title: BMDMs, Ago4-/-, Influenza A-infected rep 3

city: Boston

first: Kate

middle: L

last: Jeffrey

state: Massachusetts

address: 50 Blossom St, Thier 340

department: Medicine

institute: Massachusetts General Hospital, Harvard Medical School

description:
AGO-bound virus-derived RNA in Influenza infected AGO4 knockout bone marrow derived macrophages performed by Immunoprecipitation following by High Throughput Sequencing
Supplementary table2.pdf
This sample is Ago4 KO (1) in processed Table 2

data_processing:
TrimGalore (v0.4.2) was used to remove Illumina sequencing adaptors, quality score cutoff = 20, stringency = 3, minimum read length = 18
Reads were then aligned to mouse genome build UCSC mm10 using TopHat2 (v2.1.1 with Bowtie2 v2.2.9) maximum mismatches = 2
Unmapped reads were then algined to SP8 flu genome using Tophat2, with maximum multihit = 1.
Read length distributions were obtained using custom python scrips.
https://www.ncbi.nlm.nih.gov/nuccore/AF389115.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389116.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389117.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389118.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389119.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389120.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389121.1
https://www.ncbi.nlm.nih.gov/nuccore/AF389122.1
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary table2.pdf

source_name: mouse bone marrow derived macrophages

growth_protocol: Bone marrow was flushed from tibia and fibia and allowed to adhere to a non-treated plate for 1 day. Non-adherent cells were differentiated with 5ng/mL of IL-3 and M-CSF for 7 days

extract_protocol:
Cells UV Crosslinked, AGO IP, RNA extraced with Trizol
Libraries of small RNAs were constructed by a method depending on the 5′monophosphate of small RNAs, with a NEBNext Multiplex Small RNA Library Prep Set (Illumina) and sequenced on an Illumina HiSeq System.

treatment_protocol: Infected with Influenza A (PR/8/1034) or A/PR/8/1934 ΔNS1 , MOI 1 for 24 hours

value: Influenza (PR/8/1934, MOI 1) 24h

tag: ip antibody

value: pan Ago (2A8, Millipore)

value: Ago4 knockout

value: mouse bone marrow derived macrophages


title: Cells at timepoint Day 0, repeat 1

status: Public on Jan 01 2020

type: RNA

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

country: USA

institute: Washington University School of Medicine

description:
MSC049_D0
miRNA
Mitochondrial miRNA expression data.

hyb_protocol: The standard Affymetrix chip hybridization protocol was followed to hybridize the labeled miRNAs onto Affymtrix miRNA array 4.0 in the hybridization oven at 48 C and 60 rpm for 18 hours.

scan_protocol: After washing and staining, the chips were scanned using the Affymetrix 7G scanner with standard settings to capture the signal intensities for the miRNAs.

data_processing: The raw signal data were loaded into Affymetrix Expression Console (v1.4) and subjected to RMA background correction, median summarization of multiple probes, and quantile normalization. This was done only within the probes for Human miRNAs on chip.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cells treated with growth medium at day 0

label_protocol: 400 ng of miRNAs were first subjected to poly-A tailing with Poly A Polymerase and substrate ATP. Then the FlashTag Ligation Mix and ligase were added to carry out the ligation reaction so that the Biotin-labeled, dendritic structutre of 3DNAs were ligated onto miRNA molecules to archieve the miRNA labeling and the amplification of detection signals.

growth_protocol: MSCs were cultured and expanded in growth medium containing DMEM (low glucose), 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin and 1ng/ml basic FGF.

extract_protocol: Mitochondria were extracted from MSCs or differentiated MSCs using the human Mitochondria Isolation Kit (Milteny Biotec) which involves the use of magnetically-labeled anti-TOM22 microbeads. Total RNA was isolated from purified mitochondria extracts using the Norgen Total RNA purification kit. For both isolation of mitochondrial or RNA, the manufacturer's recommended protocol was followed carefully.

treatment_protocol: MSCs were cultured in MSC growth medium (described above) and used as controls. The treatment (differentiation) protocol involved culturing MSCs in the presence of osteogenic induction (differentiation) medium containing aMEM base medium, 10% fetal bovine serum, 2mM L-glutamine, 100U/ml penicillin, 100µg/ml streptomycin, 10mM β-glycerol phosphate, 50µM ascorbic acid and 10µM dexamethasone.

tag: cell type

value: Mesenchymal stem/stromal cells (MSCs)

tag: treatment

value: Growth medium

tag: time point

tag: subcellular compartment

value: Mitochondria

tag: repeat id


title: COAD.ct-255

type: SRA

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

institute: UCSD

library_source: genomic

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

molecule: genomic DNA

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

tag: sample type

value: cell-free DNA


title: BMDMs, Ago3-/-, Influenza A-infected rep 1

description:
AGO-bound virus-derived RNA in Influenza infected AGO3 knockout bone marrow derived macrophages performed by Immunoprecipitation following by High Throughput Sequencing
Supplementary table2.pdf

library_source: transcriptomic

organism: Mus musculus

tag: genotype

value: Ago3 knockout


title: Cells at timepoint Day 3, repeat 1

description:
MSC049_D3
miRNA
Mitochondrial miRNA expression data.

source_name: Cells treated with osteogenic induction medium at day 3

value: Osteogenic induction medium


title: Cells at timepoint Day 7, repeat 1

description:
MSC049_D7
miRNA
Mitochondrial miRNA expression data.

source_name: Cells treated with osteogenic induction medium at day 7


title: COAD.ct-256


title: BMDMs, Ago1-/-, Influenza A-infected rep 2

description:
AGO-bound virus-derived RNA in Influenza infected AGO1 knockout bone marrow derived macrophages performed by Immunoprecipitation following by High Throughput Sequencing
Supplementary table2.pdf

value: Ago1 knockout


title: Cells at timepoint Day 0, repeat 2

description:
MSC139_D0
miRNA
Mitochondrial miRNA expression data.


title: COAD.ct-252


title: BMDMs, Ago1-/-, Influenza A-infected rep 1


title: COAD.ct-253


title: P493_wt_8h-1

city: Singapore

first: Julius

last: Müller

address: 61 Biopolis Drive

department: IMCB

country: Singapore

institute: A*Star Singapore

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with beadarray in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: cell line

tag: time (release)


title: BMDMs, WT, Influenza A-infected rep 3

description:
AGO-bound virus-derived RNA in Influenza infected WT bone marrow derived macrophages performed by Immunoprecipitation following by High Throughput Sequencing
Supplementary table2.pdf

value: wild-type


title: COAD.ct-251


title: P493_wt_4h-2

description: replicate 2


title: P493_wt_4h-3

description: replicate 3


title: P493_wt_0h-3

description: replicate 3


title: P493_wt_4h-1

description: replicate 1


title: P493_wt_0h-1

description: replicate 1


title: 32k: B1_503_5mCG_ZTA_N182Q

type: protein

city: Bethesda

first: Charles

last: Vinson

state: MD

address: 37 Convent Drive

department: National Cancer Institute

institute: National Institutes of Health

description: ZTA(N182Q) PBM experiment, 5mCG

hyb_protocol: The double-stranded arrays were blocked with 4% milk for 1 hour and washed with 0.1% Tween-20 in 1x PBS.  Freshly synthesized protein (25 µL) was mixed with 125 µL of protein binding reaction mixture consisting of 4% milk in 1x PBS, 50 ng of salmon testes DNA and 0.2 µg/µL bovine serum albumin and added to double-stranded array.  The protein binding reactions were carried out in hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS.  The protein bound array was incubated with Alexa Fluor 647 conjugated Anti-GST antibody for 1 hour, followed by three washes with 0.05 % Tween-20.  Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 micron resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: For all possible 65,536 8-mers, a transformed 8-mer median intensity (Z-score) was calculated from the median signal intensity across array probes containing each 8-mer.  8-mer Z-scores of the modified strand (the reverse complement of the array probe sequence) were used for downstream analyses.

molecule: protein

source_name: ZTA(N182Q), HK design

label_protocol: Zta constructs were expressed using the PURExpress In vitro protein synthesis kit (NEB) according to the manufacturer’s protocol as previously described (Mann, 2013).  Protein expression was monitored using a western blot anti GST HRP conjugated antibody and similar protein expression was confirmed by western blot.

extract_protocol: We used an N-terminal GST fusion construct of the wild-type construct of the DNA binding domain of Zta plus 50 flanking amino acids cloned into a modified pDEST15 MAGIC vector (Sharrocks, 1994).  Mutant constructs of Zta(N182S, N182Q, N182I, N182V, N182T) were generated via site-directed mutagenesis of the wild-type plasmid (GenScript, USA).

treatment_protocol: The single-stranded oligonucleotide microarrays were double-stranded by primer extension as described in Badis et al. Science (2009).   Arrays were double-stranded using either cytosine, 5-methylcytosine (5mC, NEB) or 5-hydroxymethylcytosine (5hmC, Zymo Research). The resulting double-stranded DNA on the array thus contained probes with either cytosine on both strands or modified cytosine (5mC/5hmC) on one strand and cytosine on the second strand. This results in a hemi-methylated or hemi-hydroxymethylated state.

