title: RNA-Seq_TS543_shH2AFV#2_rep3

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

description:
shH2AFV#2
H2AFV_KD_RNA-seq_TS543_TPM.txt

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and overrepresented sequences have been removed using cutadapt software (https://cutadapt.readthedocs.io/ en/stable/).
Further reads preprocessing was performed by Trimmomatic (version 0.36) with the parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50.
Mapping of RNA-seq reads was done using STAR_2.5.0a (Dobin et al., 2013) with default parameters for RNA-seq data; the human ENSEMBL gene annotation model (GRCh37).
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; TPM values for three experimental conditions with 3 replicates each.

source_name: Cancer stem cells

growth_protocol: The GSCs were cultured in human neural stem cell Maintenance Media (Millipore), 1% Penicillin-Streptomycin (PS) supplemented with EGF and  FGF (20 ng/ml each) to maintain stemness.

extract_protocol:
Tree days after treatment, cells were harvested and total RNA were extracted with RNeasy® Micro Kit (Qiagen).
After the QC procedures, mRNA  is enriched using oligo(dT) beads. The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: TS543 cells were treated with either with non-targeting or targeting shRNA.

value: Glioblastoma patient derived cancer stem cell

tag: passage


title: G11P2KD_Tam 2

status: Public on Jan 15 2022

type: SRA

city: Ithaca

first: Scott

last: Coonrod

state: New York

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

country: USA

institute: Cornell University

description:
D2_15
Nascent RNA

library_source: transcriptomic

data_processing:
Library strategy: PRO-seq
Paired end sequencing data were preprocessed to remove the adapter sequences and trim based on base quality, and deduplicating the reads based on unique molecular identifiers in RNA adapters.
Sequencing reads were mapped into a human genome assembly (hg19) using the Burrows-Wheeler Aligner software package.
Aligned BAM files were converted into bigWig format.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: BigWig files were generated from aligned BAM files by proseq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).

molecule: total RNA

organism: Homo sapiens

source_name: G11_PADI2 KD

growth_protocol: MCF7 cells were routinely grown in 10% Bovine Calf Serum in DMEM. 5x 10^6 cells were plated in 15 cm dish prior to the treatment.

extract_protocol:
Cells were washed with ice-cold PBS and lysed with NP-40 lysis buffer (Horibata S, et al., 2016). Nuclei were isolated and snap-frozen.
Precision run-on sequencing libraries were prepared following PRO-seq protocol (Mahat DB et al., Nat Protoc. 2016).

treatment_protocol: Cells in 15 cm dish were pre-treated in charcoal stripped serum media for 3 days. On the day of experiment, charcoal stripped serum pre-treated cells were treated with control (EtOH), E2 (100 nM estradiol), Tam (1 micro M Tamoxifen) for 40 min.

tag: cell line

tag: cell type

value: ER+ breast cancer cell line

tag: treatment

value: Tamoxifen

tag: tamoxifen sensitivity

value: Resistant

tag: shRNA knockdown

value: PADI2 shRNA


title: RNA-Seq_TS543_shH2AFV#2_rep2


title: B7P2KD_E2 1

description:
D1_11
Nascent RNA

source_name: B7_PADI2 KD

value: Estradiol

value: Sensitive


title: B7P2KD_EtOH 1

description:
D1_10
Nascent RNA

value: EtOH


title: RNA-Seq_TS543_shH2AFV#1_rep3

description:
shH2AFV#1
H2AFV_KD_RNA-seq_TS543_TPM.txt


title: B7_Tam 1

description:
D1_9
Nascent RNA

source_name: B7 (Tam Sen MCF7)


title: AlbCre-Hnf4a fl/fl_Liver_biological replicate 3

type: RNA

city: Heraklion

first: Dimitris

last: Kardassis

address: Vassilika Vouton

department: Medical School

country: Greece

institute: University of Crete

scan_protocol: GeneChip® Scanner 3000 7G (Affymetrix/ThermoFisher Scientific)

data_processing:
Affymetrix Transcriptome Analysis Console (TAC) Software Version 4.0.2 was used for the normalization, summarization and quality control of the microarray data. In the next step, TAC was used for the determination of the differentially expressed genes by performing p-value and fold change thresholds: p-value <0.05 and absolute fold change >1.5).
Expression values of probe sets after the analysis by Affymetrix Expression Console Software Version 4.0.2

label: biotin

organism: Mus musculus

source_name: AlbCre-Hnf4a fl/fl, 6-weeks, Liver, biological replicate 3

label_protocol: The aRNA was purified, reverse transcribed and the resulting cDNA was fragmented, labelled and hybridized overnight to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays.

growth_protocol: Alb-Cre and Hnf4αfl/fl mice were kindly provided by Dr I. Talianidis (Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece). Heterozygous animals carrying one floxed (fl; flanked by loxP) and one wild-type allele were crossed with animals hemizygous for the albumin-Cre transgene (AlbCre). Heterozygous (fl/+) animals carrying one copy of the AlbCre transgene were then bred with  Hnf4αfl/fl mice to generate Hnf4a liver knockout mice (AlbCre-Hnf4a fl/fl) and littermate control mice (Hnf4a fl/fl). All mice were maintained on a 12/12-h light/dark cycle and were given free access to food and water. All animals received human care and the study protocols comply with the guidelines of the Institute of Molecular Biology and Biotechnology, Heraklion, Greece.

extract_protocol: PureLink® RNA Mini Kit (ThermoFisher Scientific) was used for RNA isolation according to the manufacturer's instructions. Sample processing was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix/ThermoFisher Scientific). Starting from total RNA, first and second strand cDNA synthesis was performed. The double stranded cDNA was transcribed to aRNA (amplified RNA) during in vitro transcription (IVT).

treatment_protocol: All mice were fed a standard chow diet (Mucedola diet, 4RF25). At 6 weeks of age Hnf4a liver knockout mice (AlbCre-Hnf4a fl/fl) and control (Hnf4a fl/fl) mice were anesthetized with isoflurane and euthanized by cardiac puncture.

tag: genotyp

value: AlbCre-Hnf4a fl/fl

tag: tissue

value: liver


title: Hnf4a fl/fl_Liver_biological replicate 3

hyb_protocol: hybridized overnight to GeneChip™ Mouse Gene 2.0 ST Affymetrix expression arrays.

source_name: Hnf4a fl/fl, 6-weeks, Liver, biological replicate 3

value: Hnf4a fl/fl


title: AlbCre-Hnf4a fl/fl_Liver_biological replicate 1

source_name: AlbCre-Hnf4a fl/fl, 6-weeks, Liver, biological replicate 1


title: B7_EtOH 1

description:
D1_7
Nascent RNA


title: AlbCre-Hnf4a fl/fl_Liver_biological replicate 4

source_name: AlbCre-Hnf4a fl/fl, 6-weeks, Liver, biological replicate 4


title: B7_E2 1

description:
D1_8
Nascent RNA


title: B7P2KD_Tam 1

description:
D1_12
Nascent RNA


title: RNA-Seq_TS543_shH2AFV#1_rep2


title: G11P2KD_Tam 1

description:
D1_6
Nascent RNA


title: Hnf4a fl/fl_Liver_biological replicate 1

source_name: Hnf4a fl/fl, 6-weeks, Liver, biological replicate 1


title: RNA-Seq_TS543_shH2AFV#1_rep1


title: Hnf4a fl/fl_Liver_biological replicate 4

source_name: Hnf4a fl/fl, 6-weeks, Liver, biological replicate 4


title: AlbCre-Hnf4a fl/fl_Liver_biological replicate 2

source_name: AlbCre-Hnf4a fl/fl, 6-weeks, Liver, biological replicate 2


title: G11P2KD_E2 1

description:
D1_5
Nascent RNA


title: RNA-Seq_TS543_NT_rep1

description:
Control
H2AFV_KD_RNA-seq_TS543_TPM.txt


title: RNA-Seq_TS543_NT_rep3

description:
Control
H2AFV_KD_RNA-seq_TS543_TPM.txt


title: RNA-Seq_TS543_NT_rep2

description:
Control
H2AFV_KD_RNA-seq_TS543_TPM.txt


title: G11P2KD_EtOH 1

description:
D1_4
Nascent RNA


title: Hnf4a fl/fl_Liver_biological replicate 2

source_name: Hnf4a fl/fl, 6-weeks, Liver, biological replicate 2


title: ProSys(1-178) 22-rep3

city: Portici

first: Mariangela

last: Coppola

address: Via Università 100

country: Italy

institute: University of Naples "Federico II"

description: Biological replicate 3 of 3

hyb_protocol: Equal amounts of cRNAs (825 ng) from control and a transgenic line were mixed together and hybridized to the Tomato Gene Expression Microarray 4x44K (Agilent Technologies) at 65 °C for 17 hours in an Agilent Hybridization Oven (G2545A) at 10 rpm. Slides were washed with the Gene Expression Wash buffer 1 for 1 minute at room temperature, the Gene Expression Wash buffer 2 for 1 minute at 37°C, and treated with the Stabilization and Drying Solution for 30 seconds at room temperature.

