title: bone marrow (BM) mononuclear cells at disease relapse [R2_Relapse]

type: genomic

city: Bari

first: Francesco

last: Albano

state: Bari

address: P.zza G. Cesare, 11

department: Department of Emergency and Organ Transplantation (D.E.T.O.) - Hematology and Stem Cell Transplantation Unit

country: Italy

institute: University of Bari "Aldo Moro", School of Medicine Policlinico Hospital

hyb_protocol: Genomic DNA (500 ng) was bisulfate converted according to the manufacturer's recommendations for the Illumina Infinium Assay. Bisulfite-treated samples were processed using the EPIC array (Illumina, San Diego, CA, USA), following manufacturer’s instructions

scan_protocol: Microarrays were scanned using an IScan scanner (Illumina).

data_processing: Genome Studio V2011.1 and Methylation Module 1.9.0

label: Cy3 and Cy5

source_name: AML disease relapse sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit according to standard instructions

value: Bone marrow mononuclear cells

tag: disease state

value: Disease relapse


title: RNA_Binding_ChIP_seq_CTCF_mAux_rep2

status: Public on May 10 2022

type: SRA

city: Daejeon

first: Sungwook

last: Han

address: Deahakro 291

department: Biological Science

country: South Korea

institute: KAIST(Korea Advanced Institute of Science and Technology)

library_source: genomic

data_processing:
For Hi-C analysis, we analyzed our in situ Hi-C data using HiC-Pro (Servant et al., 2015). This includes alignment to the mouse genome (UCSC mm10), extracting valid Hi-C interactions, merging replicates, building Hi-C matrix, and performing ICE normalization.  We applied reciprocal insulation scores to identify TADs (topologically associating domains) by using CaTCH (Zhan et al., 2017).   For most of Hi-C related analysis including RCP (relative contact probability), ATA (aggregate TAD analysis), or APA (aggregate peak analysis), we used GENOVA (Van der Weide et al., 2021).
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: Using HiC-Pro, we generated ICE-normalized Hi-C matrix (.matrix file) for 20kb and 40kb resolution and annotation file that indicates the genomic bins (abs.bed).
For Mnase-seq, ATAC-seq, ChIP-seq, CUT&RUN, and GRO-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).
For TotalRNA-seq and mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

molecule: genomic DNA

organism: Mus musculus

source_name: E14Tg2a (mESCs)

growth_protocol: E14Tg2a mouse embryonic stem cells (mESCs) : cultured in feeder-free gelatin-coated plates in Glasgow minimum essential medium (GMEM, Gibco) supplemented with 10% knockout serum replacement (Gibco), 1% Defined fetal bovine serum (FBS, Hyclone), 1% non-essential amino acids (NEAA, Gibco), 1% sodium pyruvate (Gibco), 0.5% antibiotic-antimycotic (penicillin-streptomycin containing, Hyclone), 0.1mM β-mercaptoethanol (Gibco), and 1000 U/ml Leukemia Inhibitory Factor (LIF, Millipore).

extract_protocol:
in situ Hi-C :    For Control and Chd4KD cells : in situ Hi-C was performed as previously described (Rao et al., 2014). Briefly: 1.5 million mESCs were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI (R0147, NEB); 5’ ends were filled by incorporation of biotinylated-dCTP (19524-016, Life Technologies); proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads (65601, Life Technologies); and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform.    For Aux and +Aux cells : in situ HiC was performed using the Arima Hi-C kit following the manufacturer’s protocols. Breifly, 1.5 million mESCs were crosslinked with 2% formaldehyde and 150ng of sheared DNA was used for biotin enrichment. Hi-C libraries were prepared using the Kapa Library Prep Kit with a modified protocol provided by Arima. Each Hi-C library was amplified for seven cycles and then subjected to deep sequencing on a Novaseq6000 Illumina platform.
Mnase-seq : Cells cultured in 60Ф culture dishes were washed with PBS and incubated with modified PBS (150 mM NaCl, 0.02% Tween-20, 0.02% Triton X-100) at 25°C for 5 min. The cells were then fixed with 1% formaldehyde at 25°C for 10 min, quenched with 125 mM glycine at 25°C for 5 min, washed, and suspended with lysis buffer (18% Ficoll-400, 10 mM KH2PO4, 10 mM K2HPO4, 1 mM MgCl2, 250 nM EGTA). The lysates were centrifuged at 12,000 rpm for 40 min at 4°C, and the pelleted chromatin was resuspended in A buffer (10 mM Tris-Cl, pH 7.4, 150 mM NaCl, 5 mM KCl, 1 mM EDTA). CaCl2 (5 mM) was added to the samples, which were immediately digested with MNase (M0247S, NEB) at 37°C for 60 min. The reaction was inactivated with 1% SDS and 500 mM EDTA, and reverse-crosslinking was performed overnight at 68°C. Proteinase K and RNase were added sequentially to the samples, and DNAs were recovered using phenol-chloroform-isoamyl alcohol extraction. The MNase-digested DNAs were separated on a 1.5% agarose gel, and mono-nucleosomal DNAs were extracted using a QIAEX II gel extraction kit (20021, Qiagen) according to the manufacturer’s manual. The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
ATAC-seq : ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with minor modification. Briefly, 50,000 mESCs were harvested, washed with cold PBS, lysed with cold lysis buffer, and immediately centrifuged. The nuclear pellets were resuspended in 25 μl of 2X tagmentation reaction buffer (10 mM Tris, pH 8.0, 5 mM MgCl2, 10% dimethylformamide), 23 μl of nuclease-free water, and 2 μl of Tn5 transposase (in-house generated), and incubated at 37°C for 30 min. The samples were then immediately purified using a QIAquick PCR purification kit (28106, Qiagen). The libraries were pre-enriched for five cycles using the KAPA HiFi Hotstart ready mix (KK2601, Kapa Biosystems), and the threshold cycle (Ct) was monitored using qPCR to determine the additional enrichment cycles, which were then applied. The final libraries were purified again with a QIAquick PCR purification kit, and sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates.
ChIP : E14Tg2a mESCs (1x10^6cells/well) were seeded to 100-mm dish. After treatment (siRNA transfection or auxin treatment), cells were cross-linked using fresh 1% formaldehyde solution at 25°C for 10 min. This crosslinking was quenched with 125 mM glycine at 25°C for 5 minutes, and the cells were harvested with cold PBS and suspended in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA). The chromatin was sheared to mono- or dinucleosome sizes using a focused ultrasonicator (Covaris S220). Immunoprecipitated DNA and input DNA were purified by treatment with proteinase K (40 µg, at 55°C for 3 hours), RNase A (20 µg, at 37°C for 1 hour), and phenol:chloroform:isoamyl alcohol extractions.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
CUT&RUN assays were performed as previously described (Meers et al., 2019; Skene and Henikoff, 2017), with minor modification. Briefly, 4 million mESCs were harvested and washed with 1.5 ml Wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine) three times. Cells were bound to activated Concanavalin A-coated magnetic beads (at 25°C for 10 min on a nutator), then permeabilized with Antibody buffer (Wash buffer containing 0.05% Digitonin and 4 mM EDTA). The bead-cell slurry was incubated with 3 μl relevant antibody (see below) in a 150 μl volume at 25°C for 2 hours on a nutator. After two washes in 1 ml Dig-wash buffer (Wash buffer containing 0.05% Digitonin), beads were resuspended in 150 μl pAG/MNase and incubated at 4°C for 1 hour on a nutator. After two washes in 1 ml Dig-wash buffer, beads were gently vortexed with 100 μl Dig-wash buffer. Tubes were chilled to 0°C for 5min and ice-cold 2.2 mM CaCl2 was added while gently vortexing. Tubes were immediately placed on ice and incubated at 4°C for 1 hour on a nutator, followed by addition of 100 μl 2xSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.1 mg/ml RNase A, 50 μg/ml glycogen) and incubated at 37°C for 30min on a nutator. Beads were placed on a magnet stand and the liquid was removed to a fresh tube, followed by addition of 2 μl 10% SDS and 2.5 μl proteinase K (20mg/ml) and incubated at 50°C for 1 hour. DNA was extracted using phenol chloroform as described at https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn. CUT&RUN libraries were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT), according to the manufacturer’s guidelines. The libraries were then sequenced using an Illumina Novaseq 6000 platform. The libraries were generated from two sets of biological replicates.
CUT&RUN libraries for genome-wide sequencing were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
Total RNA-seq : total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25 °C for 10 minutes to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 minutes at 4 °C, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 minutes at 4°C. The RNA pellets were dried and dissolved in RNase-free water.
Total RNA-seq libraries were prepared using a TruSeq stranded RNA kit (RS-122-2301, Illumina) according to the manufacturer’s manual.
mRNA-seq : To isolate mRNA, total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The

treatment_protocol: In genral, mESCs were transfected with 50 nM of the indicated siRNA using DharmaFECT I (T-2001-03, Dharmacon) according to the manufacturer’s protocol. Briefly, mESCs were seeded to 6-well plates. One day later, 50 nM of siRNAs and DharmaFECT reagent were diluted in Opti-MEM (Gibco), incubated separately at 25°C for 5 min, and then mixed together. The mixtures were incubated at 25°C for 20 min and added to the mESC cultures. The culture medium was replaced after 24 hours. Transfected mESCs were harvested at 48 hours after transfection.    For auxin treatment and temporal aspect siRNA / auxin withdrawal / RNA binding ChIP-seq experiments, we treated siRNA or auxin as indicated.

tag: genotype

tag: chip antibody

value: CTCF (07-729, Millipore)

tag: treatment

value: -Aux


title: RNA_Binding_ChIP_seq_CTCF_ppAux_rep1

value: ++Aux (auxin treated for 48 hours)


title: ChIP_seq_H3K27me3_Control_rep2

value: Wild-type Control

value: H3K27me3 (07-449, Millipore)

value: siRNA against EGFP


title: KPC_ACVR2B/Fc_Late [71]