tag: dbd

value: bZIP

tag: protein

tag: double-stranding treatment


title: 32k: A2_503_5mCG_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5mCG

source_name: ZTA(N182T), HK design


title: BMDMs, Ago3-/-, Influenza A-infected rep 2

description:
AGO-bound virus-derived RNA in Influenza infected AGO3 knockout bone marrow derived macrophages performed by Immunoprecipitation following by High Throughput Sequencing
Supplementary table2.pdf
This sample is Ago3 KO (3) in processed table 2


title: adrenal gland LR2016

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

country: Germany

institute: FBN

description: Gene expression data from adrenal gland of adult pig, low-reactive coping pattern

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: Adrenal gland from adult pig

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: tissue

value: adrenal gland

tag: breed

value: German Landrace

tag: developmental stage

value: adult


title: H_9_29_360

city: Wageningen

first: Juri

middle: C

last: Matualatupauw

address: PO Box 17

department: Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: The amount of biotinylated cRNA which was hybridized onto the Illumina HumanHt12-v4 Expression Beadchip was 750 ng.

scan_protocol: The samples were scanned using the Illumina iScan array scanner according to the manufacturer's protocol.

data_processing:
Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina was used for Gene Expression analysis.
Microarray QC and pre-processing were performed using Arrayanalysis.org. Three samples did not pass QC-criteria and were left out of further analysis. Probe expression values were calculated using the neqc algorithm from the limma package, which performs background correction, quantile normalization and log2-transformation of the data. We filtered out low expressing probes by selecting only the probes with a detection p-value < 0.01  in at least 5 arrays for further analysis.

label_protocol: The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art.No.AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA.

growth_protocol: Men aged between 35 and 65 years were recruited from a pool of volunteers from the Netherlands Organisation for Applied Scientific Research (TNO) database and with the assistance of a recruitment agency. In total, 20 men participated in the study. Of these men, 10 were presumably healthy, and 10 had two or more characteristics of MetS. Inclusion criteria for the healthy men were age 35–65 yr, BMI 23–30 kg/m2, normal Dutch eating habits and eating without restriction, defined as a score of <3.25 on the Dutch Restrained Eating Questionnaire. Inclusion criteria for the MetS group were age 35–65 yr, BMI 23–40 kg/m2, normal Dutch eating habits , and 2 or more cardiometabolic risk factors, defined as waist circumference ≥ 94 cm, TGs ≥ 1.7 mM, HDL cholesterol < 0.9 mM, systolic blood pressure ≥ 130 mm Hg and diastolic blood pressure ≥ 85 mm Hg and fasting glucose ≥ 5.6 mM. Exclusion criteria for both groups were a history of medical or surgical events that may significantly affect the study outcome, including medication for diabetes, cholesterol-lowering medication, eating disorders, food allergy, smoking, consuming more than 28 U/wk of alcohol, and exercising more than 3 h/wk.

extract_protocol: Total RNA was extracted using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands). RNA integrity was examined using the RNA 6000 Nano Lab-on-a-Chip kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).

treatment_protocol: The healthy subjects underwent a 4 week high-fat high-calorie dietary intervention. The intervention diet consisted of a fixed amount of commercially available foods high in fat, sugar, or both and was consumed on top of their habitual diet (see below for details). Before and after the 4 week intervention period, the healthy subjects underwent a high-fat challenge consisting of whipping cream, water and a bit of sugar (see below for details). The MetS subjects underwent the high-fat challenge once.

tag: disease

value: Healty

tag: subject id

tag: day

value: Whole blood


title: 32k: HK_537_D2_5mCG_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5mCG

source_name: ZTA(N182V), HK design


title: COAD.ct-250


title: P493_wt_0h-2

description: replicate 2

tag: treatment


title: COAD.ct-249


title: PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors, biological rep3

city: University Pk

first: Robert

last: Paulson

state: PA

address: 115 Henning Building, Penn State University

department: Veterinary and Biomedical Sciences

institute: Penn State University

description: Gene expression data from in-vitro cultured mouse PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors

hyb_protocol: Labeled samples were incubated with rotation at 60 rpm for 16 hours at 45C for hybridization to Mouse Clariom D Pico Assay microarrays. Washing and staining of the arrays were performed on GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS3000 scanner as recommended by the manufacturer.

data_processing: Raw gene expression profiles were normalized using Robust Multi-arry Average (RMA) approach in Affymetrix Expression Console Software. Normalized data were analyzed with Transcriptome Analysis Console (TAC) Software.

source_name: In-vitro cultured mouse PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors

label_protocol: cRNA was labeled using Affymetrix GeneChip WT Pico Reagent Kit according to the manufacturer’s protocol from 5ng total RNA. (Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays User Guide, 2017, Affymetrix)

growth_protocol: Unfractionated mouse bone marrow cells were isolated, stained with PKH26 dye and then cultured in stress erythropoiesis expansion media (SEEM) for 6 days. Detailed isolation and culture protocols can be found in our lab's previous publication (Xiang, 2015).

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit according to the manufacturer's recommendations.

treatment_protocol: Cultured bone marrow cells were harvested, washed with PBS, stained with erythroid progenitor cell surface markers and then sorted by Astrios cell sorter.

value: Bone marrow

tag: strain

tag: cell type


title: BMDMs, WT, Influenza A-infected rep 1

value: Influenza (PR/8/1934, MOI 1) 24h

tag: ip antibody

value: pan Ago (2A8, Millipore)


title: BMDMs, WT, Influenza A-infected rep 2

value: mouse bone marrow derived macrophages


title: 32k: HK_537_C2_5mCG_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5mCG

source_name: ZTA(N182I), HK design


title: CC068_lung_rna

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 120 Mason Farm Road

institute: University of North Carolina, Chapel Hill

data_processing:
Sequencing reads in FASTQ files were filtered (sequence quality score ≥ 20 for ≥ 90% of bases) and adapter contamination was removed using TagDust
Reads were mapped to strain-specific pseudo-genomes (Build37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) and psuedo-transcriptomes (C57BL/6J RefSeq annotations mapped to pseudo-genomes) using the RSEM command rsem-calculate-expression with STAR (v2.5.3a) [82] as the specified aligner (parameter set: --star)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited file containing gene abundance estimates per RefSeq gene annotation

source_name: lung tissue

growth_protocol: Adult male mice (8-12 weeks old) from 47 CC strains were acquired from the University of North Carolina Systems Genetics Core and maintained on an NTP 2000 wafer diet (Zeigler Brothers, Inc., Gardners, PA) and water ad libitum. The housing room was maintained on a 12-h light-dark cycle

extract_protocol:
Mice were euthanized by exsanguination following deep nembutal (100 mg/kg intraperitoneal injection) anesthesia. Lungs, livers, and kidneys were excised, snap-frozen in liquid nitrogen, and stored at –80°C. Total RNA was isolated from flash-frozen tissue samples using a Qiagen miRNeasy Kit (Valencia, CA) according to the manufacturer’s protocol
RNA purity and integrity were evaluated using a Thermo Scientific Nanodrop 2000 (Waltham, MA) and an Agilent 2100 Bioanalyzer (Santa Clara, CA), respectively. A minimum RNA integrity value of 7.0 was required for RNA samples to be used for library preparation and sequencing. Libraries for samples with a sufficient RNA integrity value were prepared using the Illumina TruSeq Total RNA Sample Prep Kit (Illumina, Inc., San Diego, USA) with ribosomal depletion

treatment_protocol: Mice were placed in cylindrical, metal mesh exposure chambers emitting clear air for 6 hours a day, Monday-Friday, across a two week period

value: lung


title: COAD.ct-247

tag: sample type


title: CC068_liver_rna

source_name: liver tissue

value: liver


title: 32k: ZTA-GST_5mCG_283_H1

description: ZTA PBM experiment, 5mCG

source_name: ZTA, HK design

value: ZTA


title: COAD.ct-246

value: cell-free DNA


title: PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors, biological rep1

value: In-vitro cultured mouse PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors


title: PKH26highCD133+Kit+Sca1+ stress erythroid progenitors, biological rep2

description: Gene expression data from in-vitro cultured mouse PKH26highCD133+Kit+Sca1+ stress erythroid progenitors

source_name: In-vitro cultured mouse PKH26highCD133+Kit+Sca1+ stress erythroid progenitors


title: CC068_kidney_rna

source_name: kidney tissue

value: kidney


title: COAD.ct-245


title: PKH26lowCD133-Kit+Sca1+ stress erythroid progenitors, biological rep2


title: 32k: D2_503_5mCG_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5mCG