scan_protocol: Slides were scanned with a dual laser microarray scanner (G2565AA, Agilent Technologies)

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Solanum lycopersicum

source_name: Transgenic tomato genotype ProSys(1-178) 22

label_protocol: Samples were amplified in the presence of cyanine-3 or cyanine-5 labelled CTP using the Agilent Low Input Quick Amp Labeling kit (Agilent Technologies). Samples were purified using the RNeasy mini spin columns (Qiagen).

growth_protocol: Seeds of Solanun lycopersicum L. “Red Setter” were sterilized and germinated in vitro. A. tumefaciens-mediated transformation of tomato cotyledons was performed. Putative transfomants were selected on kanamycin (50 mgl-1) and transferred to sterile soil in an environmental chamber 26+2 oC with a photoperiod of 16:8 hr light/dark.

extract_protocol: Total RNA was extracted using Plant RNeasy mini kit (Qiagen) according to manufacturer’s protocol.

tag: cultivar

value: Red Setter

value: leaves

source_name: Untransformed control


title: ProSys(1-178) 16-rep2

description: Biological replicate 2 of 3

source_name: Transgenic tomato genotype ProSys(1-178) 16


title: ProSys(1-178) 22-rep1

description: Biological replicate 1 of 3


title: ProSys(1-178) 16-rep1

description: Biological replicate 1 of 1


title: G11_Tam 1

description:
D1_3
Nascent RNA

source_name: G11 (Tam Res MCF7)


title: ProSys(1-178) 22-rep2

description: Biological replicate 2 of 3


title: ATAC-Seq_TS543_shH2AFV#2_rep2

library_source: genomic

data_processing:
ATAC-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were filtered based on quality and adapter sequences were removed from the ATAC-Seq experiments using Trim_galore (https://github.com/FelixKrueger/TrimGalore) with the default options.
The resulting fastq files were aligned to the human reference genome (hg19) using STAR (Dobin et al., 2013) with the following parameters: "--alignIntronMax 1", "--outFilterMismatchNoverLmax 0.09", "--alignMatesGapMax 2000", "--outFilterMultimapNmax 1", "--alignEndsType EndToEnd"; the rest of the options were set to the default.
Picard-tools MarkDuplicates was used to remove read duplicates.
Bam files were converted to bigWig for visualization purposes using deepTools (Ramirez  et al,Nucleic acids research,  2014) normalizing by library size and transforming the values to "counts per million".
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of normalized ATAC-Seq signal

molecule: genomic DNA

extract_protocol:
Cells were harvested and frozen in culture media containing 5% DMSO. Frozen cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al, Nature Methods 2013), with some modifications based on Corces et al., Nature methods, 2017. Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified.
Extracted material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).


title: G11_E2 1

description:
D1_2
Nascent RNA


title: ATAC-Seq_TS543_shH2AFV#2_rep1


title: ATAC-Seq_TS543_shH2AFV#1_rep2


title: ProSys(1-178) 16-rep3

description: Biological replicate 3 of 3


title: ATAC-Seq_TS543_NT_rep2


title: ATAC-Seq_TS543_NT_rep1


title: BBCA_Tam_PAD2 3

description:
C4_33
Replicate set 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using bowtie2.
Mapped reads were sorted and compressed in BAM format, and then bedGraph was converted to bigWig.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig

source_name: ER+ breast cancer cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: pre-treatment

value: BBCA

tag: chip antibody


title: WT_MPI2_E1

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description:
WT cultured Macrophages transferred into lungs of neonal Csf2Rb KO mice
result--Condition6--16_20--over--15_19.txt
19_WT_MPI2

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped and annotated to GRCm38.p5 STAR with cmdOptions --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
the read counts were scaled with the use of the trimmed mean of M-values (TMM) method
Genome_build: GRCm38.p5 Release_91-2018-02-26
Supplementary_files_format_and_content: tab-delimited text files, the processed data file includes Gene Identifier, gene name, description, log2 Ratio, pValue, fdr, normalized count (between-sample-normalization)

source_name: Macrophages

growth_protocol: Sorted cells were then seeded at a density of 1 × 105 cells/mL in untreated 24-well plates (Sarstedt, 83.3922.500) or 12-well plates (Sarstedt, 83.3921.500) and maintained in GlutaMAX supplement RPMI 1640 (Gibco, 61870036), containing 10% FCS, 10 mM Hepes, 50uM 2-mercaptoethanol, 100 U/ml penicillin, 100 U/ml streptomycin, in the presence of 30 ng/mL murine GM-CSF (PeproTech, 315-03) in vitro. Cells were sub-cultured when cell density reached 5 × 105 cells/mL, normally every 3-4 days. After 2 weeks culter cells were either sequenced or transferred into Csf2Ra deficinet neonates. 8 weeks later cells were isolated from bronchoalveolar lavage and sequenced

extract_protocol:
RNeasy kit was used for RNA isolation (Qiagen)
RNA libraries were prepared for sequencing using standard NextSeq protocols

treatment_protocol: In vitro cells were treated with 30 ng/mL murine GM-CSF (PeproTech, 315-03)

tag: strain

value: WT cultured Macrophages


title: ATAC-Seq_TS543_shH2AFV#1_rep1

source_name: Cancer stem cells


title: BBCA_Tam_RIgG 3

description:
C4_35
Replicate set 3

value: Rabbit IgG


title: BBCA_Tam_Cit 3

description:
C4_34
Replicate set 3


title: BBCA_Tam_MIgG 3

description:
C4_36
Replicate set 3

value: Mouse IgG


title: G11_EtOH 1

description:
D1_1
Nascent RNA


title: WT_MPI_AM2_E1

description:
WT cultured Macrophages
result--Condition6--16_20--over--15_19.txt
20_WT_MPI_AM2

source_name: Alveolar Macrophages


title: BBCA_E2_MIgG 3

description:
C3_30
Replicate set 3


title: BBCA_Tam_ER 3

description:
C4_32
Replicate set 3

value: Estrogen Receptor


title: WT_MPI_AM_E1

description:
WT cultured Macrophages
result--Condition6--16_20--over--15_19.txt
16_WT_MPI_AM


title: BBCA_Tam_Input 3

description:
C4_31
Replicate set 3

value: ER+ breast cancer cell line


title: BBCA_E2_RIgG 3

description:
C3_29
Replicate set 3


title: WT_MPI_E1

description:
WT cultured Macrophages transferred into lungs of neonal Csf2Rb KO mice
result--Condition6--16_20--over--15_19.txt
15_WT_MPI


title: BBCA_E2_Cit 3

description:
C3_28
Replicate set 3


title: CTR-20mM G [7-CTRHG-4]

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

institute: University of Padova

data_processing:
Data analysis was performed using CLC Genomics Workbench software v.20 (Quiagen)
Reads from FASTq files was filtered for quality and aligned to the Ensembl-v99-hg38 version of the reference human genome.
Normalization of the data was performed using TMM method (trimmed Mean of M-values
Statistically differentially expressed (DEG) transcripts were performed using Empirical analysis of Differential Gene Expression (EDGE, a count based statistics) with expression values
Genome_build: Ensembl-v99-hg38
Supplementary_files_format_and_content: raw data and cpm values (TMM-adjusted) for each Sample

source_name: CTR-20mM G

growth_protocol: Cells were cultured in RPMI 1640 medium (Sigma) supplemented with 10 % FBS, 1% L-glutamine and 1% antibiotic solution in a humid atmosphere containing 5% CO2 at 37°C

extract_protocol:
Total RNA was isolated from cells by RNeasy Mini kit (Qiagen).
200 ng of RNA was used for RNA-seq library preparation using the Illumina Stranded mRNA prep. (Illumina, USA)

treatment_protocol: THP1 cells  were plated in 6 well plates coated with Matrigel (Corning Incorporated Life Sciences, Tewksbury, MA) for 3 weeks in the complete osteogenic medium.THP-1 cells were cultured in osteogenic medium with high glucose (20 mM) or normal  5 mM glucose.

