title: sc_his-0_rep2

description: BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
HT5Pseq reads were demultiplexed using bcl2fastq (v2) and  trimmed 3’-sequencing adapter using cutadapt V1.16 (http://gensoft.pasteur.fr/docs/cutadapt/1.6/index.html). After that the 8-nt random barcodes located on the 5´ ends of reads were extracted and added to the fastq file header as UMIs using UMI-tools (Smith, Heger and Sudbery, 2017). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome, GCF_000009045.1_ASM904v1 for B. subtilis  genome) by star/2.7.0 (Dobin et al., 2013) with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5´ end. Duplicated 5´ ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMI-tools (Smith, Heger and Sudbery, 2017).
Analysis of 5´ ends positions was performed using Fivepseq package (Nersisyan, Ropat and Pelechano, 2020) (http://pelechanolab.com/software/fivepseq). This included analysis of the relative positions of the 5' ends of the mRNA reads with respect to the start codon, stop codon, and codon-specific pausing. Specifically, the unique 5´mRNA reads in biological samples were averaged and normalized to reads per million (rpm). The relative position of 5´mRNA reads at each codon were summed up  and used for all additional analyses. Metagene plots for frame preference were showed as the sum value (in rpm) of each frame versus the relative from the sliding window's average (in rpm) for 20 codons located at the beginning, middle, and end of each gene.
Assembly: Saccharomyces cerevisiae R64-1-1, GCA_000009045.1 for B. subtilis
Supplementary files format and content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.
Library strategy: 5PSeq

growth_protocol: All yeast experiments were performed using Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). S. cerevisiae was grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose), Complete Supplement Mixture (CSM from Formedium™) or Synthetic Complete (SC from MP Biomedicals™) medium. Bacteria of the strain B. subtilis 168 (trpC2) were pre-cultivated at 37°C with rotating in LB and minimal growth medium (per 50 ml:  5X minimal salts solution,10 ml;  glucose (50% (w/v)), 0.5 ml; casamino acids (2% (w/v)), 0.5 ml; tryptophan (10 mg/ml), 0.1 ml; iron ammonium citrate (2.2 mg/ml), 0.05 ml, deonized water, 39 ml) with tryptophan supplementation at OD600 < 0.8. Cultures were diluted to  OD600~0.05 and collected until reaching the mid-exponential phase (OD600~0.6).

extract_protocol:
Total RNA was isolated by the standard phenol chloroform method and DNA was removed by DNase I treatment, as described in Zhang & Pelechano, 2021 (PMID:33870233). RNA concentration was measured with Qubit and RNA quality was checked by 1.2% Agarose Gel or on a BioAnalyzer using an RNA Nano 6000 chip according (Agilent Technologies).
HT-5Pseq libraries were prepared following a previously established protocol (Zhang & Pelechano, 2021) if not stated otherwise. To briefly summarize, 6 μg of RNA was subjected to DNase treatment, and the resulting DNA-free total RNA was ligated with an RNA/RNA oligo containing UMI (RNA rP5_RND oligo). The ligated RNA was reverse transcribed using Illumina PE2 compatible oligos with random hexamers and oligo-dT as primers. To eliminate RNA in RNA/DNA hybrids, samples were treated with sodium hydroxide at 65°C for 20 minutes. Ribosomal RNAs were depleted using DSN (Duplex-specific nuclease) and a mixture of ribosomal DNA probes. To deplete Ribosomal RNAs in B. subtilis 168 (trpC2), we used the in-house rRNA DNA oligo depletion mixes described previously (Huch, Nersisyan et.al, doi.org/10.1101/2021.04.08.439066). Finally, the samples were amplified by PCR and sequenced on an Illumina NextSeq 2000 instrument using average of 45 cycles for read1.

treatment_protocol: Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). To induce disomes,S. cerevisiae cells grown in SC overnight and transfer to SC without histidine for 30 mins. S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.

value: Cells were harvested at exponential growth after being growing overnight in a SC media and transfer to SC without histidine for 30 mins


title: YPD_H2O2_t5_rep3

status: Public on May 14 2025

type: SRA

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

library_source: transcriptomic

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
HT5Pseq reads were demultiplexed using bcl2fastq (v2) and  trimmed 3’-sequencing adapter using cutadapt V1.16 (http://gensoft.pasteur.fr/docs/cutadapt/1.6/index.html). After that the 8-nt random barcodes located on the 5´ ends of reads were extracted and added to the fastq file header as UMIs using UMI-tools (Smith, Heger and Sudbery, 2017). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome, GCF_000009045.1_ASM904v1 for B. subtilis  genome) by star/2.7.0 (Dobin et al., 2013) with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5´ end. Duplicated 5´ ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMI-tools (Smith, Heger and Sudbery, 2017).
Analysis of 5´ ends positions was performed using Fivepseq package (Nersisyan, Ropat and Pelechano, 2020) (http://pelechanolab.com/software/fivepseq). This included analysis of the relative positions of the 5' ends of the mRNA reads with respect to the start codon, stop codon, and codon-specific pausing. Specifically, the unique 5´mRNA reads in biological samples were averaged and normalized to reads per million (rpm). The relative position of 5´mRNA reads at each codon were summed up  and used for all additional analyses. Metagene plots for frame preference were showed as the sum value (in rpm) of each frame versus the relative from the sliding window's average (in rpm) for 20 codons located at the beginning, middle, and end of each gene.
Assembly: Saccharomyces cerevisiae R64-1-1, GCA_000009045.1 for B. subtilis
Supplementary files format and content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: All yeast experiments were performed using Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). S. cerevisiae was grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose), Complete Supplement Mixture (CSM from Formedium™) or Synthetic Complete (SC from MP Biomedicals™) medium. Bacteria of the strain B. subtilis 168 (trpC2) were pre-cultivated at 37°C with rotating in LB and minimal growth medium (per 50 ml:  5X minimal salts solution,10 ml;  glucose (50% (w/v)), 0.5 ml; casamino acids (2% (w/v)), 0.5 ml; tryptophan (10 mg/ml), 0.1 ml; iron ammonium citrate (2.2 mg/ml), 0.05 ml, demonized water, 39 ml) with tryptophan supplementation at OD600 < 0.8. Cultures were diluted to  OD600~0.05 and collected until reaching the mid-exponential phase (OD600~0.6).

extract_protocol:
Total RNA was isolated by the standard phenol chloroform method and DNA was removed by DNase I treatment, as described in Zhang & Pelechano, 2021 (PMID:33870233). RNA concentration was measured with Qubit and RNA quality was checked by 1.2% Agarose Gel or on a BioAnalyzer using an RNA Nano 6000 chip according (Agilent Technologies).
HT-5Pseq libraries were prepared following a previously established protocol (Zhang & Pelechano, 2021) if not stated otherwise. To briefly summarize, 6 μg of RNA was subjected to DNase treatment, and the resulting DNA-free total RNA was ligated with an RNA/RNA oligo containing UMI (RNA rP5_RND oligo). The ligated RNA was reverse transcribed using Illumina PE2 compatible oligos with random hexamers and oligo-dT as primers. To eliminate RNA in RNA/DNA hybrids, samples were treated with sodium hydroxide at 65°C for 20 minutes. Ribosomal RNAs were depleted using DSN (Duplex-specific nuclease) and a mixture of ribosomal DNA probes. To deplete Ribosomal RNAs in B. subtilis 168 (trpC2), we used the in-house rRNA DNA oligo depletion mixes described previously (Huch, Nersisyan et.al, doi.org/10.1101/2021.04.08.439066). Finally, the samples were amplified by PCR and sequenced on an Illumina NextSeq 2000 instrument using average of 45 cycles for read1.
OTHER: 5PSeq

treatment_protocol:
Cells grew in YPD medium to exponential phase and treated with 0.2 mM H2O2 for 5 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.

tag: cell type

value: yeast

tag: genotype

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: YPD_H2O2_t5_rep2

treatment_protocol:
Cells grew in  YPD medium to exponential phase and treated with 0.2 mM H2O2 for 5 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 4

city: New York

first: Nicholas

last: Arpaia

state: NY

department: Microbiology & Immunology

country: USA

institute: Columbia University

description:
BulkIAV_counts.txt
BulkIAV_normalizedcounts.txt

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000, yielding paired-end 100bp reads
RTA (Illumina) for base calling and bcl2fastq2 (v2.19) for converting BCL to fastq, Trim Galore for adapter trimming
Pseudoalignment using Salmon (1.10.2) from transcriptomic data (Ensembl v96, Mouse GRCm38 p6)
DESeq2 for analysis
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tab delimited .txt file with raw counts for each gene/sample
Supplementary files format and content: tab delimited .txt file with normalized DESeq2 values for each gene/sample

organism: Mus musculus

source_name: lung

extract_protocol:
Cells were lysed with Trizol Reagent, and RNA was extracted using a Qiagen kit
PolyA pulldown of RNA, then cDNA library synthesis with NexteraXT Kit

treatment_protocol: Thy1.1- (Areg non-producing) and Thy1.1+ (Areg-producing) lung Treg cells were sorted and prepared for bulk RNA-seq.

tag: tissue

value: lung

value: Treg cells

value: C57BL/6 male; Foxp3GFPAregThy1.1/Thy1.1

tag: treatment

value: Influenza A Virus


title: Recurrent08,snRNAseq

city: Seoul

first: Ji Yoon

last: Lee

address: 161, Jeongneung-ro, Seongbuk-gu

country: South Korea

institute: Korea university

description:
10x Genomics
matrix.mtx.gz
features.tsv.gz
barcodes.tsv.gz

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Surgical samples were either snap-frozen using liquid nitrogen for genomic analysis or enzymatically dissociated into single cells using Liberase TM (Roche Diagnostics, Basel, Switzerland)
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x genomics).

value: Brain

tag: patient diagnosis

value: meningioma


title: sc_his-0_rep1


title: YPD_HS_t30_rep1

treatment_protocol:
Cells grew in YPD medium to exponential phase and exposed to 42°C for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Primary06,snRNAseq