source_name: ZTA(N182S), HK design


title: CC062_lung_rna


title: 32k: HK_504_A2_Zta_N182T_C

description: ZTA(N182T) PBM experiment, cytosine

value: cytosine


title: 32k: HK_504_B2_Zta_N182Q_C

description: ZTA(N182Q) PBM experiment, cytosine

value: bZIP


title: COAD.ct-244


title: PKH26highCD133+Kit+Sca1+ stress erythroid progenitors, biological rep1

value: In-vitro cultured mouse PKH26highCD133+Kit+Sca1+ stress erythroid progenitors


title: CC062_kidney_rna


title: COAD.ct-243


title: AI8_MDA-MB-231_Anillin knockout sgRNA4

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Quality control at each processing step was performed using the FastQC tool (quality base calls, CG content distribution, duplicate levels, complexity level) https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Single-end reads were adapter-trimmed using Trimmomatic [Bolger et al., 2014] and aligned using the subread v.1.6.2 aligner [Liao et al., 2013] and the latest assembly of the human genome (GRCh38/hg38). Gene counts were obtained using the feature Counts v1.6.2 software [Liao et al., 2014] and analyzed for differential expression using the edgeR v3.24.3 R package. The sequences from two replicates were merged together. Variability (batch effect) due to the “merged” status of one set of replicates was accounted for in the detection of differentially expressed genes. P-values were corrected for multiple testing using a False Discovery Rate (FDR) multiple testing correction method [https://www.jstor.org/stable/2346101]. Genes at FDR<0.1 were selected as differentially expressed. Gene set enrichment analysis [Mootha et al., 2003] was performed on a list of 275 genes differentially expressed in both CRISPR experiments using the clusterProfiler v3.10.1 R package. All analyses were performed in R/Bioconductor v3.5.3 statistical environment.
Gene set enrichment analysis [Mootha et al., 2003] was performed on a list of 275 genes differentially expressed in both CRISPR experiments using the clusterProfiler v3.10.1 R package. All analyses were performed in R/Bioconductor v3.5.3 statistical environment.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated text, counts

growth_protocol: MDA-MB-231 cells were grown in the Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine sarum and antibiotics.

extract_protocol: Total RNA was extracted from either control, or anillin deficient (two different CRISPR probes, referred hereafter as CRISPR1 and CRISPR2) MDA-MB-231 cell lines using mirVana miRNA Isolation Kit (ThermoFisher Scientific, Cat #AM1560). The RNA quality was determined by Bioanalyzer (Agilent, Santa Clara, CA). To isolate the polyA RNA, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) combined with SMARTer Apollo NGS library preparation system (Takara, Mountain View, CA) were used with a total of 1 µg of good quality total RNA as input. The NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) was then used for polyA RNA library preparation, which is dUTP-based stranded library. The library was indexed and amplified under PCR cycle number of 11. After library Bioanalyzer QC analysis and quantification, individually indexed and compatible libraries were proportionally pooled and sequenced using Illumina HiSeq 1000 sequencer.

treatment_protocol: Cells were infected with lentiviruses bearing Cas9 and anillin-specific sigle guide RNAs (or non-trageted sgRNA) and stable anillin-deficient or control cell lines were obtained by puromycin selection.

tag: cell line background

value: Anillin knockout sgRNA4 cell line

tag: merged

tag: replicate


title: 32k: HK_504_D1_Zta_N182S_C

description: ZTA(N182S) PBM experiment, cytosine

tag: dbd


title: CC062_liver_rna


title: PKH26highCD133+Kit+Sca1+ stress erythroid progenitors, biological rep3


title: AI7_MDA-MB-231_Anillin knockout sgRNA3

value: Anillin knockout sgRNA3 cell line


title: COAD.ct-242


title: 32k: HK_485_C2_Zta_N182I_C

description: ZTA(N182I) PBM experiment, cytosine

tag: protein


title: COAD.ct-241


title: CC061_lung_rna


title: AI6_MDA-MB-231_Non-targeted CRISPR

source_name: noCRISPR

value: Non-targeted CRISPR cell line


title: AI4_MDA-MB-231_Anillin knockout sgRNA4


title: COAD.ct-240


title: CC061_liver_rna


title: COAD.ct-239


title: 32k: A1_503_5mCG_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5mCG

tag: double-stranding treatment


title: 32k: HK_485_A2_Zta_WT_C

description: ZTA PBM experiment, cytosine


title: CC061_kidney_rna

tag: tissue


title: 32k: B2_503_5mCG_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, 5mCG


title: CC059_lung_rna


title: AI3_MDA-MB-231_Anillin knockout sgRNA3


title: 32k: HK_508_B2_Zta_N182V_C

description: ZTA(N182V) PBM experiment, cytosine


title: COAD.ct-238


title: CC059_liver_rna


title: AI2_MDA-MB-231_Non-targeted CRISPR


title: COAD.ct-237


title: CC059_kidney_rna


title: 32k: D1_503_5mCG_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5mCG


title: 32k: HK_537_C1_5mCG_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5mCG


title: 507Pos

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent)
Reads were aligned against the Mm10 build of the mouse genome (2014.11.26). Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained.
Normalization was performed with the DESeq algorithm
Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue and those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
For statistical analysis of differential expression, a one-way ANOVA or two-way ANOVA with the factors of TRAP fraction and treatment and a Benjamini-Hochberg Multiple Testing Correction followed by Student-Newman Keuls post hoc test were used. For those transcripts meeting this statistical criterion, a fold change >|1.25| cutoff was used to eliminate those genes which were statistically significant but unlikely to be biologically significant and orthogonally confirmable due to their very small magnitude of change.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Brain

extract_protocol:
The purification of cell-specific RNA from brain tissue from Tam-induced Aldh1l1-cre/ERT2+; NuTRAP+ and Cx3cr1-cre/ERT2+; NuTRAP+ mice was achieved by following an established protocol, with slight modifications.11,50 For each mouse, a hemisected half-brain was minced into small pieces and homogenized in 2 ml ice-cold homogenization buffer (50 mM Tris, pH 7.4; 12 mM MgCl2; 100 mM KCl; 1% NP-40; 1 mg/mL sodium heparin; 1 mM DTT) supplemented with 100 ug/mL cycloheximide (#C4859-1ML, Millipore Sigma), 200 units/mL RNaseOUT™ Recombinant Ribonuclease Inhibitor (#10777019; Thermofisher), and 1X cOmplete™, EDTA-free Protease Inhibitor Cocktail (#11836170001; Millipore Sigma) with a glass dounce tissue grinder set (#D8938; 10 times with pestle A and 10 times with pestle B). Homogenate was transferred to a 2 mL round-bottom tube and centrifuged at 12,000 x g for 10 minutes at 4°C. After centrifugation, 100 uL of the supernatant was saved as input. The remaining supernatant was transferred to a 2 mL round-bottom tube and incubated with 5 ug/uL of anti-GFP antibody (ab290; Abcam) at 4°C with end-over-end rotation for one hour. Dynabeads™ Protein G for Immunoprecipitation (#10003D; Thermofisher) were washed three times in 1 mL ice-cold low-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 100mM KCl; 1% NP-40; 100μg/ml cycloheximide; 1mM DTT). After removal of the last wash, the homogenate/antibody mixture was transferred to the 2 mL round-bottom tube containing the washed Protein-G Dynabeads and incubated at 4°C with end-over-end rotation for an additional two hours. Magnetic beads were collected using a DynaMag-2 magnet and the unbound- ribosomes and associated RNA saved as the “negative” fraction. Beads were then washed three times with 1 mL of high-salt wash buffer (50mM Tris, pH 7.5; 12mM MgCl2; 300mM KCl; 1% NP-40; 100μg/ml cycloheximide; 2mM DTT). Following the last wash, 350 uL of Buffer RLT (Qiagen) supplemented with 3.5 uL 2-β mercaptoethanol was added directly to the beads and incubated with mixing on a ThermoMixer (Eppendorf) for 10 minutes at room temperature. The beads were magnetically separated and the supernatant containing the target bead-bound ribosomes and associated RNA was transferred to a new tube. 350 uL of 100% ethanol was added to the tube (“positive” fraction) and then loaded onto an RNeasy MinElute column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies).
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used on 25 ng of total RNA for the preparation of strand-specific sequencing libraries from each TRAP-isolated RNA sample (input, negative fraction, and positive fraction) and from conventionally isolated RNA samples from brain (tissue), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS RNA ScreenTape (#5067-5579; Agilent Technologies) and libraries were quantified by qPCR (Kappa Biosystems, Inc., Wilmington, MA). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NovaSeq 6000 system (SP PE150bp) at the Oklahoma Medical Research Foundation Genomics Facility.

treatment_protocol: At 3-4 weeks post-Tam treatment, Cx3cr1-cre/ERT2+; NuTRAP+ mice were systemically administered 5 mg/kg LPS31 (#L2262, 1 mg/ml stock solution; Millipore Sigma) or vehicle (PBS) by ip injection.