value: Peripheral blood

value: human monocytic cell line


title: CTR-20mM G [6-CTRHG-3]


title: CTR-20mM G [5-CTRHG-2]


title: CTR-20mM G [4-CTRHG-1]


title: CTR-5mM G [5-CTR-4]

source_name: CTR-5mM G


title: CTR-5mM G [4-CTR-3]


title: CTR-5mM G [3-CTR-2]


title: BBCA_EtOH_RIgG 3

description:
C2_23
Replicate set 3


title: CTR-5mM G [2-CTR-1]


title: BBCA_E2_Input 3

description:
C3_25
Replicate set 3


title: BBCA_EtOH_MIgG 3

description:
C2_24
Replicate set 3


title: BBCA_EtOH_Cit 3

description:
C2_22
Replicate set 3


title: BBCA_EtOH_Input 3

description:
C2_19
Replicate set 3


title: DMSO_Tam_RIgG 3

description:
C2_17
Replicate set 3

value: DMSO

value: Tamoxifen


title: TAF1B_8hrs_rep2_ChIP-Seq

city: Philadelphia

first: Vikram

middle: R

last: Paralkar

state: PA

address: 421 Curie Boulevard

department: Division of Hematology and Oncology, Department of Medicine

institute: University of Pennsylvania Perelman School of Medicine

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 -TAF1B ChIP-Seq Replicate 2

data_processing:
FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
Reads were mapped to a custom mm9_rDNA genome using Bowtie2 with the following parameter: -X 2000. This genome is the mm9 genome with a single 45,306 nt mouse rDNA repeat unit sequence (NCBI BK000964.3) inserted into chr12:2501-47806.
SAM files from Bowtie2 were converted to BAM using Samtools View with the following parameters: -F 4 -q 0. BAM files were sorted using Samtools Sort, and indexed using Samtools Index. Picard MarkDuplicates tool was used to remove PCR duplicate reads.
The IGVtools count feature was used to extract density across the rDNA sequence (chr12:2501-47806) from the BAM files.
Each FASTQ was also mapped in parallel to a Drosophila dm3 genome to quantify number of Drosophila reads pulled down by anti-H2av antibody. This read number was used to normalized rDNA mapping signal in each sample.
Genome_build: Custom-made mm9 genome with a single 45,306 nt mouse rDNA repeat unit sequence (NCBI BK000964.3) inserted into chr12:2501-47806
Supplementary_files_format_and_content: Excel spreadsheets showing normalized ChIP-Seq mapping signals across mouse rDNA sequence

source_name: ER-HoxA9 cell line with FKBPV-FLAG integrated into CEBPA locus

growth_protocol: ER-HoxA9 cell line was cultured at 37 °C in a 5 % CO2 atmosphere using RPMI-1640 media, supplemented with 10 % fetal bovine serum, 2 % stem cell factor [SCF] conditioned media (prepared from a Chinese hamster ovary cell line that stably secretes SCF), 0.5 µM β-Estradiol, and Penicillin/Streptomycin.

extract_protocol:
25 x 10^6 cells were crosslinked in 1% formaldehyde for 15 min at RT, and crosslinking reaction was quenched with glycine. To rupture cell and nuclear membranes, pelleted cells were snap-frozen in liquid nitrogen (30 sec), followed by thawing in 37 °C (1 min) for a total of three cycles, following which the cell pellet was stored at -80 °C. On the day of ChIP-Seq, cells were lysed in buffer containing MNase for chromatin fragmentation. MNase reaction was quenched by EGTA, and lysate was further sheared using a Bioruptor machine with two cycles of 30 sec ON and 30 sec OFF. Sheared extract was clarified by centrifugation, and to the clarified extract, 5 µl (50 ng) of Drosophila chromatin from S2 cells (Active Motif, #53083) was added as spike-in control. To ensure quantitative accuracy of spike-in, exactly 25 x 10^6 starting cells were used for each sample, and comparative samples were harvested and processed together. Extract was precleared by incubating overnight with mouse polyclonal IgG. The next morning, extract was clarified, and IgG was removed with Dynabeads. To the resultant supernatant (ChIP Input Lysate), 10 µg of the desired ChIP antibody was added, along with 2 µg of anti-H2Av (Active Motif, #61686) [which recognizes Drosophila-specific histone variant H2Av in spike-in chromatin], and incubated overnight at 4 °C with rotation. Lysate was clarified the next morning, and antibody-bound chromatin was pulled down with Dynabeads. Chromatin was eluted from Dynabeads, and treated with high salt, RNase A and Proteinase K. DNA was recovered using a Qiagen PCR purification kit, and eluted in 50 µl of 1X TE buffer.
All of the eluted DNA was used to construct NextSseq DNA libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina, quantified using KAPA Quantification Kit, and sequenced on an Illumina Nextseq 500 platform.

treatment_protocol: For all experiments involving dTAGV-1 treatment, cells were seeded at a density of 2 x 10^5 cells/ml, and maintained below a maximum concentration of 1 x 10^6 cells/ml. Based on the requirements of individual experiments, 500 nM dTAGV-1 or DMSO were added to media at appropriate time points prior to cell harvest. For timecourse experiments, ‘0 hr’ samples was treated with DMSO for a period of time equal to the maximum duration of dTagV-1 treatment in that experiment.

tag: agent

tag: time point

value: 8 hrs

value: provided by Tom Moss lab


title: UBTF_0hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - UBTF ChIP-Seq Replicate 1

value: 0 hrs

value: Santa Cruz Biotechnology, #sc-13125


title: BBCA_EtOH_ER 3

description:
C2_20
Replicate set 3

value: EtOH


title: UBTF_0hrs_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - UBTF ChIP-Seq Replicate 2


title: DMSO_Tam_MIgG 3

description:
C2_18
Replicate set 3


title: DMSO_Tam_PAD2 3

description:
C2_15
Replicate set 3


title: BBCA_E2_PAD2 3

description:
C3_27
Replicate set 3

value: Estradiol


title: TAF1B_0hrs_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - TAF1B ChIP-Seq Replicate 2


title: BBCA_EtOH_PAD2 3

description:
C2_21
Replicate set 3


title: UBTF_8hrs_dTag_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - UBTF ChIP-Seq Replicate 2


title: Spleen sample - 74_DI_L001

city: Ås

first: Jeleel

middle: Opeyemi

last: Agboola

address: Høgskoleveien 3B

department: Animal and Aquacultural Science

country: Norway

institute: Norwegian University of Life Science

data_processing:
RNA sequence data analysis was performed using the publicly available nf-core/RNA-seq pipeline version 3.3 implemented in Nextflow 21.04.0.
Raw reads were trimmed using Trim Galore and clean reads were thereafter aligned to Salmo salar genome Ssal_v3.1 (GenBank assembly accession: GCA_905237065.2) by STAR_RSEM. Gene-level assignment was performed using featureCounts (v1.4.6).
Differentially expressed genes (DEGs) between diets were estimated using DESeqe2 (v1.22.1) and SARTools (v1.7.3) R packages.
Genome_build: Ssal_v3.1 (GenBank assembly accession: GCA_905237065.2)
Supplementary_files_format_and_content: *.markdup.counts.txt: Tab-delimited count files generated with featureCounts.

organism: Salmo salar

source_name: Spleen sample

growth_protocol: Atlantic salmon smolts were fed experimental diets for 42 days in seawater. At the end of the experiment, distal intestine and spleen tissue were collected from 2 fish per tank (3 replicate tanks per diet) for transcriptomic analysis.

extract_protocol:
Total RNA was extracted from distal intestine and spleen tissue from 6 fish per dietary group.
Total RNA was extracted using Qiazol and chloroform protocol.
Libraries were prepared using TruSeq stranded mRNA library preparation according to Illumina standard protocol.

