title: MCF10A cells, Cas9-expressing controls, 2D culture, biol rep 2


title: p53MDM2_162_6hr

status: Public on Jan 07 2026

type: RNA

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

country: USA

institute: University of Michigan

hyb_protocol: Hybridized to Human GeneChipTM Human Gene 1.0 ST Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize and fit log2 transformed expression values.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: purified AML cells from PBMCs

label_protocol: Biotinylated cDNA were prepared according to the Nugen WT-Pico Ovation kit protocol from 10 ng total RNA (WT-Pico Ovation RNA Amplification System Manual, 2007, NuGEN). Subsequently cDNA is made double stranded fragmented and end-labeled following manufacturers standard protocol (NuGEN encore end-labeling module).

growth_protocol: Mononuclear cells from blood or marrow from AML patients were isolated by Ficoll gradient centrifugation (GE Healthcare), aliquoted into FCS with 10% DMSO, and cryopreserved in liquid nitrogen. For purification of AML blasts using negative selection, cryopreserved PBMCs were washed and recovered by centrifugation and then treated with anti-human CD3 (Miltenyi Biotec #130-050-101), anti-human CD14 microbeads (if blasts were negative for CD14 expression; Miltenyi Biotec #130-050-201), anti-human CD19 (if blasts were negative for CD19 expression; Miltenyi Biotec #130-050-301) and anti-human CD235a (Miltenyi Biotec #130-050-501) per manufacturer’s recommendations. Cell suspensions were run through Miltenyi MACS separation LS columns (#130-042-401) to negatively enrich for AML blasts.  All blast preps were analyzed by cytospins for purity. This schema resulted in greater than 90%-95% blast purity.

extract_protocol: RNA was extracted using the Trizol reagent. RNA was further purified using the RNeasy kit (Qiagen 74104) and the integrity analyzed using the bioanalyzer platform (Agilent).

treatment_protocol: Blasts enriched to >90% purity were incubated in serum-supplemented RPMI medium at 2.5x105 cells in 100 µl final volume in the presence of 0.625-20µM of the MDM2 inhibitor MI-219

tag: gender

value: m

tag: mdm2 inhibitor sensitivity

value: Sensitive

tag: time point (h)

tag: aml type

value: de novo

tag: age


title: 810_Quad

type: SRA

city: Rochester

first: Chantal

last: McCabe

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description: Library name: 810_Quad

library_source: transcriptomic

data_processing:
Data processing for FeatureCounts done with Galaxy using HISAT2 and FeatureCount Packages
Assembly: mm10
Supplementary files format and content: FeatureCounts in a tabular format

organism: Mus musculus

source_name: Quadricep

extract_protocol:
Tissues collected and homogenized in QIAZOL and totalRNA extracted via Qiagen's mRNeasy kit
Library construction via LibStrmRNA(MRNA)

treatment_protocol: Mice dosed with either Vehicle or AP over a 16-week timecourse (2x per week)

tag: tissue

value: Quadricep

tag: genotype

tag: treatment

value: AP


title: VGLUT1_CTRL_2

city: Houston

first: Jacob

middle: Michael

last: Dundee

state: Texas

address: 1 Baylor Plaza

department: Neuroscience

institute: Baylor College of Medicine

description:
Library name: S2_8179_9307
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Modified mouse mm10 with transgenes information (APP695S, R26LNL, CaMK2TTA, GAD2Cre) to check the expression of transgenes in each model.
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Frontal cortex

extract_protocol:
Mouse brain cortex tissues (one hemisphere of the cortex for each animal) were collected and put into 1.5ml RNAase free Eppendorf tubes, flash-frozen using liquid nitrogen, and stored at –80 ̊C. For each sample, we pooled 2 mouse brain cortex tissues into one tube for Single-nucleus suspensions. Single-nucleus suspensions were prepared following the protocol we described previously (McLaughlin et al., 2022). Nuclei were stained by Hoechst-33342 (1:1000; >5min). Next, we collected nuclei using Fluorescence activated cell sorting (FACS) to remove debris. We used the BD Aria III sorter for collecting nuclei. Hoechst+ nuclei were collected during sorting into a 1.5ml tube with 200ul 1x PBS with 0.5% BSA as the receiving buffer (RNase inhibitor added). For each 10x Genomics run, 80k–150k nuclei were collected. Nuclei were spun down for 10 min at 950g at 4 ̊C, and then resuspended using 40ul of 1x PBS with 0.5% BSA (RNase inhibitor added). 2ul nucleus suspension was used for counting the nuclei with hemocytometers to calculate the concentration. 20K nuclei were loaded into the 10X chip for each capture to target 10k nuclei for each run.
10x Genomics sequencing libraries were prepared following the standard protocol from Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with following settings. All PCR reactions were performed using the Biorad C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Cycle numbers were used as the 10x protocol recommended for cDNA amplification and sample index PCR. As per 10x protocol, 1:10 dilutions of amplified cDNA and final libraries were evaluated on Agilent TapeStation. The final library was sent to Novogene Corporation Inc. for Illumina NovaSeq PE150 S4 lane sequencing with the dual index configuration Read 1 28 cycles, Index 1 (i7) 10 cycles, Index 2 (i5) 10 cycles, and Read 2 90 cycles. A PhiX control library was spiked in at 1% concentration. The sequencing depth is about 43-60K reads per nucleus.

value: Frontal cortex

value: VGLUT1 control

tag: batch


title: VGLUT1_APP_1

description:
Library name: S3_9028_1385
10x Genomics

value: VGLUT1 APP


title: VGLUT1_APP_2

description:
Library name: S4_9037_7286
10x Genomics


title: VGLUT1_CTRL_1

description:
Library name: S1_9027_7278
10x Genomics


title: p53MDM2_162_2hr


title: 603_Quad

description: Library name: 603_Quad


title: p53MDM2_150_u


title: Plasmid library_TYC_STARR8_replicate2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Library name: G202M22
Plasmid DNA, stranded library

library_source: other

data_processing:
READ MAPPING: reads were aligned to the mm9 mouse genome using Bowtie2 (Langmead et al 2009, Genome Biology) with default settings. Reads were filtered so that only uniquely-aligned reads were used for downstream analysis.
Assembly: mm9
Supplementary files format and content: Excel workbook; In vivo global STARR-seq assay on 23,912 reporter regions. These 23,912 reporters represet 1,839 ATAC regions selected from ATAC peak identified by 10x Genomic Multiome datasets.
Supplementary files format and content: Excel workbook; mapped read counts

molecule: other

source_name: liver

growth_protocol: Male and female CD1 mice (ICR strain) were purchased from Charles River Laboratories (Wilmington, MA) and kept on a 12-hour light/dark cycle with food and water without restriction.

extract_protocol:
The extraction methods, adapted from the published STARR-seq protocol (Neumayr, Pagani et al. 2019), were used in a nested PCR amplification protocol to characterize the transcriptional activity of each DHS sequence (putative regulatory region) to be assayed by HDI-STARR-seq: 1) a library prepared from the same batch of purified plasmid DNA injected into each mouse by HDI, which was used directly as a PCR template in a nested PCR reaction for library construction (primers ON8381, ON8382; see STARR_seq_primer.txt); 2) a library prepared from DNA extracted from flash frozen liver tissue collected 10 days after in vivo transfection by HDI (primers ON8381, ON8382); and 3) a library prepared from the transcribed RNA (reporter sequences) extracted from each HDI-transfected liver (primers ON8379, ON8380; see STARR_seq_primer.txt) . STARR-seq reporter plasmid DNA remaining in the liver 10 days after HDI was extracted using a commercial QIAprep spin miniprep kit (QIAgen, cat. # 27106). The liver tissue (200 mg frozen liver) was initially homogenized in 750 ul of QIAgen Buffer P1 using a rubber-tipped micropestle and passed through a 20G needle three times to homogenize large tissue pieces. The extracted plasmid DNA was bound to a QIAprep spin column, eluted in EB buffer and used as a PCR template in a subsequent nested PCR reaction using primers ON8381 and ON8382 (see STARR_seq_primer.txt). To extract transcribed reporter RNA, 120 ug of total liver RNA was isolated from 60-100 mg liver tissue from each mouse by TRIzol guanidinium thiocyanate-phenol-chloroform extraction then purified by polyA selection using oligo(dT) beads (New England Biolabs, cat. #E7490L). The transcribed RNA was digested with Turbo DNase I (Ambion, cat. # AM2238) at 37°C for 30 min, reverse transcribed using primer ON8731 (see STARR_seq_primer.txt) for STARR-seq RNA first strand synthesis and Superscript III first-strand synthesis supermix (Invitrogen, cat. # 18080-400), and treated with 10 mg RNase A per ml (Fermentas, cat. # EN0531) for 1 h at 37 degrees Celsius. The cDNA obtained was purified using 1.8x SPRI beads then used as a PCR template in the nested PCR reaction.
The nested PCR requires one set of primers specificially targeting DNA or RNA form of STARR-seq reporter followed by generalized illumina dual index primers. A primer set, ON8381 and ON8382 (see STARR_seq_primer.txt), was designed to amplify the STARR-seq plasmid DNA libraries by specifically targeting the unspliced intron incorporated into original plasmid and present in the plasmid and DNA libraries but spliced out of the reporter RNA sequences. Another primer set, ON8379 and ON8380 primer (see STARR_seq_primer.txt), which straddles the splice junction, was designed to specifically amplify only the transcribed and spliced RNA molecules. The nested PCR was completed by using  NEBNext® Multiplex Oligos for Illumina (#E7600S) for all three library types (plasmid, DNA and RNA) to further amplify the material and attach Illumina i5 and i7 barcoded sequences to allow for multiplex sequencing on an Illumina sequencer (Novogene, Sacramento, CA).

treatment_protocol: In vivo HDI transfection: Plasmid DNA to be delivered to each mouse was resuspended in TransIT-EE delivery solution (MIR 5340, Mirus, Inc, Madison, WI) in a final volume of ~3 ml, equivalent to 10% of the mouse body weight (vol/weight) within 5-8 seconds and delivered by HDI. For HDI-STARR-seq studies, 30 ug of STARR-seq library plasmid DNA was mixed with 3 ug of Renilla reporter plasmid DNA was injected per mouse at day 0. Male mice (7-9 wk of age) were anesthetized with isoflurane and implanted subcutaneously with an Alzet osmotic minipump (cat. # 2002; Durect Corp., Cupertino, CA) at day 1 to deliver recombinant rat growth hormone (GH) as a continuous infusion (cGH) at 25 ng/g BW/h then euthanized on day 11. Recombinant rat GH (bacterial lipopolysaccharide depleted (7.7 to 15.5 EU/mg); purchased from Dr. Arieh Gertler, Protein Laboratories Rehovot, Ltd., Rehovot, Israel) was dissolved in 30 mM NaHCO3 and 0.15 M NaCl containing 0.1 mg/ml rat albumin (Sigma-Aldrich, catalog no. A6414). Mice were euthanized between 10:30 AM and 12 noon under CO2 followed by cervical dislocation (Boston University animal facility light cycle: lights on from 7:30 AM to 7:30 PM). Livers were excised and flash frozen in liquid nitrogen then stored at -80° C.