value: Brain

tag: genotype

value: Cx3cr1-Cre/Ert2+; NuTRAP+

tag: fraction

value: Positive

tag: animal number

tag: lps or pbs

value: LPS

tag: Sex

value: female

tag: library type

value: RNA Sequencing

tag: library prep kit

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: 507Input

value: Input


title: COAD.ct-235

source_name: blood serum

value: cell-free DNA


title: COAD.ct-236


title: CC057_lung_rna

tag: strain

value: lung


title: COAD.ct-234


title: COAD.ct-233


title: 32k: HK_537_D1_5mCG_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5mCG


title: 506Pos

value: PBS


title: 506Input


title: 32k: A1_475_5mCG_ZTA_WT

description: ZTA PBM experiment, 5mCG

value: ZTA


title: 273Pos

value: male


title: CC057_kidney_rna

value: kidney


title: CC057_liver_rna

value: liver


title: 32k: B1_504_C_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, cytosine

value: bZIP

value: cytosine


title: 32k: A1_504_C_ZTA_N182T

description: ZTA(N182T) PBM experiment, cytosine


title: CC055_lung_rna


title: COAD.ct-232


title: 273Input

value: Brain


title: CC055_liver_rna


title: 32k: HK_508_C_B1_ZTA_N182V

description: ZTA(N182V) PBM experiment, cytosine


title: COAD.ct-231


title: 32k: D2_504_C_ZTA_N182S

description: ZTA(N182S) PBM experiment, cytosine


title: CC055_kidney_rna


title: 32k: HK_485_C_C1_ZTA_N182I

description: ZTA(N182I) PBM experiment, cytosine


title: 272Input

value: Cx3cr1-Cre/Ert2+; NuTRAP+


title: COAD.ct-230


title: COAD.ct-229


title: CC053_lung_rna


title: 32k: A1_485_C_ZTA_WT

description: ZTA PBM experiment, cytosine


title: 271Pos

value: Positive


title: CC053_kidney_rna


title: COAD.ct-228


title: 271Input

value: LPS


title: 65k: HK_535_F2_50PMT_5hmC_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, 5hmC


title: COAD.ct-227


title: CC049_lung_rna


title: mut_samp1

type: genomic

city: Bronx

first: Amit

last: Verma

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ,Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details.

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as failed. These failed loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, Methylated loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background.PCR-amplifying fragments (those not flagged as either methylated or failed) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.)

label_protocol: Random 9-mers pre-labeled with Cy3 or Cy5, for MspI or HpaII, respectively.

extract_protocol: Genomic DNA was isolated as per dialysis tubing method. in summary, genomic DNA was isolated from cell lysates (0.1 M Tris-HCL pH 8.0; 10 mM EDTA pH 8.0 and 1% SDS), digested overnight at 50C on Proteinase K, follow by several organic extractions (TE-saturated phenol and Phenol-Chloroform-Isoamyl alcohol), DNA was purified and concentrated by ethanol precipitation and resuspended in LOTE pH 7.5 (3 mM Tris-Hcl and 0.2 mM EDTA).

value: mspi

tag: genotype/variation

value: Jak2 mutant

value: HpaII


title: 270Pos

value: female

value: RNA Sequencing

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: COAD.ct-226

tag: sample type

value: cell-free DNA


title: 270Input

value: Input


title: CC053_liver_rna


title: 65k: HK_505_5hmC_A2_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5hmC


title: 65k: HK_505_5hmC_D2_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5hmC


title: mut_samp2


title: COAD.ct-225


title: 65k: HK_535_E2_50PMT_5hmC_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5hmC


title: COAD.ct-248


title: CC049_kidney_rna


title: 268Pos

value: PBS


title: COAD.ct-224


title: 65k: HK_505_5hmC_C2_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5hmC


title: COAD.ct-223


title: 65k: HK_536_E1_50PMT_5hmC_ZTA_WT

description: ZTA PBM experiment, 5hmC

value: ZTA


title: CC046_liver_rna

value: liver


title: CC046_lung_rna

value: lung


title: COAD.ct-222


title: wt_samp2

value: wildtype

source_name: 388259_JAK2  hpaii


title: COAD.ct-221


title: 266Pos

value: Brain


title: 267Input

value: Cx3cr1-Cre/Ert2+; NuTRAP+

value: male


title: 65k: HK_507_5mC_A2_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5mC

value: bZIP


title: 267Pos

value: Positive

value: LPS


title: CC046_kidney_rna

value: kidney


title: 65k: HK_535_D2_10PMT_5mC_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, 5mC


title: 65k: HK_536_50PMT_C1_5mC_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5mC


title: COAD.ct-220


title: CC045_liver_rna


title: COAD.ct-219


title: 268Input

value: female


title: 266Input

value: RNA Sequencing


title: 272Pos

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: CC045_kidney_rna


title: 65k: HK_536_50PMT_D1_5mC_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5mC


title: C277Slice

source_name: Cx3cr1-Cre/Ert2+; NuTRAP+_Whole tissue

value: brain

value: Whole tissue


title: CC044_lung_rna


title: CC044_liver_rna


title: COAD.ct-217

value: cell-free DNA


title: 65k: HK_536_A2_10PMT_5mC_ZTA_WT

description: ZTA PBM experiment, 5mC

value: ZTA


title: C277Neg

source_name: Cx3cr1-Cre/Ert2+; NuTRAP+_Negative

value: Negative


title: C277Pos

source_name: Cx3cr1-Cre/Ert2+; NuTRAP+_Positive


title: COAD.ct-216


title: C277Input

source_name: Cx3cr1-Cre/Ert2+; NuTRAP+_Input

value: Input


title: CC045_lung_rna

value: lung


title: CC044_kidney_rna


title: COAD.ct-215


title: wt_samp1

value: mspi

value: wildtype

value: HpaII


title: C210Slice

value: Cx3cr1-Cre/Ert2+; NuTRAP+


title: 65k: A2_504_C_ZTA_N182T

description: ZTA(N182T) PBM experiment, cytosine

source_name: ZTA(N182T), HK design

value: bZIP

value: cytosine


title: 65k: B2_504_C_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, cytosine

source_name: ZTA(N182Q), HK design


title: COAD.ct-214


title: CC043_lung_rna


title: COAD.ct-218


title: 65k: HK_535_C2_10PMT_5mC_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5mC


title: CC043_liver_rna

value: liver


title: 65k: HK_508_C_B2_ZTA_N182V

description: ZTA(N182V) PBM experiment, cytosine

source_name: ZTA(N182V), HK design


title: COAD.ct-213


title: C210Neg


title: CC043_kidney_rna

value: kidney


title: COAD.ct-212


title: 65k: D1_504_C_ZTA_N182S

description: ZTA(N182S) PBM experiment, cytosine


title: C210Input


title: 65k: A2_485_C_ZTA_WT

description: ZTA PBM experiment, cytosine


title: COAD.ct-211


title: 65k: HK_505_5hmC_A1_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5hmC


title: COAD.ct-210


title: CC042_kidney_rna


title: C209Pos

value: Positive


title: C209Slice


title: C209Neg


title: CC042_liver_rna


title: 65k: HK_535_F1_50PMT_5hmC_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, 5hmC


title: C209Input


title: 65k: HK_505_5hmC_D1_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5hmC


title: COAD.ct-208


title: CC041_lung_rna

source_name: lung tissue


title: CC041_liver_rna

source_name: liver tissue


title: 65k: HK_535_E1_50PMT_5hmC_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5hmC


title: COAD.ct-207


title: CC041_kidney_rna


title: CC042_lung_rna


title: C194Slice


title: 65k: HK_485_C_C1_ZTA_N182I

description: ZTA(N182I) PBM experiment, cytosine

source_name: ZTA(N182I), HK design


title: C210Pos


title: COAD.ct-206


title: C194Pos


title: CC049_liver_rna


title: C194Neg


title: COAD.ct-205


title: COAD.ct-209


title: 65k: HK_505_5hmC_C1_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5hmC


title: COAD.ct-204


title: C194Input


title: 65k: HK_536_E2_50PMT_5hmC_ZTA_WT

description: ZTA PBM experiment, 5hmC

source_name: ZTA, HK design


title: CC040_liver_rna


title: CC040_lung_rna


title: CC040_kidney_rna

source_name: kidney tissue


title: COAD.ct-203


title: 65k: HK_507_5mC_A1_ZTA_N182T

description: ZTA(N182T) PBM experiment, 5mC


title: C192Slice


title: C192Pos


title: 65k: HK_536_50PMT_C2_5mC_ZTA_N182V

description: ZTA(N182V) PBM experiment, 5mC


title: COAD.ct-202


title: CC039_liver_rna


title: CC039_lung_rna


title: COAD.ct-201


title: C192Neg


title: 65k: HK_536_50PMT_D2_5mC_ZTA_N182I

description: ZTA(N182I) PBM experiment, 5mC


title: COAD.ct-200


title: COAD.ct-198


title: COAD.ct-199


title: 65k: HK_536_A1_10PMT_5mC_ZTA_WT

description: ZTA PBM experiment, 5mC


title: 65k: A1_504_C_ZTA_N182T

description: ZTA(N182T) PBM experiment, cytosine


title: CC038_kidney_rna


title: CC038_lung_rna


title: 65k: B1_504_C_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, cytosine