value: Spleen

tag: diet

value: 30% SBM + autolyzed Wickerhamomyces anomalus (AWA)

tag: FISH id


title: UBTF_8hrs_dTag_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - UBTF ChIP-Seq Replicate 1


title: TAF1B_0hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - TAF1B ChIP-Seq Replicate 1


title: BBCA_E2_ER 3

description:
C3_26
Replicate set 3

value: BBCA


title: Spleen sample - 73_DI_L001


title: DMSO_Tam_ER 3

description:
C2_14
Replicate set 3


title: Spleen sample - 21_DI_L001


title: Spleen sample - 57_DI_L001


title: Spleen sample - 56_DI_L001


title: RRN3_8hrs_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - RRN3 ChIP-Seq Replicate 2


title: DMSO_Tam_Cit 3

description:
C2_16
Replicate set 3


title: Spleen sample - 19_DI_L001


title: TAF1B_8hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 -TAF1B ChIP-Seq Replicate 1


title: RRN3_8hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - RRN3 ChIP-Seq Replicate 1


title: Spleen sample - 88_DI_L001

value: 30% SBM + spray-dried Wickerhamomyces anomalus (IWA)


title: Spleen sample - 62_DI_L001


title: DMSO_E2_MIgG 3

description:
C1_12
Replicate set 3

value: Mouse IgG


title: DMSO_Tam_Input 3

description:
C2_13
Replicate set 3


title: Spleen sample - 61_DI_L001


title: RNA-Seq_TS543_shH2AFV#2_rep1

value: Glioblastoma patient derived cancer stem cell


title: DMSO_E2_RIgG 3

description:
C1_11
Replicate set 3

value: ER+ breast cancer cell line

value: Rabbit IgG


title: RRN3_0hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - RRN3 ChIP-Seq Replicate 1


title: Spleen sample - 02_DI_L001


title: Spleen sample - 01_DI_L001


title: DMSO_E2_Cit 3

description:
C1_10
Replicate set 3


title: Spleen sample - 81_DI_L001

value: 30% SBM + autolyzed Cyberlindnera jadinii (ACJ)


title: RRN3_0hrs_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - RRN3 ChIP-Seq Replicate 2

value: DMSO


title: DMSO_E2_PAD2 3

description:
C1_9
Replicate set 3


title: RPA194_10hrs_dTag_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 10hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 1

value: 10 hrs

value: Santa Cruz Biotechnology, #sc-48385


title: Spleen sample - 79_DI_L001


title: Spleen sample - 85_DI_L001


title: DMSO_E2_ER 3

description:
C1_8
Replicate set 3

value: Estrogen Receptor


title: Spleen sample - 44_DI_L001


title: Spleen sample - 27_DI_L001


title: Spleen sample - 43_DI_L001


title: RPA194_8hrs_dTag_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 2

value: 8 hrs


title: Spleen sample - 105_DI_L001

value: 30% SBM + spray-dried Cyberlindnera jadinii (ICJ)


title: DMSO_E2_Input 3

description:
C1_7
Replicate set 3


title: Spleen sample - 26_DI_L001


title: Spleen sample - 104_DI_L001


title: DMSO_EtOH_MIgG 3

description:
C1_6
Replicate set 3

value: EtOH


title: RPA194_4hrs_dTag_rep2_ChIP-Se9

description: CEBPA Degron ER-HoxA9 line, treated with 4hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 2

value: 4 hrs


title: RPA194_8hrs_dTag_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 8hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 1


title: Spleen sample - 38_DI_L001

value: Spleen


title: RPA194_4hrs_dTag_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 4hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 1


title: RPA194_10hrs_dTag_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with 10hrs dTagV1 - RPA194 (Pol I) ChIP-Seq Replicate 2


title: DMSO_EtOH_Cit 3

description:
C1_4
Replicate set 3


title: Spleen sample - 37_DI_L001


title: RPA194_0hrs_rep2_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - RPA194 (Pol I) ChIP-Seq Replicate 2

value: 0 hrs


title: Spleen sample - 07_DI_L001


title: Spleen sample - 09_DI_L001


title: Spleen sample - 93_DI_L001

value: 30% soybean meal (SBM)


title: Spleen sample - 95_DI_L001


title: Spleen sample - 33_DI_L001


title: DMSO_EtOH_PAD2 3

description:
C1_3
Replicate set 3


title: Spleen sample - 67_DI_L001


title: DMSO_EtOH_Input 3

description:
C1_1
Replicate set 3


title: DMSO_EtOH_ER 3

description:
C1_2
Replicate set 3


title: Spleen sample - 70_DI_L001


title: CEBPA-FLAG_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line - CEBPA-FLAG ChIP-Seq

value: Sigma, #F1804


title: RPA194_0hrs_rep1_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line, treated with DMSO (0hrs) - RPA194 (Pol I) ChIP-Seq Replicate 1


title: Spleen sample - 101_DI_L001

value: Fishmeal (FM)


title: IgG_ChIP-Seq

description: CEBPA Degron ER-HoxA9 line - IgG

value: Invitrogen, #31903


title: Spleen sample - 31_DI_L001


title: Spleen sample - 51_DI_L001


title: BBCA_Tam_MIgG 2

description:
B3_36
Replicate set 2

value: ER+ breast cancer cell line

value: BBCA

value: Tamoxifen

value: Mouse IgG


title: Spleen sample - 98_DI_L001


title: Input DNA

description: CEBPA Degron ER-HoxA9 line - Input


title: Spleen sample - 49_DI_L001


title: BBCA_Tam_RIgG 2

description:
B3_35
Replicate set 2

value: Rabbit IgG


title: DMSO_EtOH_RIgG 3

description:
C1_5
Replicate set 3

value: DMSO


title: Control group, scRNA-seq library of mouse brain cells

city: Dallas

first: Boxun

last: Li

state: Texas

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

data_processing:
BCL files generated by Illumina sequencing systems were demultiplexed and converted to standard FASTQ files using mkfastq function from Cell Ranger pipeline (version 3.0.2).
Reads were processed to generate expression (UMI count) matrices using Cell Ranger pipeline (version 3.1.0) with default parameters, except the parameter of expected number of cells, which was adjusted based on individual experiment.
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI count matrices representing gene expression values (.h5 format) were generated as described above. Each column represents a single cell, each row represents a single gene.

source_name: tdTomato+ cells from Aldh1l1-Ai14 mouse brain striatum, 4 weeks post lentivirus injection

growth_protocol: Aldh1L1-A14 mice treated with tamoxifen were bilateral injected with LV-hGFAP-GFP (n=4) or LV-hGFAP-Dlx2-IRES-GFP (n=5)

extract_protocol:
Cells were left to stay for 2min and the supernatant was transferred to a new 50ml tube. Volume was topped to 1ml with HABG+1%BSA. Cells were triturated using 1ml low binding barrier tip (Genesee Scientific, #23-430) for 10 times. Cells were combined and filtered through 40 um cell strainer (FALCON, REF352340). Cells were pellet down and resuspended in HABG+1% BSA for FACS sorting. Cells were sorted into HABG+1%BSA and followed by exchanging buffer to DPBS+0.05%BSA for 10x Genomics library construction.
Single cell RNA sequencing libraries were constructed following the manufacturer’s instructions (Zheng et al., 2017).

treatment_protocol: At 4wpi, mice were enthusized with isoflurane and perfused with cold 0.9% NaCl solution to remove blood. Brains were collected and dissected in HABG containing Hibernate A (BrainBits), B27 (Gibco) and Glutamine (Gibco) on ice. Tissues were chopped into 0.5~1mm3 pieces and digested using papain in Hibernate A minus Ca medium (1mg/ml papain, 0.125x Glutamine, 0.5mM EDTA, 0.05mg/ml DNaseI, 2.5mM MgCl2) at 37 oC for 45min. Digestion was terminated by adding equal volume of HABG+2% BSA and cells were dispensed using 10ml serological pipette triturating 12 times.