value: liver

tag: Sex

tag: strain

tag: age at_euthanasia


title: 737_Quad

description: Library name: 737_Quad

value: Vehicle


title: 608_Quad

description: Library name: 608_Quad


title: Plasmid library_TYC_STARR8_replicate1

description:
Library name: G202M21
liver-extracted plasmid DNA, stranded library


title: 670_Quad

description: Library name: 670_Quad


title: MCF10A cells, Cas9-expressing controls, 2D culture, biol rep 1

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

data_processing:
Reads were mapped to hg38 with STAR v2.7.3a and counted with HTSeq v0.12.4.
Differential expression analysis was performed with DESeq2 v1.38.3.
Assembly: hg38
Supplementary files format and content: rawcount.txt : HTseq Count output, tabular file

molecule: polyA RNA

growth_protocol: MCF10A cells were maintained in DMEM/F12 medium supplemented with 5% fetal bovine serum (FBS), insulin (10 µg/mL), epidermal growth factor (20 ng/mL), hydrocortisone (500 ng/mL), cholera toxin (100ng/mL), and 1% penicillin/streptomycin, in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). 2ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) following the manufacturer's protocol.

tag: cell line

tag: cell type

value: Non-tumorigenic mammary cells

value: Cas9-expressing control


title: GAD2_CTRL_2

description:
Library name: G
10x Genomics

value: GAD2 control


title: p53MDM2_150_6hr


title: p53MDM2_150_2hr


title: GAD2_APP_1

description:
Library name: F
10x Genomics

value: GAD2 APP


title: Female-Vehicle_TYC_STARR8_DNA_replicate2

description:
Library name: G202M20
liver-extracted plasmid DNA, stranded library

value: Female

value: 9-10 weeks

value: no treatment


title: 446_Quad

description: Library name: 446_Quad


title: Female-Vehicle_TYC_STARR8_RNA_replicate2

description:
Library name: G202M11
polyA-selected RNA, stranded library


title: p53MDM2_139_2hr

value: f

value: Resistant


title: 567_Quad

description: Library name: 567_Quad


title: Male+cGH_10days_TYC_STARR8_DNA_replicate1

description:
Library name: G202M17
polyA-selected RNA, stranded library

value: Male

value: cGH (continuous GH infusion)


title: 445_Quad

description: Library name: 445_Quad

value: Quadricep


title: CAMKII_APP_2

description:
Library name: D
10x Genomics

value: Frontal cortex

value: CAMKII APP


title: Female-Vehicle_TYC_STARR8_DNA_replicate1

description:
Library name: G202M19
liver-extracted plasmid DNA, stranded library


title: Female-Vehicle_TYC_STARR8_RNA_replicate1

description:
Library name: G202M9
polyA-selected RNA, stranded library


title: 444_Quad

description: Library name: 444_Quad


title: 568_Quad

description: Library name: 568_Quad

value: AP


title: GAD2_APP_2

description:
Library name: H
10x Genomics


title: p53MDM2_139_u

value: de novo


title: CAMKII_CTRL_2

description:
Library name: C
10x Genomics

value: CAMKII control


title: p53MDM2_138_6hr


title: Male-Vehicle_TYC_STARR8_RNA_replicate1

description:
Library name: G202M5
polyA-selected RNA, stranded library

value: liver


title: GAD2_CTRL_1

description:
Library name: E
10x Genomics


title: CAMKII_CTRL_1

description:
Library name: A
10x Genomics


title: p53MDM2_139_6hr


title: Male+cGH_10days_TYC_STARR8_RNA_replicate2

description:
Library name: G202M4
polyA-selected RNA, stranded library


title: Male-Vehicle_TYC_STARR8_RNA_replicate3

description:
Library name: G202M8
polyA-selected RNA, stranded library


title: p53MDM2_138_2hr


title: 443_Quad

description: Library name: 443_Quad

value: Vehicle


title: Orai1Sox9 mouse, AP1

city: Beijing

first: Xiaoyu

last: Guo

state: Beijing

address: Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.

country: China

institute: Peking Union Medical College Hospital

description: Library name: PECD-B16

data_processing:
Quality control and mapping
Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment
Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment
Gene structure extension and novel transcripts identification
Alternatively splicing analysis and SNP-INDEL calling
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and counts values for each Sample

source_name: pancreas

extract_protocol:
Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols.

value: pancreas

value: primary cells

value: primary pancreatic ductal epithelial cells

value: palmitoleic acid plus ethanol


title: Orai1Sox9 mouse, AP2

description: Library name: PECD-B18


title: Male-Vehicle_TYC_STARR8_RNA_replicate2

description:
Library name: G202M7
polyA-selected RNA, stranded library

value: 9-10 weeks

value: no treatment


title: 207_Quad

description: Library name: 207_Quad


title: p53MDM2_101_u

value: f

value: Resistant


title: p53MDM2_122_u

value: m


title: 442_Quad

description: Library name: 442_Quad

value: Quadricep


title: 101_Quad

description: Library name: 101_Quad


title: CAMKII_APP_1

description:
Library name: B
10x Genomics

value: Frontal cortex


title: Orai1f/f mouse, AP5

description: Library name: PECD-B36


title: 441_Quad

description: Library name: 441_Quad


title: old

city: Bad Nauheim

first: Yousef

last: Alayoubi

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max-Planck-Institute for Heart and Lung Research

description: Library name: sample_old

library_source: genomic single cell

data_processing:
The libraries were sequenced on Illumina NextSeq500 on 2 separate high75 cartridges, resulting in ca 400-500M reads per run. The sequencing data (fastq files) were demultiplexed using the 10x Cell Ranger pipeline. The Cell Ranger pipeline included the following steps: 1) the sequencing reads were demultiplexed based on the unique bead barcode. 2) The demultiplexed reads were trimmed, aligned to the reference genome (mm10), counted and normalized. 3) The individual runs (young1, young2, old1 and old2) were merged and re-normalized.
Assembly: mm10 / gencode.vM17.basic
Supplementary files format and content: The Cell Ranger pipeline outputs were analyzed with the Signac R package (extension of the Seurat package). There dataset was additionally filtered based on QC parameters, then dimensional reductions and clustering were performed. All chromatin accessibility peaks, located in the genebody and +2kb upstream, were annotated to the respective genes and referred to as pseudoexpression for further analysis.

molecule: genomic DNA

source_name: heart

extract_protocol:
Whole hearts (both ventricles and atriums) were isolated from 3 young (14 weeks) and 3 old (98 weeks) mice. Washed in PBS and snap-frozen in liquid nitrogen. Hearts from each condition were stored at -80 C. 4 hearts (2 young and 2 old) were mechanically disrupted, isolated nuclei were stained for DAPI (nuclear marker) and PCM1 (cardiomyocyte nuclear envelope marker). Afterwards nuclei were FAC-Sorted based on forward and side scatters and DAPI signal to get nuclei suspension.
FAC-Sorted nuclei were used for scATAC-seq, using the 10x Chromium kit. Nuclei were tagmented by Tn5 transposase (cut fragments stay inside the nuclei) and then encapsulated into droplets with barcoded beads. Droplets contain compounds, which release Tn5-cut DNA fragments from the nuclei. Barcoded beads have primers attached to their surface. These primers contain unique bead-barcode, as well as complimentary sequence to adapters, inserted by Tn5 during tagmentation. Therefore, Tn5-cut fragments attach to the bead. On-the-beads PCR enriches attached fragments, incorporating unique bead- barcodes into library. Fragments are released from the beads, additionally enriched (with universal primers) by PCR. The final libraries were cleaned with SPRI magnetic beads and size-selected for 200-1000bp library size. Concentration was assessed by Qubit and library size distribution was assessed by PerkinElmer LabChip.

value: heart

value: heart nuclei

value: cardiac cells

value: old


title: Orai1Sox9 mouse, AP3

description: Library name: PECD-B35


title: young_2

description: Library name: sample_young_2

value: young


title: Orai1f/f mouse, AP3

description: Library name: PECD-B27


title: p53MDM2_101_6hr

value: de novo


title: p53MDM2_122_6hr


title: RNA-seq, wildtype mouse, MEF cells, biological replicate 2

city: Bethesda

first: Emma

last: Price

state: MD

address: 9000 Rockville Pike, Bld 29B

department: LIG

institute: NIAID/NIH

description: Library name: MEF_WT_RNAseq_Rep2

data_processing:
Raw RNA-seq reads were assessed for quality using FastQC (v0.11.9) and adapter-trimmed using Trimmomatic (v0.39). Trimmed reads were aligned to the mouse reference genome (mm10) using HISAT2 (v2.2.1). Gene-level read counts were generated with featureCounts (v2.0.1). Differential gene expression analysis was performed in R using DESeq2 (v1.30.1).
Assembly: mm10
Supplementary files format and content: Counts were generated separately for tissue samples and MEF samples due to independent library preparation and processing. Rows correspond to genes and columns correspond to individual samples. These count matrices represent the primary processed RNA-seq data.

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM with L-glutamine supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C in 5% CO₂. For ChIP, 2 × 10⁶ cells were plated in 15-cm dish in fresh growth medium one day prior to cross-linking. Cell number and viability were assessed at harvest, and viability exceeded 90%.

extract_protocol:
Mice were euthanized via carbon dioxide asphyxiation followed by cervical dislocation, in accordance with institutional animal care guidelines. Tissues were immediately harvested, briefly rinsed in ice-cold phosphate-buffered saline (PBS), and placed in RNAlater (Invitrogen) and stored at −20 °C until RNA extraction. For RNA isolation, tissues were removed from RNAlater and washed in ice cold PBS prior to homogenization in TRIzol reagent. MEFs were washed with PBS and lysed directly in plates using TRIzol for RNA extraction. Total RNA was extracted by column-based purification with the Direct-zol RNA MiniPrep Kit (Zymo Research), according to the manufacturers’ instructions. Genomic DNA was removed during purification using DNaseI supplied with kit.
RNA quality and integrity were assessed using an Agilent Bioanalyzer, and only samples with high RNA integrity numbers (RIN) and A260/A280 ratios between 1.8–2.1 were used for library preparation. Purified RNA was stored at −80 °C until processing. Polyadenylated mRNA was isolated from 1 µg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and converted into sequencing libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina, according to the manufacturer’s instructions. Libraries were fragmented, reverse transcribed, end-repaired, adapter-ligated, and amplified by limited-cycle PCR. Library size distribution (200–400 bp) was confirmed using an Agilent Bioanalyzer. Sequencing was performed on an Illumina NovaSeq platform to generate paired-end reads.

value: MEF

value: Mouse embryonic fibroblasts

value: Wildtype

tag: developmental stage


title: p53MDM2_122_2hr


title: Orai1f/f mouse, AP4

description: Library name: PECD-B34

value: pancreas

value: primary cells

value: primary pancreatic ductal epithelial cells

value: palmitoleic acid plus ethanol


title: RNA-seq, wildtype mouse, MEF cells, biological replicate 1

description: Library name: MEF_WT_RNAseq_Rep1


title: RES_MNP_mouse_IgG1_rep3

city: Cincinnati

first: Samantha

last: Brugmann

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Library name: RES_MNP_mouse_IgG1_rep3

library_source: genomic

data_processing:
A quality control check on the generated fastq files was performed using FastQC basic quality metrics.
The reads were mapped to a reference genome using Bowtie2, and peaks were called with MACS2.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Run

source_name: Mandible

extract_protocol:
Genomic DNA from liberase-digested mandibles (300-400K cells) for CUT&Run assay was prepared according to manufacturer's protocol (Epicypher CUTANA CUT&RUN Protocol) and FLAG-M2 antibody (Sigma F3165).
Using 5-10 ng purified CUT&RUN-enriched DNA, prepare Illumina library using the NEBNext Ultra II Library Prep Kit for Illumina per manufacturer's instructions. Each created library was dual-indexed with NEBNext Multiplex Oligos for Illumina. Completed libraries were sequenced on an Illumina Nextseq-500 sequencer, generating 5 million or more high quality, 100 base length read pairs per sample.