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 4


title: YPD_H2O2_t5_rep1


title: CMV_2

city: Xuzhou

first: qianqian

last: Li

address: No.46 Heping Road

country: China

institute: Xuzhou maternal and child Health care hospital

description: Library name: CMV_2

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp [ 1 ] with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 [ 2 ] software. The mapped reads of each sample were assembled by StringTie [ 3 ] in a reference- based approach
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: blood

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions. Then RNA quality was determined by 53 0 0 Bioanalyser(Agilent) and quantified using the ND-2 0 0 0 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280= 1.8~2.2, OD260/230≥2.0, RQN≥ 6.5, 28S:18S≥ 1.0, >1g) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double- stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq X plus sequencer (2 × 150bp read length).

value: blood

value: PBMCs

value: WT


title: YPD_H2O2_t30_rep3

treatment_protocol:
Cells grew in YPD medium to exponential phase and treated with 0.2 mM H2O2 for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 1

description:
BulkBleo_counts.txt
BulkBleo_normalizedcounts.txt

value: Bleomycin


title: CMV_3

description: Library name: CMV_3


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 3


title: CMV_1

description: Library name: CMV_1


title: Recurrent07,snRNAseq


title: YPD_H2O2_t30_rep2

treatment_protocol:
Cells grew in  YPD medium to exponential phase and treated with 0.2 mM H2O2 for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 2


title: Primary05,snRNAseq


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 3


title: sc_his-0_rep3


title: Fluoxetine Treated S-180 cells1

type: RNA

city: Purulia

first: Sankar

last: Bhattacharyya

state: West Bengal

address: Ranchi Road Sainik School

department: Zoology

country: India

institute: Sidho Kanho Birsha University

description: Gene expression of S-180 tumor cells treated with Fluoxetine

hyb_protocol: Fragmentation of 600ng cRNA done by incubating at 60o for 30 minutes in 25x fragmentation buffer and 10x Gene Expression Blocking Agent in 25ul of total reaction volume. After completion of hybridisation reaction 25ul of 2xHi-RPM Hybridization Buffer is added to stop fragmentation reaction. 40ul of hybridization sample is dispense in the SureHyb gasket slide. Further the Gasket slides were assembled with gene expression microarray slide (G3 Mouse GE 8x60k microarray, Agilent whole genome microarray) . Hybridisation done at 65o C for 17 hours in Agilent hybridisation oven. Slides were afterwards using Gene expression wash buffers.

scan_protocol: Slides were scanned using SureScan Microarray scanner system with one color scan setting for 8X60K array slides immediately after washing followed by manufacturers guidelines.

data_processing: Image generated after scanning were analysed using Agilent feature extraction Software version 11.5.1. using default parameters (Protocol in use:GE1_1200_Jun14, Grid template no: 074809_D_F_20181026 at saturation value 778020 g). Further processing of data were done using GeneSpring 14.9 (Agilent Technologies).

source_name: S-180 Tumour Cells

label_protocol: Using Low Input Quick Amp Labeling Kit, One color Cyanine-3 (Cy3) labelled complementary RNA were prepared from 10ng of RNA (Agilent technologies). Purification of amplified cRNA performed using RNeasy Mini Kit (QIAGEN, Valencia, CA). NanoDrop ND-1000 UV-VIS Spectrophotometer were used to quitify cRNA yield and dye incorporation.

growth_protocol: S-180 tumor cells were purchased from National Centre for Cell Science (NCCS), India and maitained in presence  of RPMI supplimented with 10% FBS in proper cell culture environment.

extract_protocol: RNA isolation from total cells were performed by isopropyl alcohol precipitation method. RNA from Control and 20uM Fluoxetine treated group of S-180 with two biological replicates were verified for RNA integrity in 1% agarose gel electrophoresis.

treatment_protocol: 5x105 S-180 cells cultured in 12 well plate for 12hr in presence and absence of 20uM Fluoxetine. Cells were harvested using 1XPBS after 12hr then transferred to 1000ul of TRIzol reagent (ambionÒ, life technologiesTM).

value: S-180 tumor cells

value: 20uM Fluoxetine for 12hr


title: YPD_H2O2_t30_rep1


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 1


title: Fluoxetine Treated S-180 cells2


title: Not treated Control S-180 cells1

description: Gene expression of S-180 tumor cells


title: CON_3

description: Library name: CON_3


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 2


title: Recurrent06,snRNAseq


title: Not treated Control S-180 cells2

description: Gene expression of S-180 tumor cells


title: YPD_AA_t30_rep3

treatment_protocol:
Cells grew in YPD medium to exponential phase and transfer in CSM without  amino acids for 30 minutes incubation
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: CON_1

description: Library name: CON_1


title: Primary04,snRNAseq


title: YPD_AA_t30_rep2

treatment_protocol:
Cells grew in  YPD medium to exponential phase and transfer in CSM without  amino acids for 30 minutes incubation
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 2


title: CON_2

description: Library name: CON_2


title: Recurrent05,snRNAseq


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 1


title: Primary03,snRNAseq


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Influenza A Virus, Bulk RNA-seq, Sample 1


title: Recurrent04,snRNAseq


title: MDA-MB-231 cells, shPDCD11, Repeat-2

city: Yangzhou

first: Li

last: Ding

state: Jiangsu

address: No. 88, Daxuenan Road

department: College of Bioscience and Biotechnology

institute: Yangzhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
Differential expression analysis and functional enrichment
Assembly: HiSat2(http://ccb.jhu.edu/software/hisat2/index.shtml)
Supplementary files format and content: CSV file includes raw conunts for each sample
Supplementary files format and content: CSV file includes differential genes with the fold changes, p values, and p-adj values

growth_protocol: MDA-MB-231 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent
The ranscriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline for 4 days to induce expression of shLuc or shPDCD11

tag: cell line

value: Breast cancer cells

value: PDCD11 knockdown

value: doxycycline treatment to induce expression of shPDCD11

tag: time

value: day 4


title: CSM_ctrl_rep2

treatment_protocol:
Cells grew in  CSM medium to exponential phase as a control for stress condition
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.

value: yeast

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: MDA-MB-231 cells, shPDCD11, Repeat-3


title: Panc-Smad4OFF_m3_multiome_ATAC

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics

library_source: genomic single cell

data_processing:
Sequencing data was demultiplexed, mapped, and processed into gene/cell expression matrices using 10X Genomics' Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). Gene expression reads were aligned to the mouse reference genome version gex-mm10-2020-A, available from the 10X Genomics website.
Assembly: mm10
Supplementary files format and content: Filtered single cell 3' cell/gene matrices in .h5 format generated by Cell Ranger
Supplementary files format and content: single cell atac fragments generated by Cell Ranger

molecule: genomic DNA

source_name: PDAC Primary Tumor

growth_protocol: Mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse.

extract_protocol:
Single Cell Multiome ATAC + Gene Expression was performed with 10X Genomics system using Chromium Next GEM Single Cell Multiome Reagent Kit A (catalog #1000282) and ATAC Kit A (catalog #1000280) following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and demonstrated protocol, Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing.
Briefly, cells (viability 95%) were lysed for 4 min and resuspended in Diluted Nuclei Buffer (10X Genomics #PN-2000207). Lysis efficiency and nuclei concentration was evaluated on Countess II automatic cell counter by trypan blue and DAPI staining. 11,000 nuclei were loaded per transposition reaction, targeting recovery of 7,000 nuclei after sequencing. After transposition reaction, nuclei were encapsulated and barcoded.
Next-generation sequencing libraries were constructed following Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide and sequenced on an Illumina NovaSeq 6000 system.

value: PDAC Primary Tumor

value: DoxON

tag: Sex

value: M


title: MDA-MB-231 cells, shPDCD11, Repeat-1


title: Panc-Smad4OFF_m3_multiome_RNA

description: 10x Genomics


title: Recurrent03,snRNAseq

value: Brain


title: MDA-MB-231 cells, shLuc, Repeat-3

value: doxycycline treatment to induce expression of shLuc


title: CSM_ctrl_rep1

treatment_protocol:
Cells grew in CSM medium to exponential phase as a control for stress condition
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: MDA-MB-231 cells, shLuc, Repeat-2


title: CSM_HS_t30_rep3

treatment_protocol:
Cells grew in CSM medium to exponential phase and exposed to 42°C for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: CSM_ctrl_rep3


title: Recurrent02,snRNAseq

value: meningioma


title: Panc-Smad4OFF_m2_multiome_ATAC

description: 10x Genomics


title: Primary02,snRNAseq


title: Panc-Smad4OFF_m2_multiome_RNA

description: 10x Genomics


title: MDA-MB-231 cells, shLuc, Repeat-1


title: Recurrent01,snRNAseq


title: CSM_HS_t30_rep2


title: YPD_AA_t30_rep1

treatment_protocol:
Cells grew  in YPD medium to exponential phase and transfer in CSM without  amino acids for 30 minutes incubation
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: CSM_HS_t30_rep1


title: Panc-Smad4OFF_m1_multiome_ATAC

description: 10x Genomics


title: scRNAseq_VSV-infected

city: Düsseldorf

first: Lang

middle: A.

last: Philipp

state: NRW

address: Universitätsstrasse 1

department: Department of Molecular Medicine II

country: Germany

institute: University Hospital Duesseldorf

description: Library name: 550-3 VSV-infected

data_processing:
Raw sequencing data were processed using the 10X Genomics CellRanger software (v6.1.2). Raw BCL-files were demultipexed and processed to Fastq-files using the CellRanger mkfastq pipeline. Alignment of reads to the mm10 genome, UMI counting as well as sample demultiplexing were performed via the CellRanger multi pipieline to generate a gene-barcode matrix. The Cellranger aggr pipeline was used for aggregation and sequencing depth normalization.
Quality control, preprocessing and analysis of single cell RNA-sequencing data were performed using the python package Scanpy. During quality control, cells were removed when they contain less than 400 genes, less than 3,500 reads, more than 100,000 reads or over 10% of mitochondrial genes to total transcripts. In addition, genes expressed in less than three cells were also removed. After the quality control, 7,358 cells of the naïve sample, 11,869 cells of the VSV exposed sample, and 30,949 genes remained for analysis. The total gene count per barcode was normalized to 10,000 reads and reads were transformed to log(x+1). Lastly, count depth effects were regressed out and gene counts were scaled to unit variance and zero mean. Principle component analysis was carried out using the 2,000 most variable genes. For clustering and visualization, we calculated a Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) representation. Clusters were detected using the Leiden algorithm with a resolution of 0.7.
Assembly: mm10
Supplementary files format and content: mtx. File contains matrix data
Supplementary files format and content: TSV File contains a list of anlayzed genes

source_name: kidney (cell line)

growth_protocol: HEK293 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and 1% Pen Strep Glutamine.