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Cell, Developmental & Cancer Biology

country: USA

institute: Oregon Health & Science University

library_source: transcriptomic

data_processing:
Base calling and quality scoreing were performed in Illumina HiSeq
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode M15 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) < 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw count

molecule: total RNA

source_name: Quadriceps muscle

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit.
The Illumina TruSeq Standed mRNA standard methods were used for RNA sequencing (RNAseq). Total RNA extracted from the mouse quadriceps skeletal muscles was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. For RNA quality, a RIN number (RNA Integrity Number) of 7 or higher is desired. Five hundred nanograms of total RNA was used for library preparation. Briefly, cDNA library preparation included mRNA enrichment/purification, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the TruSeq Stranded mRNA Sample Preparation Guide, RS-122-9004DOC, Part# 15031047 Rev. E (Illumina, Inc.). Each resulting indexed library with average insert size of 150-200b was quantified and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. Five microliters of 2 nM pooled libraries per lane were then denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading to HiSeq 4000 for 75b paired-end read sequencing (Illumina, Inc.). Approximately 30M reads per library were generated. A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

treatment_protocol: RNA isolation, sequencing for all quadriceps samples were done at one time.

tag: strain

tag: Sex

value: Male

tag: agent

tag: time point

value: Late

tag: tissue

value: Muscle


title: RNA_Binding_ChIP_seq_CTCF_mAux_rep1


title: SPRI: Claret Library without Heatshock

city: Los Angeles

first: Jordan

last: Cheng

institute: UCLA

data_processing:
Demultiplexed using SRSLYumi:SRSLYumi (0.4 version), Claret Bioscience
Fastq trimmed with fastp:fastp (0.23.1 version)
Align with bwa mem:BWA-mem (0.7.17)
sam to bam and indexing with Samtools:Samtools (1.9 version)
Quality Cotrol using Qualimap:Qualimap (2.2.2c version)
Move UMI tags with SRSLYumi (srslyumi-bamtag):SRSLYumi (0.4 version), Claret Bioscience
Mark UMI with umi-tools:umi-tools (11.2 version)
Remove duplicates with Picard:Picard (2.27.0 version)
Files split by alignmentsieve (uscfDNA 25-100 and mncfDNA 101-250) with alignmentsieve in deep tools:DeepTools (3.31 version).
Functional peaks called with macs2 :Macs2 (2.2.7.1 version)
Assembly: GRC38
Assembly: LambdaPhage
Supplementary files format and content: Functional Elements called with HOMERannotatePeaks:HOMERannotatePeaks (version 4.11.1).

organism: Homo sapiens

source_name: Plasma

extract_protocol:
QiaM extracted cfDNA
SRSLYTM PicoPlus DNA NGS Library Preparation  CBS-K250B-24

treatment_protocol: No treatment

tag: organism

value: Human + Lambda Genome


title: bone marrow (BM) mononuclear cells at diagnosis [R2_Diagnosis]

source_name: AML diagnosis sample

tag: gender

tag: cell type

value: Diagnosis


title: KPC_Vehicle_Late [64]


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_12hr_rep2

description: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_12hr.bw

value: +Aux for 6hr, withdraw Aux for 12hr


title: SPRI: Exo1 Treatment


title: ChIP_seq_H3K27me3_Control_rep1


title: SPRI: Claret Library with Heatshock (Normal Control)


title: Control_Late [63]

value: Control


title: SPRI: dsDNA Library Kit Preparation


title: KPC_ACVR2B/Fc_Late [54]


title: bone marrow (BM) mononuclear cells at complete remission [R2_Remission]

source_name: AML complete remission sample

value: Complete remission


title: KPC_ACVR2B/Fc_Late [75]


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_3hr_rep2

description: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_3hr.bw

value: +Aux for 6hr, withdraw Aux for 3hr


title: bone marrow (BM) mononuclear cells at diagnosis [R1_Diagnosis]

value: Bone marrow mononuclear cells


title: ChIP_seq_H3K4me3_Control_rep1

value: In-house generated


title: bone marrow (BM) mononuclear cells at complete remission [R1_Remission]


title: SPRI: Claret ssDNA Library with no Heatshock


title: KPC_ACVR2B/Fc_Late [52]


title: SPRI: DsDnase Treatment


title: ChIP_seq_H3K4me1_Control_rep2


title: ChIP_seq_H3K27ac_Control_rep1

value: H3K27ac (ab4729, Abcam)


title: KPC_Vehicle_Late [50]

value: Female


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_3hr_rep1


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_30m_rep2

description: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_30m.bw

value: +Aux for 6hr, withdraw Aux for 30min


title: ChIP_seq_H3K4me1_Control_rep1

value: Wild-type Control


title: bone marrow (BM) mononuclear cells at disease relapse [R1_Relapse]

value: Disease relapse


title: Qiam: NEB Nick Repair Treatment

data_processing:
Demultiplexed using SRSLYumi: SRSLYumi (0.4 version), Claret Bioscience
Fastq trimmed with fastp: fastp (0.23.1 version)
Align with bwa mem: BWA-mem (0.7.17)
sam to bam and indexing with Samtools: Samtools (1.9 version)
Quality Cotrol using Qualimap: Qualimap (2.2.2c version)
Move UMI tags with SRSLYumi (srslyumi-bamtag): SRSLYumi (0.4 version), Claret Bioscience
Mark UMI with umi-tools: umi-tools (11.2 version)
Remove duplicates with Picard: Picard (2.27.0 version)
Files split by alignmentsieve (uscfDNA 25-100 and mncfDNA 101-250) with alignmentsieve in deep tools: DeepTools (3.31 version).
Functional peaks called with macs2 : Macs2 (2.2.7.1 version)
Assembly: GRC38
Assembly: LambdaPhage
Supplementary files format and content: Functional Elements called with HOMERannotatePeaks: HOMERannotatePeaks (version 4.11.1).

extract_protocol:
QiaM
SRSLYTM PicoPlus DNA NGS Library Preparation  CBS-K250B-24

tag: extraction method

value: QiaM extracted cfDNA


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_12hr_rep1


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_30m_rep1


title: ChIP_seq_Input_forRad21_Chd4KD_rep1

value: Wild-type Chd4KD

value: siRNA against Chd4


title: Qiam: P1 Treatment


title: ChIP_seq_Input_forRad21_Chd4KD_rep2


title: Control_Late [33]

value: Late

value: Muscle


title: ChIP_seq_Input_forRad21_Control_rep2

value: siRNA against EGFP


title: ChIP_seq_H3K4me3_Control_rep2


title: Qiam: Claret Library without Heatshock

value: Human + Lambda Genome


title: ChIP_seq_H3K27ac_Control_rep2


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_0m_rep1

description: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_0m.bw

value: +Aux for 6hr, withdraw Aux for 0min


title: KPC_Vehicle_Late [32]


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_mAux_rep1

description: AuxWithdraw_ChIP_seq_Input_forCTCFH3_mAux.bw

value: -Aux


title: Control_Late [22]

value: Male

value: Control


title: KPC_ACVR2B/Fc_Late [28]


title: SPRI: DNase1 Treatment


title: N2_noGo1

city: Cologne

first: Bjoern

last: Schumacher

state: NRW

address: Joseph-Stelzmann-Strasse 26

department: Institute for Genome Stability in Ageing and Disease

country: Germany

institute: CECAD Cologne

data_processing:
Reads were mapped to the Caenorhabditis elegans
Differential gene expression was analyzed using the DESeq2
Results were uploaded into the QuickNGS database
Genome_build: Caenorhabditis elegans (Ensembl Version 87)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

growth_protocol: growth in liquid culture for 12 hours

extract_protocol:
500 animals in trizol, homogenizer with beads, phenol-chlorform extraction, RNA isolation via RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina® TruSeq stranded® RNA sample preparation Kit.  The pool was sequenced by using an Illumina HiSeq 4000 sequencer with a paired-end protocol

treatment_protocol: treatment with either GO or GONH2 or mock

tag: genotype/variation

value: wild type

value: none (control)

value: whole animal


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_mAux_rep2


title: Control_Late [49]

value: Female


title: Qiam: S1 Treatment


title: ChIP_seq_Rad21_Control_rep2

value: Wild-type Control

value: Rad21 (ab992, Abcam)


title: Control_Early [46]

value: Early


title: ChIP_seq_Input_forRad21_Control_rep1


title: KPC_Vehicle_Late [79]


title: AuxWithdraw_ChIP_seq_Input_forCTCFH3_pAux_0m_rep2


title: AuxWithdraw_ChIP_seq_H3_pAux_3hr_rep1

value: H3 (ab1791, Abcam)

value: +Aux for 6hr, withdraw Aux for 3hr


title: Qiam: Claret Library with Heatshock (Normal Control)

value: QiaM extracted cfDNA


title: ChIP_seq_Rad21_Chd4KD_rep1

value: Wild-type Chd4KD

value: siRNA against Chd4


title: Qiam: Claret ssDNA Library with no Heatshock

value: Human + Lambda Genome


title: AuxWithdraw_ChIP_seq_H3_pAux_12hr_rep1

value: +Aux for 6hr, withdraw Aux for 12hr


title: Qiam: Exo1 Treatment


title: AuxWithdraw_ChIP_seq_H3_pAux_12hr_rep2


title: AuxWithdraw_ChIP_seq_H3_pAux_30m_rep2

value: +Aux for 6hr, withdraw Aux for 30min


title: ChIP_seq_Rad21_Control_rep1

value: siRNA against EGFP


title: AuxWithdraw_ChIP_seq_H3_pAux_3hr_rep2


title: AuxWithdraw_ChIP_seq_H3_pAux_30m_rep1


title: KPC_Vehicle_Late [21]

value: Male

value: Late

value: Muscle


title: Qiam: DNase1 Treatment


title: Qiam: DsDnase Treatment


title: ChIP_seq_Input_forCTCF_pAux_rep2

value: +Aux


title: Qiam: dsDNA Library Kit Preparation


title: QiaC extracted cfDNA with Lambda DNA Spike-In

extract_protocol:
QiaC or QiaM or SPRI
SRSLYTM PicoPlus DNA NGS Library Preparation  CBS-K250B-24

value: QiaC extracted cfDNA


title: AuxWithdraw_ChIP_seq_H3_pAux_0m_rep2

value: +Aux for 6hr, withdraw Aux for 0min


title: AuxWithdraw_ChIP_seq_H3_pAux_0m_rep1


title: ChIP_seq_Input_forCTCF_pAux_rep1

value: +Aux (auxin treated for 12 hours)


title: 20SP_no toxicity_non-irradiated

type: RNA

city: Barcelona

first: Ester

last: Aguado-Flor

state: Barcelona

address: c/Natzaret, 115-117

country: Spain

institute: Vall Hebron Institute of Oncology (VHIO)

hyb_protocol: Affymetrix GeneChip Human Exon 1.0 ST Array manufacturer's protocol.