value: Mandible

value: mouse IgG1


title: 208_Quad

description: Library name: 208_Quad

value: Quadricep

value: Vehicle


title: p53MDM2_101_2hr

value: f

value: Resistant


title: p53MDM2_138_u


title: Male+cGH_10days_TYC_STARR8_RNA_replicate1

description:
Library name: G202M3
polyA-selected RNA, stranded library

value: liver

value: Male

value: 9-10 weeks

value: cGH (continuous GH infusion)


title: 810_Fat

description: Library name: 810_Fat

source_name: Inquinal Fat

value: Inquinal Fat

value: AP


title: old_2

description: Library name: sample_old_2

value: heart

value: heart nuclei

value: cardiac cells

value: old


title: RES_MNP_mouse_IgG1_rep2

description: Library name: RES_MNP_mouse_IgG1_rep2


title: 117_Quad

description: Library name: 117_Quad


title: 737_Fat

description: Library name: 737_Fat


title: Orai1Sox9 mouse, control5

description: Library name: PECD-B33

value: pancreas

value: primary cells

value: primary pancreatic ductal epithelial cells

value: palmitoleic acid plus ethanol


title: RNA-seq, humanized mouse, MEF cells, biological replicate 2

description: Library name: MEF_HUM_RNAseq_Rep2

value: MEF

value: Mouse embryonic fibroblasts

value: Humanized CTCFL


title: RNA-seq, humanized mouse, MEF cells, biological replicate 1

description: Library name: MEF_HUM_RNAseq_Rep1


title: 670_Fat

description: Library name: 670_Fat


title: young

description: Library name: sample_young

value: young


title: Orai1f/f mouse, AP1

description: Library name: PECD-B20


title: RNA-seq, wildtype mouse, MEF cells, biological replicate 3

description: Library name: MEF_WT_RNAseq_Rep3

value: Wildtype


title: RNA-seq, wildtype mouse, testis tissue, biological replicate 2

description: Library name: Testis_WT_RNAseq_Rep2

source_name: Testis

value: Testis

value: Whole testis tissue

value: Adult


title: RES_MNP_FLAG_rep3

description: Library name: RES_MNP_FLAG_rep3

value: Mandible

value: FLAG antibody


title: Orai1f/f mouse, AP2

description: Library name: PECD-B26


title: RES_MNP_FLAG_rep1

description: Library name: RES_MNP_FLAG_rep1


title: 811_Fat

description: Library name: 811_Fat

value: Inquinal Fat

value: AP


title: RNA-seq, wildtype mouse, testis tissue, biological replicate 1

description: Library name: Testis_WT_RNAseq_Rep1


title: Orai1Sox9 mouse, control1

description: Library name: PECD-B38


title: RNA-seq, humanized mouse, MEF cells, biological replicate 3

description: Library name: MEF_HUM_RNAseq_Rep3


title: Orai1f/f mouse, control5

description: Library name: PECD-B42


title: MUT_MNP_mouse_IgG1_rep1

description: Library name: MUT_MNP_mouse_IgG1_rep1

value: Kif3a fl/fl;Wnt1Cre;Gli3 BioFLAG/+

value: mouse IgG1


title: 568_Fat

description: Library name: 568_Fat


title: RES_MNP_mouse_IgG1_rep1

description: Library name: RES_MNP_mouse_IgG1_rep1


title: 736_Fat

description: Library name: 736_Fat

value: Vehicle


title: RNA-seq, humanized mouse, testis tissue, biological replicate 1

description: Library name: Testis_HUM_RNAseq_Rep1


title: RES_MNP_FLAG_rep2

description: Library name: RES_MNP_FLAG_rep2


title: Orai1Sox9 mouse, control3

description: Library name: PECD-B31

value: pancreas

value: primary cells

value: primary pancreatic ductal epithelial cells


title: Orai1f/f mouse, control3

description: Library name: PECD-B40

value: palmitoleic acid plus ethanol


title: MUT_MNP_mouse_IgG1_rep2

description: Library name: MUT_MNP_mouse_IgG1_rep2


title: 608_Fat

description: Library name: 608_Fat


title: 603_Fat

description: Library name: 603_Fat


title: Orai1f/f mouse, control2

description: Library name: PECD-B39


title: 445_Fat

description: Library name: 445_Fat


title: WT_MNP_mouse_IgG1_rep3

description: Library name: WT_MNP_mouse_IgG1_rep3

value: Gli3 BioFLAG/BioFLAG Wild type


title: RNA-seq, humanized mouse, liver tissue, biological replicate 2

description: Library name: Liver_HUM_RNAseq_Rep2

source_name: Liver

value: Liver

value: Whole liver tissue

value: Humanized CTCFL


title: 044_Quad

description: Library name: 044_Quad

value: Quadricep


title: RNA-seq, humanized mouse, liver tissue, biological replicate 1

description: Library name: Liver_HUM_RNAseq_Rep1

value: Adult


title: RNA-seq, humanized mouse, testis tissue, biological replicate 2

description: Library name: Testis_HUM_RNAseq_Rep2

value: Testis

value: Whole testis tissue


title: MUT_MNP_FLAG_rep2

description: Library name: MUT_MNP_FLAG_rep2

value: Mandible

value: FLAG antibody


title: 567_Fat

description: Library name: 567_Fat

value: Inquinal Fat

value: AP


title: Orai1Sox9 mouse, control4

description: Library name: PECD-B32


title: Orai1f/f mouse, control4

description: Library name: PECD-B41


title: N2, 100 mM NaCl, biol rep 3

city: Shanghai

first: Rong

last: Huang

address: Shanghai Jiao Tong University, Minhang Campus, 800 Dongchuan Road, Minhang District, Shanghai 200240, China

institute: Shanghai Jiao Tong university

description: Library name: NaCl-3

data_processing:
FASTQ files were aligned to C. elegans WBcel269 using STAR (version 2.7.1a) with a 2-pass alignment procedure.
Gene and transcript quantification was performed using RSEM (version 1.3.3).
Differential expression analysis was conducted in R (version 4.3.1) using the DESeq2 package (version 1.40.2).
Differentially expressed genes were defined with an adjusted P value (false discovery rate, FDR) < 0.05.
Assembly: C. elegans WBcel269
Supplementary files format and content: csv files include raw counts for each Sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were maintained at 15°C or 20°C on standard nematode growth medium (NGM) agar plates seeded with Escherichia coli OP50-1 (a streptomycin-resistant strain for worm food).

extract_protocol:
Total RNA was extracted and purified from all samples using the M5 HiPer Universal Plus RNA Mini Kit (MF167, Mei5 Biotech, Beijing, China) according to the manufacturer’s instructions. RNA quality and integrity were assessed prior to library preparation.
All RNA samples were sent to Novogene Co., Ltd (Beijing, China) for quality control (Sample QC). After RNA library preparation, cDNA libraries are sequenced on Illumina NovaSeq platforms using a paired-end 150 bp sequencing strategy. Approximately 6 Gb of clean data per sample was obtained, with a uniquely mapped read rate exceeding 75%. Three biological replicates were included.

treatment_protocol: For solid agar plate assay, approximately 2,000 synchronized L4-stage wild type (N2) animals were washed twice in either 100 mM NaCl, 100 mM KCl, or NGM solution (51 mM NaCl, 25 mM KPB) and then transferred to agar plates supplemented with 100 mM NaCl, 100 mM KCl, or NGM solution (51 mM NaCl, 25 mM KPB). These plates were seeded with OP50-1 bacteria that had been treated with the corresponding solutions. After 4 hours, the animals were collected and flash-frozen in liquid nitrogen.

value: whole animal

value: N2 (wild type)

value: 100 mM NaCl


title: 442_Fat

description: Library name: 442_Fat


title: N2, 100 mM NaCl, biol rep 2

description: Library name: NaCl-2


title: RNA-seq, wildtype mouse, spleen tissue, biological replicate 2

description: Library name: Spleen_WT_RNAseq_Rep2

source_name: Spleen

value: Spleen

value: Whole spleen tissue

value: Wildtype


title: RNA-seq, wildtype mouse, liver tissue, biological replicate 2

description: Library name: Liver_WT_RNAseq_Rep2

value: Liver


title: RNA-seq, wildtype mouse, liver tissue, biological replicate 1

description: Library name: Liver_WT_RNAseq_Rep1

value: Whole liver tissue


title: WT_MNP_FLAG_rep3

description: Library name: WT_MNP_FLAG_rep3

value: Gli3 BioFLAG/BioFLAG Wild type


title: RNA-seq, wildtype mouse, spleen tissue, biological replicate 1

description: Library name: Spleen_WT_RNAseq_Rep1


title: 446_Fat

description: Library name: 446_Fat


title: Orai1Sox9 mouse, control2

description: Library name: PECD-B29

value: pancreas

value: primary cells

value: primary pancreatic ductal epithelial cells

value: palmitoleic acid plus ethanol


title: 441_Fat

description: Library name: 441_Fat


title: RNA-seq, humanized mouse, spleen tissue, biological replicate 2

description: Library name: Spleen_HUM_RNAseq_Rep2

value: Humanized CTCFL

value: Adult


title: MUT_MNP_FLAG_rep1

description: Library name: MUT_MNP_FLAG_rep1

value: Mandible

value: Kif3a fl/fl;Wnt1Cre;Gli3 BioFLAG/+

value: FLAG antibody


title: 208_Fat

description: Library name: 208_Fat

value: Inquinal Fat

value: Vehicle


title: N2, 100 mM KCl, biol rep 3

description: Library name: KCl-3

value: whole animal

value: N2 (wild type)

value: 100 mM KCl


title: 444_Fat

description: Library name: 444_Fat


title: 443_Fat

description: Library name: 443_Fat


title: WT_MNP_mouse_IgG1_rep2

description: Library name: WT_MNP_mouse_IgG1_rep2

value: mouse IgG1


title: Orai1f/f mouse, control1

description: Library name: PECD-B37


title: WT_MNP_mouse_IgG1_rep1

description: Library name: WT_MNP_mouse_IgG1_rep1


title: RNA-seq, humanized mouse, spleen tissue, biological replicate 1

description: Library name: Spleen_HUM_RNAseq_Rep1

value: Spleen

value: Whole spleen tissue


title: WT_MNP_FLAG_rep2

description: Library name: WT_MNP_FLAG_rep2

value: Gli3 BioFLAG/BioFLAG Wild type


title: 101_Fat

description: Library name: 101_Fat


title: N2, 100 mM NaCl, biol rep 1

description: Library name: NaCl-1

value: 100 mM NaCl


title: 117_Fat

description: Library name: 117_Fat


title: WT_MNP_FLAG_rep1

description: Library name: WT_MNP_FLAG_rep1


title: N2, NGM solution, biol rep 3

description: Library name: SB-3

value: NGM solution


title: Input alphaKO

city: Napoli

first: Dario

last: Antonini

address: Strada Vicinale Cupa Cintia, 21

country: Italy

institute: University of Naples "Federico II"