title: CC038_liver_rna


title: COAD.ct-196


title: 65k: HK_535_D1_10PMT_5mC_ZTA_N182Q

description: ZTA(N182Q) PBM experiment, 5mC


title: 65k: HK_508_C_B1_ZTA_N182V

description: ZTA(N182V) PBM experiment, cytosine


title: COAD.ct-195


title: 65k: D2_504_C_ZTA_N182S

description: ZTA(N182S) PBM experiment, cytosine

source_name: ZTA(N182S), HK design


title: CC037_kidney_rna


title: C192Input


title: C155Neg


title: 65k: HK_485_C_C2_ZTA_N182I

description: ZTA(N182I) PBM experiment, cytosine


title: C155Pos


title: 65k: HK_535_C1_10PMT_5mC_ZTA_N182S

description: ZTA(N182S) PBM experiment, 5mC


title: 65k: A1_485_C_ZTA_WT

description: ZTA PBM experiment, cytosine


title: COAD.ct-197


title: CC037_lung_rna


title: CC036_liver_rna


title: CC036_kidney_rna


title: CC036_lung_rna


title: CC037_liver_rna


title: A294Pos

source_name: Aldh1l1-Cre/Ert2+; NuTRAP+_Positive

value: Aldh1l1-Cre/Ert2+; NuTRAP+


title: CC039_kidney_rna


title: A290Neg

source_name: Aldh1l1-Cre/Ert2+; NuTRAP+_Negative

value: brain


title: A294Neg


title: CC035_lung_rna


title: A290Pos


title: A293Neg


title: COAD.ct-191

source_name: blood serum


title: A293Pos


title: COAD.ct-190


title: CC035_liver_rna


title: COAD.ct-192


title: COAD.ct-193


title: COAD.ct-194


title: CC035_kidney_rna


title: COAD.ct-189


title: mut_CH12+AZFmutant_ChIP-seq_Input

first: Elena

last: Pugacheva

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to either the hg19 (Human) or mm9 (Mouse) genome assembly using Bowtie program (http://bowtie-bio.sourceforge.net) with default parameters
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) and MACS2 (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (MACS) to call sub-peaks, summit of peaks and improve peak resolution.
RNA-seq reads were aligned  to UCSC Human reference (build mm9) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
RNA-seq aligned reads (BAM files) were analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build mm9). The expression of each transcript was quantified as the number of reads mapped to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19 (for human), mm9 (for mouse)
Supplementary_files_format_and_content: Narrow peak (bed), bdg, and wig files were generated either by MACS or MACS2

source_name: Mouse B lymphoma cell

growth_protocol: K562 and MCF7 cell lines (obtained from ATCC) were grown in Dulbecco's modified Eagle medium (DMEM) supplemented with 10 % fetal calf serum and penicillin-streptomycin. CH12, B-cell lymphoma, cell line was maintained in RPMI 1640 supplemented with 10% FBS, 1% penicillin/streptomycin and 55 μM 2-β mercaptoethanol. CH12 wild type (wt) and mutant (mut) cells were described previously in (PMID: 29706548 ) and obtained as a gift from Dr. Rafael Casellas.

extract_protocol:
Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch). DNA concentration was assessed with a Qubit4 (ThermoFisher) and 5–10 ng was used to generate sequencing libraries using a TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA).
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For ChIP-seq 60 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.

tag: cell line

value: mutant (mut)

tag: expressed vector

value: mut_CH12 stably expressed CTCF mutant with 3 AZF, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

tag: treatment

tag: chip antibody

tag: mutation

value: homozygous deletion of ZF9-11 in CTCF gene


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with IGG_Abs_Control

value: mut_CH12 stably expressed mutant CTCF (CTCF with the first two ZFs deleted), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: Mouse IGG, Diagenode (C15400001-15)


title: mut_CH12+ChimeraAZF_ChIP-seq_with_IGG_Abs_Control

value: mut_CH12 stably expressed Chimera AZF:CTCF mutant with 3 AZFs + the first 2 CTCF ZFs, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: C155Input

value: Input


title: CC033_lung_rna

value: lung


title: mut_CH12+AZFmutant_ChIP-seq_with IGG Abs_Control


title: C12-OXBS

data_processing:
Sequencing reads were trimmed using trimmomatic 0.35 with the follwing settings: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 SLIDINGWINDOW:5:30 LEADING:25 TRAILING:25 HEADCROP:4 MINLEN:25 AVGQUAL:25
mm10 genome was prepared with in silico bisulfite conversion using Bismark 0.16.3-intel-2016a "bismark_genome_preparation" with Bowtie2/2.3.41-foss-2017b
Paired, trimmed fastqs were aligned to mm10 using Bismark 0.16.3-intel-2016a with the following settings: -p 6 -N 1 --bowtie2 --non_bs_mm --un
Bams were deduplicated using Bismark 0.16.3-intel-2016a "deduplicate_bam" function
Deduplicated bams were run through Bismark 0.16.3-intel-2016a "bismark_methylation_extractor" with the following settings: -p --comprehensive --bedgraph --buffer_size 20G --no_overlap --report --genome_folder /path/to/directory/mm10/
Genome_build: mm10
Supplementary_files_format_and_content: Deduplicated BAM file were run through MethylKit 1.10.0 to generate context-specific (CpG/CH) coverage text files

source_name: Brain

extract_protocol:
The purification of viable, cell-specific nuclei from brain tissue from Tam-induced Aldh1l1-cre/ERT2+; NuTRAP+ and Cx3cr1-cre/ERT2+; NuTRAP+ mice was achieved by combining two previously published protocols, with modifications.10,43 For each mouse, a hemisected half-brain was rinsed in ice-cold 1X PBS, minced into small pieces and homogenized in 4 ml ice-cold nuclei EZ lysis buffer (#NUC-101, Millipore Sigma) supplemented with 1X HaltTM protease inhibitor cocktail (ThermoFisher Scientific) using a glass dounce tissue grinder set (#D9063; Millipore Sigma: 20 times with pestle A and 20 times with pestle B).43 Undissociated tissue, largely composed of blood vessels, was removed by centrifugation at 200 x g for 1.5 min at 4°C,44 and the supernatant containing the nuclear material filtered through a 30 µm strainer and centrifuged at 500 x g for 5 min at 4°C. The resulting nuclear pellet was resuspended in nuclei lysis EZ buffer, incubated on ice for 5 min, washed by centrifugation, and resuspended in 300 µl nuclei EZ storage buffer by gentle trituration with a micropipette. From the total resuspended pellet volume, 10% was reserved as input nuclei fraction and the rest was diluted with 1.6 ml nuclei purification buffer (NPB: 20 mM HEPES, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 1X HaltTM protease inhibitor cocktail), and subjected to the INTACT protocol.10 Briefly, 30 µl of resuspended M-280 Streptavidin Dynabeads (#11205, ThermoFisher Scientific) were added into a fresh 2 ml microcentrifuge tube and washed with 1ml of NPB using a DynaMag-2 magnet (#12321; ThermoFisher Scientific) for a total of three washes (1 min incubation/each). The washed beads were reconstituted to their initial volume (30 µl) with NPB and gently mixed with the nuclear suspension. The mixture of nuclei and magnetic beads was incubated at 4°C for 40 min under gentle rotation settings to allow the affinity binding of streptavidin beads to the cell-specific, biotinylated nuclei. After incubation, the streptavidin-bound nuclei were magnetically separated with the DynaMag-2 magnet for a period of 3 min and the unbound nuclei collected in a fresh 2 ml microcentrifuge tube, centrifuged at 4°C (1,000 x g, 3 min), resuspended in 100 µl of NPB and reserved as the negative nuclei fraction. The nuclei bound to the beads were washed in the magnet for three washes (1 min/each), resuspended in 30 µl of NPB, and reserved as the positive nuclei fraction. From each nuclear fraction (input, negative, and positive), a 3 µl aliquot was mixed with equal volume of DAPI counterstain and used for confocal microscopy visualization and calculation of purity percentage (3-5 fields of view per sample).
The AllPrep DNA/RNA kit Micro (#80284, Qiagen, Germantown, MD) was used to extract gDNA from each sample.10 gDNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by genomic DNA D1000 (#5067-5582) with a 2200 Tapestation analyzer (Agilent Technologies, Santa Clara, CA). For each input, negative, and positive INTACT-isolated sample 400 ng of gDNA was brought up to 50 µl volume with 1X low-EDTA TE buffer and sheared with a Covaris E220 sonicator (Covaris, Inc., Woburn, MA) to an average 200 base pair size using the following settings: intensity of 5, duty cycle of 10%, 200 cycles per burst, 2 cycles of 60 seconds, at 7 °C. The size of sheared products was confirmed by capillary electrophoresis (DNA D1000, Agilent).  gDNA fragments were cleaned by an Agencourt bead-based purification protocol, after which gDNA was quantified (QubitTM dsDNA, Thermofisher Scientific). Two aliquots of 200 ng gDNA fragments were prepared in a 12 µl volume to which 1µl of spike-in control DNA (0.08 ng/ul) with known levels of specific mC, hmC, and fC at individual sites was added. Whole genome oxidative bisulfite (WGoxBS) libraries were constructed with NuGen Ovation Ultra-low Methyl Seq Library System with True-Methyl OXBS module.