data_processing:
Raw data were processed using Expression Command Console software from Affymetrix. RMA normalization method was used for background correction, normalization and probesets summarization,
probe group file: HuEx-1_0-st-v1.r2.pgf
meta-probeset file: HuEx-1_0-st-v1.r2.dt1.mm8.mps

label: Biotin

source_name: isolated PBMCs from human blood

growth_protocol: Peripheral blood mononuclar cells (PBMCs) were isolated using Lymphoprep (Stemcell Technologies) density gradient medium from an average of 17mL of whole blood. Two PBMC cultures, in 19.5mL RPMI 1640 supplemented with 20% foetal bovine serum with an average of 8.5x10^6 cells per 20mL of culture were set up for each patient.

extract_protocol: After 48h of incubation total RNA was isolated using TRIzol Isolation Reagent (Invitrogen Life Technologies). RNA was purified using Rneasy Minikit (QIAGEN) and DNA traces were digested with Rnase-Free Dnase Set (QIAGEN). Ribosomal RNA was removed using RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Thermo Fisher Scientific).

treatment_protocol: One culture was treated with 8Gy at room temperature at dose of 3 Gy/min with 6MV photon beam and one culture was the control sham-irradiated. Both cultures were then placed into a 37ªC incubator with 5% of CO2 for 48h.

tag: irradiation

value: non-irradiated

tag: late toxicity

value: yes


title: 20SP _no toxicity_irradiated

scan_protocol: Affymetrix GeneChip Human Exon 1.0 ST Array manufacturer's protocol.

value: irradiated


title: ChIP_seq_Input_forCTCF_mAux_rep2

value: -Aux


title: 19SP _toxicity_irradiated

label_protocol: Affymetrix GeneChip Human Exon 1.0 ST Array manufacturer's protocol.

value: no


title: ChIP_seq_Rad21_Chd4KD_rep2

value: Wild-type Chd4KD

value: Rad21 (ab992, Abcam)

value: siRNA against Chd4


title: SPRI extracted cfDNA with Lambda DNA Spike-In

value: Human + Lambda Genome

value: SPRI extracted cfDNA


title: ChIP_seq_Input_forCTCF_Control_rep2

value: Wild-type Control

value: siRNA against EGFP


title: 19SP_toxicity_non-irradiated


title: 17SP_no toxicity_non-irradiated


title: 18SP _toxicity_irradiated


title: ChIP_seq_Input_forCTCF_Chd4KD_rep2


title: ChIP_seq_Input_forCTCF_mAux_rep1


title: AuxWithdraw_ChIP_seq_CTCF_pAux_12hr_rep2

value: CTCF (07-729, Millipore)

value: +Aux for 6hr, withdraw Aux for 12hr


title: ChIP_seq_CTCF_pAux_rep2

value: +Aux


title: AuxWithdraw_ChIP_seq_CTCF_pAux_12hr_rep1


title: HepG2 cells - Ethanol vehicle treatment - replicate 2

city: Atlanta

first: Michael

middle: Lee

last: Cato

state: GA

address: 1510 Clifton Rd. NE

department: Biochemistry

institute: Emory University

data_processing:
Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina).
Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding ~35 million reads per sample.
Alignments were performed using BioJupies.
Data were subsequently analyzed using the R/Bioconductor package “DESeq2” to identify differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (generated with DESeq2)

source_name: HepG2 cells

growth_protocol: Cultured in DMEM + 10% FBS.

extract_protocol:
Cells were washed with PBS, extracted in RLT buffer, and stored at -80°C until use.
Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding ~35 million reads per sample.

treatment_protocol: Experiments were conducted with cells in DMEM + 10% charcoal-stripped FBS

tag: cell line

value: HepG2 cells

value: Ethanol (0.1%)


title: 18SP_toxicity_non-irradiated

value: non-irradiated


title: HepG2 cells - DLPC treatment - replicate 2

value: phospholipid DLPC (100 µM)


title: ChIP_seq_Input_forCTCF_Chd4KD_rep1


title: HepG2 cells - DLPC treatment - replicate 3


title: AuxWithdraw_ChIP_seq_CTCF_pAux_3hr_rep2

value: +Aux for 6hr, withdraw Aux for 3hr


title: AuxWithdraw_ChIP_seq_H3_mAux_rep1

value: H3 (ab1791, Abcam)

value: -Aux


title: ChIP_seq_Input_forCTCF_Control_rep1


title: QiaM extracted cfDNA with Lambda DNA Spike-In

value: QiaM extracted cfDNA


title: AuxWithdraw_ChIP_seq_H3_mAux_rep2


title: HepG2 cells - DLPC treatment - replicate 1


title: HepG2 cells - Ethanol vehicle treatment - replicate 3


title: HepG2 cells - Ethanol vehicle treatment - replicate 1


title: ChIP_seq_CTCF_pAux_rep1

value: +Aux (auxin treated for 12 hours)


title: ChIP_seq_CTCF_mAux_rep2


title: HepG2 cells - 6N-10CA treatment - replicate 3

value: small molecule 6N-10CA (10 µM)


title: AuxWithdraw_ChIP_seq_CTCF_pAux_3hr_rep1


title: 16 SP _toxicity_irradiated

value: irradiated

value: no


title: HepG2 cells - 6N-10CA treatment - replicate 2


title: AuxWithdraw_ChIP_seq_CTCF_pAux_30m_rep2

value: +Aux for 6hr, withdraw Aux for 30min


title: 16 SP_toxicity_non-irradiated


title: 17 SP _no toxicity_irradiated

value: yes


title: 15SP_no toxicity_non-irradiated


title: ChIP_seq_CTCF_mAux_rep1

value: CTCF (07-729, Millipore)


title: ChIP_seq_CTCF_Chd4KD_rep2

value: Wild-type Chd4KD

value: siRNA against Chd4


title: AuxWithdraw_ChIP_seq_CTCF_pAux_30m_rep1


title: 15SP _no toxicity_irradiated


title: ChIP_seq_CTCF_Chd4KD_rep1


title: HepG2 cells - 6N-10CA treatment - replicate 1

value: HepG2 cells


title: 14SP_no toxicity_non-irradiated


title: HepG2 cells - 10CA treatment - replicate 3

value: small molecule 10CA (10 µM)


title: AuxWithdraw_ChIP_seq_CTCF_pAux_0m_rep1

value: +Aux for 6hr, withdraw Aux for 0min


title: HepG2 cells - 10CA treatment - replicate 2


title: AuxWithdraw_ChIP_seq_CTCF_mAux_rep2


title: ChIP_seq_CTCF_Control_rep2

value: Wild-type Control

value: siRNA against EGFP


title: 13SP_toxicity_non-irradiated

value: non-irradiated


title: AuxWithdraw_ChIP_seq_CTCF_mAux_rep1

value: -Aux


title: ATAC_seq_Chd4KD_rep2


title: HepG2 cells - 6N treatment - replicate 3

value: small molecule 6N (10 µM)


title: AuxWithdraw_ChIP_seq_CTCF_pAux_0m_rep2


title: ATAC_seq_Chd4KD_rep1


title: 12SP_toxicity_non-irradiated


title: HepG2 cells - 10CA treatment - replicate 1


title: 14SP _no toxicity_irradiated


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_48hr_rep1

description: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_48hr.bw

value: siRNA against Chd4 treated for 48hr


title: ChIP_seq_CTCF_Control_rep1


title: ATAC_seq_Control_rep1


title: ATAC_seq_Control_rep2


title: HepG2 cells - 6N treatment - replicate 1


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_12hr_rep2

description: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_12hr.bw

value: siRNA against Chd4 treated for 12hr


title: 13SP _toxicity_irradiated

value: irradiated


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_48hr_rep2


title: HepG2 cells - DMSO vehicle treatment - replicate 3


title: Mnase_seq_Chd4KD_rep2


title: 11 SP_toxicity_irradiated

value: no


title: 11SP _toxicity_non-irradiated


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_06hr_rep2

description: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_06hr.bw

value: siRNA against Chd4 treated for 6hr


title: HepG2 cells - 6N treatment - replicate 2


title: Mnase_seq_Chd4KD_rep1


title: 10 SP _no toxicity_irradiated

value: yes


title: 10 SP_no toxicity_non-irradiated


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_06hr_rep1


title: HepG2 cells - DMSO vehicle treatment - replicate 2


title: Mnase_seq_Control_rep2


title: Temporal_siRNA_ChIP_seq_Input_forCTCFH3_Chd4KD_12hr_rep1


title: Mnase_seq_Control_rep1


title: 9SP_no toxicity_non-irradiated


title: Cirrhotic_1

city: Chengdu

first: Liangliang

last: Xu

state: Sichuan

address: Number 37 Guoxue Lane

country: China

institute: West China Hospital of Sichuan University

data_processing:
Raw data of fastq format were firstly processed through in-house perlscripts. After filtering low quality data using NGSQC software (v2.3.2), the clean reads with high quality were used for downstream analyses.
Tophat2 software (v2.0.13) was employed to align clean reads with the human reference genome (GRCh38/hg38). The sequencing data that cannot aligned to reference genome directly were subjected to the subsequent circRNA analysis by recognition of the reverse splicing event using Find_circ (v1.0) and CIRCexplorer2 softwares.
DESeq2 R package (2.15.13) was employed to analyze the differentially expressed circRNAs between non-cirrhotic and cirrhotic HCC tissues.
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatocellular carcinoma tissue

extract_protocol:
Total RNA was extracted from the HCC tissues using TRIzol reagent according to the manufacturer’s instructions. RNA degradation and contamination were monitored on 1% agarose gels. RNA concentration and purity were assessed using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). A total amount of 5 μg high-quality RNA per sample was used as input material for the RNA sample preparations. Ribosomal and linear RNA were removed by Epicentre RibozeroTM rRNA Removal Kit (Epicentre, USA) and RNase R (Epicentre, USA) respectively.Subsequently, circRNA was enriched by using acid phenol/ chloroform (pH 4.5).
The sequencing libraries were prepared by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: disease state

value: cirrhotic hepatocellular carcinoma

value: Hepatocellular carcinoma

tag: age

value: 61 years old

tag: ishak score


title: Cirrhotic_3

value: 50 years old


title: Cirrhotic_2

value: 47 years old


title: HepG2 cells - DMSO vehicle treatment - replicate 1

value: HepG2 cells

tag: treatment


title: Non_cirrhotic_3

value: non-cirrhotic hepatocellular carcinoma


title: mRNA_Smarcb1KD_NIH_MEF_2

description: CuffDiff_MEF_NIH3T3_siEgfp_vs_siSmarcb1.diff

data_processing:
For mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
For ChIP-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome: mm10
Supplementary_files_format_and_content: For mRNA-seq analysis, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression and the data were processed into .diff file.  For ChIP-seq analysis, we used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.