description: Library name: Sample 3

data_processing:
mapping performed using Bowtie2
peak calling performed using MACS  2.1.1.20160309
Assembly: mm10
Supplementary files format and content: Tabular files containing peak name, coordinates, lenght, summit, pileup, fold of enrichment, -log of pvalue and -log of FDR

source_name: epidermis

extract_protocol:
QiaQuick columns (ThermoFisher Scientific)
KAPA Hyper prep kit (Roche)

value: epidermis

value: p63 alphaKO


title: N2, NGM solution, biol rep 2

description: Library name: SB-2


title: N2, 100 mM KCl, biol rep 1

description: Library name: KCl-1


title: N2, NGM solution, biol rep 1

description: Library name: SB-1


title: 207_Fat

description: Library name: 207_Fat

value: AP


title: ChIP ab-p63 alphaKO

description: Library name: Sample 4

tag: antibody

value: p63-specific antibodies (EPR570, Abcam)


title: RNA-seq, wildtype mouse, brain tissue, biological replicate 2

description: Library name: Brain_WT_RNAseq_Rep2

source_name: Brain

value: Brain

value: Whole brain tissue

value: Wildtype

value: Adult


title: 810_Dia

description: Library name: 810_Dia

source_name: Flushed Diaphysis

value: Flushed Diaphysis


title: 811_Dia

description: Library name: 811_Dia


title: 044_Fat

description: Library name: 044_Fat

value: Inquinal Fat

value: Vehicle


title: RNA-seq, wildtype mouse, brain tissue, biological replicate 1

description: Library name: Brain_WT_RNAseq_Rep1


title: RNA-seq, humanized mouse, brain tissue, biological replicate 2

description: Library name: Brain_HUM_RNAseq_Rep2

value: Humanized CTCFL


title: ChIP-seq, CTCF antibody, wildtype mouse, MEFs, biological replicate 1

description: Library name: MEF_WT_ChIP_CTCF_Rep1

data_processing:
Sequencing quality was assessed using FastQC (v0.11.9), and adapter trimming was performed with Trim Galore (v0.6.6) using default settings. Reads were aligned to the mm10 reference genome with Bowtie2 (v2.4.5) using the “--very-sensitive” preset. Aligned reads were filtered with SAMtools (v1.15) to retain uniquely mapped, high-quality reads (MAPQ ≥ 30). Peak calling was performed with MACS2 (v2.2.7.1) using default parameters (q-value < 0.05). Signal tracks were generated in bigWig format using bedtools (v2.30.0) and deeptools (v3.5.1) for visualization in IGV.
Assembly: mm10
Supplementary files format and content: Processed bigWig files were generated from BAM alignment files using deepTools (v3.5.1) with the bamCoverage function. Reads were normalized using RPGC (Reads Per Genomic Content) with a bin size of 10 bp, allowing for high-resolution visualization. These files provide genome-wide signal tracks for use in IGV or other genome browsers.

source_name: MEFs

extract_protocol:
Mice were euthanized via carbon dioxide asphyxiation followed by cervical dislocation, in accordance with institutional animal care guidelines. Tissues were immediately harvested and placed in ice-cold phosphate-buffered saline (PBS). For tissue dissociation, samples were transferred to a sterile dish containing PBS (250 µL per 50 mg of tissue) and finely minced. The minced tissue was then transferred to a 50 mL Falcon tube and further homogenized by repeated passage through an 18-gauge needle (10 times) followed by a 21-gauge needle (20 times). Large debris and clumps were removed using a 70 µm cell strainer. Cells were pelleted by centrifugation and resuspended in 2 mL Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). To crosslink chromatin (from tissues and MEFs), formaldehyde was added to the cell suspension to a final concentration of 1%, and samples were incubated on a rocker at room temperature for 10 minutes. The reaction was quenched by the addition of glycine (final concentration 125 mM) and incubated for an additional 10 minutes. Cells were washed twice with ice-cold PBS and pelleted by centrifugation. Cell pellets were stored at -80°C until further use. For chromatin immunoprecipitation (ChIP), cells were thawed on ice and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 20 mM Tris–HCl pH 8.0, 2 mM EDTA). Chromatin was sheared to a fragment size of 200–600 bp using sonication. Immunoprecipitation was performed using 5 µg of the appropriate antibody. Immunoprecipitated DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research, catalog #D5205).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, catalog #E7645S), following the manufacturer’s protocol. Libraries were amplified using 10 cycles of PCR and size-selected to 250–450 bp using AMPure XP beads (Beckman Coulter, catalog #A63881). Library quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies, catalog #5067-4626) on an Agilent 2100 Bioanalyzer.

value: MEFs

value: Mouse embryonic fibroblasts

tag: chip antibody

value: CTCF B-5 (Santa Cruz, sc-271514)


title: Input WT

description: Library name: Sample 1

value: wild type


title: 737_Dia

description: Library name: 737_Dia


title: RNA-seq, humanized mouse, brain tissue, biological replicate 1

description: Library name: Brain_HUM_RNAseq_Rep1


title: pmk-1, NaCl, biol rep 2

description: Library name: pmk-1NaCl2

treatment_protocol: Approximately 1,000 synchronized day 1 adult N2 or pmk-1(km25) animals were quickly washed twice in either 100 mM NaCl or 100 mM KCl solution and then transferred to 100 mM NaCl or 100 mM KCl solution without OP50-1. After 4 hours, the animals were collected and flash-frozen in liquid nitrogen.

value: whole animal

value: 100 mM NaCl


title: N2, 100 mM KCl, biol rep 2

description: Library name: KCl-2

value: N2 (wild type)

value: 100 mM KCl


title: ChIP ab-p63 WT

description: Library name: Sample 2

value: epidermis

value: p63-specific antibodies (EPR570, Abcam)


title: 736_Dia

description: Library name: 736_Dia


title: Mono_Old_4

description: Library name: sample_8

data_processing:
The European Galaxy server (UseGalaxy.eu)
HISAT2 (v 2.0.5.2) of individual unpaired reads; aligned to mus musculus (mm10 FULL)
FeatureCounts (Galaxy Version 1.4.6.p5)
Assembly: mm10
Supplementary files format and content: FeatureCounts outputs tabular file containing counted reads per gene per row

source_name: bone

growth_protocol: Primary mouse bone marrow stromal cells (BMSCs) were generated from 6- or 24-mo deriving from flushed bone marrow, RBC lysed, and MACs sorted via Miltenyi's Moncoyte Isolation Kit (BM), mouse.

extract_protocol:
Purification of RNA was performed with RNeasy Mini Columns (QIAGEN, Valencia, CA) with RNase-free DNase solution (QIAGEN) applied to degrade contaminating genomic DNA. RNA quantity was assessed with Nanodrop spectrophotometry (ThermoFisher).
cDNA libraries were prepared using 100 ng of total RNA according to the manufacturer’s instructions for the Illumina Stranded mRNA Prep, Ligation (Illumina, San Diego, CA). The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation’s D1000 ScreenTape and Qubit fluorometry.

value: bone

value: Monocyte

value: Wild-Type


title: ChIP-seq, CTCF antibody, humanized mouse, MEFs, biological replicate 1

description: Library name: MEF_HUM_ChIP_CTCF_Rep1


title: pmk-1, NaCl, biol rep 3

description: Library name: pmk-1NaCl3


title: Mono_Old_3

description: Library name: sample_7


title: Mono_Young_4

description: Library name: sample_4


title: 670_Dia

description: Library name: 670_Dia

value: Flushed Diaphysis

value: AP


title: Mono_Old_2

description: Library name: sample_6


title: Mono_Old_1

description: Library name: sample_5


title: ChIP-seq, CTCF antibody, wildtype mouse, MEFs, biological replicate 2

description: Library name: MEF_WT_ChIP_CTCF_Rep2

value: Wildtype


title: pmk-1, KCl, biol rep 1

description: Library name: pmk-1KCl1


title: ChIP-seq, CTCFL antibody, humanized mouse, MEFs, biological replicate 2

description: Library name: MEF_HUM_ChIP_CTCFL_Rep2

value: Humanized CTCFL

value: custom CTCFL monoclonal


title: 603_Dia

description: Library name: 603_Dia


title: 608_Dia

description: Library name: 608_Dia


title: pmk-1, KCl, biol rep 2

description: Library name: pmk-1KCl2


title: ChIP-seq, CTCFL antibody, humanized mouse, MEFs, biological replicate 1

description: Library name: MEF_HUM_ChIP_CTCFL_Rep1

value: MEFs

value: Mouse embryonic fibroblasts


title: pmk-1, KCl, biol rep 3

description: Library name: pmk-1KCl3


title: Mono_Young_3

description: Library name: sample_3


title: pmk-1, NaCl, biol rep 1

description: Library name: pmk-1NaCl1


title: N2, NaCl, biol rep 2

description: Library name: N2NaCl2


title: 446_Dia

description: Library name: 446_Dia


title: 568_Dia

description: Library name: 568_Dia


title: Mono_Young_1

description: Library name: sample_1


title: ChIP-seq, CTCF antibody, humanized mouse, MEFs, biological replicate 2

description: Library name: MEF_HUM_ChIP_CTCF_Rep2

value: CTCF B-5 (Santa Cruz, sc-271514)


title: ChIP-seq, shared input control, humanized mouse, MEFs, single biological replicate

description: Library name: MEF_Shared_Input


title: N2, NaCl, biol rep 3

description: Library name: N2NaCl3

value: whole animal


title: Mono_Young_2

description: Library name: sample_2


title: 444_Dia

description: Library name: 444_Dia

value: Vehicle


title: Liver, sgBap1 CCl4 , rep 2

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description: Library name: x1240.8

data_processing:
Reads were aligned with STAR 2.7.6a
counts were generated with Salmon 1.4.0 in alignment mode
Assembly: GRCm38
Supplementary files format and content: csv matrix of raw counts for each sample

extract_protocol:
RNA was extracted from fresh frozen liver using Applied Biosystems MagMax mirVana Total RNA Isolation Kit
TruSEQ Stranded mRNA kit

treatment_protocol: Mice were treated with either CRISPR/CAS9 guide RNAs targeting a non-targeting control or BAP1. After 10 days mice were then treated with either carbon tetracholoride or olive oil vehicle control. Tissue was harvested 48 hours after treatment.