tag: lentivirus

value: LV-hGFAP-GFP


title: BBCA_Tam_Cit 2

description:
B3_34
Replicate set 2


title: DLX2 group, scRNA-seq library of mouse brain cells

description: 10x Genomics


title: Distal intestine sample - 74_DI_L001

source_name: Distal intestine sample

value: Distal intestine

value: 30% SBM + autolyzed Wickerhamomyces anomalus (AWA)


title: BBCA_Tam_PAD2 2

description:
B3_33
Replicate set 2


title: Distal intestine sample - 57_DI_L001


title: BBCA_Tam_ER 2

description:
B3_32
Replicate set 2

value: Estrogen Receptor


title: Distal intestine sample - 21_DI_L001


title: Distal intestine sample - 88_DI_L001

value: 30% SBM + spray-dried Wickerhamomyces anomalus (IWA)


title: Distal intestine sample - 85_DI_L001


title: Distal intestine sample - 56_DI_L001


title: Distal intestine sample - 62_DI_L001


title: BBCA_E2_MIgG 2

description:
B3_30
Replicate set 2

value: Estradiol


title: BBCA_Tam_Input 2

description:
B3_31
Replicate set 2


title: M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep2

city: Hefei

first: Xucong

last: Teng

address: No. 96, Jinzhai Road

department: Hefei National Laboratory of Physical Science at Microscale

country: China

institute: University of Science and Technology of China

data_processing:
Library strategy: LiveG4ID-seq
[Trimming] Raw reads were trimmed with Trim Galore (version: 0.4.4).
[Read alignment] Trimmed reads were filtered for repeat elements using sequences obtained from RepBase (v26.08) with bowtie2 (v.2.3.5.1). Then reads were aligned with bowtie2 (v.2.3.5.1) using -I 25 -X 500 -N 1 -L 25 and samtools (v1.10).
[Deduplication] BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[Genome coverage] Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: hg19 for human cell lines; mm9 for mouse cell lines
Supplementary_files_format_and_content: Normalized genomic tracks in BigWig format; Expression matirx of RNA-seq data in TXT format

growth_protocol: HEK293T cells, HEK293FT cells, HeLa cells and N2a cells were obtained from National Infrastructure of Cell Line Resource (NICLR, China). The cell lines were checked free of mycoplasma contamination by PCR. Their species origins were confirmed with PCR. The identity of the cell line was authenticated with STR profiling (FBI, CODIS). All the results can be viewed on the website (http://cellresource.cn). HEK293T cells, HEK293FT cells, HeLa cells and N2a cells were maintained in Dulbecco’s modified eagle medium (DMEM, Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Macklin) at 37 °C/5% CO2. LiveG4ID lentivirus was produced in HEK293FT cells. HEK293T cells, HeLa cells, N2a cells were transfected with LiveG4ID lentivirus to generate HEK293T-LiveG4ID cell line, HeLa-LiveG4ID cell line, N2a-LiveG4ID cell line. These stably transfected cell lines had the ability to express LiveG4ID upon induced by Dox.

extract_protocol:
Purified genomic DNA from LiveG4ID-seq were mixed with the universal i5 primer and barcoded i7 primer, and amplified with 5X Ampli PCR Mix (Novoprotein, Shanghai). The library PCR products were cleaned up with DNA Clean Beads (Vazyme, Nanjing).
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).

treatment_protocol: For the expression of LiveG4ID, HEK293T-LiveG4ID cells, HeLa-LiveG4ID cells, or N2a-LiveG4ID cells were treated in complete media supplemented with 1 ng/mL (Low Dox), 1 ug/mL (High Dox), respectively.  For G1/S arrest, cells were incubated in complete media supplemented with 300 μM L-Mimosine (SM9070, Solarbio) for 24 hrs. Early S phase arrest was obtained by cells treated with 300 μM L-Mimosine in complete media for 16 hrs, followed by 3 hrs in complete media. Synchronisation at G2/M was attained by incubating cells with 9 μM RO-3306 (HY-12529, MCE) supplemented complete media for 24 hrs. M arrest was achieved by incubating cells with 0.1 µg/mL colcemid (12-004-1D, BI) in complete media for 24 hrs.

value: HEK293T with Dox-induced expressing of LiveG4ID

value: M arrest was achieved by incubating cells with 0.1 ug/mL colcemid (12-004-1D, BI) in complete media for 24 hrs.


title: Distal intestine sample - 02_DI_L001


title: Distal intestine sample - 61_DI_L001


title: G2-M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep3

value: Synchronisation at G2/M was attained by incubating cells with 9 uM RO-3306 (HY-12529, MCE) supplemented complete media for 24 hrs.


title: M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep1


title: Distal intestine sample - 01_DI_L001


title: M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep3


title: G2-M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: Distal intestine sample - 19_DI_L001


title: Spleen sample - 15_DI_L001

value: Spleen

value: Fishmeal (FM)


title: Spleen sample - 13_DI_L001


title: BBCA_E2_Cit 2

description:
B3_28
Replicate set 2

value: ER+ breast cancer cell line


title: G2-M_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep1


title: Distal intestine sample - 81_DI_L001

value: 30% SBM + autolyzed Cyberlindnera jadinii (ACJ)


title: Distal intestine sample - 79_DI_L001


title: Distal intestine sample - 73_DI_L001


title: BBCA_E2_PAD2 2

description:
B3_27
Replicate set 2

value: BBCA


title: Distal intestine sample - 44_DI_L001


title: BBCA_E2_ER 2

description:
B3_26
Replicate set 2


title: S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep3

value: Early S phase arrest was obtained by cells treated with 300 uM L-Mimosine in complete media for 16 hrs, followed by 3 hrs in complete media.


title: Distal intestine sample - 27_DI_L001


title: S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: Distal intestine sample - 26_DI_L001


title: BBCA_E2_RIgG 2

description:
B3_29
Replicate set 2

value: Rabbit IgG


title: Distal intestine sample - 104_DI_L001

value: 30% SBM + spray-dried Cyberlindnera jadinii (ICJ)


title: Distal intestine sample - 38_DI_L001


title: Distal intestine sample - 37_DI_L001


title: BBCA_E2_Input 2

description:
B3_25
Replicate set 2


title: Distal intestine sample - 07_DI_L001


title: G1-S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep3

value: For G1/S arrest, cells were incubated in complete media supplemented with 300 uM L-Mimosine (SM9070, Solarbio) for 24 hrs.


title: G1-S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: BBCA_EtOH_RIgG 2

description:
B2_23
Replicate set 2

value: EtOH


title: Distal intestine sample - 95_DI_L001

value: Distal intestine

value: 30% soybean meal (SBM)


title: G1-S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep1


title: Distal intestine sample - 93_DI_L001


title: Distal intestine sample - 70_DI_L001


title: HeLa-LiveG4ID_LowDox_LiveG4ID-seq_rep3

value: HeLa with Dox-induced expressing of LiveG4ID

value: 1 ng/mL Dox for 48 h


title: Distal intestine sample - 67_DI_L001


title: BBCA_EtOH_ER 2

description:
B2_20
Replicate set 2

value: Estrogen Receptor


title: Distal intestine sample - 31_DI_L001


title: BBCA_EtOH_Input 2

description:
B2_19
Replicate set 2


title: Distal intestine sample - 43_DI_L001


title: S_HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep1

value: HEK293T with Dox-induced expressing of LiveG4ID


title: HeLa-LiveG4ID_LowDox_LiveG4ID-seq_rep1


title: BBCA_EtOH_MIgG 2

description:
B2_24
Replicate set 2

value: Mouse IgG


title: Distal intestine sample - 49_DI_L001


title: DMSO_Tam_MIgG 2

description:
B2_18
Replicate set 2

value: DMSO

value: Tamoxifen


title: DMSO_Tam_RIgG 2

description:
B2_17
Replicate set 2

value: ER+ breast cancer cell line


title: Distal intestine sample - 15_DI_L001

value: Fishmeal (FM)


title: DMSO_Tam_Cit 2

description:
B2_16
Replicate set 2


title: HEK293T-LiveG4ID_HighDox_RNA-seq_rep3

data_processing:
[Trimming] Raw reads were trimmed with Trim Galore (version: 0.4.4).
[Read alignment] Trimmed reads were filtered for repeat elements using sequences obtained from RepBase (v26.08) with bowtie2 (v.2.3.5.1). Then reads were aligned with bowtie2 (v.2.3.5.1) using -I 25 -X 500 -N 1 -L 25 and samtools (v1.10).
[Deduplication] BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[Genome coverage] Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: hg19 for human cell lines; mm9 for mouse cell lines
Supplementary_files_format_and_content: Normalized genomic tracks in BigWig format; Expression matirx of RNA-seq data in TXT format

molecule: polyA RNA

extract_protocol:
RNA-seq was performed using Hieff NGS® MaxUp II Dual-mode mRNA Library Prep Kit for Illumina® MaxUp II kit under the manufacturer's protocol.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).