molecule: polyA RNA

source_name: NIH3T3 (MEFs)

growth_protocol:
E14Tg2a mouse embryonic stem cells (mESCs) : cultured in feeder-free gelatin-coated plates in Glasgow minimum essential medium (GMEM, Gibco) supplemented with 10% knockout serum replacement (Gibco), 1% Defined fetal bovine serum (FBS, Hyclone), 1% non-essential amino acids (NEAA, Gibco), 1% sodium pyruvate (Gibco), 0.5% antibiotic-antimycotic (penicillin-streptomycin containing, Hyclone), 0.1mM β-mercaptoethanol (Gibco), and 1000 U/ml Leukemia Inhibitory Factor (LIF, Millipore).
NIH3T3 mouse embryonic fibroblasts and human embryonic kidney (HEK)-293T cells : grown in high-glucose DMEM supplemented with 10% FBS,  2 mM L-glutamine, and penicillin/streptomycin (100 mg/ml), maintained in a humid atmosphere of 5% CO2 at 37 °C.

extract_protocol:
To isolate mRNA, total RNAs were purified from mESCs or MEFs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs of MEFs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25 °C for 10 minutes to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 minutes at 4 °C, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 minutes at 4°C. The RNA pellets were dried and dissolved in RNase-free water.  Finally, mRNAs were isolated from total RNA using a Magnetic mRNA isolation kit (S1550S, NEB).
mRNA-seq libraries were made using NEXTflex™ Rapid Directional mRNA-Seq kit (5138-10, BIOO) from purified mRNA.

value: MEFs

tag: genotype


title: mRNA_Smarcb1KD_NIH_MEF_1


title: Non_cirrhotic_2

value: 49 years old


title: Temporal_siRNA_ChIP_seq_Input_forH3_Control_rep2

description: Temporal_siRNA_ChIP_seq_Input_forH3_Control.bw

value: Wild-type Control

value: siRNA against EGFP treated for 48hr


title: Temporal_siRNA_ChIP_seq_Input_forH3_Control_rep1


title: mRNA_IpmkKD_NIH_MEF_2

description: CuffDiff_MEF_NIH3T3_siEgfp_vs_siIpmk.diff

value: IpmkKD


title: 9SP _no toxicity_irradiated


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_48hr_rep2

description: Temporal_siRNA_ChIP_seq_H3_Chd4KD_48hr.bw

value: Wild-type Chd4KD

tag: chip antibody

value: H3 (ab1791, Abcam)

value: siRNA against Chd4 treated for 48hr


title: Temporal_siRNA_ChIP_seq_Input_forCTCF_Control_rep1

description: Temporal_siRNA_ChIP_seq_Input_forCTCF_Control.bw


title: Temporal_siRNA_ChIP_seq_Input_forCTCF_Control_rep2


title: mRNA_IpmkKD_NIH_MEF_1


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_48hr_rep1


title: mRNA_Control_NIH_MEF_2

description:
CuffDiff_MEF_NIH3T3_siEgfp_vs_siIpmk.diff
CuffDiff_MEF_NIH3T3_siEgfp_vs_siSmarcb1.diff

value: Control (EgfpKD)


title: 12 SP _toxicity_irradiated

value: irradiated

value: no


title: 8SP_toxicity_non-irradiated

value: non-irradiated


title: 7SP_toxicity_non-irradiated


title: 8SP _toxicity_irradiated


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_12hr_rep2

description: Temporal_siRNA_ChIP_seq_H3_Chd4KD_12hr.bw

value: siRNA against Chd4 treated for 12hr


title: 7SP ._toxicity_irradiated


title: Non_cirrhotic_1

value: Hepatocellular carcinoma

value: 69 years old


title: 6SP_toxicity_non-irradiated


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_12hr_rep1


title: 6SP _toxicity_irradiated


title: 5SP_no toxicity_non-irradiated

value: yes


title: mRNA_Smarcb1KD_E14_mESC_2

description: CuffDiff_mESC_E14Tg2a_siEgfp_vs_siSmarcb1.diff

value: mESCs


title: Naïve B cell Donor 186 (RNA-seq)

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
TPM values of bulk RNA-seq data were calculated using the pseudo-aligner Kallisto quant 0.46.2 with fastq files with the default parameters except with --rf-stranded set
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes TPM for each sample

source_name: Naïve B cell Donor 186

extract_protocol:
Tonsillar mononuclear cells were isolated from tissues by mechanical disruption (tonsils were minced and pressed through a 70-micron cell screen) followed by Ficoll-Paque centrifugation
RNA was isolated from ~1 million of each cell type using Trizol Re- agent (Invitrogen), purified using the Directzol RNA Miniprep Kit (Zymo Research), and depleted of contaminating genomic DNA using DNAse I. Purified RNA was checked for quality on a Bioanlayzer 2100 using the Nano RNA Chip and samples with RIN>7 were used for RNA-seq library preparation. RNA samples were depleted of rRNA using QIAseq Fastselect RNA removal kit (Qiagen).
RNA samples were depleted of rRNA using the QIAseq FastSelect RNA Removal Kit then processed into libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to manufacturer’s instructions. Quality and quantity of the libraries was measured using the Bioanalyzer 2100 DNA chip and Qubit Fluorometer. Libraries were pooled and sequenced on the NovaSeq 6000 platform using paired-end 51bp reads at the Center for Spatial and Functional Genomics at CHOP.

value: Sorted Naive B Cells from Tonsil

tag: markers


title: mRNA_IpmkKD_E14_mESC_2

description: CuffDiff_mESC_E14Tg2a_siEgfp_vs_siIpmk.diff


title: Germinal Center B cell Donor 186 (RNA-seq)

department: Center for Spatial and Functional Genomics

source_name: Germinal Center B cell Donor 186

value: Sorted Germinal Center B Cells from Tonsil


title: mRNA_Control_NIH_MEF_1

value: MEFs


title: Temporal_siRNA_ChIP_seq_H3_Control_rep2

value: Wild-type Control

value: siRNA against EGFP treated for 48hr


title: 5SP _no toxicity_irradiated


title: Naïve B cell Donor 184 (RNA-seq)

source_name: Naïve B cell Donor 184


title: 4SP._toxicity_non-irradiated


title: Germinal Center B cell Donor 184 (RNA-seq)

source_name: Germinal Center B cell Donor 184


title: mRNA_IpmkKD_E14_mESC_1

value: IpmkKD


title: Naïve B cell Donor 181 (RNA-seq)

source_name: Naïve B cell Donor 181


title: Naïve B cell Donor 180 (RNA-seq)

source_name: Naïve B cell Donor 180


title: mRNA_Control_E14_mESC_2

description:
CuffDiff_mESC_E14Tg2a_siEgfp_vs_siIpmk.diff
CuffDiff_mESC_E14Tg2a_siEgfp_vs_siSmarcb1.diff


title: Temporal_siRNA_ChIP_seq_H3_Control_rep1

value: H3 (ab1791, Abcam)


title: Germinal Center B cell Donor 180 (RNA-seq)

source_name: Germinal Center B cell Donor 180


title: 3SP_no toxicity_non-irradiated


title: mRNA_Smarcb1KD_E14_mESC_1


title: mRNA_Control_E14_mESC_1


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_06hr_rep2

description: Temporal_siRNA_ChIP_seq_H3_Chd4KD_06hr.bw

value: Wild-type Chd4KD

value: siRNA against Chd4 treated for 6hr


title: Temporal_siRNA_ChIP_seq_H3_Chd4KD_06hr_rep1


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_48hr_rep2

description: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_48hr.bw

value: CTCF (07-729, Millipore)

value: siRNA against Chd4 treated for 48hr


title: 3SP _no toxicity_irradiated

value: irradiated


title: Naïve B cell Donor 99 (Capture-C)

description:
NaiveB_chicago.1frag.ibed
NaiveB_chicago.4frag.ibed

data_processing:
Library strategy: Capture-C
Bases were called using Illumina bcl2fastq2 conversion v2.29
Paired-end reads from three replicates of Naive B and GCB cells as well as five replicates of Monocytes were pre-processed using the HICUP pipeline (v0.5.9) with the default parameters. Reads were aligned to hg19 using bowtie2. We called call significant promoter interactions using the read count from promoters included in our reference bait.
Significant interactions were called CHiCAGO (v1.1.8) with default parameters except for bin-size set to 2,500. In addition to our analysis per individual DpnII fragment (1frag), we also called interactions by binning four fragments, which improves detection of long-distance interactions. Significant interactions at 4-DpnII fragment resolution were also called using CHiCAGO with artificial baitmap and .rmap files where four DpnII fragments were concatenated. Interactions with a CHiCAGO score > 5 in at least one cell type in either 1-fragment or 4-fragment resolution were considered significant.
Genome_build: hg19
Supplementary_files_format_and_content: ibed

source_name: Naïve B cell Donor 99

extract_protocol:
Tonsillar mononuclear cells were isolated from tissues by mechanical disruption (tonsils were minced and pressed through a 70-micron cell screen) followed by Ficoll-Paque centrifugation
For each library, 10e7 fixed cells were thawed at 37ºC, followed by centrifugation at RT for 5 mins at 14,000 rpm. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 μL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 μL in dH2O.
Both samples underwent a pre-digestion incubation with the addition of 0.3% SDS, 1x NEBuffer DpnII, and dH2O for 1hr at 37ºC in a Thermomixer shaking at 1,000rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After the pre-digestion incubation, 10 μL of DpnII (was added only to each sample tube, and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digestion continued overnight. The next day, another additional 10 µL of DpnII was added and the incubation continued for another 2-3 hours. 100 μL of each digestion reaction was then removed, pooled into one 1.5 mL tube. The remaining samples were heat inactivated at 65°C for 20 min at 1000 rpm in a Thermomixer, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 μL of T4 DNA ligase (HC 30U/uL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a Thermomixer. The next day, an additional 2 µL of T4 DNA ligase was spiked into each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K along with the pre-digestion and digestion controls. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation at -20°C. The 3C libraries were centrifuged at 3000 rpm for 45 min at 4°C 14,000 rpm, to pellet the samples. DNA pellets were resuspended in 70% ethanol and again centrifuged as described above. The 3C library pellets were resuspended in 300 μL dH2O and stored at −20°C. 10 μg of isolated DNA from 3C libraries of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp.  After shearing, DNA was purified using AMPure XP beads. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C probe set.
Promoter Focused Capture C