value: Whole genome oxidative bisulfite

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: C11-OXBS

value: Cx3cr1-Cre/Ert2+; NuTRAP+

value: Negative


title: C10-OXBS


title: COAD.ct-187

value: cell-free DNA


title: CC033_liver_rna

value: liver


title: COAD.ct-186


title: mut_CH12+Chimera4_ChIP-seq_with RAD21 Abs_Rep5

description: mut_CH12+Chimera4_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera4, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: RAD21 ABs Abcam (ab992)


title: COAD.ct-185


title: mut_CH12+Chimera2_ChIP-seq_with RAD21 Abs_Rep5

description: mut_CH12+Chimera2_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera2, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC032_liver_rna


title: COAD.ct-183


title: C7-OXBS


title: CC032_lung_rna


title: COAD.ct-184


title: mut CH12 cells_RNA-seq_Rep2

description: CuffDiff_gene_exp.diff_CH12_WTversusMUT.txt

value: mutant (mut)


title: mut CH12 cells_RNA-seq_Rep1


title: wt CH12 cells_RNA-seq_Rep2

value: wild type (wt)


title: COAD.ct-188


title: C5-OXBS


title: CC032_kidney_rna

value: kidney


title: COAD.ct-182


title: COAD.ct-181


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with CTCF Abs_Rep3

description: mut_CH12+deltaZFs1_2_CTCF_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed mutant CTCF (CTCF with the first two ZFs deleted), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)

value: homozygous deletion of ZF9-11 in CTCF gene


title: wt CH12 cells_RNA-seq_Rep1


title: C9-OXBS

value: Positive


title: CC033_kidney_rna


title: CC031_liver_rna


title: C8-OXBS


title: mut_CH12+BORIS_ChIP-seq_with V5 Abs

description: mut_CH12+BORIS_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-180


title: C2-OXBS

value: Whole genome oxidative bisulfite

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: wt_CH12+BORIS_ChIP-seq_with V5 Abs

description: wt_CH12+BORIS_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: wt_CH12 stably expressed BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: wild type


title: C3-OXBS

value: Cx3cr1-Cre/Ert2+; NuTRAP+


title: COAD.ct-179

value: cell-free DNA


title: C6-OXBS


title: wt_CH12_TreatedWith_DMSO_ChIP-seq_with_RAD21_Abs

description: wt_CH12_ChIP_seq_RAD21_ABs_DMSO_treat_pileup.bdg.gz

value: CH12 cells were cultured for 3 days with DMSO (8mM)

value: RAD21 ABs Abcam (ab992)


title: C4-OXBS

value: Input


title: COAD.ct-178


title: CC030_lung_rna

value: lung


title: CC030_liver_rna

value: liver


title: COAD.ct-177


title: wt_CH12_TreatedWith_DMSO_ChIP-seq_with_CTCF_Abs

description: wt_CH12_ChIP_seq_CTCF_ABs_DMSO_treat_pileup.bdg.gz

value: wild type (wt)


title: CC030_kidney_rna

value: kidney


title: C12-BS

value: Whole genome bisulfite


title: wt_CH12_TreatedWith_8mM_ABA_ChIP-seq_with_RAD21_Abs

description: wt_CH12_ChIP_seq_RAD21_ABs_3ABA_8mM_treat_pileup.bdg.gz

value: CH12 cells were cultured for 3 days with 8mM of the PARP-1 inhibitor 3-aminobenzamide (3-ABA)


title: C11-BS

value: Negative


title: COAD.ct-176


title: C10-BS


title: COAD.ct-175


title: wt_CH12_TreatedWith_8mM_ABA_ChIP-seq_with_CTCF_Abs

description: wt_CH12_ChIP_seq_CTCF_ABs_3ABA_8mM_treat_pileup.bdg.gz

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: CC029_lung_rna


title: COAD.ct-174


title: CC029_liver_rna


title: C9-BS

value: Positive


title: CC031_kidney_rna


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+deltaZFs1_2_CTCF_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mutant (mut)

value: mut_CH12 stably expressed mutant CTCF (CTCF with the first two ZFs deleted), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)

value: homozygous deletion of ZF9-11 in CTCF gene


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with V5 Abs_Rep3


title: C1-OXBS

value: Cx3cr1-Cre/Ert2+; NuTRAP+

value: Whole genome oxidative bisulfite

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: CC031_lung_rna


title: C8-BS


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with V5 Abs_Rep1


title: COAD.ct-173

value: cell-free DNA


title: CC029_kidney_rna


title: COAD.ct-172


title: C7-BS

value: Input


title: COAD.ct-171


title: C5-BS


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+deltaZFs1_2_CTCF_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: RAD21 ABs Abcam (ab992)


title: CC028_kidney_rna


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with RAD21 Abs_Rep2


title: C6-BS


title: COAD.ct-170


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with RAD21 Abs_Rep1


title: COAD.ct-169


title: CC027_lung_rna

value: lung


title: C4-BS


title: CC027_liver_rna

value: liver


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with CTCF Abs_Rep2


title: C3-BS

value: Whole genome bisulfite


title: COAD.ct-168


title: CC027_kidney_rna

value: kidney


title: CC028_lung_rna


title: C2-BS

value: Negative


title: COAD.ct-166


title: COAD.ct-167


title: mut_CH12+ChimeraAZF_ChIP-seq_with V5 Abs

description: mut_CH12+ChimeraAZF_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera AZF:CTCF mutant with 3 AZFs + the first 2 CTCF ZFs, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC025_liver_rna


title: mut_CH12+CTCFmutant(deltaZFs1-2)_ChIP-seq_with CTCF Abs_Rep1

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: mut_CH12+ChimeraAZF_ChIP-seq_with RAD21 Abs

description: mut_CH12+ChimeraAZF_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: mutant (mut)


title: CC028_liver_rna


title: C1-BS


title: A12-OXBS

value: Aldh1l1-Cre/Ert2+; NuTRAP+

value: Positive


title: CC025_lung_rna


title: COAD.ct-165


title: mut_CH12+ChimeraAZF_ChIP-seq_with CTCF Abs

description: mut_CH12+ChimeraAZF_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: homozygous deletion of ZF9-11 in CTCF gene


title: CC024_lung_rna


title: A10-OXBS


title: mut_CH12+AZFmutant_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+AZF_CTCF_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed CTCF mutant with 3 AZF, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-163


title: COAD.ct-162


title: mut_CH12+AZFmutant_ChIP-seq_with V5 Abs_Rep1


title: A8-OXBS

value: Whole genome oxidative bisulfite

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: CC024_liver_rna


title: A9-OXBS


title: mut_CH12+AZFmutant_ChIP-seq_with RAD21 Abs_Rep2

description: mut_CH12+AZF_CTCF_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz


title: COAD.ct-161

value: cell-free DNA


title: mut_CH12+AZFmutant_ChIP-seq_with RAD21 Abs_Rep1

value: RAD21 ABs Abcam (ab992)


title: COAD.ct-160


title: CC023_liver_rna


title: A11-OXBS


title: COAD.ct-164


title: CC023_kidney_rna


title: CC025_kidney_rna


title: CC021_lung_rna

value: lung


title: mut_CH12+AZFmutant_ChIP-seq_with CTCF Abs

description: mut_CH12+AZF_CTCF_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz


title: mut_CH12+N5mutant_ChIP-seq_with V5 Abs_Rep3

description: mut_CH12+N5mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N6mutant of CTCF(The N-terminus truncated to aa187-265), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: mut_CH12+N5mutant_ChIP-seq_with V5 Abs_Rep2


title: COAD.ct-159


title: A5-OXBS


title: A6-OXBS


title: A7-OXBS

value: Input


title: A4-OXBS


title: COAD.ct-157


title: COAD.ct-158


title: A3-OXBS


title: CC021_liver_rna

value: liver


title: CC024_kidney_rna

value: kidney


title: CC021_kidney_rna


title: A2-OXBS

value: Negative


title: COAD.ct-155


title: mut_CH12+N5mutant_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+N5mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz


title: COAD.ct-156


title: mut_CH12+N5mutant_ChIP-seq_with RAD21 Abs_Rep2


title: A1-OXBS


title: CC020_liver_rna


title: CC020_lung_rna


title: mut_CH12+N5mutant_ChIP-seq_with RAD21 Abs_Rep1


title: A12-BS

value: Whole genome bisulfite


title: COAD.ct-154


title: A11-BS


title: mut_CH12+N5mutant_ChIP-seq_with CTCF Abs_Rep3

description: mut_CH12+N5mutant_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: mutant (mut)