extract_protocol:
Single cell suspensions were used as input for the single cell droplet libraries generation on the 10X Chromium Controller system utilizing the Chromium Single Cell 3’ NextGEM Reagent Kit v3.1 according to manufacturer’s protocol.
Sequencing was carried out on a NextSeq 2000 system (Illumina Inc. San Diego, USA) with a mean sequencing depth of 45,000 reads/cell.

treatment_protocol: HEK cells were divided into 6 samples, three control samples and three samples infected with VSV at MOI=0.1 for 4h (106 cells per sample). Cells were labelled with 3' CellPlex Kit following manufacturer’s protocol, and the samples from the same treatment group were pooled together. Viable cells were enriched by BD FACS-Melody.

value: kidney (cell line)

value: VSV-infected


title: Primary01,snRNAseq


title: Panc-Smad4OFF_m1_multiome_RNA

description: 10x Genomics


title: scRNAseq_control

description: Library name: 550-1_GE_S1 control

value: control


title: CSM_H2O2_t5_rep3

treatment_protocol:
Cells grew in CSM medium to exponential phase and treated with 0.2 mM H2O2 for 5 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: CITEseq_3' CellPlex_VSV-infected

description:
Library name: 550-3
Hashtag-derived oligonucleotide (HTO), 3' CellPlex Kit

library_source: other

data_processing:
Raw sequencing data were processed using the 10X Genomics CellRanger software (v6.1.2). Raw BCL-files were demultipexed and processed to Fastq-files using the CellRanger mkfastq pipeline. Alignment of reads to the mm10 genome, UMI counting as well as sample demultiplexing were performed via the CellRanger multi pipieline to generate a gene-barcode matrix. The Cellranger aggr pipeline was used for aggregation and sequencing depth normalization.
Quality control, preprocessing and analysis of single cell RNA-sequencing data were performed using the python package Scanpy. During quality control, cells were removed when they contain less than 400 genes, less than 3,500 reads, more than 100,000 reads or over 10% of mitochondrial genes to total transcripts. In addition, genes expressed in less than three cells were also removed. After the quality control, 7,358 cells of the naïve sample, 11,869 cells of the VSV exposed sample, and 30,949 genes remained for analysis. The total gene count per barcode was normalized to 10,000 reads and reads were transformed to log(x+1). Lastly, count depth effects were regressed out and gene counts were scaled to unit variance and zero mean. Principle component analysis was carried out using the 2,000 most variable genes. For clustering and visualization, we calculated a Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) representation. Clusters were detected using the Leiden algorithm with a resolution of 0.7.
Assembly: mm10
Supplementary files format and content: mtx. File contains matrix data
Supplementary files format and content: TSV File contains a list of anlayzed genes
Library strategy: CITE-seq

molecule: other


title: ATAC sequencing, BCPAP, 5-Azacytidine treated, rep2

first: Yeongun

state: State...

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei university

description: paired-end 101bp

library_source: genomic

data_processing:
ATAC sequencing data from BCPAP cell line were processed using the PEPATAC pipeline. PEPATAC employs the refgenie asset manager for consistent reference genome annotations, crucial for reproducibility. Adapters and mitochondrial DNA content were trimmed using trimmomatic, and read alignment and deduplication were performed using bowtie2 and Picard, respectively.
Assembly: hg19
Supplementary files format and content: Peak calling was conducted using MACS2 with standard settings, including parameters for shifting (--shift 75), extension size (--extsize 150), along with directives to forgo the model (--nomodel), pinpoint summit locations (--call-summits), retain all duplicates (--keep-dup all), and set a significance threshold (p-value of 0.01). Subsequently, peak scores were adjusted to a normalized score per million, achieved by dividing the cumulative scores by one million.

source_name: BCPAP

extract_protocol:
genomic DNA was extracted from the collected tissue samples using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). as outlined in the manufacturer's recommendations and guideline. After DNA extraction, the DNA concentration and purity were assessed using Nanodrop (Thermo Fisher, Carlsbad, CA, US).
ATAC libraries of BCPAP were prepared as done in previous study. In brief, the procedure is as follows. Cells are lysed following preparation guidelines, with fresh ATAC-seq lysis and wash buffers. Cells are pelleted and supernatant removed before resuspension in lysis buffer. After incubation, samples are diluted, washed, and pelleted again. The transposition mix is applied, followed by incubation. Post-incubation, DNA is cleaned and concentrated. Barcoding involves assigning unique adapters, PCR amplification, and cleanup. Library concentrations are quantified for sequencing. Then, the libraries were sequenced on a HiSeq2500 sequencer (Illumina, San Diego, CA, USA) with 2X 100bp paired-end reads featuring unique dual index, generating 2Gb of sequencing data from each sample.

value: BCPAP


title: ATAC sequencing, BCPAP, 5-Azacytidine treated, rep1

description: paired-end 101bp


title: PND7, replicate 1, scRNAseq

city: Urbana

first: CheMyong

middle: Jay

last: Ko

state: Illinois

address: 2001 S. Lincoln Ave.

department: Comparative Biosciences

institute: University of Illinois at Urbana Champaign

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting 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) using a custom reference made for genome GRM38 and Gencode release M16 gene models
Assembly: Gencode GRCm38, release M16
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ovary

extract_protocol:
After collagenase-assisted tissue dissociation, single-cell suspensions were converted into individually barcoded cDNA libraries with the Chromium Single Cell 3′ Library & Gel Bead Kit v2 from 10X Genomics.
All 3 libraries were sequenced on a 2x150nt lane in a HiSeq 4000; Reads are 26nt (read1) and 98nt (read2) nt in length.

value: Mixed

value: Ovary

tag: strain

tag: age

value: Postnatal day 7

value: female


title: CSM_H2O2_t5_rep2


title: CITEseq_3' CellPlex_control

description:
Library name: 550-1
Hashtag-derived oligonucleotide (HTO), 3' CellPlex Kit


title: PND14, replicate 1, scRNAseq

description: 10x Genomics

value: Postnatal day 14


title: Blood neutrophil, 0h, ERA replicate 13

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

data_processing:
Reads were aligned to the human genome (hg38) using TopHat2 (v2.1.1)
Counts were generated using featureCounts in R (v3.6.3) profiving the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: Neutrophils were isolated from whole blood by centrifugation through density-gradient reagent (Polymorphprep or Ficoll-Paque). Erythrocytes were removed by hypotonic lysis with ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
50bp Single-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: peripheral blood

value: Neutrophil

tag: subject status

value: Early RA


title: CSM_H2O2_t30_rep3

treatment_protocol:
Cells grew in CSM medium to exponential phase and treated with 0.2 mM H2O2 for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.

value: yeast

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: ATAC sequencing, BCPAP, untreated, rep2

description: paired-end 101bp

value: untreated


title: Blood neutrophil, 0h, ERA replicate 12


title: CSM_H2O2_t30_rep2


title: Targeted bisulfite sequencing, 10495043, Normal thyroid tissue

description: paired-end 101bp

data_processing:
The generated sequencing data was quality controlled with FastQC (version 0.11.9). Trim Galore (version 0.6.7) and Cutadapt (version 2.8) were used to remove the adaptor sequences and low-quality sequences. Based on the human CpG island reference hg19, Bismark (version 0.22.3) was used to align sequencing reads with Bowtie2 (version 2.4.4). Alignment of each data was assessed by Picard CollectHsMetrics and every QC data was summarized by multiQC. Sort and index commands from Samtools were utilized. The number of methylated and unmethylated cytosines at each CpG site was listed using Bismark methylation extractor from post-indexed data, and only those 10X or higher were selected for downstream analysis. Finally, the methylation values of CpG sites included in the same CpG island were calculated by averaging the methylation value based on the hg19.
Assembly: hg19
Supplementary files format and content: DNA methylation levels of CpG sites extracted in a text file by Bismark methylation extractor

source_name: Normal thyroid

extract_protocol:
genomic DNA was extracted from the collected tissue samples using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). as outlined in the manufacturer's recommendations and guideline. After DNA extraction, the DNA concentration and purity were assessed using Nanodrop (Thermo Fisher, Carlsbad, CA, US).
A total 500ng of genomic DNA was fragmented using M220 Focused-ultrasonicator (Covaris, Woburn, MA, US) with low-EDTA TE buffer. The quality, quantity, and fragment size (major peak in 250–300 bp) of sheared genomic DNA was verified using a 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) prior to library preparation. The DNA library was bisulfite-converted using the EZ DNA Methylation-Gold™ Kit (Zymo Research, Irvine, CA, USA). Then, the library was prepared using the Accel-NGS® Methyl-Seq DNA library kit (Swift Biosciences, Ann Arbor, MI, USA) and other specified enzymes, buffers, and reagents in manufacturer’s protocol. Finally, 8 libraries were pooled and incubated with probe pool designed for targeting the regions of our interest. After clean-up, the libraries were sequenced on HiSeq2500 sequencer (Illumina, San Diego, CA, US) with 2 X 100bp pair-end reads with unique dual index and generated 2Gb of sequencing data from each sample.

value: Normal thyroid

value: Female

tag: metastasis

value: N


title: ED17, replicate 1, scRNAseq

description: 10x Genomics

value: Embryonic day 16.5


title: TN7-4

city: Taichung City

first: Yuan-Kai

last: Tu

address: No.189, Zhongzheng Rd., Wufeng Dist.