value: Naive B cells

tag: restriction enzyme

value: DpnII


title: 2SP_no toxicity_non-irradiated

value: non-irradiated


title: 4SP _toxicity_irradiated

value: no


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_48hr_rep1

source_name: E14Tg2a (mESCs)


title: 2SP _no toxicity_irradiated

value: yes


title: Germinal Center B cell Donor 181 (RNA-seq)

source_name: Germinal Center B cell Donor 181


title: Naïve B cell Donor 104 (Capture-C)

source_name: Naïve B cell Donor 104


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_06hr_rep2

description: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_06hr.bw


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_12hr_rep1

description: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_12hr.bw

value: siRNA against Chd4 treated for 12hr


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_12hr_rep2


title: Naïve B cell Donor 103 (Capture-C)

source_name: Naïve B cell Donor 103


title: Schwann Cell 7d post-crush 2

city: Stanford

first: Tawaun

middle: Autry

last: Lucas

state: CA

address: 1201 Welch Rd

institute: Stanford University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rnor 6.0 whole genome using STAR(v1.26)
Aligned reads were quantified with RSEM
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: tab-delimited files with counts and TPM and FPKM values

organism: Rattus norvegicus

source_name: Sciatic Nerve

extract_protocol:
A minimum of 10 sciatic nerves was used for the generation of each sample of purified cells. Schwann cells were acutely purified using immunopanning from the injured or uninjured Rat sciatic nerve according to (Lutz, 2014). For injured nerves, only the nerve segment distal to the site of crush injury was included. For uninjured nerves the anatomically equivalent nerve segment was isolated.
RNA from whole nerves was purified according to the RNeasy Fibrous Tissue kit. For injured nerves, only the nerve segment distal to the site of crush injury was included. For uninjured nerves the anatomically equivalent nerve segment was isolated.
Total RNA that passed QC standards proceeded to library synthesis using the Ovation® RNA-seq system V2 (Nugen 7102).

value: Schwann Cell from Sciatic nerve

tag: tissue

value: Sciatic Nerve

value: postnatal day 18

tag: time point

value: 7d post-crush


title: Whole Nerve 7d post-crush 2

value: Whole Nerve/Sciatic Nerve


title: Whole Nerve 7d post-crush 1


title: Lazer dissected epidermis at CT20, WT

city: Sakyo-ku

first: Hitoshi

last: Okamura

state: Kyoto

address: Yoshida-Konoe-cho

department: Division of Physiology and Neurobiology

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Gene expression data from lazer dissected epidermis at CT20, WT

hyb_protocol: Hybridization was performed with GeneChip Mouse Genome 430 2.0 array according to the manufacture’ protocol.

scan_protocol: The GeneChip was scanned with the GeneChip Scanner 3000 (Affymetrix) following the manufacturer's instructions.

data_processing: Values were normalized with the MAS5 (GCOS 1.4) algorithm, using the default analysis settings and global scaling as normalization method.

source_name: Lazer dissected epidermis from foot pad

label_protocol: Biotynylated cRNA labelling were performed using the One-Cycle Target Labelling and Control Reagents Kit (Affymetrix)

growth_protocol: Animals (12 wildtype mice, and 12 Cry-null mice) were sacrificed by cervical dislocation under a safety red light at the indicated time points in DD.

extract_protocol: Lazer dissected epidermis was lysed in Trizol reagent (Invitrogen), and total RNA was purified using the RNeasy micro kit (Qiagen).

treatment_protocol: Skin section (30 μm thick) containing the cross-section of footpad was prepared using a cryostat microtome (CM3050S, Leica) and mounted on POL-membrane slides (Leica). Sections were fixed for 3 min in an ice-cold mixture of ethanol and acetic acid (19:1), rinsed briefly in ice-cold water, stained for 30 seconds in ice-cold water containing 0.05% toluidine blue, followed by two brief washes in ice-cold water (all the solutions were RNase-free). After wiping off excess water, slides were quickly air dried at room temperature. As soon as moistures in the skin sections decreased enough for laser-cutting, cells in the epidermis were microdissected using a LMD7000 device (Leica; 20× magnification)

value: epidermis

value: WT

tag: time


title: Temporal_siRNA_ChIP_seq_CTCF_Chd4KD_06hr_rep1

value: Wild-type Chd4KD

value: siRNA against Chd4 treated for 6hr


title: Germinal Center B cell Donor 104 (Capture-C)

description:
GCB_chicago.1frag.ibed
GCB_chicago.4frag.ibed

source_name: Germinal Center B cell Donor 104

tag: cell type

value: Germinal Center B cells


title: Temporal_siRNA_ChIP_seq_CTCF_Control_rep2

value: Wild-type Control

value: CTCF (07-729, Millipore)

value: siRNA against EGFP treated for 48hr


title: Germinal Center B cell Donor 103 (Capture-C)

source_name: Germinal Center B cell Donor 103

value: DpnII


title: Temporal_siRNA_ChIP_seq_CTCF_Control_rep1


title: Whole Nerve 5d post-crush 2

value: 5d post-crush


title: 1SP_no toxicity_non-irradiated

source_name: isolated PBMCs from human blood

value: non-irradiated

value: yes


title: Germinal Center B cell Donor 99 (Capture-C)

source_name: Germinal Center B cell Donor 99


title: 1SP _no toxicity_irradiated

value: irradiated


title: Whole Nerve 5d post-crush 1

value: Sciatic Nerve


title: CUTnRUN_Rad21_pAux_rep2

data_processing:
Library strategy: CUT&RUN
For Hi-C analysis, we analyzed our in situ Hi-C data using HiC-Pro (Servant et al., 2015). This includes alignment to the mouse genome (UCSC mm10), extracting valid Hi-C interactions, merging replicates, building Hi-C matrix, and performing ICE normalization.  We applied reciprocal insulation scores to identify TADs (topologically associating domains) by using CaTCH (Zhan et al., 2017).   For most of Hi-C related analysis including RCP (relative contact probability), ATA (aggregate TAD analysis), or APA (aggregate peak analysis), we used GENOVA (Van der Weide et al., 2021).
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: Using HiC-Pro, we generated ICE-normalized Hi-C matrix (.matrix file) for 20kb and 40kb resolution and annotation file that indicates the genomic bins (abs.bed).
For Mnase-seq, ATAC-seq, ChIP-seq, CUT&RUN, and GRO-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).
For TotalRNA-seq and mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).

value: Rad21 (ab992, Abcam)

value: +Aux


title: Monocyte Donor 509 (Capture-C)

description:
Monocyte_chicago.1frag.ibed
Monocyte_chicago.4frag.ibed

source_name: Monocyte Donor 509

extract_protocol:
Primary monocytes were obtained from a University of Pennsylvania campus core facility under an Institutional Review Board–approved protocol
For each library, 10e7 fixed cells were thawed at 37ºC, followed by centrifugation at RT for 5 mins at 14,000 rpm. The cell pellet was resuspended in 1 mL of dH2O supplemented with 5 μL 200X protease inhibitor cocktail, incubated on ice for 10 mins, then centrifuged. The cell pellet was resuspended to a total volume of 650 μL in dH2O.
Both samples underwent a pre-digestion incubation with the addition of 0.3% SDS, 1x NEBuffer DpnII, and dH2O for 1hr at 37ºC in a Thermomixer shaking at 1,000rpm. A 1.7% solution of Triton X-100 was added to each tube and shaking was continued for another hour. After the pre-digestion incubation, 10 μL of DpnII (was added only to each sample tube, and continued shaking until the end of the day. An additional 10 µL of DpnII was added to each digestion reaction and digestion continued overnight. The next day, another additional 10 µL of DpnII was added and the incubation continued for another 2-3 hours. 100 μL of each digestion reaction was then removed, pooled into one 1.5 mL tube. The remaining samples were heat inactivated at 65°C for 20 min at 1000 rpm in a Thermomixer, and cooled on ice for 20 additional minutes. Digested samples were ligated with 8 μL of T4 DNA ligase (HC 30U/uL) and 1X ligase buffer at 1,000 rpm overnight at 16°C in a Thermomixer. The next day, an additional 2 µL of T4 DNA ligase was spiked into each sample and incubated for another few hours. The ligated samples were then de-crosslinked overnight at 65°C with Proteinase K along with the pre-digestion and digestion controls. The following morning, both controls and ligated samples were incubated for 30 min at 37°C with RNase A, followed by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation at -20°C. The 3C libraries were centrifuged at 3000 rpm for 45 min at 4°C 14,000 rpm, to pellet the samples. DNA pellets were resuspended in 70% ethanol and again centrifuged as described above. The 3C library pellets were resuspended in 300 μL dH2O and stored at −20°C. 10 μg of isolated DNA from 3C libraries of each library was sheared in dH2O using a QSonica Q800R to an average fragment size of 350bp.  After shearing, DNA was purified using AMPure XP beads. One microgram of adaptor-ligated library was used as input for the SureSelect XT capture kit using manufacturer protocol and our custom-designed 41K promoter Capture-C probe set.
Promoter Focused Capture C

value: Monocyte


title: Schwann Cell 7d post-crush 1

value: Schwann Cell from Sciatic nerve

value: postnatal day 18

value: 7d post-crush


title: CUTnRUN_Rad21_pAux_rep1

value: +Aux (auxin treated for 12 hours)


title: Monocyte Donor 500 (Capture-C)

source_name: Monocyte Donor 500


title: Lazer dissected epidermis at CT12, WT

description: Gene expression data from lazer dissected epidermis at CT12, WT

value: epidermis

value: WT


title: Lazer dissected epidermis at CT8, WT

description: Gene expression data from lazer dissected epidermis at CT8, WT


title: Lazer dissected epidermis at CT16, WT

description: Gene expression data from lazer dissected epidermis at CT16, WT


title: Lazer dissected epidermis at CT0, WT

description: Gene expression data from lazer dissected epidermis at CT0, WT


title: Monocyte Donor 410 (Capture-C)