value: 10 ug/mL Dox for 48 h


title: Distal intestine sample - 09_DI_L001


title: BBCA_EtOH_Cit 2

description:
B2_22
Replicate set 2

value: BBCA


title: BBCA_EtOH_PAD2 2

description:
B2_21
Replicate set 2


title: DMSO_Tam_PAD2 2

description:
B2_15
Replicate set 2


title: HEK293T-LiveG4ID_HighDox_RNA-seq_rep1


title: HEK293T-LiveG4ID_LowDox_RNA-seq_rep3


title: Distal intestine sample - 33_DI_L001


title: HeLa-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: Cx_former

city: Daejeon

first: Haemin

last: Chon

address: Daehak-ro 291

department: Graduate school of medical science and engineering

country: South Korea

institute: KAIST

description:
Cortex_former
tdTomato +
Single-cell RNA

data_processing:
Cell Ranger (v3.0.2) with tdTomato and EGFRvIII sequence inserted was used to process single cell 3' RNA-seq output. First, cell ranger mkfastq demultiplexed Illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.4) and cell-gene raw expression matrices were made. Then, immune cell contaminates (Itgam and/or Ptprc expression), low quality cells (expressing less then 200 genes), potential dead cells (>=25% mitochondrial gene percentage) were removed.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files. Batch removal was done using 2500 anchon features.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.h5: HDF5 files.

source_name: glioblastoma

extract_protocol:
FACS-sorted tumor cells were processed on the 10X Chromium system following the manufacturer's protocols.
Using 10X single-cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X Genomics), cDNA libraries were constructed.

value: GBM model

value: Cortex

value: FACS-sorted cancer cells

tag: age

value: Adult

tag: batch


title: Cx_latter

description:
Cortex_latter
tdTomato +
Single-cell RNA

tag: cell type


title: Co_former

description:
Core_former
tdTomato +
Single-cell RNA

value: Tumor center


title: DMSO_Tam_ER 2

description:
B2_14
Replicate set 2

tag: cell line

tag: treatment


title: Co_latter

description:
Core_latter
tdTomato +
Single-cell RNA


title: CC_latter

description:
Corpus callosum_latter
tdTomato +
Single-cell RNA

value: Corpus callosum


title: Distal intestine sample - 101_DI_L001

value: Distal intestine


title: HEK293T-LiveG4ID_LowDox_RNA-seq_rep2

value: 1 ng/mL Dox for 48 h


title: Distal intestine sample - 98_DI_L001


title: CC_former

description:
Corpus callosum_former
tdTomato +
Single-cell RNA


title: HEK293T-LiveG4ID_LowDox_RNA-seq_rep1


title: Distal intestine sample - 51_DI_L001


title: Distal intestine sample - 13_DI_L001


title: N2a-LiveG4ID_LowDox_LiveG4ID-seq_rep1

value: N2a with Dox-induced expressing of LiveG4ID


title: N2a-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: DMSO_E2_MIgG 2

description:
B1_12
Replicate set 2

value: Estradiol


title: HEK293T-LiveG4ID_NoDox_RNA-seq_rep3

value: HEK293T with Dox-induced expressing of LiveG4ID


title: DMSO_E2_RIgG 2

description:
B1_11
Replicate set 2

value: DMSO

value: Rabbit IgG


title: HEK293T-LiveG4ID_HighDox_RNA-seq_rep2


title: HEK293T-LiveG4ID_NoDox_RNA-seq_rep2


title: DMSO_E2_Cit 2

description:
B1_10
Replicate set 2

value: ER+ breast cancer cell line


title: 35248

type: genomic

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio with GT module (Illumina).

organism: Canis lupus familiaris

source_name: blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.

tag: origin

value: Argentina

tag: breed

value: Ovejero Argentino


title: 35250


title: 35254


title: 35253


title: 35249


title: HEK293T-LiveG4ID_NoDox_RNA-seq_rep1


title: 35252


title: 35251


title: 34861

value: Chile

value: Border Collie


title: HEK293T-LiveG4ID_HighDox_competitive_G4_antibody_binding_seq_rep3

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG12ID and chromatin G-quadruplexes.

data_processing:
Library strategy: CUT&TAG
[Trimming] Raw reads were trimmed with Trim Galore (version: 0.4.4).
[Read alignment] Trimmed reads were filtered for repeat elements using sequences obtained from RepBase (v26.08) with bowtie2 (v.2.3.5.1). Then reads were aligned with bowtie2 (v.2.3.5.1) using -I 25 -X 500 -N 1 -L 25 and samtools (v1.10).
[Deduplication] BAM files were deduplicated with picard (v2.23.4) MarkDuplicates
[Genome coverage] Normalized (RPGC, 1x Genome Coverage) coverage tracks were generated using deepTools (v3.3.2) bamCoverage using parameters -binSize 5 --normalizeUsing RPGC
Genome_build: hg19 for human cell lines; mm9 for mouse cell lines
Supplementary_files_format_and_content: Normalized genomic tracks in BigWig format; Expression matirx of RNA-seq data in TXT format

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG12ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).

value: 10 ug/mL Dox for 48 h


title: HEK293T-LiveG4ID_HighDox_competitive_G4_antibody_binding_seq_rep2

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG11ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG11ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: DMSO_E2_PAD2 2

description:
B1_9
Replicate set 2


title: Distal intestine sample - 105_DI_L001

tag: tissue

value: 30% SBM + spray-dried Cyberlindnera jadinii (ICJ)


title: 34855

value: Kelpie


title: DMSO_E2_ER 2

description:
B1_8
Replicate set 2

value: Estrogen Receptor


title: 34860


title: 34854

value: Magallenas region, Chile

value: Patagonian Ovejero Dog


title: DMSO_Tam_Input 2

description:
B2_13
Replicate set 2

value: Tamoxifen


title: DMSO_E2_Input 2

description:
B1_7
Replicate set 2


title: 34858


title: 34853


title: DMSO_EtOH_MIgG 2

description:
B1_6
Replicate set 2

value: EtOH

value: Mouse IgG


title: HEK293T-LiveG4ID_LowDox_competitive_G4_antibody_binding_seq_rep3

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG9ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG9ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).

value: HEK293T with Dox-induced expressing of LiveG4ID

value: 1 ng/mL Dox for 48 h


title: 34852


title: 34859


title: 34857


title: DMSO_EtOH_RIgG 2

description:
B1_5
Replicate set 2

value: DMSO

value: Rabbit IgG


title: HEK293T-LiveG4ID_LowDox_competitive_G4_antibody_binding_seq_rep2

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG8ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG8ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: DMSO_EtOH_Cit 2

description:
B1_4
Replicate set 2

value: ER+ breast cancer cell line


title: HEK293T-LiveG4ID_LowDox_competitive_G4_antibody_binding_seq_rep1

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG7ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG7ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: 34856


title: 34850


title: 34851


title: 34849


title: DMSO_EtOH_PAD2 2

description:
B1_3
Replicate set 2


title: 34848


title: HEK293T-LiveG4ID_NoDox_competitive_G4_antibody_binding_seq_rep3

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG6ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG6ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: 34843


title: DMSO_EtOH_Input 2

description:
B1_1
Replicate set 2


title: DMSO_EtOH_ER 2

description:
B1_2
Replicate set 2


title: BBCA_Tam_MIgG 1

description:
A3_30
Replicate set 1

value: BBCA


title: HEK293T-LiveG4ID_NoDox_competitive_G4_antibody_binding_seq_rep2

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG5ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG5ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: 34842


title: HEK293T-LiveG4ID_HighDox_competitive_G4_antibody_binding_seq_rep1

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG10ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG10ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: 34846


title: 34841


title: BBCA_Tam_Cit 1

description:
A3_29
Replicate set 1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.


title: HEK293T-LiveG4ID_NoDox_competitive_G4_antibody_binding_seq_rep1

description: After Dox-induced LiveG4ID expression, the chromatin G-quadruplex landscape was detected by conventianal CUT&Tag using Mouse IgG1 BG4 antibody to evaluate the binding between LiveG4ID and chromatin G-quadruplexes.