department: Crop Genetic Resources and Biotechnology

country: Taiwan

institute: Taiwan Agricultural Research Institute, Ministry of Agriculture

description:
Library name: Sample19
peach accession with Gg genotype

data_processing:
For FASTQ data pre-processing, Fastp (version 0.23.2) was used to eliminate adapters and undergo quality filtering.
The peach genome annotation file and genetic information for chromosomes were sourced from the Joint Genomics Institute (https://phytozome-next.jgi.doe.gov/info/Ppersica_v2_1). Further refinement of the genomic annotation file involved the exon column was extracted and information of coding sequences (CDS) was added.
RSEM (version 1.2.31) coupled with Bowtie2 (version 2.5.1) alignment was performed for gene and transcript abundance quantification against a reference transcriptome.
The analysis of differential expression genes utilized the DESeq2 package (version v1.34.0) within the R software environment (version 4.1.1).
Assembly: The peach genome annotation file and genetic information for chromosomes were sourced from the Joint Genomics Institute (https://phytozome-next.jgi.doe.gov/info/Ppersica_v2_1)
Supplementary files format and content: After RSEM analysis, files of raw read counts were extracted using the 'rsem-generate-data-matrix' command and combined into a single file, except for TN7-4, which was excluded due to unexpectedly long alignment time compared to other samples.

organism: Prunus persica

source_name: fruit at the fruit set stage

extract_protocol:
Total RNA were extracted at the fruit set stage (n = 5 per accession) by RNeasy Plant Mini Kit (Qiagen, Germany).
Library preparation was performed by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instruction.

value: fruit at the fruit set stage

value: Gg


title: Blood neutrophil, 0h, ERA replicate 11


title: CSM_H2O2_t30_rep1


title: Targeted bisulfite sequencing, 10495043, Tumor

description: paired-end 101bp

source_name: Papillary thyroid cancer

value: Papillary thyroid cancer


title: Blood neutrophil, 0h, ERA replicate 10


title: CSM_AA_t30_rep3

treatment_protocol:
Cells grew in CSM medium to exponential phase and transfer to CSM without  amino acids for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: TN7-3

description:
Library name: Sample18
peach accession with Gg genotype


title: Blood neutrophil, 0h, ERA replicate 9


title: TN7-2

description:
Library name: Sample17
peach accession with Gg genotype


title: Targeted bisulfite sequencing, 10496904, Normal thyroid tissue

description: paired-end 101bp


title: Targeted bisulfite sequencing, 10496904, Tumor

description: paired-end 101bp


title: TN7-1

description:
Library name: Sample16
peach accession with Gg genotype


title: Blood neutrophil, 0h, ERA replicate 8


title: CSM_H2O2_t5_rep1


title: Targeted bisulfite sequencing, 10503094, Normal thyroid tissue

description: paired-end 101bp


title: ATAC sequencing, BCPAP, untreated, rep1

description: paired-end 101bp

value: BCPAP


title: Blood neutrophil, 0h, ERA replicate 7


title: TN11-5

description:
Library name: Sample15
peach accession with GG genotype

value: GG


title: TN11-4

description:
Library name: Sample14
peach accession with GG genotype


title: CSM-serine_rep3

treatment_protocol:
Cells were harvested at exponential growth after being growing overnight in a CSM media supplemented with Serine to a final concentration of 85.6 mg/L
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: TN7-5

description:
Library name: Sample20
peach accession with Gg genotype


title: Blood neutrophil, 0h, ERA replicate 6


title: Targeted bisulfite sequencing, 10503094, Tumor

description: paired-end 101bp


title: CSM-serine_rep2


title: Blood neutrophil, 0h, ERA replicate 5


title: CSM-serine_rep1


title: Targeted bisulfite sequencing, 2036341, Tumor

description: paired-end 101bp


title: TN11-3

description:
Library name: Sample13
peach accession with GG genotype


title: TN11-2

description:
Library name: Sample12
peach accession with GG genotype


title: Blood neutrophil, 0h, ERA replicate 4


title: CSM_AA_t30_rep2


title: Sr-4

description:
Library name: Sample10
a commercial nectarine accession

value: gg


title: CSM-proline_rep3

treatment_protocol:
Cells were harvested at exponential growth after being growing overnight in a CSM media supplemented with Proline to a final concentration of 85.6 mg/L
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: TN11-1

description:
Library name: Sample11
peach accession with GG genotype


title: Blood neutrophil, 0h, ERA replicate 3


title: CSM-proline_rep2


title: Targeted bisulfite sequencing, 5683060, Normal thyroid tissue

description: paired-end 101bp


title: CSM_AA_t30_rep1


title: Targeted bisulfite sequencing, 5683060, Tumor

description: paired-end 101bp


title: Blood neutrophil, 0h, ERA replicate 2


title: Sr-3

description:
Library name: Sample9
a commercial nectarine accession


title: Targeted bisulfite sequencing, 6246356, Normal thyroid tissue

description: paired-end 101bp

value: Male


title: CSM-proline_rep1


title: Blood neutrophil, 0h, ERA replicate 1

value: peripheral blood


title: CSM-ctrl_rep3

treatment_protocol:
Cells were harvested at exponential growth after being growing overnight in a CSM media as a control
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Targeted bisulfite sequencing, 6246356, Tumor

description: paired-end 101bp


title: Sr-2

description:
Library name: Sample8
a commercial nectarine accession


title: Blood neutrophil, 0h, HC replicate 6

value: Neutrophil

value: Healthy control


title: Sr-1

description:
Library name: Sample7
a commercial nectarine accession


title: Blood neutrophil, 0h, HC replicate 5


title: CSM-ctrl_rep1

value: yeast


title: CSM-ctrl_rep2

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: Blood neutrophil, 0h, HC replicate 4


title: Targeted bisulfite sequencing, 2036341, Normal thyroid tissue

description: paired-end 101bp


title: CSM-arginine_rep3

treatment_protocol:
Cells were harvested at exponential growth after being growing overnight in a CSM media supplemented with Arginine to a final concentration of 85.6 mg/L
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Targeted bisulfite sequencing, 6600984, Normal thyroid tissue

description: paired-end 101bp

value: Y


title: Targeted bisulfite sequencing, 6554789, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 6554789, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: MN-6

description:
Library name: Sample5
a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN)


title: Targeted bisulfite sequencing, 6600984, Tumor

description: paired-end 101bp

value: Female


title: Blood neutrophil, 0h, HC replicate 2


title: CSM-arginine_rep1


title: CSM-arginine_rep2


title: Targeted bisulfite sequencing, 6715626, Normal thyroid tissue

description: paired-end 101bp

value: N


title: Blood neutrophil, 0h, HC replicate 3


title: MN-5

description:
Library name: Sample4
a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN)


title: MN-4

description:
Library name: Sample3
a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN)


title: M18-Old

type: genomic

city: New Haven

first: Jessica

middle: Yuki

last: Kasamoto

state: CT

address: 300 George Street

department: Computational Biology and Bioinformatics

institute: Yale University

description: Old (20 months)

hyb_protocol: The Clock Foundation performed the following steps. The Bisulfite converted DNA was amplified, fragmented, and hybirdized to Illumina Horvath Mammalian Methylation 320k Chip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Illumina sequencing platform using standard recommended Illumina scanner setting

data_processing: BetaMatrix_ProcessedFinal.txt represents Average Beta

label: Cy3 and Cy5

source_name: Liver

label_protocol: Standard Illumina Protocol

growth_protocol: Male C57BL/6J mice aged 6 months (young) and 20 months (old) were obtained from The Jackson Laboratory (stock number: 000664).

extract_protocol: Frozen liver tissues collected immediately following hyperinsulinemic-euglycemic clamp and used for nucleic acid extraction. DNA was extracted according to the manufacturer’s protocols for each kit. Extractions were done using either the AllPrep DNA/RNA Mini Kit (Qiagen, 80204; samples M4, M5, M9, and M10) or the DNeasy Blood & Tissue Kit (Qiagen, 69504; samples M1, M2, M3, M6, M7, M8, M11, M12, M13, M14, M15, M16, M17, and M18). DNA quantification was performed using both NanoDrop spectrophotometry and Qubit fluorometry. All samples were stored at –80°C until further processing.

value: Liver

tag: metaboliccageid

tag: agecategory

value: Old

tag: isold

tag: dosactifice


title: Blood neutrophil, 0h, HC replicate 1


title: M17-Old

description: Old (20 months)


title: Targeted bisulfite sequencing, 6715626, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 6767830, Normal thyroid tissue

description: paired-end 101bp


title: MN-1

description:
Library name: Sample1
a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN)

value: fruit at the fruit set stage

value: Gg


title: Blood neutrophil, 0h, SRA replicate21

value: Severe RA


title: M16-Old

description: Old (20 months)


title: Sr-10

description:
Library name: Sample6
a commercial nectarine accession


title: NF54, HP1, wholeparasites, low input, 10k, rep2

city: Nijmegen

first: Jonas

last: Gockel

email: jonas-gockel@web.de, jonas.gockel@ru.nl

address: Geert Grooteplein-Zuid 8

country: Netherlands

institute: Radboud University

description: Library name: NF54_10k_wholeparasites_antiHP1_rep2

data_processing:
Sequencing reads were mapped against the reference genome PlasmoDB v26 3D7 with bowtie2 (v2.5.2)
Reads were filtered for mapping quality higher or equal than 30 and mitrochondrial and apicoplast reads were removed with samtools (v1.18)
BigWig files normalised to RPMK were generated with deeptools (v3.5.4)
Bedgraphs were generated for visualisation on UCSC genome browser with bedtools (v2.31.0) normalised to reads per million
Assembly: PlasmoDB v26 3D7
Supplementary files format and content: bedGraph
Library strategy: CUT&Tag

organism: Plasmodium falciparum

source_name: NF54 wt

growth_protocol: RPMI 1640 medium supplemented with 0.2% NaHCO3 and 10% human serum at 37 °C under low oxygen conditions (3% O2, 4% CO2 and 93% N2) in human red blood cells at 5% hematocrit. For DiBioCUT&Tag, parasites were grown in biotin-free RPMI supplemented with 0.2% NaHCO3, 200 µM Hypoxyxanthine and 0.5% AlbuMAX TM II. Medium was furthermore supplemented with 250 nM Rapalog 1h before harvest for RAPA samples and 50 µm Biotin 30 min before harvest for plusBiotin samples.