source_name: Monocyte Donor 410


title: Whole Nerve 3d post-crush 2

value: Whole Nerve/Sciatic Nerve

value: 3d post-crush


title: Schwann Cell 5d post-crush 1


title: Monocyte Donor 527 (Capture-C)

source_name: Monocyte Donor 527

value: DpnII


title: Lazer dissected epidermis at CT20, Cry-null

description: Gene expression data from lazer dissected epidermis at CT20, Cry-null


title: Monocyte Donor 451 (Capture-C)

source_name: Monocyte Donor 451


title: CUTnRUN_Rad21_mAux_rep1

value: -Aux


title: CUTnRUN_Rad21_mAux_rep2


title: Naive B cells Donor T99 tonsil (ATAC-seq)

data_processing:
Bases were called using Illumina bcl2fastq2 conversion v2.29
Reads were aligned using bowtie2 implimented in the ENCODE pipeline. Reads alignment by offsetting +4bp for all the reads aligned to the forward strand, and -5bp for all the reads aligned to the reverse strand
Open chromatin regions (OCRs) were called using MACS2 implimented in the ENCODE pipeline with the following parameters -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits. The encode blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were removed from called peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files and ENCODE idr optimal peakcalls

source_name: Naive B cells Donor T99 tonsil

extract_protocol:
Tonsillar mononuclear cells were isolated from tissues by mechanical disruption (tonsils were minced and pressed through a 70-micron cell screen) followed by Ficoll-Paque centrifugation
A total of 50,000 cells were centrifuged at 550xg for 5 min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 xg for 10 min at 4°C. The tagmented DNA was then purified using the Qiagen MinElute kit and eluted in 10.5 μL Elution Buffer.
Ten microliters of purified tagmented DNA was PCR amplified using the Nextera Indexing Kit for 12 cycles to generate each library. The PCR reaction was subsequently purified using 1.8x AMPure XP beads, and concentrations were measured by Qubit Fluorometer.  Quality of completed libraries was assessed on a Bioanalyzer 2100 high sensitivity DNA Chip.  Libraries were paired-end sequenced at the Center for Spatial and Functional Genomics on the Novaseq 6000 platform (50 bp read length).

value: Sorted Naive B Cells from Tonsil


title: Whole Nerve 3d post-crush 1


title: Lazer dissected epidermis at CT4, WT

description: Gene expression data from lazer dissected epidermis at CT4, WT


title: Schwann Cell 5d post-crush 2

value: 5d post-crush


title: CUTnRUN_IgG_mouse

value: Wild-type

value: IgG (12-371, Millipore)


title: CUTnRUN_IgG_rabbit

value: In-house generated


title: scRNA_CK_1wk_rep3

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description:
processed data file:
scRNA_CKp25_count_matrix_all.tsv
scRNA_CKp25_count_matrix_metadata_QCd_only.tsv
scRNA_CKp25_count_matrix_rowname_symb_all.tsv
scRNA_CKp25_count_matrix_columnnames_all.tsv
scRNA_CKP25_count_matrix_metadata_all.tsv

data_processing:
bulk RNA-seq: From the paired-end fastq files, the first three nucleotides were trimmed off the second sequencing read using cutadapt version 1.16. TrimGalore version 0.4.5 was used in paired mode to trim adapters and low-quality portions of reads. Reads were aligned using Salmon version 0.12.0 to mouse genome version GRCm38.94 and human genome version GRCh38.94. For downstream analysis, TPM files from Salmon were imported into R version 3.6.1 using tximport version 1.14.0 with the option to generate estimated counts using abundance estimates scaled up to library size, and additionally scaled using the average transcript length over samples and the library size (countsFromAbundance = lengthScaledTPM).
scRNA-seq: We aligned 40-bp paired-end reads to the mm10 genome for each of 1,357 single nuclei from 12 mice (64 cells each for 6 CK controls and an average of 162 cells in each of 6 CKp25 mice) using bwa mem (options: -k 15 -M) and filtered out improperly aligned reads and secondary alignments with samtools (options: -f 3 -F 1280). We ran HTSeq-count10 on each cell’s filtered bam file to compute the cell’s transcriptomic coverage over each gene’s exons in vM25 GENCODE gene annotation.
Genome_build: mm10
Supplementary_files_format_and_content: TPM, raw counts

molecule: nuclear RNA

source_name: cortex

growth_protocol: CK-p25 double transgenic mice were raised and maintained on a doxycycline diet. All mice were induced by removing doxycycline from their diet to drive the expression of p25-GFP in forebrain excitatory neurons. All mice were induced at 3-4 months old.

extract_protocol: Single nuclei were sorted into a 96-well plate then transported immediately to the MIT BioMicro Center for library preparation. Libraries were prepped using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara bio, cat no. 634891) according to manufacturer’s instructions. Single-end sequencing was performed using the Illumina MiSeq platform according to standard operating procedures.

treatment_protocol: no treatment

tag: strain

value: CK

tag: timepoint


title: CUTnRUN_CHD4-2_Abcam_rep2

source_name: E14Tg2a (mESCs)

extract_protocol:
in situ Hi-C :    For Control and Chd4KD cells : in situ Hi-C was performed as previously described (Rao et al., 2014). Briefly: 1.5 million mESCs were crosslinked with 1% formaldehyde; nuclei were isolated; chromatin was digested with MboI (R0147, NEB); 5’ ends were filled by incorporation of biotinylated-dCTP (19524-016, Life Technologies); proximity ligation, reverse-crosslinking, and DNA shearing were performed; biotinylated junctions were isolated with streptavidin beads (65601, Life Technologies); and DNA libraries were prepared. Each Hi-C library was amplified for six cycles and then subjected to deep sequencing on a Hiseq4000 Illumina platform.    For Aux and +Aux cells : in situ HiC was performed using the Arima Hi-C kit following the manufacturer’s protocols. Breifly, 1.5 million mESCs were crosslinked with 2% formaldehyde and 150ng of sheared DNA was used for biotin enrichment. Hi-C libraries were prepared using the Kapa Library Prep Kit with a modified protocol provided by Arima. Each Hi-C library was amplified for seven cycles and then subjected to deep sequencing on a Novaseq6000 Illumina platform.
Mnase-seq : Cells cultured in 60Ф culture dishes were washed with PBS and incubated with modified PBS (150 mM NaCl, 0.02% Tween-20, 0.02% Triton X-100) at 25°C for 5 min. The cells were then fixed with 1% formaldehyde at 25°C for 10 min, quenched with 125 mM glycine at 25°C for 5 min, washed, and suspended with lysis buffer (18% Ficoll-400, 10 mM KH2PO4, 10 mM K2HPO4, 1 mM MgCl2, 250 nM EGTA). The lysates were centrifuged at 12,000 rpm for 40 min at 4°C, and the pelleted chromatin was resuspended in A buffer (10 mM Tris-Cl, pH 7.4, 150 mM NaCl, 5 mM KCl, 1 mM EDTA). CaCl2 (5 mM) was added to the samples, which were immediately digested with MNase (M0247S, NEB) at 37°C for 60 min. The reaction was inactivated with 1% SDS and 500 mM EDTA, and reverse-crosslinking was performed overnight at 68°C. Proteinase K and RNase were added sequentially to the samples, and DNAs were recovered using phenol-chloroform-isoamyl alcohol extraction. The MNase-digested DNAs were separated on a 1.5% agarose gel, and mono-nucleosomal DNAs were extracted using a QIAEX II gel extraction kit (20021, Qiagen) according to the manufacturer’s manual. The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
The purified mono-nucleosomal DNAs were subjected to sequencing using a TruSeq DNA library prep kit (FC-121-2001, Illumina).
ATAC-seq : ATAC-seq libraries were prepared as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015), with minor modification. Briefly, 50,000 mESCs were harvested, washed with cold PBS, lysed with cold lysis buffer, and immediately centrifuged. The nuclear pellets were resuspended in 25 μl of 2X tagmentation reaction buffer (10 mM Tris, pH 8.0, 5 mM MgCl2, 10% dimethylformamide), 23 μl of nuclease-free water, and 2 μl of Tn5 transposase (in-house generated), and incubated at 37°C for 30 min. The samples were then immediately purified using a QIAquick PCR purification kit (28106, Qiagen). The libraries were pre-enriched for five cycles using the KAPA HiFi Hotstart ready mix (KK2601, Kapa Biosystems), and the threshold cycle (Ct) was monitored using qPCR to determine the additional enrichment cycles, which were then applied. The final libraries were purified again with a QIAquick PCR purification kit, and sequenced using an Illumina HiSeq 2500 platform. The libraries were generated from two sets of biological replicates.
ChIP : E14Tg2a mESCs (1x10^6cells/well) were seeded to 100-mm dish. After treatment (siRNA transfection or auxin treatment), cells were cross-linked using fresh 1% formaldehyde solution at 25°C for 10 min. This crosslinking was quenched with 125 mM glycine at 25°C for 5 minutes, and the cells were harvested with cold PBS and suspended in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 1% SDS, 10 mM EDTA). The chromatin was sheared to mono- or dinucleosome sizes using a focused ultrasonicator (Covaris S220). Immunoprecipitated DNA and input DNA were purified by treatment with proteinase K (40 µg, at 55°C for 3 hours), RNase A (20 µg, at 37°C for 1 hour), and phenol:chloroform:isoamyl alcohol extractions.
ChIP-seq libraries for genome-wide sequencing were prepared using either a NEXTflex™ Illumina ChIP-Seq Library Prep kit (5143-02, BIOO) or Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
CUT&RUN assays were performed as previously described (Meers et al., 2019; Skene and Henikoff, 2017), with minor modification. Briefly, 4 million mESCs were harvested and washed with 1.5 ml Wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine) three times. Cells were bound to activated Concanavalin A-coated magnetic beads (at 25°C for 10 min on a nutator), then permeabilized with Antibody buffer (Wash buffer containing 0.05% Digitonin and 4 mM EDTA). The bead-cell slurry was incubated with 3 μl relevant antibody (see below) in a 150 μl volume at 25°C for 2 hours on a nutator. After two washes in 1 ml Dig-wash buffer (Wash buffer containing 0.05% Digitonin), beads were resuspended in 150 μl pAG/MNase and incubated at 4°C for 1 hour on a nutator. After two washes in 1 ml Dig-wash buffer, beads were gently vortexed with 100 μl Dig-wash buffer. Tubes were chilled to 0°C for 5min and ice-cold 2.2 mM CaCl2 was added while gently vortexing. Tubes were immediately placed on ice and incubated at 4°C for 1 hour on a nutator, followed by addition of 100 μl 2xSTOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 0.1 mg/ml RNase A, 50 μg/ml glycogen) and incubated at 37°C for 30min on a nutator. Beads were placed on a magnet stand and the liquid was removed to a fresh tube, followed by addition of 2 μl 10% SDS and 2.5 μl proteinase K (20mg/ml) and incubated at 50°C for 1 hour. DNA was extracted using phenol chloroform as described at https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn. CUT&RUN libraries were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT), according to the manufacturer’s guidelines. The libraries were then sequenced using an Illumina Novaseq 6000 platform. The libraries were generated from two sets of biological replicates.
CUT&RUN libraries for genome-wide sequencing were prepared using either a Accel-NGS 2S Plus DNA Library Kit (21024, SWIFT).
Total RNA-seq : total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The mixtures were incubated at 25 °C for 10 minutes to precipitate total RNAs. The samples were centrifuged at 12,000 rpm for 10 minutes at 4 °C, washed with 75% ethanol, and centrifuged again at 10,000 rpm for 5 minutes at 4°C. The RNA pellets were dried and dissolved in RNase-free water.
Total RNA-seq libraries were prepared using a TruSeq stranded RNA kit (RS-122-2301, Illumina) according to the manufacturer’s manual.
mRNA-seq : To isolate mRNA, total RNAs were purified from mESCs using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Briefly, mESCs were harvested and homogenized with 1 ml of TRIzol reagent. Chloroform (200 μL/sample) was added, and the samples were mixed vigorously by hand for 15 seconds and incubated at 25 °C for 2 minutes. The mixtures were centrifuged at 12,000 rpm for 15 minutes at 4 °C, and 500 μL of each aqueous phase was transferred to a new Eppendorf tube and mixed with the same volume of isopropanol. The