extract_protocol:
For CUT&Tag with BG4 antibody to evluate the binding specificity between LiveG4ID and chromatin G-quadruplexes by competitive binding of BG4 antibody and LiveG4ID protein, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 BG4 Mouse IgG1 antibody (Absolute Antibody, Ab00174-30.126) dilution at RT by rotating for 2 h. Then the BG4 Mouse IgG1 antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 Goat anti-Mouse IgG antibody (Abcam, ab6708) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG4ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: 34845


title: 34839


title: HEK293T_purified_LiveG4ID_CUT&Tag_rep3

extract_protocol:
For CUT&Tag with purified G4ID protein to identify the chromatin G-quadruplexes in permeabilized cells, the protocol is a little different from LiveG4ID-seq. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 10 ug/mL G4ID protein at RT by rotating for 2 h. Then the G4ID protein buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. The following steps were the same as LiveG4ID-seq.
The first antibody for the identification of chromatin G-quadruplexes was expressed as LiveG4ID in living cells. Then LiveG4ID-seq experiment was performed according to a protocol similar to CUT&Tag. Briefly, 20 K cells were harvested, washed with wash buffer (20mM HEPES pH 7.5, 150mM NaCl, 0.5mM spermidine), and immobilized to concanavalin A–coated beads (Novoprotein, Shanghai) with incubation at room temperature for 10 min. The beads-bound cells were incubated in 50 μl of buffer (wash buffer with 2mM EDTA, 0.1% BSA and 0.05% digitonin) with 1:100 Rabbit anti-GFP antibody (Yeasen, Shanghai) dilution at RT by rotating for 2 h. Then the Rabbit anti-GFP antibody buffer was removed. The incubated cells were then resuspended with 100 ul of dig-wash buffer with 1:200 dilution of Goat anti-Rabbit IgG antibody (Abcam, ab6702) and incubated at room temperature for 1 hour by rotating. After wash with 500 uL dig-wash buffer twice, cells were resuspended in 60 ul of dig-300 buffer (20mM HEPES pH 7.5, 300mM NaCl and 0.5mM spermidine, 0.01% digitonin) with 1:100 dilution of pA/G-Tn5 transposome and incubated at room temperature for 1 hour by rotating. pA/G-Tn5-bound cells were washed with 500 ul of dig-300 buffer twice, followed by tagmentation in 50ul of tagmentation buffer (dig-300 buffer with 10mM MgCl2) at 37℃ for 1 hour. After tagmentation, 1 uL of 10% SDS was added and further incubated at 55℃ for 10 min to stop tagmentation and detach Tn5 from DNA. The DNA fragments were extracted by 3:1 v/v Tagment DNA Extract Beads (Novoprotein, Shanghai).


title: HEK293T_purified_LiveG4ID_CUT&Tag_rep2


title: 34837


title: 34838


title: HEK293T_purified_LiveG4ID_CUT&Tag_rep1


title: BBCA_Tam_PAD2 1

description:
A3_28
Replicate set 1


title: 34844


title: BBCA_Tam_ER 1

description:
A3_27
Replicate set 1


title: 34836


title: 34829


title: 34818


title: 34835


title: HEK293T-LiveG4ID_HighDox_LiveG4ID-seq_rep2


title: BBCA_E2_MIgG 1

description:
A3_25
Replicate set 1

value: Estradiol


title: BBCA_Tam_Input 1

description:
A3_26
Replicate set 1


title: HEK293T-LiveG4ID_HighDox_LiveG4ID-seq_rep1


title: 34834


title: HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep3


title: 34817


title: 34833


title: 34847


title: BBCA_E2_Cit 1

description:
A3_24
Replicate set 1


title: 34816


title: HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep2


title: 34815


title: 34830


title: HEK293T-LiveG4ID_LowDox_LiveG4ID-seq_rep1


title: BBCA_E2_ER 1

description:
A3_22
Replicate set 1


title: BBCA_E2_PAD2 1

description:
A3_23
Replicate set 1


title: BBCA_E2_Input 1

description:
A3_21
Replicate set 1


title: HEK293T-LiveG4ID_NoDox_LiveG4ID-seq_rep3


title: 34803


title: 34814

value: Aysen region, Chile


title: BBCA_EtOH_MIgG 1

description:
A2_20
Replicate set 1


title: 34813


title: HEK293T-LiveG4ID_NoDox_LiveG4ID-seq_rep2


title: HEK293T-LiveG4ID_HighDox_LiveG4ID-seq_rep3

value: 10 ug/mL Dox for 48 h


title: 34812


title: 34802


title: 34810


title: HEK293T-LiveG4ID_NoDox_LiveG4ID-seq_rep1


title: 34801


title: BBCA_EtOH_Cit 1

description:
A2_19
Replicate set 1


title: BBCA_EtOH_PAD2 1

description:
A2_18
Replicate set 1


title: 34806


title: 34798


title: 34799


title: ChIP-Seq_GATA_A333fs-rep1 [G2021_113_15]

city: Grand Forks

first: Motoki

last: Takaku

state: North Dakota

address: 501 N Columbia Road,

institute: University of North Dakota

data_processing:
Base calling in illumina HiSeq X
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2
reads mapping to annotated genes were counted using featureCounts
differential gene expression analysis using DESeq2
Reads were filtered based on a mean base quality score >20.
For ChIP-seq analysis, reads were mapped to hg19 genome using Bowtie 0.12.8. Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package. Paired-end reads were converted to a single fragment for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each data set, bigWig files were generated to visualize the genomic coverage. Peak calling was performed with HOMER v4.1 at default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Cells were cultured in DMEM-F12 supplemented with 15% FBS, 2 mM L-glutamine, Insulin-transferrin-selenium (1x), 450 µM 1-Thioglycerol, and 50 µg/ml Ascorbic acid. Cells are maintained on Collagen-treated plates.

extract_protocol: RNAs from various cells were purified by the Direct-zol RNA kit (Zymo). RNA-seq libraries were prepared using NEBNext Ultra II RNA-Seq Kit (NEB) as per the manufacturer’s instruction with duel indexing. Quality of libraries was assessed in Tapestation (Agilent technologies) using D1000 Tape. Libraries were quantified using a well plate reader (Bio Tek) and pooled at a concentration of 12nM. Pooled libraries were quantified using the Droplet PCR system (Bio-Rad), and pooled libraries were sequenced in one lane Nova-Seq S4 as 150 bp Paired-end reads.

treatment_protocol: Cells were treated with a hypotonic buffer, and lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Covaris. DNA was precipitated with antibody against each target protein.

value: breast cancer

tag: cell subtype

value: luminal

tag: genotype/variation

value: A333fs expressed

tag: passages

tag: antibody

value: GATA3 (Cell Signaling, D13C9)


title: BBCA_EtOH_Input 1

description:
A2_16
Replicate set 1

tag: pre-treatment

tag: chip antibody


title: 34805

value: Magallenas region, Chile

value: Patagonian Ovejero Dog


title: BBCA_EtOH_ER 1

description:
A2_17
Replicate set 1

value: EtOH

value: Estrogen Receptor


title: ChIP-Seq_GATA_A333fs-rep1 [G2021_113_16]


title: 34831


title: 34804


title: 34796


title: 34797


title: ChIP-Seq_GATA_C321fs-rep1 [G2021_113_13]

value: C321fs expressed


title: ChIP-Seq_GATA_Splice-rep2 [G2021_113_12]

value: Splice del expressed


title: DMSO_Tam_MIgG 1

description:
A2_15
Replicate set 1

value: DMSO

value: Tamoxifen

value: Mouse IgG


title: DMSO_Tam_Cit 1

description:
A2_14
Replicate set 1

value: ER+ breast cancer cell line


title: 34795


title: 34786


title: DMSO_Tam_PAD2 1

description:
A2_13
Replicate set 1


title: 34787


title: ChIP-Seq_GATA_Empty-rep2 [G2021_113_10]

value: Negative control


title: ChIP-Seq_GATA_Splice-rep1 [G2021_113_11]


title: 34791


title: 34790


title: 34758


title: 34759


title: DMSO_Tam_Input 1

description:
A2_11
Replicate set 1


title: DMSO_Tam_ER 1

description:
A2_12
Replicate set 1


title: ChIP-Seq_TY1_A333fs-rep1 [G2021_113_8]

value: Ty1 (Diagenode, C15200054)


title: 34789


title: ChIP-Seq_GATA_Empty-rep1 [G2021_113_9]


title: 34757


title: ChIP-Seq_TY1_A333fs-rep1 [G2021_113_7]


title: 34754


title: DMSO_E2_Cit 1

description:
A1_9
Replicate set 1

value: Estradiol


title: 34788


title: ChIP-Seq_TY1_C321fs-rep2 [G2021_113_6]

value: breast cancer


title: 34753


title: 34751


title: 34752


title: DMSO_E2_ER 1

description:
A1_7
Replicate set 1


title: 34750


title: ChIP-Seq_TY1_C321fs-rep1 [G2021_113_5]