extract_protocol:
For nuclei isolation, parasite cultures were lightly crosslinked with 0.1% formaldehyde (Sigma, F8775), incubating for 2 min at 37 °C while shaking. Crosslinking was stopped by addition of glycine to 0.125 M final concentration. Samples were handled on ice from here onwards. Cells were harvested by 440 g centrifugation for 8 min at 4 °C, and washed with ice-cold PBS. Centrifugation was repeated and the pellet was washed with PBS supplemented with 1x EDTA-free Protease Inhibitor (Roche, 04693132001). Parasites were extracted by adding saponin (0.05% total concentration) and incubating at room temperature (RT) for 10 min. Nuclei were isolated by carefully transferring the extracted parasite mixture on top of a 0.25 M to 0.1 M sucrose gradient in cell lysis buffer (10 mM Tris pH 8, 3 mM MgCl2, 0.2% NP-40, 1x EDTA free Protease inhibitor (Roche, 04693132001); 15 mL 0.25 M Sucrose and 17.5 mL 0.1M Sucrose for 50 mL tubes, 4 mL 0.25 M Sucrose and 6 mL 0.1 M Sucrose for 15 mL tubes) and centrifuging for 12 min, 3100 g, 4 °C with acceleration and deceleration set to 1 (Eppendorf 5910 Ri, Rotor S-4x400). Supernatant was removed and nuclei washed in cell lysis buffer (10 min, 3500 g, 4 °C; Heraeus Fresco 21). Nuclei were counted in an automatic hemocytometer (BioRad, TC10 Automated Cell Counter) and were directly used for CUT&Tag. Optionally, nuclei were washed with cell lysis buffer containing 20% Glycerol and nuclei pellet was snap frozen in liquid nitrogen prior to storage at -80°C. For parasite isolations, parasite cultures were harvested by 440 g centrifugation for 8 min at RT and pellet was resuspended in 1 mL of 0.15% Saponin/PBS per 10 mL culture and incubated for 5 min on ice. Samples were vortexed shortly every minute. Samples were washed three times with ice-cold PBS (3500 g centrifugation for 3 min at 4 °C; Heraeus Fresco 21). Intact parasites were counted in an automatic hemocytometer and were directly used for CUT&Tag. Optionally, parasites were washed with PBS containing 20% Glycerol and parasite pellets snap frozen in liquid nitrogen prior to storage at -80 °C. Nuclei or whole parasite were resuspended in CUT&Tag wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor) containing 0.1% Triton X-100 and permeabilized for 10 min on ice. Nuclei / parasites were pelleted by centrifugation (3500 g, 10 min, 4 °C) and resuspended in CUT&Tag wash buffer. Concanavalin A beads (Bangs Laboratories, BP531) were activated by resuspending into 10 volumes of Bead Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), washed once on a magnetic rack and resuspended in the starting volume of bead slurry. Purified nuclei or parasites were bound to 10 µL beads per reaction by incubating for 10 min rotating at RT. The supernatant was removed and 50 µL antibody buffer (CUT&Tag wash buffer; 2 mM EDTA, 0.1% BSA) with primary Antibody (0.25 µL polyclonal rabbit αHP1; 0.5 µg αH3K9me3, Abcam 8988; 0.5 µL αBiotin (Cell Signaling Technology #D5A7; for DiBioCUT&Tag); 0.25µg αGFP, Roche 11814460001; or 0.5 µg normal rabbit IgG (MERCK, #12-370)) was added and incubated nutating over night at 4 °C. Unbound primary antibody was removed by washing once with 100 µL CUT&Tag wash buffer and samples were then incubated with secondary antibody (1.2 µg guinea pig anti-rabbit antibody, Antibodies-Online ABIN101961; or 0.5 µg goat anti-mouse antibody, EpiCypher 13-0048; in 100 µL CUT&Tag wash buffer, 1:100 dilution) for 1h on RT, nutating. The nuclei or parasites were washed on a magnetic stand twice with 100 µL CUT&Tag wash buffer and once with 100 µL CUT&Tag 300 Wash Buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0,5 mM Spermidine, 1x EDTA-free protease inhibitor). For all following wash steps CUT&Tag 300 wash buffer was used in order to quench potential affinity of protA-Tn5 to accessible chromatin regions. 2.5 µL commercial proteinA/G-Tn5 fusion protein (CUTANA™ pAG-Tn5 for CUT&Tag, Epicypher, 15-1017) was added in 50 µL CUT&Tag 300 wash buffer and incubated nutating for 1 h. Unbound proteinA/G-Tn5 fusion protein was removed by thrice washing with 100 µL CUT&Tag 300 wash buffer. The supernatant was removed and the nuclei or parasites were resuspended in 200 µL freshly prepared tagmentation buffer (CUT&Tag 300 wash buffer, 10 mM MgCl2). To perform tagmentation, samples were incubated in a PCR thermocycler (BioRad, T100) at 37 °C for 1h. Tagmentation was stopped and nuclei or parasite lysis was facilitated by addition of 10 µL of 0.5M EDTA pH8, 3 µL of 10% SDS and 1 µL of 50 mg/mL proteinase K. Samples were briefly vortexed and then incubated at 55 °C for 1 h. DNA fragments were extracted utilizing the DNA Clean & Concentrator - 5 kit (Zymogen, D4014) following manufactures instructions. DNA was eluted from the column with 26 µL of prewarmed elution buffer and DNA concentrations were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231).
Libraries were generated using maximal 50 ng of extracted DNA from CUT&Tag experiments and tagged fragments were amplified with unique combinations of i5 and i7 barcoded primers, enabling tracing the DNA fragments originating from separate experiments in the sequencing data. PCRs were performed in a total reaction volume of 50 µL using Kapa HiFi polymerase (use non-hotstart version for gap filling; Roche, KK2102) in a thermocycler with the following program: 58 °C for 5 min, 62 °C for 5 min (gap filling), 98 °C for 2 min, 12-16 cycles of 98 °C for 20 second and 62 °C for 10 seconds, 62 °C for 1 min and hold at 4 °C. Post-PCR DNA cleanup was performed by adding 50 µL (1x volume) of AMPure XP bead slurry (Beckman Coulter, A63882) and incubating for 10 min at RT, washing twice with 80% EtOH on a magnetic rack, and eluting in 16.5 µL of 10 mM Tris-HCl pH 8 for 5 min at RT. DNA concentrations of libraries were assessed with Qubit dsDNA High Sensitivity Assay kit (Invitrogen, Q33231) and library fragment size distribution was accessed by microfluidic gel electrophoresis (Agilent 2100 Bioanalyser) with the corresponding High Sensitivity DNA Kit (Agilent, 5067-4626). Sequencing was performed using an Illumina NextSeq 2000 instrument for 3-10 M reads per CUT&Tag sample; 59bp paired-end reads were generated.

tag: chip /cut&tag_antibody

value: HP1 (Brancucci et. al, 2014)

value: NF54 wt

tag: starting material

value: isolated parasites


title: Blood neutrophil, 0h, SRA replicate20

value: peripheral blood

tag: cell type


title: M15-Old

description: Old (20 months)

tag: tissue


title: Targeted bisulfite sequencing, 6767830, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: Targeted bisulfite sequencing, 8243164, Normal thyroid tissue

description: paired-end 101bp


title: NF54, HP1, wholeparasites, low input, 10k, rep1

description: Library name: NF54_10k_wholeparasites_antiHP1_rep1


title: Blood neutrophil, 0h, SRA replicate19

value: Neutrophil


title: M14-Old

description: Old (20 months)


title: NF54, HP1, wholeparasites, low input, 50k, rep2

description: Library name: NF54_50k_wholeparasites_antiHP1_rep2


title: Targeted bisulfite sequencing, 8243164, Tumor

description: paired-end 101bp


title: Blood neutrophil, 0h, SRA replicate18


title: M9-Old

description: Old (20 months)


title: Targeted bisulfite sequencing, 8745550, Normal thyroid tissue

description: paired-end 101bp


title: NF54, HP1, wholeparasites, low input, 50k, rep1

description: Library name: NF54_50k_wholeparasites_antiHP1_rep1


title: Blood neutrophil, 0h, SRA replicate17


title: MN-3

description:
Library name: Sample2
a peach to nectarine mutant, named Maravilha Nectarine Mutant (MN)

tag: genotype


title: M8-Old

description: Old (20 months)


title: NF54, HP1, wholeparasites, low input, 100k, rep2

description: Library name: NF54_100k_wholeparasites_antiHP1_rep2


title: Targeted bisulfite sequencing, 8745550, Tumor

description: paired-end 101bp


title: Blood neutrophil, 0h, SRA replicate16


title: Blood neutrophil, 0h, SRA replicate22


title: M7-Old

description: Old (20 months)


title: Blood neutrophil, 0h, SRA replicate15


title: M6-Old

description: Old (20 months)


title: Targeted bisulfite sequencing, 901063, Normal thyroid tissue

description: paired-end 101bp


title: Targeted bisulfite sequencing, 901063, Tumor

description: paired-end 101bp


title: NF54, HP1, wholeparasites, low input, 100k, rep1

description: Library name: NF54_100k_wholeparasites_antiHP1_rep1


title: NF54, H3K9me3, diagenode, 100K

description:
Library name: NF54_100K_H3K9me3_diagenode
NF54-H3K9me3_CT_log2ratio_2000bpbins.bedgraph.gz

value: H3K9me3(Diagenode, Cat#C15410193)

value: isolated nuclei


title: M5-Old

description: Old (20 months)