value: Liver


title: 567_Dia

description: Library name: 567_Dia


title: N2, KCl, biol rep 2

description: Library name: N2KCl2

value: N2 (wild type)

value: 100 mM KCl


title: Liver, sgBap1 CCl4 , rep 3

description: Library name: x1240.9


title: ChIP-seq, CTCF antibody, wildtype mouse, testis tissue, biological replicate 1

description: Library name: Testis_WT_ChIP_CTCF_Rep1

value: Testis

value: Whole testis tissue

value: Adult


title: 445_Dia

description: Library name: 445_Dia


title: N2, NaCl, biol rep 1

description: Library name: N2NaCl1

value: 100 mM NaCl


title: ChIP-seq, CTCFL antibody, humanized mouse, testis tissue, biological replicate 2

description: Library name: Testis_HUM_ChIP_CTCFL_Rep2


title: ChIP-seq, CTCF antibody, wildtype mouse, testis tissue, biological replicate 2

description: Library name: Testis_WT_ChIP_CTCF_Rep2


title: N2, KCl, biol rep 3

description: Library name: N2KCl3


title: 442_Dia

description: Library name: 442_Dia

value: Flushed Diaphysis


title: ChIP-seq, CTCFL antibody, humanized mouse, testis tissue, biological replicate 1

description: Library name: Testis_HUM_ChIP_CTCFL_Rep1


title: Liver, NTC Veh , rep 2

description: Library name: x1240.5

value: NTC

value: Veh


title: ChIP-seq, CTCF antibody, humanized mouse, testis tissue, biological replicate 2

description: Library name: Testis_HUM_ChIP_CTCF_Rep2

value: Humanized CTCFL


title: Liver, sgBap1 Veh , rep 1

description: Library name: x1240.6


title: Danio rerio, wild-type larvae, 81-96 hpf, hypoxia, rep3

first: Hui

last: Xu

state: Michigan

address: 500 S State St

description: Library name: H3_lib1

data_processing:
Raw sequencing reads were processed to remove low-quality bases and adapter sequences using Trimmomatic (v0.39)
Read quality was evaluated before and after trimming using FastQC (v0.12.1)
Trimmed reads were then aligned to the zebrafish reference genome (GRCz11, Ensembl release 113) using STAR (v2.7.10), with gene annotations obtained from Ensembl
Gene counts were obtained with featureCount (v2.0.7）
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Danio rerio

source_name: whole body

extract_protocol:
Total RNA was extracted using the PureLinkTM RNA Mini Kit (Invitrogen) and treated with DNase using the PureLinkTM DNase Set (Invitrogen).
Poly(A) RNA libraries were constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs).

value: whole body

value: wild type

value: Hypoxia


title: N2, KCl, biol rep 1

description: Library name: N2KCl1


title: 441_Dia

description: Library name: 441_Dia

value: AP


title: Liver, NTC Veh , rep 1

description: Library name: x1240.4


title: ChIP-seq, shared input control, humanized mouse, testis tissue, single biological replicate

description: Library name: Testis_Shared_Input


title: 208_Dia

description: Library name: 208_Dia


title: Liver, NTC CCl4 , rep 2

description: Library name: x1240.2


title: ChIP-seq, CTCF antibody, wildtype mouse, liver tissue, biological replicate 2

description: Library name: Liver_WT_ChIP_CTCF_Rep2

value: Whole liver tissue

value: Wildtype

value: CTCF B-5 (Santa Cruz, sc-271514)


title: 443_Dia

description: Library name: 443_Dia

value: Vehicle


title: Danio rerio, wild-type larvae, 81-96 hpf, hypoxia, rep1

description: Library name: H1_lib1


title: Danio rerio, wild-type larvae, 81-96 hpf, hypoxia, rep2

description: Library name: H2_lib1


title: Liver, NTC CCl4 , rep 3

description: Library name: x1240.3

value: Liver


title: ChIP-seq, CTCF antibody, humanized mouse, testis tissue, biological replicate 1

description: Library name: Testis_HUM_ChIP_CTCF_Rep1

value: Testis


title: ChIP-seq, CTCF antibody, humanized mouse, liver tissue, biological replicate 2

description: Library name: Liver_HUM_ChIP_CTCF_Rep2


title: 117_Dia

description: Library name: 117_Dia


title: Liver, sgBap1 CCl4 , rep 1

description: Library name: x1240.10


title: Liver, sgBap1 Veh , rep 2

description: Library name: x1240.7


title: ChIP-seq, CTCF antibody, wildtype mouse, liver tissue, biological replicate 1

description: Library name: Liver_WT_ChIP_CTCF_Rep1


title: Danio rerio, wild-type larvae, 81-96 hpf, normoxia, rep4

description: Library name: N4_lib1

value: Normoxia


title: Danio rerio, wild-type larvae, 81-96 hpf, normoxia, rep3

description: Library name: N3_lib1


title: 207_Dia

description: Library name: 207_Dia


title: ChIP-seq, CTCF antibody, humanized mouse, liver tissue, biological replicate 1

description: Library name: Liver_HUM_ChIP_CTCF_Rep1

value: Adult


title: Liver, NTC CCl4 , rep 1

description: Library name: x1240.1


title: Danio rerio, wild-type larvae, 81-96 hpf, normoxia, rep2

description: Library name: N2_lib1


title: 101_Dia

description: Library name: 101_Dia


title: ChIP-seq, CTCFL antibody, humanized mouse, liver tissue, biological replicate 2

description: Library name: Liver_HUM_ChIP_CTCFL_Rep2

value: custom CTCFL monoclonal


title: Danio rerio, wild-type larvae, 81-96 hpf, normoxia, rep1

description: Library name: N1_lib1


title: 044_Dia

description: Library name: 044_Dia

value: Flushed Diaphysis


title: 811_Spleen

description: Library name: 811_Spleen

value: Spleen


title: ChIP-seq, CTCFL antibody, humanized mouse, liver tissue, biological replicate 1

description: Library name: Liver_HUM_ChIP_CTCFL_Rep1


title: BMDM_Etoposide_3

description: Library name: sample_14

growth_protocol:
Primary mouse bone marrow stromal cells (BMSCs) were generated from 6-month-old C57BL/6N mice using collagenase digestion and grown in low-glucose DMEM + 10% fetal bovine serum + antibiotics in a hypoxic incubator (humidified, 37 degree, 2% oxygen).
Primary mouse bone marrow-derived macrophages (BMDMs) were generated from 6-month-old C57BL/6N bone marrow treated with MCSF (10 ng/mL) for 7 days, and subsequently cultured in high-glucose DMEM + 10% fetal bovine serum + antibiotics in a standard cell culture incubator (humidified, 37 degree, normal/atmospheric oxygen).

extract_protocol:
Purification of RNA was performed with RNeasy Mini Columns (QIAGEN, Valencia, CA) with RNase-free DNase solution (QIAGEN) applied to degrade contaminating genomic DNA. RNA quantity was assessed with Nanodrop spectrophotometry (ThermoFisher).
RNA libraries for RNA-seq were prepared using Illumina Total RNA Prep Kit following manufacturer's protocols.

treatment_protocol: BMSCs and BMDMs were treated with 20 uM etoposide for 48 hours, followed by maintenance in growth media for 14 days (Day 14). Untreated control cells at Day 0 were collected prior to etoposide treatments.

value: bone

value: Macrophage

value: Wild-Type


title: BMDM_Etoposide_1

description: Library name: sample_12


title: larval guts, yw LpWJL, Late L3 (S2), replicate D

first: Longwei

last: Bai

address: 32-34 Avenue Tony Garnier

institute: ENS Lyon

description: Library name: WJL_S2D

data_processing:
Sequencing data were analyzed using the DAVID Bioinformatics Resources online software (https://david.ncifcrf.gov/) on 2633 annotated genes across both sizes groups which were organized into a functional annotation chart and subsequently grouped into 91 clusters.
An enrichment score (ES) was calculated and 53 of the clusters were found to be significantly enriched.
Genes from the two sizes were split into early L3 and late L3 groups and further analyzed by Biological Process Direct and presented as pie charts.
Volcano plots were generated using GraphPad Prism 10.
Assembly: genome build: BDGP6.32.104 genome build accession: GCA_000001215.4
Supplementary files format and content: tab delimited csv file that contains TPM values for all Samples.
Supplementary files format and content: tab delimited csv files that are the gene level expression estimates from RSEM program. Each csv file notably contains TPM values (second to last column) for each Sample.

organism: Drosophila melanogaster

source_name: larval guts

growth_protocol: The nutritional challenge was performed using a low yeast diet containing 7.2 g/L agar, 80 g/L cornmeal flour, 7 g/L inactivated yeast, and supplemented with 5.2 g/L Methyl 4-hydroxybenzoate sodium salt and 4 mL/L of propionic acid.

extract_protocol:
RNA was extracted using the NucleoSpin kit (Macherey Nagel, #740955) following the manufacturer’s protocol, and quantified using the Nanodrop spectrophotometer (Thermofisher, ND-2000).
For RNA sequencing, samples were treated by the IGFL sequencing platform. Purification, quantification and quality checks were performed using the Qubit 2.0 – RNA BR Assay Kit (Thermofisher) and the TypeStation 2200 (Agilent). Libraries were generated following the online protocol (https://www.hexabiogen.com), quantified via the TapeSation D1000 ScreenTape Assay (Agilent), and the raw data were subsequently processed to generate final genes regulation datasets

treatment_protocol: GF or Lp-associated yw axenic embryos were reared on a low-yeast diet. Gut collection from L3 larvae was performed to obtain size-matched larvae: early L3 samples (15 guts/replicate, 5 replicates) were collected at 4 days AEL for Lp and 8 days AEL for GF, while late L3 samples (10 guts/replicate, 5 replicates) were collected at 6 days AEL for Lp and 10 days AEL for GF.

value: larval guts

value: yw LpWJL

value: Late L3 (S2)


title: ChIP-seq, CTCF antibody, wildtype mouse, spleen tissue, biological replicate 2

description: Library name: Spleen_WT_ChIP_CTCF_Rep2

value: Whole spleen tissue


title: 810_Spleen

description: Library name: 810_Spleen

value: AP


title: ChIP-seq, shared input control, humanized mouse, liver tissue, single biological replicate

description: Library name: Liver_Shared_Input

value: Whole liver tissue

value: Humanized CTCFL


title: larval guts, yw LpWJL, Late L3 (S2), replicate C

description: Library name: WJL_S2C


title: ChIP-seq, CTCF antibody, wildtype mouse, spleen tissue, biological replicate 1

description: Library name: Spleen_WT_ChIP_CTCF_Rep1

value: Wildtype

value: CTCF B-5 (Santa Cruz, sc-271514)


title: 737_Spleen

description: Library name: 737_Spleen

value: Vehicle


title: 736_Spleen

description: Library name: 736_Spleen


title: larval guts, yw LpWJL, Late L3 (S2), replicate B

description: Library name: WJL_S2B


title: 670_Spleen

description: Library name: 670_Spleen


title: BMDM_Control_2

description: Library name: sample_10


title: BMDM_Control_3

description: Library name: sample_11


title: BMDM_Etoposide_4

description: Library name: sample_15


title: BMDM_Control_1

description: Library name: sample_9


title: larval guts, yw LpWJL, Late L3 (S2), replicate A

description: Library name: WJL_S2A


title: larval guts, yw LpWJL, Late L3 (S2), replicate E

description: Library name: WJL_S2E


title: ChIP-seq, CTCF antibody, humanized mouse, spleen tissue, biological replicate 1

description: Library name: Spleen_HUM_ChIP_CTCF_Rep1

value: Adult


title: ChIP-seq, CTCF antibody, humanized mouse, spleen tissue, biological replicate 2

description: Library name: Spleen_HUM_ChIP_CTCF_Rep2


title: 603_Spleen

description: Library name: 603_Spleen


title: larval guts, yw (GF), Late L3 (S2), replicate D

description: Library name: GF_S2D

value: yw (GF)


title: ChIP-seq, CTCFL antibody, humanized mouse, spleen tissue, biological replicate 1

description: Library name: Spleen_HUM_ChIP_CTCFL_Rep1

value: custom CTCFL monoclonal


title: BMSC_Etoposide_3

description: Library name: sample_7

value: BMSC


title: ChIP-seq, CTCFL antibody, humanized mouse, spleen tissue, biological replicate 2