value: Chd4 (ab70469, Abcam)


title: Lazer dissected epidermis at CT16, Cry-null

description: Gene expression data from lazer dissected epidermis at CT16, Cry-null


title: Lazer dissected epidermis at CT4, Cry-null

description: Gene expression data from lazer dissected epidermis at CT4, Cry-null


title: Lazer dissected epidermis at CT12, Cry-null

description: Gene expression data from lazer dissected epidermis at CT12, Cry-null


title: Germinal Center B cells Donor TC99 tonsil (ATAC-seq)

value: Sorted Germinal Center B Cells from Tonsil


title: scRNA_CK_1wk_rep2


title: Lazer dissected epidermis at CT0, Cry-null

description: Gene expression data from lazer dissected epidermis at CT0, Cry-null


title: scRNA_CK_2wk_rep3


title: Naive B cells Donor T104 tonsil (ATAC-seq)

source_name: Naive B cells Donor T104 tonsil


title: CUTnRUN_CHD4-1_R1_rep2


title: Schwann Cell 3d post-crush 2

value: Schwann Cell from Sciatic nerve

value: Sciatic Nerve

value: postnatal day 18


title: Whole Nerve Uncrushed 2

value: Uncrushed


title: Germinal Center B cells Donor TC104 tonsil (ATAC-seq)


title: Lazer dissected epidermis at CT8, Cry-null

description: Gene expression data from lazer dissected epidermis at CT8, Cry-null

value: epidermis


title: CUTnRUN_CHD4-1_R1_rep1


title: CUTnRUN_CHD4-2_Abcam_rep1


title: Naive B cells Donor 103 tonsil (ATAC-seq)

source_name: Naive B cells Donor 103 tonsil


title: Whole Nerve Uncrushed 1

value: Whole Nerve/Sciatic Nerve


title: Schwann Cell Uncrushed 1


title: ATAC_seq_pAux_rep2

value: +Aux


title: Monocytes Control 4 (ATAC-seq)

description: Monocytes_control_ppr.IDR0.1.filt.narrowPeak.gz

source_name: Monocytes Control

extract_protocol:
Primary monocytes were obtained from a University of Pennsylvania campus core facility under an Institutional Review Board–approved protocol
A total of 50,000 cells were centrifuged at 550xg for 5 min at 4°C. The cell pellet was washed with cold PBS and resuspended in 50 μL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40/IGEPAL CA-630) and immediately centrifuged at 550 xg for 10 min at 4°C. The tagmented DNA was then purified using the Qiagen MinElute kit and eluted in 10.5 μL Elution Buffer.
Ten microliters of purified tagmented DNA was PCR amplified using the Nextera Indexing Kit for 12 cycles to generate each library. The PCR reaction was subsequently purified using 1.8x AMPure XP beads, and concentrations were measured by Qubit Fluorometer.  Quality of completed libraries was assessed on a Bioanalyzer 2100 high sensitivity DNA Chip.  Libraries were paired-end sequenced at the Center for Spatial and Functional Genomics on the Novaseq 6000 platform (50 bp read length).

value: Sorted monocytes from blood

value: donor 4


title: scRNA_CK_1wk_rep1


title: scRNA_CK_2wk_rep1


title: ATAC_seq_pAux_rep1

value: +Aux (auxin treated for 12 hours)


title: ATAC_seq_mAux_rep1

value: -Aux


title: Schwann Cell Uncrushed 2

source_name: Sciatic Nerve


title: Simonsiella muelleri in BSTSY+FBS stationary, replicate2

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads mapping to rRNA were removed using sortmerna v4.1.0 against the pre-built sortmerna rRNA databases and the organism-specific rRNA sequences. Reads were mapped against the reference genomes (XXX upload Csteedae) using bowtie2 v2.4.4, and Q>30 filtered and index-sorted using samtools v1.9. Reads were counted using featureCounts of the subread-package v2.0.0 in paired-end mode (-s 2 -p -B -C) against the ”gene” features of the reference genomes’ gff-file (see supplementary file).
Genome_build: NZ_CP083930.1
Supplementary_files_format_and_content: raw counts

organism: Simonsiella muelleri

source_name: bacterial cells

growth_protocol: Cells grown in BSTSY+FBS 37°C 350 rpm

extract_protocol:
500 µl liquid culture were fixed with 1 ml RNAprotect Bacteria Reagent (Qiagen), and cells grown on solid medium scraped off and resuspended in 1 ml thereof, and stored at -70°C until the next day. Total RNA was extracted using the RNeasy® Mini Kit (Qiagen) for low cell numbers, including the on-column DNA digestion. Eluted RNA (30 ul) was treated with 2 U of DNase for 30 min using the TURBO DNA-free kit (Invitrogen). RNA was cleaned up using the RNA Clean & Concentrator-25 kit (Zymo) including the on-column DNA digestion. Absence of DNA was checked via PCR (35 cycles) against a ~200 bp fragment of gyrB.
RNA was quality checked (all samples had a RIN > 9), rRNA depleted using an in-facility developed protocol, and reverse-stranded sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).


title: Simonsiella muelleri in BSTSY+FBS stationary, replicate3


title: HiC_pAux_rep2

description:
pAux_20kb_abs.bed
pAux_20kb_ICE.matrix
pAux_40kb_abs.bed
pAux_40kb_ICE.matrix

data_processing:
For Hi-C analysis, we analyzed our in situ Hi-C data using HiC-Pro (Servant et al., 2015). This includes alignment to the mouse genome (UCSC mm10), extracting valid Hi-C interactions, merging replicates, building Hi-C matrix, and performing ICE normalization.  We applied reciprocal insulation scores to identify TADs (topologically associating domains) by using CaTCH (Zhan et al., 2017).   For most of Hi-C related analysis including RCP (relative contact probability), ATA (aggregate TAD analysis), or APA (aggregate peak analysis), we used GENOVA (Van der Weide et al., 2021).
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: Using HiC-Pro, we generated ICE-normalized Hi-C matrix (.matrix file) for 20kb and 40kb resolution and annotation file that indicates the genomic bins (abs.bed).
For Mnase-seq, ATAC-seq, ChIP-seq, CUT&RUN, and GRO-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using Bowtie2 (version 2.2.9) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and normalized the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).
For TotalRNA-seq and mRNA-seq analysis, raw reads were aligned to the mouse genome (UCSC mm10) using STAR (version 2.5.2a) with default parameters.  We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts.  Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files.  The bigWig files were used as input files for bwtool (matrix and aggregate option) to quantify the intensity of the relevant sequencing data.  Finally, we used Cufflinks (Cuffdiff option, fr-firststrand) to assess the gene expression.
Genome_build: mouse genome : mm10
Supplementary_files_format_and_content: We used MACS2 to convert the aligned BAM files into bedGraph files, and the data with respect to the total read counts. Then, we used bedGraphToBigWig to convert the bedGraph files into bigWig files (.bw).


title: Monocytes Control 2 (ATAC-seq)

value: donor 2


title: Monocytes Control 3 (ATAC-seq)

value: donor 3


title: cell line: AGS-EBV transduced with: sheIF4A3 lentivirus replicate3

city: Changsha

first: siwei

last: Zhang

state: Hunan

address: 87 Xiangya Road

department: Department of Microbiology

institute: Central South University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to human reference genome
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
bowtie2 mapping to lentivirus reference genome
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38/ASM240226v1 Human gammaherpesvirus 4 genome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human gastric adenocarcinoma

growth_protocol: EBV positive AGS-cell were grown in RPMI-1640 with 10% FBS.

extract_protocol:
total RNA isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-sequencing analysis was performed with AGS-EBV cells transduced with either pLVX ncsh, shBC200 or  sheIF4A3 lentivirus after 10 days of puromycin selection.