title: Blood neutrophil, 0h, SRA replicate14


title: CenH3, DiBioCUT&Tag, plusBiotin, plusRapa, rep2

description: Library name: CenH3_plusBiotin_plusRapa_rep2

value: Biotin (CST, #D5A7)


title: M13-Young

description: Young (6 months)

value: Young


title: Blood neutrophil, 0h, SRA replicate13


title: Targeted bisulfite sequencing, 9213165, Tumor

description: paired-end 101bp

value: Female


title: CenH3, DiBioCUT&Tag, plusBiotin, plusRapa, rep1

description: Library name: CenH3_plusBiotin_plusRapa_rep1


title: Targeted bisulfite sequencing, 9221121, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: Male

value: Y


title: Blood neutrophil, 0h, SRA replicate11


title: CenH3, DiBioCUT&Tag, plusBiotin, noRapa, rep2

description: Library name: CenH3_noBiotin_plusRapa_rep2


title: M11-Young

description: Young (6 months)

value: Liver


title: CenH3, DiBioCUT&Tag, plusBiotin, noRapa, rep1

description: Library name: CenH3_noBiotin_plusRapa_rep1


title: Targeted bisulfite sequencing, 9221121, Tumor

description: paired-end 101bp


title: M10-Young

description: Young (6 months)


title: CenH3, DiBioCUT&Tag, noBiotin, noRapa, rep2

description: Library name: CenH3_noBiotin_noRapa_rep2


title: Targeted bisulfite sequencing, 9238665, Normal thyroid tissue

description: paired-end 101bp

value: N


title: M4-Young

description: Young (6 months)


title: M3-Young

description: Young (6 months)


title: CenH3, DiBioCUT&Tag, noBiotin, noRapa, rep1

description: Library name: CenH3_noBiotin_noRapa_rep1


title: Blood neutrophil, 0h, SRA replicate9

value: Severe RA


title: Targeted bisulfite sequencing, 9213165, Normal thyroid tissue

description: paired-end 101bp


title: CenH3, ChIP

description:
Library name: CenH3_ChIP
NF54-H3K9me3_CT_log2ratio_2000bpbins.bedgraph.gz

data_processing:
Sequencing reads were mapped against the reference genome PlasmoDB v26 3D7 with bowtie2 (v2.5.2)
Reads were filtered for mapping quality higher or equal than 30 and mitrochondrial and apicoplast reads were removed with samtools (v1.18)
BigWig files normalised to RPMK were generated with deeptools (v3.5.4)
Bedgraphs were generated for visualisation on UCSC genome browser with bedtools (v2.31.0) normalised to reads per million
Assembly: PlasmoDB v26 3D7
Supplementary files format and content: bedGraph

source_name: 3D7 wt

value: PfCENH3 (Volz et al. 2010)

value: 3D7 wt

value: chromatin


title: Blood neutrophil, 0h, SRA replicate7

value: peripheral blood


title: Targeted bisulfite sequencing, 9238665, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: M2-Young

description: Young (6 months)


title: CenH3, ChIP, Input

description:
Library name: CenH3_ChIP_Input
NF54-H3K9me3_CT_log2ratio_2000bpbins.bedgraph.gz


title: Blood neutrophil, 0h, SRA replicate12

value: Neutrophil


title: M1-Young

description: Young (6 months)


title: M12-Young

description: Young (6 months)


title: Blood neutrophil, 0h, SRA replicate6


title: Blood neutrophil, 0h, SRA replicate5


title: Blood neutrophil, 0h, SRA replicate8


title: Targeted bisulfite sequencing, 9358028, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 9367012, Normal thyroid tissue

description: paired-end 101bp


title: SAFA depletion, SAFA-WT-GFP_rep2

city: Boston

first: Michael

middle: D

last: Blower

state: MA

address: 72 E. Concord St. K123C

department: Biochemistry and Cell Biology

institute: Boston University

description:
SAF-A_WT_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_WT_chrX.txt
RPE1vsSAFAWT_DGE.txt
RPE14_SAFAWTGFP_SE.MATS.JC.txt

data_processing:
Duplicates were removed, adaptors were trimmed, and low quality reads were removed using fastp.
For DGE reads were aligned to hg38 using Subread, counted vs. EntrezGenes using FeatureCounts, and DGE was performed using EdgeR
for splicing analysis reads were aligned to hg38 using STAR and splicing was anayzed using rMATS
for allele-specific gene expression analysis reads were aligned and quantified against hg38 using PAC
Assembly: hg38
Supplementary files format and content: tab delimited text file for PAC counts per gene and tab delimited text file for DGE analysis of chrX genes from PAC data
Supplementary files format and content: tab deliimited text file for junction counts from rMATS output
Supplementary files format and content: tab delimited text file for read counts per gene and EdgeR output

growth_protocol: hTERT-RPE-1 cells were cultured in DMEM/F-12 supplemented with 10% FBS (HyClone Laboratories), penicillin/streptomycin, 2 mM glutamine, and 7.5% sodium bicarbonate.

extract_protocol:
Total RNA was harvested using Trizol Reagent(InvitrogenTM  #15596018), 1 micro gram of total RNA was used for library preparation.
Libraries were prepared by NEB Next rRNA depletion kit v2 (NEB #E7405) and NEBNext® Ultra™ II Directional RNA Library Prep kit(NEB #E7765) following manufacturer's instructions

treatment_protocol: To induce SAF-A depletion +/- SAF-A-GFP expression, cells were treated with 0.5 μg/mL doxycycline (D3447; MilliporeSigma) and 100 μg/mL 3-indole acetic acid (IAA, I-5148 MilliporeSigma) for 24 hours.

value: Retinal Pigment Epithelial Cells

value: SAFA depletion, SAFA-WT rescue

tag: treatment

value: dox, aux 24h


title: upf1gcn1delta_3_ypd_t30

description: Library name: upf1gcn1delta_3_ypd_t30

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
SLAM-Seq data analysed was performed with slamdunk (v0.4.3) provided by nfcore pipeline(v1.0.0)(https://nf-co.re/slamseq). Firstly, fastq compressed files (fastq.gz) were first converted to reverse complementary reads method in order to feed into slamdunk nf core pipeline as stranded libraries were prepared with dUTP.  Adapter contamination and low-quality bases were trimmed using TrimGalore(v 0.6.4) (trim length 27bp). Slamdunk was used for mapping, quantifying nucleotide-conversions and collapsing quantifications on gene level.  At least 2 T>C conversions per read was regarded as a confident call for labelled RNA reads. Genes with less than 10 reads were filter out. SNP masking was employed to distinguish filter T>C SNPs from converted nucleotides. T > C reads counts in each library were normalized to total library read counts. To calculate RNA half-lives , T>C conversions were normalized to chase-onset (t0). Curve fitting was performed followed by non-linear decay model equations in R using the minpack.lm package.  Degradation rate is calculated as 60 * ln(2) / t1/2 (t1/2 is half-time of gene).
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Bedgraph files for collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.
Library strategy: SLAM-seq

source_name: yeast cells

growth_protocol: S. cerevisiae (wildtype and upf1 mutant) were grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose) or  Complete Supplement Mixture (CSM from Formedium™).

extract_protocol:
Metabolic labelling of newly synthesized RNA molecules was performed as previously described [PMID: 28945705, PMID: 36838506].  Briefly, 4tU (Sigma)  was dissolved in NaOH (83 mM) used for labelling RNA molecules. The final concentration of 4tU for YPD and CSM is 5mM (PMID: 26941319) and 0.2 mM (PMID: 30192227), respectively. MES buffer (pH 5.9) with a final concentration 10 mM was prepared with media to avoid the PH change due to 4tU addition. To perform pulse and chase experiment, RNA molecules were labelled with 4tU (prepared as above) for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without  4tU and time points were collected at 0, 15 and 30 mins by centrifugation and snap frozen in liquid nitrogen immediately.
To perform thiol(SH)-linked alkylation, the reaction including 5 μg of RNA  was incubated with iodoacetamide (final concentration at 0.5 M) at 50 oC for 15 minutes [PMID: 28945705]. The reaction was stopped by adding 0.1 M DTT (final concentration at 20 mM). RNA was then precipitated by 3 M of sodium acetate and pure ethanol.  Purified RNA was subjected for ribosomal RNA depletion using RiboPools Depletion Kit (siTOOLs Biotech). Libraries were prepared by  Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacture instructions.  Sequencing was performed on Illumina Nextseq 2000 sequencer with single end read length for 150 cycles.

value: yeast cells

value: gcn1deltaupf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1deltaupf1delta)

value: Pulse for 1 h and chase for 30 min


title: Targeted bisulfite sequencing, 9367012, Tumor

description: paired-end 101bp

value: Female


title: upf1gcn1delta_3_ypd_t15

description: Library name: upf1gcn1delta_3_ypd_t15

value: Pulse for 1 h and chase for 15 min


title: Blood neutrophil, 0h, SRA replicate10


title: SAFA depletion, SAFA-WT-GFP_rep1

description:
SAF-A_WT_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_WT_chrX.txt
RPE1vsSAFAWT_DGE.txt
RPE14_SAFAWTGFP_SE.MATS.JC.txt

tag: cell line


title: upf1gcn1delta_3_ypd_t0

description: Library name: upf1gcn1delta_3_ypd_t0

value: Pulse for 1 h and chase for 0 min


title: Targeted bisulfite sequencing, 9368480, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: N


title: SAFA depletion, SAFA-SAP-GFP_rep2

description:
SAF-A_SAP_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_SAP_chrX.txt
RPE1vsSAFAdeltaSAP_DGE.txt
RPE14_SAFASAP_SE.MATS.JC.txt

value: SAFA depletion, SAFA-SAP rescue


title: Targeted bisulfite sequencing, 9368480, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 9358028, Normal thyroid tissue

description: paired-end 101bp


title: Blood neutrophil, 0h, SRA replicate2

value: Severe RA


title: SAFA depletion, SAFA-SAP-GFP_rep1

description:
SAF-A_SAP_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_SAP_chrX.txt
RPE1vsSAFAdeltaSAP_DGE.txt
RPE14_SAFASAP_SE.MATS.JC.txt


title: upf1gcn1delta_2_ypd_t30

description: Library name: upf1gcn1delta_2_ypd_t30


title: Targeted bisulfite sequencing, 9372803, Normal thyroid tissue

description: paired-end 101bp

value: Y


title: Blood neutrophil, 0h, SRA replicate1

value: peripheral blood


title: SAFA depletion, SAFA-DD-GFP_rep2

description:
SAF-A_DD_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_DD_chrX.txt
RPE1vsSAFADD_DGE.txt
RPE14_SAFADD_SE.MATS.JC.txt

value: SAFA depletion, SAFA-DD rescue


title: Targeted bisulfite sequencing, 9372803, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: upf1gcn1delta_2_ypd_t0

description: Library name: upf1gcn1delta_2_ypd_t0


title: parental MDA-MB-231 cell line expressing GFP, replicate 2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description:
Library name: 231Pa_Luc+GFP_RNA_rep2
q2_FPKM

data_processing:
Raw sequencing data of replicate 1 and 2 were combined for the following process.
Reference files of the human genome hg38 (NCBI build 38, Dec. 2013) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat2 (2.0.8)/Cufflinks with the default parameter settings (Trapnell et al., 2012).
Assembly: hg38
Supplementary files format and content: Txt files include FPKM values of genes for each sample.