description: Library name: Spleen_HUM_ChIP_CTCFL_Rep2

value: Spleen


title: BMSC_Etoposide_4

description: Library name: sample_8

value: bone


title: BMDM_Etoposide_2

description: Library name: sample_13

value: Macrophage

value: Wild-Type


title: larval guts, yw (GF), Late L3 (S2), replicate C

description: Library name: GF_S2C

value: larval guts


title: larval guts, yw (GF), Late L3 (S2), replicate E

description: Library name: GF_S2E

value: Late L3 (S2)


title: BMSC_Etoposide_2

description: Library name: sample_6


title: 567_Spleen

description: Library name: 567_Spleen


title: ChIP-seq, shared input control, humanized mouse, spleen tissue, single biological replicate

description: Library name: Spleen_Shared_Input

value: Whole spleen tissue


title: BMSC_Etoposide_1

description: Library name: sample_5


title: larval guts, yw (GF), Late L3 (S2), replicate B

description: Library name: GF_S2B


title: ChIP-seq, CTCF antibody, wildtype mouse, brain tissue, biological replicate 2

description: Library name: Brain_WT_ChIP_CTCF_Rep2

extract_protocol:
Mice were euthanized via carbon dioxide asphyxiation followed by cervical dislocation, in accordance with institutional animal care guidelines. Tissues were immediately harvested and placed in ice-cold phosphate-buffered saline (PBS). For tissue dissociation, samples were transferred to a sterile dish containing PBS (250 µL per 50 mg of tissue) and finely minced. The minced tissue was then transferred to a 50 mL Falcon tube and further homogenized by repeated passage through an 18-gauge needle (10 times) followed by a 21-gauge needle (20 times). Large debris and clumps were removed using a 70 µm cell strainer. Cells were pelleted by centrifugation and resuspended in 2 mL Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). To crosslink chromatin, formaldehyde was added to the cell suspension to a final concentration of 1%, and samples were incubated on a rocker at room temperature for 10 minutes. The reaction was quenched by the addition of glycine (final concentration 125 mM) and incubated for an additional 10 minutes. Cells were washed twice with ice-cold PBS and pelleted by centrifugation. Cell pellets were stored at -80°C until further use. For chromatin immunoprecipitation (ChIP), cells were thawed on ice and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 20 mM Tris–HCl pH 8.0, 2 mM EDTA). Chromatin was sheared to a fragment size of 200–600 bp using sonication. Immunoprecipitation was performed using 5 µg of the appropriate antibody. Immunoprecipitated DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research, catalog #D5205).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, catalog #E7645S), following the manufacturer’s protocol. Libraries were amplified using 10 cycles of PCR and size-selected to 250–450 bp using AMPure XP beads (Beckman Coulter, catalog #A63881). Library quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies, catalog #5067-4626) on an Agilent 2100 Bioanalyzer

value: Brain

value: Whole brain tissue


title: 568_Spleen

description: Library name: 568_Spleen

extract_protocol:
Tissues collected and homogenized in QIAZOL and totalRNA extracted via Qiagen's mRNeasy kit
Library construction via LibStrmRNA(MRNA)

value: AP


title: BMSC_Control_4

description: Library name: sample_4


title: 445_Spleen

description: Library name: 445_Spleen


title: ChIP-seq, CTCF antibody, wildtype mouse, brain tissue, biological replicate 1

description: Library name: Brain_WT_ChIP_CTCF_Rep1

value: Wildtype


title: 446_Spleen

description: Library name: 446_Spleen


title: 608_Spleen

description: Library name: 608_Spleen


title: ChIP-seq, CTCF antibody, humanized mouse, brain tissue, biological replicate 2

description: Library name: Brain_HUM_ChIP_CTCF_Rep2

value: Humanized CTCFL

value: CTCF B-5 (Santa Cruz, sc-271514)


title: 444_Spleen

description: Library name: 444_Spleen

value: Vehicle


title: larval guts, yw LpWJL, Early L3 (S1), replicate D

description: Library name: WJL_S1D

value: yw LpWJL

value: Early L3 (S1)


title: ChIP-seq, CTCFL antibody, humanized mouse, brain tissue, biological replicate 2

description: Library name: Brain_HUM_ChIP_CTCFL_Rep2

value: Adult

value: custom CTCFL monoclonal


title: 443_Spleen

description: Library name: 443_Spleen

value: Spleen


title: ChIP-seq, CTCF antibody, humanized mouse, brain tissue, biological replicate 1

description: Library name: Brain_HUM_ChIP_CTCF_Rep1


title: BMSC_Control_3

description: Library name: sample_3

value: bone

value: BMSC


title: larval guts, yw LpWJL, Early L3 (S1), replicate E

description: Library name: WJL_S1E

value: larval guts


title: 442_Spleen

description: Library name: 442_Spleen


title: kd-siRNA-ctrl_3

first: Carsten

last: Kuenne

institute: Max Planck Institute for Heart and Lung Research

description: Library name: Sample 6

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 109) with STAR 2.7.11b (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a7 with FDR < 0.0001 (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Remaining peaks were unified to represent a common set of regions for all samples.
Counts were produced with featureCounts (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the promoter (TSS +- 5000 nt) of the nearest gene based on Ensembl release 109.
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: endothelium from umbilical cord vein

extract_protocol:
50.000 cells were used for ATAC library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina).
Cells were pelleted and resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer, 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and was incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform (Illumina) using P4 flowcell with 2x 36bp paired-end setup.

value: endothelium from umbilical cord vein

value: HUVEC

value: Endothelial cells

value: wt

value: negative control


title: BMSC_Control_2

description: Library name: sample_2

value: Wild-Type


title: BMSC_Control_1

description: Library name: sample_1


title: larval guts, yw LpWJL, Early L3 (S1), replicate B

description: Library name: WJL_S1B


title: ChIP-seq, CTCFL antibody, humanized mouse, brain tissue, biological replicate 1

description: Library name: Brain_HUM_ChIP_CTCFL_Rep1

value: Brain

value: Whole brain tissue

value: Humanized CTCFL


title: kd-siRNA-ctrl_2

description: Library name: Sample 5


title: ChIP-seq, shared input control, humanized mouse, brain tissue, single biological replicate

description: Library name: Brain_Shared_Input


title: larval guts, yw LpWJL, Early L3 (S1), replicate C

description: Library name: WJL_S1C

value: yw LpWJL


title: 441_Spleen

description: Library name: 441_Spleen

value: AP


title: larval guts, yw (GF), Early L3 (S1), replicate E

description: Library name: GF_S1E

value: yw (GF)

value: Early L3 (S1)


title: kd-siRNA-ctrl_1

description: Library name: Sample 4


title: 207_Spleen

description: Library name: 207_Spleen

value: Spleen


title: MCF10A cells, Cas9-expressing clone 11, gRNA library, mesenchymal cancer stem cell-like population

data_processing:
FASTQ data generated by MiSeq were first analyzed in Galaxy using the BLASTN tool (v2.5.0) to obtain gRNA read counts, by mapping of identified gRNAs against all gRNA sequences in the CRISPR library.
The differential analysis of the gRNA read counts was performed using CRISPRAnalyzeR software (DKFZ, Version: 1.50), using Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MaGeCK).
Assembly: hg38
Supplementary files format and content: bulk.txt : blastn result
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted from 2 million cells using the AllPrep DNA/RNA Mini Kit (Qiagen).
gRNAs were amplified by PCR using specific primers, and library preparation was performed with the Nextera DNA Flex Library Prep Kit (Illumina) according to the manufacturer's instructions.

value: Non-tumorigenic mammary cells


title: larval guts, yw (GF), Early L3 (S1), replicate D

description: Library name: GF_S1D


title: larval guts, yw (GF), Early L3 (S1), replicate C

description: Library name: GF_S1C


title: larval guts, yw LpWJL, Early L3 (S1), replicate A

description: Library name: WJL_S1A


title: 117_Spleen

description: Library name: 117_Spleen

data_processing:
Data processing for FeatureCounts done with Galaxy using HISAT2 and FeatureCount Packages
Assembly: mm10
Supplementary files format and content: FeatureCounts in a tabular format

value: Vehicle


title: MCF10A cells, Cas9-expressing clone 11, gRNA library, bulk


title: 101_Spleen

description: Library name: 101_Spleen


title: kd-siRNA-ZBTB16_2

description: Library name: Sample 2

value: siRNA against ZBTB16


title: MCF10A cells, Cas9-expressing clone 2, gRNA library, mesenchymal cancer stem cell-like population


title: kd-siRNA-ZBTB16_3

description: Library name: Sample 3

value: endothelium from umbilical cord vein


title: kd-siRNA-ZBTB16_1

description: Library name: Sample 1

value: HUVEC


title: 208_Spleen

description: Library name: 208_Spleen


title: M. elsdenii with N. lanati, formate added, coculture1

status: Public on Jan 06 2026

city: Santa Barbara

first: Elaina

last: Blair

state: CA

address: 3357 Engineering II Building, UCSB

institute: University of California, Santa Barbara

description: Library name: Mco_formate_105

data_processing:
Reads not containing the correct, complete adapter were discarded. Read counts were obtained only from Read 2; Read 1 contained the barcode though. Genomes from the IMG database were utilized for mapping.
Assembly: IMG 649989993, IMG 2843666722, MycoCosm Neocallimastix lanati v1.0
Supplementary files format and content: tab-delimited text file includes raw read counts for P. alactolyticus for each sample with P. alactolyticus
Supplementary files format and content: tab-delimited text file includes raw read counts for M. elsdenii for each sample with M. elsdenii

organism:
Megasphaera elsdenii
Neocallimastix lanati (nom. inval.)

extract_protocol:
RNA was extracted using the RNeasy mini kit
Libraries were constructed according to the EMBR-seq protocol for cocultures of anaerobic fungi and bacteria.

tag: condition

value: coculture


title: M. elsdenii with N. lanati, formate added, coculture3

description: Library name: Mco_formate_107


title: M. elsdenii with N. lanati, formate added, coculture2

description: Library name: Mco_formate_106


title: M. elsdenii with N. lanati, normal, coculture2

description: Library name: Mco_norm_102


title: M. elsdenii with N. lanati, normal, coculture4

description: Library name: Mco_norm_104


title: larval guts, yw (GF), Early L3 (S1), replicate A

description: Library name: GF_S1A

value: larval guts


title: M. elsdenii with N. lanati, normal, coculture1

description: Library name: Mco_norm_101


title: P. alactolyticus with N. lanati, formate added, coculture4

description: Library name: Pco_formate_53

organism:
Pseudoramibacter alactolyticus
Neocallimastix lanati (nom. inval.)