value: luminal


title: DMSO_E2_MIgG 1

description:
A1_10
Replicate set 1


title: ChIP-Seq_TY1_Splice-rep2 [G2021_113_4]


title: 34745


title: DMSO_E2_Input 1

description:
A1_6
Replicate set 1


title: 34743


title: ChIP-Seq_TY1_Splice-rep1 [G2021_113_3]


title: 34749


title: DMSO_E2_PAD2 1

description:
A1_8
Replicate set 1


title: 34748


title: 34742


title: DMSO_EtOH_Cit 1

description:
A1_4
Replicate set 1


title: DMSO_EtOH_PAD2 1

description:
A1_3
Replicate set 1


title: 34741


title: 34746


title: 34740


title: 34739


title: DMSO_EtOH_ER 1

description:
A1_2
Replicate set 1


title: ChIP-Seq_TY1_Empty-rep1 [G2021_113_1]


title: DMSO_EtOH_Input 1

description:
A1_1
Replicate set 1


title: RNA-Seq_A333fs-rep2 [G2021_53_11]

value: A333fs expressed


title: RNA-Seq_A333fs-rep1 [G2021_53_10]


title: RNA-Seq_A333fs-rep3 [G2021_53_12]


title: 34737


title: small RNA selection, vector, 8 dpi, b

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

data_processing:
Reads aligned to a combined A. aegypti, B. malayi, and wBm reference using BWA-ALN (v 0.7.12)
Aligned reads were used to predict microRNAs using mirDeep2 (v. 0.1.2) with nematode microRNAs from miRBase as a guide
MicroRNA reads were quantified using HTSEQ v0.5.3p9 with mode set to Union
TPM values were calculated from microRNA genes
Expression Modules for Differentially Expressed MicroRNA were identified for Brugia malayi using WGCNA v1.61
Protein-coding genes that contain microRNA targets were identified using Miranda v3.3
Differentially expressed protein-coding genes with inverse WGCNA modules to microRNAs that they have targets for were identified as putatively regulated gene clusters
Significantly over-represented functional terms were identified using Fisher's exact test for each putatively microRNA regulated protein coding WCGNA module
Genome_build: B. malayi WS259, wBm NC_006833.1, and A. aegypti AaegL3.3
Supplementary_files_format_and_content: tab-delimited files containing counts, TPM, WGCNA module assignments for differentially expressed genes, functional term enrichment analyses for WGCNA modules

organism:
Brugia malayi
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi taken from A. aegypti 8 dpi

extract_protocol:
For nematode samples, third stage larvae of Brugia malayi strain FR3 were isolated from infected mosquitoes 9-16 days post infection (dpi) using the NIAID/NIH Filariasis Research Reagent Resource Center (FR3) Research Protocol 8.4. Larvae were isolated in RPMI + P/S, enumerated, and either flash frozen in liquid nitrogen for storage at -80°C or used for the infection of male Mongolian gerbils (Meriones unguiculatus; Charles River, Wilmington, MA, USA). Gerbils were anesthetized with 5% isoflurane and infected by introducing 400 L3s into the peritoneal cavity using a butterfly catheter. Larvae, immature adults, and mature adults were recovered by peritoneal flush using a terminal procedure. Brugia malayi embryos were collected from live gravid females as previously described. For vector samples, the Aedes aegypti black-eyed Liverpool strain was obtained from FR3 and maintained in the Biosafety Level 2 Insectary at the University of Wisconsin Oshkosh. Desiccated mosquito eggs were hatched in deoxygenated water and the resulting larvae were maintained on a slurry of ground TetraMin fish food (Blacksburg, VA) at 27°C with 80% relative humidity. Female pupae were separated using a commercial larva pupa separator (The John Hock Company, Gainesville, FL), placed in mesh-covered paper soup cartons, and enclosed adults were fed with cotton pads soaked in sucrose solution. Females were deprived of sucrose approximately twelve hours prior to blood feeding. Mosquitoes were infected with the Brugia malayi FR3 strain by feeding microfilaremic cat blood (FR3) through Parafilm via a glass-jacketed artificial membrane feeder. When necessary microfilaremic cat blood was diluted with uninfected dog blood to achieve a suitable parasite density for infection (100-250 microfilariae/20 μL). Infected mosquitoes were collected at 18 hours post infection (hpi), 4 dpi, and 8 dpi. They were anesthetized with CO2 then transferred to chilled microscope slides where the legs, wings, heads and abdomens were removed. The thoraces with and without developing B. malayi larvae were flash frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. Vector-derived Infective B. malayi L3 were isolated from whole mosquitoes in bulk using the standard FR3 protocol. For RNA isolation, mosquito thoraces were combined with TRIzol (Zymo Research, Irvine, CA) at a ratio of 1 mL TRIzol per 50-100 mg mosquito tissue, while nematode samples were processed using a 3:1 volume ratio of TRIzol to sample. For both preparations, 1 µL β-mercaptoethanol was added for every 100 µL of sample. The tissues were homogenized using a bead beater and a TissueLyser (Qiagen, Germantown, MD) at 50 Hz for 5 min. The homogenate was then transferred to a new tube and centrifuged at 12,000g for 10 min at 4°C. After incubation at room temperature for 5 min, 0.2 mL chloroform was added for every 1 mL TRIzol. The samples were shaken by hand for 15 s, incubated at room temperature for 3 min, loaded into a pre-spun Phase Lock Gel heavy tube (5Prime, Gaithersburg, MD), and centrifuged at 12,000g for 5 min at 4°C. The upper phase was extracted, one volume of 100% ethanol was added, and then loaded onto a PureLink RNA Mini column (Ambion, Austin, TX). The samples were processed following manufacturer instructions, quantified using a Qubit fluorometer (Qiagen, Germantown, MD) and Nanodrop spectrometer (Nanodrop, Wilmington, DE), and sent to Institute for Genomic Sciences at the University of Maryland Baltimore for DNase treatment and library preparation.
Small RNA sequencing libraries were constructed using the CleanTag small RNA library prep kit (TriLink Biotechnologies) according to manufacturer’s protocol. Adapters were diluted 1:2 for sample input under 150ng. Samples with input over 150 ng Used 1X adapters. Post adapter annealing and cDNA synthesis samples were subject to 15 cycles of PCR. Following PCR, samples were evaluated and size selected via 3% agarose gel. Bands ~140 bp in size were excised and purified using a QIAquick gel extraction kit (Qiagen). Post purification samples were checked for sizing, quality, and quantity on the Perkin Elmer Gx. Using the GX quantification, samples were pooled in equimolar amounts. The sample pool was further quantified using the Kapa library quantification kit (Roche). The sample pool was diluted to 2 nM, denatured with 0.1N sodium hydroxide and loaded on a MiSeq sequencing system for 50 cycles of sequencing using an MiSeq reagent kit v2 (Illumina).

tag: b. malayi strain


title: 34738


title: 34729


title: RNA-Seq_C321fs-rep3 [G2021_53_9]


title: 34735


title: 34728


title: small RNA selection, vector, 8 dpi, a


title: RNA-Seq_C321fs-rep2 [G2021_53_8]


title: DMSO_EtOH_MIgG 1

description:
A1_5
Replicate set 1


title: 34734


title: 34727


title: small RNA selection, vector, 4 dpi, b

source_name: B. malayi taken from A. aegypti 4 dpi


title: ChIP-Seq_TY1_Empty-rep2 [G2021_113_2]


title: 34747


title: RNA-Seq_C321fs-rep1 [G2021_53_7]


title: small RNA selection, vector, 4 dpi, a


title: 34726


title: small RNA selection, vector, 18 hpi, b

source_name: B. malayi taken from A. aegypti 18 hpi


title: RNA-Seq_Splice-rep3 [G2021_53_6]


title: 34725


title: RNA-Seq_Splice-rep2 [G2021_53_5]


title: small RNA selection, vector, 18 hpi, a


title: 34730


title: 33722

value: Aysen region, Chile


title: 34731

value: Magallenas region, Chile


title: 33720

value: Patagonian Ovejero Dog


title: RNA-Seq_Splice-rep1 [G2021_53_4]


title: small RNA selection, jird, 24 dpi immature female, a

source_name: B. malayi immature females taken from jirds 24 dpi


title: 33717


title: small RNA selection, jird, 24 dpi immature female, b


title: RNA-Seq_Empty-rep2 [G2021_53_2]


title: RNA-Seq_Empty-rep3 [G2021_53_3]