source_name: breast cancer cell line

growth_protocol: 231Pa_Luc+GFP cells and 231Pa_Luc+OCT-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; #11965; Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS (#SH30910.03; Thermo Fisher Scientific or #10270-106; Gibco, Thermo Fisher Scientific), 50 U·mL-1 penicillin, 50 μg·mL-1 streptomycin (penicillin–streptomycin; #15070-063; Gibco, Thermo Fisher Scientific). Cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using Dynabeads mRNA DIRECT Purification Kit and the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific).

value: breast cancer cell line

value: breast cancer

tag: transgenes

value: GFP, luciferase


title: Targeted bisulfite sequencing, 9374944, Normal thyroid tissue

description: paired-end 101bp

tag: Sex


title: SAFA depletion, SAFA-DD-GFP_rep1

description:
SAF-A_DD_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_DD_chrX.txt
RPE1vsSAFADD_DGE.txt
RPE14_SAFADD_SE.MATS.JC.txt

value: Retinal Pigment Epithelial Cells

value: dox, aux 24h


title: upf1gcn1delta_1_ypd_t30

description: Library name: upf1gcn1delta_1_ypd_t30

value: yeast cells

value: gcn1deltaupf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1deltaupf1delta)

value: Pulse for 1 h and chase for 30 min


title: parental MDA-MB-231 cell line expressing GFP, replicate 1

description:
Library name: 231Pa_Luc+GFP_RNA_rep1
q2_FPKM


title: SAFA depletion, SAFA-AA-GFP_rep2

description:
SAF-A_AA_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_AA_chrX.txt
RPE1vsSAFAAA_DGE.txt
RPE14_SAFAAA_SE.MATS.JC.txt

value: SAFA depletion, SAFA-AA rescue


title: Targeted bisulfite sequencing, 9374944, Tumor

description: paired-end 101bp

value: Female


title: upf1gcn1delta_1_ypd_t15

description: Library name: upf1gcn1delta_1_ypd_t15

value: Pulse for 1 h and chase for 15 min


title: Blood neutrophil, 0h, SRA replicate4

value: Neutrophil


title: parental MDA-MB-231 cell line expressing OCT-2, replicate 2

description:
Library name: 231Pa_Luc+OCT-2_RNA_rep2
q1_FPKM

value: OCT-2, luciferase


title: SAFA depletion, SAFA-AA-GFP_rep1

description:
SAF-A_AA_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_AA_chrX.txt
RPE1vsSAFAAA_DGE.txt
RPE14_SAFAAA_SE.MATS.JC.txt


title: Blood neutrophil, 0h, SRA replicate3

value: Severe RA


title: Targeted bisulfite sequencing, 9375380, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: Y


title: parental MDA-MB-231 cell line expressing OCT-2, replicate 1

description:
Library name: 231Pa_Luc+OCT-2_RNA_rep1
q1_FPKM


title: upf1gcn1delta_1_ypd_t0

description: Library name: upf1gcn1delta_1_ypd_t0

value: Pulse for 1 h and chase for 0 min


title: Targeted bisulfite sequencing, 9375380, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: highly metastatic clone of MDA-MB-231 cell line, no TGF-beta, replicate 2

description:
Library name: 231-D_RNA_noTGF-beta_rep2
q4_FPKM

value: breast cancer cell line

value: breast cancer

value: luciferase

value: noTGF-beta


title: upf1gcn1delta_2_ypd_t15

description: Library name: upf1gcn1delta_2_ypd_t15

value: yeast cells


title: SAFA depletion, 72h_rep1

description:
SAF-a_depletion_72h_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAF-Adepletion_72h_chrX.txt
RPEvsSAFA_Dep_72h_DGE.txt
RPE72_SAFAKD72_SE.MATS.JC.txt

value: Retinal Pigment Epithelial Cells

value: SAFA depletion

value: dox, aux 72h


title: Targeted bisulfite sequencing, 9376943, Normal thyroid tissue

description: paired-end 101bp

value: Female


title: highly metastatic clone of MDA-MB-231 cell line, no TGF-beta, replicate 1

description:
Library name: 231-D_RNA_noTGF-beta_rep1
q4_FPKM


title: upf1gcn1delta_3_csm_t0

description: Library name: upf1gcn1delta_3_csm_t0

value: gcn1deltaupf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1deltaupf1delta)


title: Targeted bisulfite sequencing, 9376943, Tumor

description: paired-end 101bp


title: SAFA depletion, 48h_rep2

description:
SAF-A_depletion_48h_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_48h_chrX.txt
RPEvsSAFA_Dep_48h_DGE.txt
RPE48_SAFAKD48_SE.MATS.JC.txt

value: dox, aux 48h


title: highly metastatic clone of MDA-MB-231 cell line, TGF-beta treated, replicate 2

description:
Library name: 231-D_RNA_TGF-beta_rep2
q3_FPKM

value: TGF-beta


title: SAFA depletion, 48h_rep1

description:
SAF-A_depletion_48h_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_48h_chrX.txt
RPEvsSAFA_Dep_48h_DGE.txt
RPE48_SAFAKD48_SE.MATS.JC.txt


title: upf1gcn1delta_2_csm_t30

description: Library name: upf1gcn1delta_2_csm_t30

value: Pulse for 1 h and chase for 30 min


title: highly metastatic clone of MDA-MB-231 cell line, TGF-beta treated, replicate 1

description:
Library name: 231-D_RNA_TGF-beta_rep1
q3_FPKM


title: Targeted bisulfite sequencing, 9377120, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: Male


title: SAFA depletion, 24h_rep1

description:
RPEvsSAFA_Dep_24h_DGE.txt
RPE24_SAFAKD24_SE.MATS.JC.txt

value: dox, aux 24h


title: parental MDA-MB-231 cell line, no TGF-beta, replicate 2

description:
Library name: 231Pa_RNA_noTGF-beta_rep2
q2_FPKM


title: Targeted bisulfite sequencing, 9378183, Normal thyroid tissue

description: paired-end 101bp

value: N


title: upf1gcn1delta_2_csm_t0

description: Library name: upf1gcn1delta_2_csm_t0

value: Pulse for 1 h and chase for 0 min


title: upf1gcn1delta_2_csm_t15

description: Library name: upf1gcn1delta_2_csm_t15

value: Pulse for 1 h and chase for 15 min


title: SAFA depletion, 72h_rep2

description:
SAF-A_depletion_72h_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAF-Adepletion_72h_chrX.txt
RPEvsSAFA_Dep_72h_DGE.txt
RPE72_SAFAKD72_SE.MATS.JC.txt


title: upf1gcn1delta_3_csm_t30

description: Library name: upf1gcn1delta_3_csm_t30


title: SAFA depletion_rep4

description:
SAF-A_depletion_4_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt

value: dox, aux


title: parental MDA-MB-231 cell line, no TGF-beta, replicate 1

description:
Library name: 231Pa_RNA_noTGF-beta_rep1
q2_FPKM

value: breast cancer cell line

value: breast cancer

value: noTGF-beta


title: upf1gcn1delta_1_csm_t30

description: Library name: upf1gcn1delta_1_csm_t30

value: yeast cells


title: Targeted bisulfite sequencing, 9378183, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: upf1gcn1delta_3_csm_t15

description: Library name: upf1gcn1delta_3_csm_t15


title: upf1gcn1delta_1_csm_t15

description: Library name: upf1gcn1delta_1_csm_t15


title: SAFA depletion_rep2

value: Retinal Pigment Epithelial Cells

value: SAFA depletion


title: parental MDA-MB-231 cell line, TGF-beta treated, replicate 1

description:
Library name: 231Pa_RNA_TGF-beta_rep1
q1_FPKM


title: Targeted bisulfite sequencing, 9385757, Normal thyroid tissue

description: paired-end 101bp

value: Female


title: upf1gcn1delta_1_csm_t0

description: Library name: upf1gcn1delta_1_csm_t0

value: gcn1deltaupf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1deltaupf1delta)


title: SAFA depletion_rep3

description:
SAF-A_depletion_3_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt


title: SAFA depletion_rep1

description:
SAF-A_depletion_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt


title: 231Pa_Luc+OCT-2 anti-OCT-2 rep2

description:
Library name: 231Pa_Luc+OCT-2_anti-OCT-2_2
OCT2 binding regions calculated from replicate 1 and 2

data_processing:
Reference files of the human reference sequence assembly (UCSC hg19 and hg38) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
ChIP-seq reads were trimmed down to 50 bp with the SamToFastq command and replicate data were combined with the cat command.
Combined read data were aligned using Bowtie (version 2.2.2.6) (Langmead et al., 2009) with the command “bowtie -p 8 -S -a --best --strata -n 1 -m 1”.
Super-enhancer regions and OCT-2 binding regions were identified using HOMER software (Model based analysis of ChIP-seq) (version) (Heinz et al, 2010) with the command "findpeaks -style superhistone" for H3K27ac ChIP-seq and "findpeaks -style factor" for POU2F2 ChIP-seq.
Identified Super-enhancer regions were compared among replicates and common Super-enhancers  among replicates were listed with the command "mergePeaks -d given". Identified OCT-2 binding regions were annotated with the annotatePeaks.pl command. RPM score were caliculated with the command bedtools multicov.
Assembly: hg19 or hg38 (specified in each sample)
Supplementary files format and content: BED files were generated using HOMER (version) as described above.