title: M. elsdenii with N. lanati, normal, coculture3

description: Library name: Mco_norm_103


title: P. alactolyticus with N. lanati, formate added, coculture3

description: Library name: Pco_formate_52


title: P. alactolyticus with N. lanati, formate added, coculture2

description: Library name: Pco_formate_51


title: P. alactolyticus with N. lanati, normal, coculture4

description: Library name: Pco_norm_49


title: P. alactolyticus with N. lanati, formate added, coculture1

description: Library name: Pco_formate_50


title: MCF10A cells, Cas9-expressing clone 2, gRNA library, bulk


title: M. elsdenii with N. lanati, formate added, coculture4

description: Library name: Mco_formate_108


title: larval guts, yw (GF), Early L3 (S1), replicate B

description: Library name: GF_S1B


title: 044_Spleen

description: Library name: 044_Spleen


title: P. alactolyticus with N. lanati, normal, coculture3

description: Library name: Pco_norm_48


title: M. elsdenii, lactate added, monoculture2

description: Library name: Mmono_118

organism: Megasphaera elsdenii

value: monoculture


title: P. alactolyticus with N. lanati, normal, coculture1

description: Library name: Pco_norm_46


title: P. alactolyticus with N. lanati, normal, coculture2

description: Library name: Pco_norm_47


title: M. elsdenii, lactate added, monoculture1

description: Library name: Mmono_117


title: M. elsdenii, lactate added, monoculture3

description: Library name: Mmono_120


title: P. alactolyticus, lactate added, monoculture1

description: Library name: Pmono_1

organism: Pseudoramibacter alactolyticus


title: P. alactolyticus, lactate added, monoculture4

description: Library name: Pmono_5


title: P. alactolyticus, lactate added, monoculture2

description: Library name: Pmono_2


title: pet309Δ, rep3

first: Yabing

last: Song

address: Chaoyang District

department: Institute of Microbiology

institute: Chinese Academy of Sciences

description: Library name: pet309_Rep3

data_processing:
Illumina Casava2.1.7 software used for basecalling.
The quality of raw sequencing data was analyzed using FastQC version 0.11.4 and processed by Trim Galore version 0.6.0 to remove adapters and low-quality reads.
Clean reads were aligned to the C. auris B8441 reference genome using the hisat2 version 2.1.0.
Read counts were then normalized to log2 transformed transcripts per kilobase million (log2TPM), followed by quantile normalization for subsequent differential expression analysis.
Significantly differential expression was detected using the DESeq2 version 1.22.1 package. Genes with a p-value < 0.05 and a log2 fold change value >= 1 were considered to represent significantly differentially expressed genes (DEGs). CGD Gene Ontology Term Finder (http://www.candidagenome.org/cgi-bin/GO/goTermFinder).
Assembly: C. auris B8441 (GCA_002759435.2)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Candidozyma auris

extract_protocol:
Hot phenol method
NEBNext Ultra II RNA Library Prep Kit (NEB, E7770)

value: pet309 KO

value: CBS10913 with pet309 knockout

value: Untreated


title: P. alactolyticus, lactate added, monoculture3

description: Library name: Pmono_3


title: pet309Δ, rep1

description: Library name: pet309_Rep1


title: pet309Δ, rep2

description: Library name: pet309_Rep2


title: WT, rep3

description: Library name: WT_Rep3

value: WT


title: larval guts, yw (GF), Late L3 (S2), replicate A

description: Library name: GF_S2A

value: Late L3 (S2)


title: WT, rep2

description: Library name: WT_Rep2


title: Input

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

description:
Library name: SP_12
Protein-DNA interaction

data_processing:
2*150 bp pair- ended reads
Adaptors were trimmed and low quality reads were filtered with Trim Galore
Alignment to genome sequence with Bowtie2
BAM files are used for peak calling with GEMv3.4, using input files as control
Assembly: S. tuberosum DMv4.03
Supplementary files format and content: Genome coverage in bigwig format
Supplementary files format and content: Significant peaks of protein-DNA interactions in narrowpeak fromat generated by GEMv3.4

organism: Solanum tuberosum

source_name: stolon

extract_protocol:
Genomic DNA extracted with the CTAB method and RNase A treated
gDNA fragmented to 200 bp fragments in average and ligated a a truncated Illumina TruSeq adapter (Y adapter). gDNA library is incubated with recombinant protein expressed in E.coli, previously immobilized with Amylose beads. After binding and washing, DNA is eluted and PCR-amplified with Truseq primers, including a double index.

value: stolon

tag: protein


title: DAP-Pti5_rep1

description:
Library name: Sample1
Input DNA for samples 1-2


title: MS057

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

country: Canada

institute: McGill University

description: Library name: MS057

data_processing:
Gene counts were generated for each sample from FASTQ files provided by Genome Quebec using the salmon aligner tool.
Assembly: GRCr8
Supplementary files format and content: *.salmon.tar.gz: tar archive of salmon outputs for each sample.

organism: Rattus norvegicus

source_name: Dissociated brain

growth_protocol: Primary culture of rat ependymal cells was performed as previously described in: Bigotte et al, 2022 (https://doi.org/10.1093/braincomms/fcac307).

extract_protocol:
Cell lysis and RNA extraction was conducted using the Norgen Single Cell RNA Isolation kit (SKU: 51800), by following the instructions provided with the kit for extraction, 48 hours following exposure. Following extraction, RNA concentration was determined using a Thermo Scientific Nanodrop instrument, and then samples were diluted to either 50 or 100 ng/uL depending on initial concentration. Resulting RNA isolates were kept at -80C until being sent off for further processing.
Library construction (with polyA enrichment) and sequencing was conducted by Genome Quebec, with a requested read number of 25M 100bp-long reads per sample.

treatment_protocol: Addition of patient CSF was done at a 1:1 ratio with culturing medium. Negative control (untreated) samples were left unperturbed.

value: Dissociated brain

value: Ependymal cells

value: MS patient CSF


title: MS061

description: Library name: MS061


title: CER6-NT

description: Library name: CER6-NT


title: CER7-NT

description: Library name: CER7-NT


title: Bos taurus, GSKA treatment_3

city: Hefei

first: Wenjie

last: Yu

address: No.130 West Changjiang Road

institute: Anhui Agricultural University

description: Library name: GSKA3

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9) was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96). The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d). The expression levels of all transcripts were estimated and performed as calculating FPKM (FPKM = [total exon fragments / mapped reads (millions) × exon length (kB)] ). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). And then the GO terms (http://www.geneontology.org/) and KEGG Pathway (http://www.genome.jp/kegg/) of these differentially expressed mRNAs were also annotated.
Assembly: ARS-UCD2.0
Supplementary files format and content: DEGs information from scRNA-Seq analysis.xlsx
Supplementary files format and content: fpkm_expression.xlsx

organism: Bos taurus

source_name: female

extract_protocol:
According the manufacturer's requirement, RNA sample was extracted with a RNeasy Plus Micro Kit (QIAGEN, Dusseldorf, Germany). Total RNA was reverse transcribed using a reverse transcription kit (Biosharp, Beijing, China).
The SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Japan) was used to prepare the low-input library following the procedures below: 1) Preparing cDNA library; 2) cDNA Purification and size selection (150-300bp); 3) Preparing sequencing ready library (add i5/i7adaptor using PCR method); 4) Library quality control (assess the size and concentration of the library using Agilent 2100 Bioanalyzer ); 5) Library sequencing performed on Illumina platforms using a 2x150bp paired-end sequencing protocol.

value: female

value: embryo


title: DAP-Pti5_rep2

description:
Library name: Sample2
Protein-DNA interaction


title: Bos taurus, GSKA treatment_1

description: Library name: GSKA1


title: Bos taurus, GSKA treatment_2

description: Library name: GSKA2


title: Bos taurus, Control_3

description: Library name: Control3


title: PDX F659 BGJ398 day 3

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

description:
Library name: PDX_F659_BGJ398_T3
10x Genomics

data_processing:
The sequencing output was processed using Cell Ranger from 10x Genomics
Assembly: hg38
Supplementary files format and content: filtered feature and barcodes matrix exported from CellRanger

organism:
Homo sapiens
Mus musculus

source_name: PDX

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
3' Reagent Kit protocol (10X Genomics)
10,000 cells were loaded per sample using the single-cell 3' Reagent Kit protocol (10X Genomics), and the cells were sequenced at a mean depth of 50,000 using a NovaSeq 6000

treatment_protocol: MGH-U3 and RT112 cells treated with DMSO or 100 nM erdafitinib for 38 h.  The PDX was treated with BGJ398, a pan‐FGFR inhibitor, for 4 days

value: PDX


title: PDX F659 BGJ398 day 4

description:
Library name: PDX_F659_BGJ398_T4
10x Genomics


title: Bos taurus, Control_2

description: Library name: Control2


title: primary normal human lung fibroblasts isolated from MVNs in devices on day  7, static culture, no flow, replicate 4

city: Cambridge

first: Charles

middle: Ara

last: Demurjian

address: 31 Ames Street

institute: BioMicro Center at MIT

description: Library name: FB static 4

data_processing:
RNA-seq data analysis was conducted using a robust R-based pipeline. BAM files were quantified with featureCounts66 to generate a counts matrix, which was processed with DESeq267 for differential gene expression analysis. Genes with low expression were filtered out, and more than four biological replicates per condition ensured statistical rigor. PCA confirmed sample clustering by condition. Pathway enrichment analysis was performed using clusterProfiler68, identifying significantly enriched pathways that contextualize the observed gene expression changes. The R code used for analyzing the counts files has been uploaded to the repository.
Assembly: hg38
Supplementary files format and content: xlsx gene count matricies

source_name: lung

extract_protocol:
For each timepoint analyzed, the fibrin hydrogel containing the MVNs was cut out of the devices and placed in 5 mL of 100 μg mL-1 Liberase (Millipore Sigma), 100 μg mL-1 DNase I (Sigma Aldrich), and 9.2 μg mL-1 Elastase (Thermo Fischer Scientific) in DMEM (Thermo Fischer Scientific) for 75 minutes at 37oC with intermittent agitation. Cells from 3-4 devices were pooled for each replicate. Dead cells were removed using the Dead Cell Removal Kit and an OctoMACS Separator (Miltenyi Biotec), cells were incubated with CD31 MicroBeads (CD31 MicroBead Kit, Miltenyi Biotec) and HUVECs and FBs were sorted using the OctoMACS Separator (Miltenyi Biotec). The sorted cells were lysed with TRIzol (Thermo Fischer) and stored at -80oC. Once the cell lysates from all timepoints were collected, the lysates were thawed, and 0.2 mL of chloroform (Millipore Sigma) per 1 mL of TRIzol reagent was added, the samples were centrifuged for 15 minutes at 12,000 x g at 4oC, and the aqueous phase was collected
Total RNA was extracted using TRIzol and processed for RNA-seq using the NEBNext Ultra II RNA Library Prep Kit for Illumina. Input RNA was fragmented for 10 minutes and cDNA synthesis was performed. Libraries were indexed using TruSeq-Singular primers, amplified for 16 cycles, and eluted in 12 µL EB. Low-concentration libraries were re-amplified with 7 additional cycles and cleaned via 2.0X SPRI. Final concentrations ranged from 1–21 ng/µL.