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: COAD.ct-153


title: COAD.ct-152


title: A10-BS

value: Aldh1l1-Cre/Ert2+; NuTRAP+


title: COAD.ct-151


title: CC023_lung_rna


title: CC019_lung_rna


title: CC019_liver_rna


title: mut_CH12+N5mutant_ChIP-seq_with CTCF Abs_Rep1

value: homozygous deletion of ZF9-11 in CTCF gene


title: CC020_kidney_rna


title: mut_CH12+N5mutant_ChIP-seq_with CTCF Abs_Rep2


title: COAD.ct-150


title: A9-BS

value: Positive


title: CC019_kidney_rna


title: CC017_lung_rna


title: mut_CH12+Chimera4_ChIP-seq_with V5 Abs_Rep3

description: mut_CH12+Chimera4_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera4, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-148


title: A7-BS

value: Nugen Ovation Ultra-Low Methyl Seq with True-Methyl OxBS module


title: COAD.ct-149

value: cell-free DNA


title: A8-BS


title: A6-BS


title: CC017_liver_rna


title: A5-BS


title: mut_CH12+Chimera4_ChIP-seq_with V5 Abs_Rep1


title: mut_CH12+Chimera4_ChIP-seq_with RAD21 Abs_Rep4

description: mut_CH12+Chimera4_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: RAD21 ABs Abcam (ab992)


title: mut_CH12+Chimera4_ChIP-seq_with RAD21 Abs_Rep3


title: A4-BS


title: COAD.ct-146


title: mut_CH12+Chimera4_ChIP-seq_with RAD21 Abs_Rep2


title: mut_CH12+Chimera4_ChIP-seq_with V5 Abs_Rep2


title: COAD.ct-145


title: COAD.ct-144


title: A2-BS


title: CC016_liver_rna


title: mut_CH12+Chimera4_ChIP-seq_with CTCF Abs

description: mut_CH12+Chimera4_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz


title: mut_CH12+Chimera4_ChIP-seq_with RAD21 Abs_Rep1


title: A3-BS


title: COAD.ct-142


title: COAD.ct-143


title: CC015_lung_rna

value: lung


title: mut_CH12+Chimera3_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+Chimera3_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera3, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: A1-BS

value: Input


title: CC015_liver_rna

value: liver


title: CC016_kidney_rna

value: kidney


title: CC017_kidney_rna


title: COAD.ct-141


title: COAD.ct-147


title: mut_CH12+N5mutant_ChIP-seq_with V5 Abs_Rep1

value: mut_CH12 stably expressed N6mutant of CTCF(The N-terminus truncated to aa187-265), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC015_kidney_rna


title: MIGA2-GFP_Day6_2

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus, Ensembl GRCm38.p5, Release_91-2018-02-26
Supplementary_files_format_and_content: tab-delimited, raw counts

growth_protocol: 3T3-L1 pre-adipocytes were purchased from American Type Culture Collection (ATCC). 3T3-L1 cells were cultured at 37°C in DMEM (Thermo-Fisher) containing 10 % calf serum (CS) (Sigma-Aldrich) in 5% CO2. The cells were cultured in 10 cm tissue culture dishes (TPP) and the medium was exchanged at least every 2 days. The pre-adipocytes never reached densities above 70% confluence unless they were subjected to differentiation.

extract_protocol:
The RNA of cell extracts of an adipocyte time course experiment was purified using RNeasy Mini Kit (Quiagen).
TruSeq RNA stranded protocol

treatment_protocol: To start differentiation the cells were cultured until they reached complete confluence, and were then further incubated for another 48 h. After 48 h at 100 % confluence the medium was exchanged with differentiation medium, (DMEM with 10% FBS, 1 µM Dexamethasone, 0.5 mM IBMX and 1 µg/mL Insulin). The time point when differentiation medium was added is defined as the start of differentiation in our time course experiments (Day 0). After two days the differentiation medium was replaced by DMEM/ 10 % FBS containing insulin (1 µg/mL). At day 4 after start of differentiation the medium was exchanged with DMEM with 10 % FBS. At day 6 after start of differentiation the cells were harvested.

tag: cell type

tag: differentiation stage

value: 6 days after differentiation

value: overexpressed MIGA2-GFP


title: MIGA2-GFP_Day6_1


title: COAD.ct-140


title: CC013_lung_rna

tag: tissue


title: COAD.ct-139


title: MIGA2-KO_Day6_3

value: MIGA2 depleted


title: mut_CH12+Chimera3_ChIP-seq_with RAD21 Abs_Rep2

description: mut_CH12+Chimera3_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

tag: genotype

value: mutant (mut)


title: MIGA2-GFP_Day6_3


title: CC013_liver_rna


title: mut_CH12+Chimera3_ChIP-seq_with RAD21 Abs_Rep1

value: homozygous deletion of ZF9-11 in CTCF gene


title: CC013_kidney_rna


title: wt_CH12_ChIP-seq_with_NIPBL_Abs

description: wt_CH12_ChIP_seq_NIPBL_ABs_treat_pileup.bdg.gz

value: Anti-NIPBL (Bethy Laboratories; catalog# A301-779A)

value: wild type


title: COAD.ct-136


title: CC012_liver_rna


title: CC012_lung_rna


title: MIGA2-KO_Day0_3

value: Start of differentiation


title: mut_CH12+Chimera2_ChIP-seq_with V5 Abs_Rep3

description: mut_CH12+Chimera2_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera2, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: MIGA2-KO_Day6_1


title: mut_CH12+Chimera2_ChIP-seq_with V5 Abs_Rep1


title: MIGA2-KO_Day0_2


title: mut_CH12+Chimera3_ChIP-seq_with V5 Abs_Rep1


title: MIGA2-KO_Day6_2


title: COAD.ct-137

value: cell-free DNA


title: COAD.ct-134


title: MIGA2-KO_Day0_1


title: COAD.ct-138


title: COAD.ct-135


title: CC011_lung_rna

value: lung


title: COAD.ct-133


title: CC011_liver_rna


title: mut_CH12+Chimera2_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+Chimera2_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: RAD21 ABs Abcam (ab992)


title: CC012_kidney_rna


title: COAD.ct-132


title: mut_CH12+Chimera2_ChIP-seq_with RAD21 Abs_Rep4


title: mut_CH12+Chimera2_ChIP-seq_with V5 Abs_Rep2


title: WT_Day6_2


title: CC010_lung_rna


title: COAD.ct-130


title: mut_CH12+Chimera2_ChIP-seq_with RAD21 Abs_Rep1


title: CC011_kidney_rna


title: WT_Day0_3


title: COAD.ct-129


title: COAD.ct-131


title: mut_CH12+Chimera2_ChIP-seq_with CTCF Abs

description: mut_CH12+Chimera2_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: CC010_liver_rna

value: liver


title: CC016_lung_rna


title: mut_CH12+Chimera1_ChIP-seq_with CTCF Abs

description: mut_CH12+Chimera1_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Chimera1, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC010_kidney_rna

value: kidney


title: mut_CH12+Chimera1_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+Chimera1_ChIP_seq_V5_ABs_treat_pileup.bdg.gz


title: CC007_lung_rna


title: CC007_liver_rna


title: WT_Day6_3

value: 6 days after differentiation


title: WT_Day0_2


title: COAD.ct-127


title: mut_CH12+Chimera1_ChIP-seq_with RAD21 Abs_Rep2

description: mut_CH12+Chimera1_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: Abcam RAD21 ABs (ab992)


title: mut_CH12+Chimera1_ChIP-seq_with V5 Abs_Rep1


title: WT_Day0_1


title: COAD.ct-126


title: COAD.ct-125


title: CC006_lung_rna


title: mut_CH12+Chimera2_ChIP-seq_with RAD21 Abs_Rep2


title: WT_Day6_1


title: mut_CH12+Chimera1_ChIP-seq_with RAD21 Abs_Rep1


title: COAD.ct-124


title: mut_CH12+Chimera1_ChIP-seq_with BORIS Abs

description: mut_CH12+Chimera1_ChIP_seq_BORIS_ABs_treat_pileup.bdg.gz

value: custom mouse monoclonal BORIS  (characterized in PMID:21659515)


title: CC006_liver_rna


title: COAD.ct-128


title: COAD.ct-123


title: mut_CH12+N6mutant_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+N6mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mutant (mut)

value: mut_CH12 stably expressed N5mutant of CTCF(11 aa mutations), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: COAD.ct-122