growth_protocol: 231Pa_Luc+GFP cells and 231Pa_Luc+OCT-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; #11965; Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS (#SH30910.03; Thermo Fisher Scientific or #10270-106; Gibco, Thermo Fisher Scientific), 50 U·mL-1 penicillin, 50 μg·mL-1 streptomycin (penicillin–streptomycin; #15070-063; Gibco, Thermo Fisher Scientific). MDA-MB-436 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). MDA-MB-436_Luc2 (436_Luc2) cells and MDA-MB-436_Luc2_No3a (436-3a) cells are cultured in RPMI 1640 medium (#11875; Gibco, Thermo Fisher Scientific supplemented with 10% FBS (#SH30910.03; Thermo Fisher Scientific or #10270-106; Gibco, Thermo Fisher Scientific), 50 U·mL-1 penicillin, 50 μg·mL-1 streptomycin (penicillin–streptomycin; #15070-063; Gibco, Thermo Fisher Scientific). These cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
ChIP-seq was performed using 5 μg of anti-H3K27ac antibody (#MABI009-100) or 5 ug of anti-OCT-2 antibody (#sc-377475, Santa Cruz Biotechnology, Dallas, TX, USA), as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

value: cancer

tag: clone

value: stable transgene expression, polyclonal

value: luciferase, POU2F2

tag: chip antibodies


title: Targeted bisulfite sequencing, 9385757, Tumor

description: paired-end 101bp

tag: age


title: Targeted bisulfite sequencing, 9387433, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: Male

tag: metastasis

value: Y


title: gcn1delta_3_ypd_t30

description: Library name: gcn1delta_3_ypd_t30

value: gcn1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1delta)

value: Pulse for 1 h and chase for 30 min


title: Targeted bisulfite sequencing, 9377120, Tumor

description: paired-end 101bp


title: SAFA depletion, 24h_rep2

description:
SAF-A_depletion_6_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPEvsSAFA_Dep_24h_DGE.txt
RPE24_SAFAKD24_SE.MATS.JC.txt

value: dox, aux 24h


title: parental MDA-MB-231 cell line, TGF-beta treated, replicate 2

description:
Library name: 231Pa_RNA_TGF-beta_rep2
q1_FPKM

value: breast cancer cell line

value: breast cancer

value: TGF-beta


title: gcn1delta_3_ypd_t15

description: Library name: gcn1delta_3_ypd_t15

value: yeast cells

value: Pulse for 1 h and chase for 15 min


title: RPE1, 72h_rep2

description:
RPE1_72h_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAF-Adepletion_72h_chrX.txt
RPEvsSAFA_Dep_72h_DGE.txt
RPE72_SAFAKD72_SE.MATS.JC.txt

value: Retinal Pigment Epithelial Cells

value: WT


title: 231-D anti-OCT-2 rep2

description:
Library name: 231-D_anti-OCT-2_2
endogenous OCT2 binding regions calculated from replicate 1 and 2

value: highly metastatic clone MDA-231-D, stable transgene expression, polyclonal

value: luciferase


title: Targeted bisulfite sequencing, 9387433, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: RPE1, 72h_rep1

description:
RPE1_72h_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAF-Adepletion_72h_chrX.txt
RPEvsSAFA_Dep_72h_DGE.txt
RPE72_SAFAKD72_SE.MATS.JC.txt


title: gcn1delta_3_ypd_t0

description: Library name: gcn1delta_3_ypd_t0

value: Pulse for 1 h and chase for 0 min


title: RPE1, 48h_rep2

description:
RPE1_48h_2_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_48h_chrX.txt
RPEvsSAFA_Dep_48h_DGE.txt
RPE48_SAFAKD48_SE.MATS.JC.txt


title: 231-D anti-OCT-2 rep1

description:
Library name: 231-D_anti-OCT-2_1
endogenous OCT2 binding regions calculated from replicate 1 and 2

value: cancer


title: Targeted bisulfite sequencing, 9388058, Tumor

description: paired-end 101bp

value: Female

value: N


title: MDA-MB-436_Luc2 input

description:
Library name: MDA-MB-436_Luc2_input
superenhancers calculated from replicate 1 and 2

value: parental cell line

value: input genome


title: Targeted bisulfite sequencing, 9388773, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid

value: Male

value: Y


title: gcn1delta_2_ypd_t15

description: Library name: gcn1delta_2_ypd_t15

value: gcn1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1delta)


title: MDA-MB-436_Luc2_No3a H3K27ac rep2

description:
Library name: MDA-MB-436_Luc2_No3a_H3K27ac_2
superenhancers calculated from replicate 1 and 2

value: breast cancer cell line

value: ex vivo culture, polyclonal


title: RPE1, 24h_rep2

description:
RPEvsSAFA_Dep_24h_DGE.txt
RPE24_SAFAKD24_SE.MATS.JC.txt

value: Retinal Pigment Epithelial Cells


title: Targeted bisulfite sequencing, 9388773, Tumor

description: paired-end 101bp


title: 231Pa_Luc+OCT-2 anti-OCT-2 rep1

description:
Library name: 231Pa_Luc+OCT-2_anti-OCT-2_1
OCT2 binding regions calculated from replicate 1 and 2

value: stable transgene expression, polyclonal

value: luciferase, POU2F2


title: RPE1, 24h_rep1

description:
RPE_6_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPEvsSAFA_Dep_24h_DGE.txt
RPE24_SAFAKD24_SE.MATS.JC.txt

value: WT


title: MDA-MB-436_Luc2_No3a H3K27ac rep1

description:
Library name: MDA-MB-436_Luc2_No3a_H3K27ac_1
superenhancers calculated from replicate 1 and 2. 230307_P015_016_017_436_Luc2_rep1-2_436_Luc2_No3a_rep1-2_commonSE_H3K27ac-superhistone_ChIP-Seq_cts.bed: superenhancers common to parental MDA-MB-436 and its No3a subline.

value: luciferase


title: gcn1delta_2_ypd_t0

description: Library name: gcn1delta_2_ypd_t0

value: yeast cells

value: Pulse for 1 h and chase for 0 min


title: MDA-MB-436_Luc2 H3K27ac rep2

description:
Library name: MDA-MB-436_Luc2_H3K27ac_2
superenhancers calculated from replicate 1 and 2

value: cancer


title: Targeted bisulfite sequencing, 9389085, Normal thyroid tissue

description: paired-end 101bp

value: Female

value: N


title: RPE1_rep4

description:
RPE_4_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt


title: gcn1delta_1_ypd_t15

description: Library name: gcn1delta_1_ypd_t15

value: Pulse for 1 h and chase for 15 min


title: Targeted bisulfite sequencing, 9389085, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: Targeted bisulfite sequencing, 9388058, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: MDA-MB-436_Luc2 H3K27ac rep1

description:
Library name: MDA-MB-436_Luc2_H3K27ac_1
superenhancers calculated from replicate 1 and 2

value: parental cell line


title: RPE1_rep3

description:
RPE3_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt


title: RPE1_rep2


title: gcn1delta_1_ypd_t0

description: Library name: gcn1delta_1_ypd_t0

value: gcn1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1delta)


title: 231Pa_Luc+GFP H3K27ac rep2

description:
Library name: 231Pa_Luc+GFP_H3K27ac_2
superenhancers calculated from replicate 1 and 2

value: breast cancer cell line

value: luciferase, GFP


title: RPE1, 48h_rep1

description:
RPE1_48h_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_48h_chrX.txt
RPEvsSAFA_Dep_48h_DGE.txt
RPE48_SAFAKD48_SE.MATS.JC.txt

value: Retinal Pigment Epithelial Cells


title: gcn1delta_3_csm_t30

description: Library name: gcn1delta_3_csm_t30

value: Pulse for 1 h and chase for 30 min


title: gcn1delta_2_ypd_t30

description: Library name: gcn1delta_2_ypd_t30


title: RPE1_rep1

description:
RPE_1_RPE1-bulk_gene_level_ae.txt
RPEvsSAFA_dep_24h_chrX.txt
RPE14_SAFAKD14_SE.MATS.JC.txt


title: Targeted bisulfite sequencing, 9393660, Normal thyroid tissue

description: paired-end 101bp

value: Male

value: Y


title: 231Pa_Luc+OCT-2 H3K27ac rep2

description:
Library name: 231Pa_Luc+OCT-2_H3K27ac_2
superenhancers calculated from replicate 1 and 2

value: stable transgene expression, polyclonal

value: luciferase, POU2F2


title: 231Pa_Luc+GFP H3K27ac rep1

description:
Library name: 231Pa_Luc+GFP_H3K27ac_1
superenhancers calculated from replicate 1 and 2


title: Targeted bisulfite sequencing, 9389355, Tumor

description: paired-end 101bp


title: gcn1delta_3_csm_t15

description: Library name: gcn1delta_3_csm_t15

value: yeast cells


title: gcn1delta_1_ypd_t30

description: Library name: gcn1delta_1_ypd_t30


title: Targeted bisulfite sequencing, 9393660, Tumor

description: paired-end 101bp


title: 231Pa_Luc+OCT-2 H3K27ac rep1

description:
Library name: 231Pa_Luc+OCT-2_H3K27ac_1
superenhancers calculated from replicate 1 and 2

value: cancer