value: lung

value: Primary human lung fibroblasts

value: Fibroblast


title: PDX F659 BGJ398 day 2

description:
Library name: PDX_F659_BGJ398_T2
10x Genomics


title: MS072

description: Library name: MS072


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 24, 17 days after flow, replicate 4

description: Library name: FB day 24 flow 4


title: primary normal human lung fibroblasts isolated from MVNs in devices on day  7, static culture, no flow, replicate 2

description: Library name: FB static 2


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 24, 17 days after flow, replicate 3

description: Library name: FB day 24 flow 3


title: primary normal human lung fibroblasts isolated from MVNs in devices on day  7, static culture, no flow, replicate 1

description: Library name: FB static 1


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 15, 8 days after flow, replicate 1

description: Library name: FB day 15 flow 1


title: CER9-NT

description: Library name: CER9-NT


title: PDX F659 BGJ398 day 1

description:
Library name: PDX_F659_BGJ398_T1
10x Genomics


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 24, 17 days after flow, replicate 1

description: Library name: FB day 24 flow 1


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 15, 8 days after flow, replicate 2

description: Library name: FB day 15 flow 2


title: immortalized HUVEC cells isolated from MVNs in devices on day  7, static culture, no flow, replicate 2

description: Library name: EC static 2

source_name: umbilical vein

value: umbilical vein

value: HUVEC (primary)

value: Endothelial cells


title: WT, rep1

description: Library name: WT_Rep1


title: MS058

description: Library name: MS058


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 15, 8 days after flow, replicate 3

description: Library name: FB day 15 flow 3


title: immortalized HUVEC cells isolated from MVNs in devices on day  7, static culture, no flow, replicate 4

description: Library name: EC static 4


title: immortalized HUVEC cells isolated from MVNs in devices on day  7, static culture, no flow, replicate 1

description: Library name: EC static 1


title: immortalized HUVEC cells isolated from MVNs in devices on day 24, 17 days after flow, replicate 3

description: Library name: EC day 24 flow 3


title: immortalized HUVEC cells isolated from MVNs in devices on day 24, 17 days after flow, replicate 4

description: Library name: EC day 24 flow 4


title: immortalized HUVEC cells isolated from MVNs in devices on day  7, static culture, no flow, replicate 3

description: Library name: EC static 3


title: primary normal human lung fibroblasts isolated from MVNs in devices on day  7, static culture, no flow, replicate 3

description: Library name: FB static 3


title: immortalized HUVEC cells isolated from MVNs in devices on day 24, 17 days after flow, replicate 2

description: Library name: EC day 24 flow 2


title: immortalized HUVEC cells isolated from MVNs in devices on day 15, 8 days after flow, replicate 1

description: Library name: EC day 15 flow 1


title: immortalized HUVEC cells isolated from MVNs in devices on day 15, 8 days after flow, replicate 2

description: Library name: EC day 15 flow 2


title: LACID piPSCs (Laminin-LDN) -12

city: Hangzhou

first: Chengchen

last: Zhao

state: Zhejiang

address: Dunyu Road No.600, Xihu District

institute: Westlake University

description: Library name: A373

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4) and then mapped to the susScr11 reference genome with HISAT2 (v2.2.1), and GFOLD (v1.1.4)was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads).
Assembly: susScr11
Supplementary files format and content: tab-delimited text file include counts values for each Sample

organism: Sus scrofa

source_name: induced pluripotent stem cells

extract_protocol:
RNAs were harvested using TRIzol Reagent (15596026, Thermo Fisher). 2 ug RNA was used for the constructing of sequencing libraries.
RNA library for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 (RK20306, ABclonal) following manufacturer's protocol.

value: induced pluripotent stem cells

value: LACID piPSCs (Laminin-LDN) -12


title: LACID piPSCs (Laminin-LDN) -10

description: Library name: A372

value: LACID piPSCs (Laminin-LDN) -10


title: immortalized HUVEC cells isolated from MVNs in devices on day 24, 17 days after flow, replicate 1

description: Library name: EC day 24 flow 1


title: LACID piPSCs (Laminin-LDN) -1

description: Library name: A371

value: LACID piPSCs (Laminin-LDN) -1


title: LACID piPSCs (Laminin) -10

description: Library name: a369

value: LACID piPSCs (Laminin) -10


title: primary normal human lung fibroblasts isolated from MVNs in devices on day 24, 17 days after flow, replicate 2

description: Library name: FB day 24 flow 2


title: LACID piPSCs (Laminin) -12

description: Library name: a370

value: LACID piPSCs (Laminin) -12


title: LACID piPSCs (N2B27)-12

description: Library name: a361

value: LACID piPSCs (N2B27)-12


title: LACID piPSCs (Laminin) -1

description: Library name: a368

value: LACID piPSCs (Laminin) -1


title: immortalized HUVEC cells isolated from MVNs in devices on day 15, 8 days after flow, replicate 3

description: Library name: EC day 15 flow 3


title: LACID piPSCs (N2B27)-1

description: Library name: a359

value: LACID piPSCs (N2B27)-1


title: LACID piPSCs (N2B27)-10

description: Library name: a360

value: LACID piPSCs (N2B27)-10


title: Cardiomyocyte-1

description: CMA

data_processing:
The RNA-seq reads were trimmed using Trim Galore (v0.6.4) and then mapped to the susScr11 reference genome with HISAT2 (v2.2.1), and GFOLD (v1.1.4)was used to quantify the transcription level of each gene in each sample into FPKM (Fragments per kilobase of exon model per million mapped reads) and gene counts.
Assembly: susScr11
Supplementary files format and content: tab-delimited text file include counts values for each sample

source_name: Cardiomyocytes

value: Cardiomyocytes


title: Cardiomyocyte-10


title: LACID piPSCs-10


title: 48_BRD4-ChIP-seq_BRD2-AID_3hH2O

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S48

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Illumina output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the hg38 and dm6 (spike-in) genomes using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments,  normalized using spike-in reads and reformatted in the bigWig file format. GFP ChIP was not spike-in normalized since different construct has different expression level except for JQ1 treatment. Spikein normalization was not used for some BRD2 and histone acetylation samples, as indicated in Methods.
Assembly: hg38, dm6 for spike-in reads
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: All cell lines were cultured in DMEM (Corning, #10013CV), supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
DNA was purified with either QIAquick PCR purification kit (Qiagen, #28106) or ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205).
Libraries were prepared by using the KAPA HTP library preparation kit (Roche, #07961901001) and sequenced on the Illumina NovaSeq 6000 or NextSeq 2000.

treatment_protocol: Auxin (#ab146403) was purchased from abcam. Doxycycline (#72742) was obtained from Stem Cell Technologies. dEBT6 (#S8762) was purchased from Selleckchem. JQ1 (#4499) was purchased from Tocris.BET and mutant expression were achieved by adding 50nM Dox into the medium and incubating for 36 or 48h.

value: colon

value: DLD-1 BRD2-AID

value: epithelial

tag: treatment 2


title: 50_H3K27ac-ChIP-seq_BRD2-AID

description: Library name: S50


title: 49_BRD4-ChIP-seq_BRD2-AID_3hAux

description: Library name: S49


title: Cardiomyocyte-12


title: LACID piPSCs-12


title: LACID piPSCs-1


title: 43_H4K12ac-ChIP-seq_BRD2-IAA7

description: Library name: S43


title: 44_H4K16ac-ChIP-seq_BRD2-IAA7

description: Library name: S44


title: 41_H4K5ac-ChIP-seq_BRD2-IAA7

description: Library name: S41


title: 42_H4K8ac-ChIP-seq_BRD2-IAA7

description: Library name: S42


title: 40_H3K27ac-ChIP-seq_BRD2-IAA7

description: Library name: S40


title: 32_Input-ChIP-seq_DLD-1_3hJQ1

description: Library name: S32


title: 39_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP-BRD2x4BD_3hAux

description: Library name: S39

value: RPB1 NTD

tag: construct

tag: treatment 1


title: Bos taurus, Control_1

description: Library name: Control1

tag: tissue

value: female

value: embryo


title: 37_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP-BRD4_3hAux

description: Library name: S37


title: 38_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP-BRD4x2BD_3hAux

description: Library name: S38


title: 30_Pol2-ChIP-seq_DLD-1_3hJQ1

description: Library name: S30


title: 36_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP-BRD3_3hAux

description: Library name: S36


title: 33_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hH2O

description: Library name: S33

value: GFP


title: 35_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP-BRD2_3hAux

description: Library name: S35


title: 34_Pol2-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hAux

description: Library name: S34


title: 31_Input-ChIP-seq_DLD-1_3hDMSO

description: Library name: S31


title: 28_BRD2-ChIP-seq_DLD-1_3hJQ1

description: Library name: S28


title: 29_Pol2-ChIP-seq_DLD-1_3hDMSO

description: Library name: S29


title: 27_BRD2-ChIP-seq_DLD-1_3hDMSO

description: Library name: S27


title: 25_TAF1-ChIP-seq_DLD-1_3hDMSO

description: Library name: S25


title: 22_TAF1-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hAux

description: Library name: S22


title: 16_BRD2-ChIP-seq_BRD2-IAA7_3hAux

description: Library name: S16


title: 20_TBP-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hAux

description: Library name: S20

value: TBP


title: 14_Pol2-ChIP-seq_DLD-1_18hDox_GFP-BRD2_3hJQ1_6hWashout

description: Library name: S14


title: 12_Pol2-ChIP-seq_DLD-1_18hDox_GFP-BRD2_3hDMSO

description: Library name: S12


title: 23_TBP-ChIP-seq_DLD-1_3hDMSO

description: Library name: S23


title: 21_TAF1-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hH2O

description: Library name: S21


title: 19_TBP-ChIP-seq_BRD2-IAA7_36hDox_GFP_3hH2O

description: Library name: S19


title: 26_TAF1-ChIP-seq_DLD-1_3hJQ1

description: Library name: S26


title: RNA-seq_DLD-1_rep2

description: Library name: S02

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Preprocessing was performed using CETO Toolbox. Sequence quality was assessed using FastQC v 0.11.2, and quality trimming was done using Trimmomatic with parameters TRAILING:30 MINLEN:20. RNA-seq reads were aligned to the GRCh38 genome using STAR v.2.5.2 and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis and quantified to the gene level using HTSeq . Output bam files were converted into bigwig track files to display coverage throughout the genome (in rpm).  Gene count tables were constructed following Ensembl GRCh38, release 78 annotation
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, 74106) using an on column DNaseI digestion step (Qiagen 79256).
RNA was subjected to polyadenylated RNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (New England Biolabs, E7490L), and libraries were synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L).

tag: genotype

value: WT


title: 15_BRD2-ChIP-seq_BRD2-IAA7_3hH2O

description: Library name: S15


title: 18_Pol2-ChIP-seq_BRD2-IAA7_3hAux

description: Library name: S18


title: RNA-seq_DLD-1_rep1

description: Library name: S01


title: 17_Pol2-ChIP-seq_BRD2-IAA7_3hH2O

description: Library name: S17


title: cWX2979_24H_Azure_10percent_Sau3AI_rep1

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: Library name: cWX2979_24H_Azure_10percent_Sau3AI_rep1

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Escherichia coli Hi-C, we mapped reads in each FASTQ file back to the genome of Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Escherichia coli W3110 genome was divided into Sau3AI restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Escherichia coli (W3110) was then divided into 10 kb bins and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads within different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Escherichia coli str. K-12 substr. W3110

source_name: bacterial culture

extract_protocol:
Wild type and mutant cells of Escherichia coli W3110 growing in Hi-Def Azure media suplemented with 0.2% glucose were crosslinked using either 10% formaldehyde for Hi-C or 3% formaldehyde for ChIP-seq and then lysed by treatment with 4 mg/ml lysozyme and 1% SDS as previouly described (Wang et al., 2022 PMID: 35101983). The solubilized chromatin was digested with Sau3AI for 2 hours at 37°C.
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: bacterial culture

value: W3110 delta_dps FRT-KanR-FRT

tag: treatment

value: Cells grown in Hi-Def Azure medium supplemented with 0.2% glucose at 37°C


title: cWX2979_exp_Azure_10percent_Sau3AI_rep1

description: Library name: cWX2979_exp_Azure_10percent_Sau3AI_rep1