value: AGS-EBV

value: EBV positive gastric adenocarcinoma

tag: transduced with

value: sheIF4A3 lentivirus


title: cell line: AGS-EBV transduced with: sheIF4A3 lentivirus replicate2


title: Simonsiella muelleri on BSTSY+FBS plate 24h, replicate2


title: ATAC_seq_mAux_rep2


title: Germinal Center B cells Donor TC103 tonsil (ATAC-seq)

value: Sorted Germinal Center B Cells from Tonsil


title: scRNA_CKp25_1wk_rep2


title: scRNA_CKp25_2wk_rep1


title: cell line: AGS-EBV transduced with: sheIF4A3 lentivirus replicate1


title: scRNA_CKp25_1wk_rep3


title: Simonsiella muelleri in BSTSY+FBS stationary, replicate1


title: HiC_pAux_rep1


title: scRNA_CKp25_2wk_rep3


title: Simonsiella muelleri in BSTSY+FBS exponential, replicate3


title: Panc1GR-SRSF3KD3

city: Fuzhou

first: Zu-wei

last: Wang

address: No. 134, East Street, Fuzhou, 350001, Fujian Province, PR China

institute: Fujian provincial hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step,  clean data (clean reads) were obtained by removing following reads: (1) reads with 5’ adapter; (2) reads  without 3’ adapter or insert sequence; (3) reads with more than 10% N; (4) reads with more than 50%  nucleotides with Qphred<=20; (5) reads with ploy A/T/G/C. Adapter trimming for the removal of adapter  sequences from the 3’ ends of reads was also performed. At the same time, Q20, Q30 and GC content of  the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Clean reads for each sample were first mapped to a reference genome with the software HISAT2. Reads alignment results were transferred to the program StringTie for transcript assembly
Quantification of the transcripts and genes was performed using StringTie software and Reads Per  Kilobase of transcript per Million mapped reads (RPKM) was obtained. Cuffdiff or edgeR was used for  differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the false discovery rate. Genes with |log2 (Fold Change) | > 0 & padj < 0.05 were  assigned as differentially expressed.

source_name: pancreatic cancer cell

extract_protocol:
A total amount of 3 µg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s  recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic  beads. Fragmentation was carried out using divalent cations under elevated temperature  in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase  H-). Second strand cDNA synthesis was subsequently performed using DNA  Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via  exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments,  NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.  In order to select cDNA fragments of preferentially 150~200 bp in length, the library  fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated  cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was  performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system
RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method. After library construction, the concentration of library was measured by the Qubit® fluorometer and adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired  library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once the  insert size and concentration of the library was identical, the samples can then be subjected for sequencing

tag: phenotype

value: gemcitabine resistance


title: Simonsiella muelleri on BSTSY+FBS plate 24h, replicate3


title: Panc1GR-SRSF3KD2

tag: cell line


title: scRNA_CKp25_1wk_rep1


title: scRNA_CK_2wk_rep2

value: CK


title: HiC_mAux_rep1

description:
mAux_20kb_abs.bed
mAux_20kb_ICE.matrix
mAux_40kb_abs.bed
mAux_40kb_ICE.matrix

value: Chd4-mAID (auxin inducible degron)

value: -Aux (auxin untreated)


title: WGBS_WAT_WT_1y

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: WGBS

data_processing:
Fastq files were algined to the mm9 genome using walt aligner form the "methpipe" software pipeline (version 3.4.3).
Aligned files were sorted using 'sort' 8.31 and duplicate reads were removed using duplicate-remover.
Methylation levels were determined using 'methcounts' and hypomethylated regions were identified using 'hmr.'
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are in a tab-delimited .meth file format and contain CpG positions and methylations levels genomewide

source_name: adipose

extract_protocol:
Samples are extracted from WT and DNMT3A-HET mouse models age matched littermates were used in all experiments. Qiagen kits were used for DNA extraction
Swift WGBS kit

value: 1 year

tag: sorting strategy

value: SVCs CD45, CD31 depleted

value: WT

value: adipose


title: scRNA_CKp25_2wk_rep2


title: HiC_mAux_rep2


title: WGBS_WAT_HET_8w

description: WGBS

tag: age

value: 8 weeks

value: DNMT3A heterozygous


title: Panc1GR-NC3

value: ctrl


title: cell line: AGS-EBV transduced with: ncsh lentivirus replicate3

value: ncsh lentivirus


title: WGBS_WAT_HET_1y

description: WGBS


title: Schwann Cell 3d post-crush 1

value: Schwann Cell from Sciatic nerve

value: Sciatic Nerve

value: postnatal day 18

value: 3d post-crush


title: Simonsiella muelleri in BSTSY+FBS stationary

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads were mapped against the reference genomes using bowtie2 v2.4.4, and index-sorted using samtools v1.9. Reads were counted using the bamCoverage program of deeptools v3.5.1 (Ramírez et al. 2016) in non-overlapping 1kb windows and the resulting bigwig file converted to human-readable format using the bigWigToWig of UCSC v391.
Genome_build: NZ_CP083930.1
Supplementary_files_format_and_content: Read counts in 1kb non-overlapping windows

extract_protocol:
Cells were lysed using lysozyme and Proteinase K, DNA extracted using Phenol-Chloform and precipitated using ammonium acetate (2.5M final concentration), 2X 100% ice-cold Ethanol, and 5 ug/ml glycogen. RNA was degraded by incubation with 10 mg/ml RNase A for 30 min at 37°C, and DNA cleaned up using DNA Clean & Concentrator-5 (Zymo).
Enzymatic shearing; NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina, 150 bp PE sequenced on NovaSeq 6000 S4
WGS


title: cell line: AGS-EBV transduced with: shBC200  lentivirus replicate3

value: AGS-EBV

value: EBV positive gastric adenocarcinoma

value: shBC200  lentivirus


title: Simonsiella muelleri in BSTSY+FBS exponential, replicate1


title: cell line: AGS-EBV transduced with: shBC200  lentivirus replicate1


title: cell line: AGS-EBV transduced with: shBC200  lentivirus replicate2


title: Panc1GR-SRSF3KD1

value: gemcitabine resistance


title: Monocytes Control 1 (ATAC-seq)

value: Sorted monocytes from blood

value: donor 1


title: cell line: AGS-EBV transduced with: ncsh lentivirus replicate2


title: Simonsiella muelleri in BSTSY+FBS late exponential


title: Panc1GR-NC2


title: ATF4 KO

city: Athens

first: Evdokia

last: Karagouni

state: Attica

address: 127 Vas. Sofias Avenue

country: Greece

institute: Hellenic Pasteur Institute

description:
98171
scRNA-Seq

data_processing:
Alignment of raw sequencing reads, pre-processing and generation of feature-barcode matrices was conducted using Cell Ranger v3.1.0 with default parameters.
Quality control, pre-processing, filtering, clustering, differential expression analysis and visualizations were performed using Seurat v3.2.1 and ggplot2 v3.2.2.
Trajectory analysis was conducted using Slingshot.
Genome_build: GRCm38
Supplementary_files_format_and_content: barcodes_*.tsv, features_*.tsv, matrix_*.mtx. Filtered feature-barcode count matrix.

source_name: B16F10 tumor

extract_protocol:
Tumors were dissociated to single cell suspension following the 10X Genomics protocol. Cells were loaded into a 10X Genomics Chromium Single-Cell controller following manufacturer's instructions using the 10X 3' RNA-Seq V3 kit.
Illumina sequencing libraries were prepared then sequenced on a NovaSeq 6000 (28bp x 91bp).

value: B16F10 tumor

tag: tumor size

value: small

tag: host genotype

tag: gender

value: Pooled male and female

value: 11 weeks


title: WGBS_WAT_WT_8w

description: WGBS

value: 8 weeks

value: SVCs CD45, CD31 depleted

tag: genotype

value: WT

value: adipose


title: Simonsiella muelleri in BSTSY+FBS early exponential


title: Panc1GR-NC1

tag: treatment

value: ctrl


title: cell line: AGS-EBV transduced with: ncsh lentivirus replicate1

value: ncsh lentivirus


title: Simonsiella muelleri in BSTSY+FBS exponential, replicate2


title: ATF4 WT

description:
98170
scRNA-Seq


title: S006778

status: Public on May 09 2022

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description: ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using HISAT2 v 2.1.0 to the human genome reference GRCh38/hg38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014) using the GENCODE release 27 transcriptome model, with default parameters except --no-unal --non-deterministic --novel-splicesite-outfile ${SPLICEFILE}  --rna-strandness RF. HISAT2 indexes were created using the --snp parameter and dbSNP build 150.
Gene expression data in FPKM ( fragments per kilobase of transcript per million mapped reads) were generated using StringTie v1.3.3b (default parameters including --rf -e) using protein coding transcripts from GENCODE release 27 as transcriptome model. Novel transcripts were discarded. An FPKM gene expression matrix was generated from .ctab files using tximport and subsequently transformed to TPM values adding to each expression measurement 0.1, followed by log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Spearman rank correlation was used to determine correlations between expression of ESR1 and ESR2. Kruskal-Wallis non-parametric test and Wilcoxon rank sum test were used to compare and plot expression of the ESR1 and ESR2 genes in various clinical groups such as PAM50 subtype and age groups in the SCAN-B cohort. Transformed ESR2 expression data was divided into tertiles, with the first tertile defined as ESR2-high, and the bottom two tertiles at ESR2-low. Mann Whitney U test and Fisher’s exact test were used to evaluate significant differences in the clinicopathological variables for the ESR2-high and ESR2-low groups. Survival analysis was performed by Kaplan-Meier and Cox regression survival analyses. All analysis was performed for a cohort of 3207 samples from patients enrolled in the SCAN-B study.
Assembly: Human genome reference GRCh38/hg38.
Supplementary files format and content: Gene expression in TPM in CSV format.

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

tag: scanb external id

tag: age at diagnosis

tag: lymph node group

tag: lymph node status

value: NodeNegative

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

value: Low

tag: nhg

tag: pam50 subtype

value: LumA

tag: clinical groups

tag: histopathological type

value: Other

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event

tag: esr1 expression

tag: esr2 expression


title: S006783

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

value: Lobular


title: S006780

tag: her2 status

tag: ki67 status

value: High

tag: nhg

tag: pam50 subtype

value: LumB

tag: clinical groups

tag: histopathological type

tag: endocrine treated


title: S006777

value: Ductal

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days

tag: relapse free interval years

tag: relapse free interval event


title: S006782

tag: scanb external id

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: esr1 expression

tag: esr2 expression


title: S006781

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: pam50 subtype

tag: clinical groups


title: S006786

tag: histopathological type

tag: endocrine treated

tag: chemo treated

tag: overall survival days

tag: overall survival years

tag: overall survival event

tag: relapse free interval days