title: CC005_lung_rna


title: COAD.ct-121


title: CC006_kidney_rna


title: mut_CH12+N6mutant_ChIP-seq_with V5 Abs_Rep1

value: homozygous deletion of ZF9-11 in CTCF gene


title: CC007_kidney_rna


title: MLL1-induced scRNA-seq

city: Aurora

first: Patricia

last: Ernst

state: CO

department: Pediatrics

institute: University of Colorado

data_processing:
Basecalls performed using RTA v3.3.3
Reads were aligned to the mm10 genome assembly using STAR aligner via Cell Ranger v2.0.2
MAPQ adjustment was performed by filtering out mapped reads with MAPQ < 255 and prioritizing exonic loci over non-exonic loci
Cell barcodes were filtered by removing cells with UMI counts less than 10 percent of the bottom percentile of UMI counts
Samples were aggregated via Cell Ranger v2.0.2 to create a single output folder containing data for both samples
Genome_build: mm10
Supplementary_files_format_and_content: Output from Cell Ranger v2.0.2 pipeline in the form of tab-delimited (barcodes.tsv, genes.tsv) and market matrix (matrix.mtx) files . Also included a key specifying which barcodes correspond to each sample (aggregation.csv)

source_name: hMLL1 clone 18 treated with doxycycline

growth_protocol: ES clones were differentiated as suspension EBs for 6 days total with doxycycline at 1 µg/mL present from day 4-day 6

extract_protocol:
RNA was extracted according to 10x Genomics Chromium Single Cell 3' Reagent Kits v2 documentation
Libraries were prepared according to 10x Genomics Chromium Single Cell 3' Reagent Kits v2 documentation
RNA High throughput sequencing using an Illumina NovaSeq 6000

treatment_protocol: At day 6, cells were dissociated with collagenase and dispase, incubated with c-Kit and CD41 antibodies and viable c-Kit/CD41 double positive cells sorted

tag: cell line background

value: hMLL1 clone 18; doxycycline-inducible MLL1 transgene

value: day 4-6 doxycycline

value: c-Kit+/CD41+ hematopoietic progenitors


title: COAD.ct-120


title: mut_CH12+N6mutant_ChIP-seq_with RAD21 Abs_Rep1

description: mut_CH12+N6mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz


title: mut_CH12+N6mutant_ChIP-seq_with RAD21 Abs_Rep2


title: CC005_kidney_rna


title: COAD.ct-119


title: LFD_PCHi-C_replicate1

city: Research Triangle Park

first: Paul

middle: A

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

data_processing:
Library strategy: PCHi-C
ChIP-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered reads were mapped to mm9 via Bowtie (v0.12.8) with parameters -m 1 -X 2000 --chunkmbs 1024.
Duplicate read pairs were removed via MarkDuplicates.jar from the Picard tools suite v1.110.
Uniquely-mapped non-duplicate reads were downsampled to 10 million prior to peak-calling with SICER. SICER parameters were window size 200, gap size 200, FDR 0.001 for H3K27ac.
For HNF4a and C/EBPa, peak calls was done by Homer with  "- factor"
Mapped read depth files were generated by BEDtools genomeCoverageBed then by UCSC utility bedGraphToBigWig, after read pairs were converted to a single fragment by filling in region between read ends with Ns. Mapped depths are normalized to 10M uniquely-mapped non-duplicate read pairs per sample.
RNA-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered read pairs were mapped to mm9 via STAR v2.5 with the following paramters: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000.
For each sample, counts per gene were extracted by subread featureCounts v1.5.0-p1 with parameters -s2 -Sfr -p.
HiC and capture HiC reads were processed by HiCUP (v0.6.1) to generate genomic alignments.
HiCExplorer was used to generate contact matrices (hicBuildMatrix with parameters --binSize 10000 --restrictionSequence AAGCTT --inputBufferSize 100000; then hicSumMatrices to combine replicates), normalize (hicCorrectMatrix), and call TADs (hicFindTADs).
CHiCAGO (v1.2.0) was used to process the capture HiC data and generate interaction calls; filtering was applied to require a minimum score of a 5 and maximum distance of 1Mb.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq normalized mapped read depth in bigWig format.
Supplementary_files_format_and_content: ChIP-seq peak calls in BED or txt format.
Supplementary_files_format_and_content: RNA-seq raw counts per gene per sample in tab-delimited text format.
Supplementary_files_format_and_content: HiC TADs in tab-delimited text format.
Supplementary_files_format_and_content: PCHiC interactions in tab-delimited text format.

extract_protocol: Chip-seq libraries were prepared by Bioo NEXTflex Rapid DNA-seq Kit (cat# 514402).

treatment_protocol: liver tissue was isolated from mice on the low fat diet and high fat diet

value: male

value: PCHi-C,Hindiii enzyme

tag: diet

value: low fat diet


title: CC005_liver_rna


title: CC004_lung_rna

value: lung


title: LFD_PCHi-C_replicate2

tag: Sex


title: COAD.ct-118

value: cell-free DNA


title: mut_CH12+N4mutant_ChIP-seq_with V5 Abs_Rep3

description: mut_CH12+N4mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N4mutant of CTCF(aa187-265), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-117


title: HFD_PCHi-C_replicate2

tag: library type

value: high fat diet


title: CC004_kidney_rna

value: kidney


title: mut_CH12+N4mutant_ChIP-seq_with V5 Abs_Rep1


title: HFD_PCHi-C_replicate1


title: COAD.ct-116


title: mut_CH12+N4mutant_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+N4mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: Abcam RAD21 ABs (ab992)


title: COAD.ct-115


title: CC003_lung_rna


title: COAD.ct-114


title: control scRNA-seq

source_name: KH2 treated with doxycycline

value: control


title: CC003_liver_rna

value: liver


title: mut_CH12+N4mutant_ChIP-seq_with RAD21 Abs_Rep2

value: mutant (mut)


title: mut_CH12+N4mutant_ChIP-seq_with RAD21 Abs_Rep1

value: homozygous deletion of ZF9-11 in CTCF gene


title: COAD.ct-113


title: LFD_Hi-C_replicate2

data_processing:
Library strategy: Hi-C
ChIP-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered reads were mapped to mm9 via Bowtie (v0.12.8) with parameters -m 1 -X 2000 --chunkmbs 1024.
Duplicate read pairs were removed via MarkDuplicates.jar from the Picard tools suite v1.110.
Uniquely-mapped non-duplicate reads were downsampled to 10 million prior to peak-calling with SICER. SICER parameters were window size 200, gap size 200, FDR 0.001 for H3K27ac.
For HNF4a and C/EBPa, peak calls was done by Homer with  "- factor"
Mapped read depth files were generated by BEDtools genomeCoverageBed then by UCSC utility bedGraphToBigWig, after read pairs were converted to a single fragment by filling in region between read ends with Ns. Mapped depths are normalized to 10M uniquely-mapped non-duplicate read pairs per sample.
RNA-seq read pairs were filtered to retain only those with mean base quality score >20.
Filtered read pairs were mapped to mm9 via STAR v2.5 with the following paramters: --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000.
For each sample, counts per gene were extracted by subread featureCounts v1.5.0-p1 with parameters -s2 -Sfr -p.
HiC and capture HiC reads were processed by HiCUP (v0.6.1) to generate genomic alignments.
HiCExplorer was used to generate contact matrices (hicBuildMatrix with parameters --binSize 10000 --restrictionSequence AAGCTT --inputBufferSize 100000; then hicSumMatrices to combine replicates), normalize (hicCorrectMatrix), and call TADs (hicFindTADs).
CHiCAGO (v1.2.0) was used to process the capture HiC data and generate interaction calls; filtering was applied to require a minimum score of a 5 and maximum distance of 1Mb.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq normalized mapped read depth in bigWig format.
Supplementary_files_format_and_content: ChIP-seq peak calls in BED or txt format.
Supplementary_files_format_and_content: RNA-seq raw counts per gene per sample in tab-delimited text format.
Supplementary_files_format_and_content: HiC TADs in tab-delimited text format.
Supplementary_files_format_and_content: PCHiC interactions in tab-delimited text format.

value: Hi-C, Hindiii enzyme


title: COAD.ct-112


title: CC003_kidney_rna


title: mut_CH12+N4mutant_ChIP-seq_with CTCF Abs_Rep2

description: mut_CH12+N4mutant_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: CC004_liver_rna


title: HFD_Hi-C_replicate2


title: HFD_Hi-C_replicate1


title: mut_CH12+N4mutant_ChIP-seq_with V5 Abs_Rep2


title: CC002_liver_rna


title: mut_CH12+N3mutant_ChIP-seq_with V5 Abs_Rep2

description:
mut_CH12+N3mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz
mut_CH12+N3mutant_ChIP_seq_V5_ABs_Rep2_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N3mutant of CTCF(aa90-186), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC002_kidney_rna


title: CC002_lung_rna


title: COAD.ct-110


title: KO 826

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

country: China

institute: Wuhan university

data_processing:
Quality control of mRNA-seq data was performed by using Fatsqc and low-quality bases were trimmed by Cutadapt
All RNA-seq data were mapped to the mouse genome (mm9) by TopHat (version 2.1.1) and allow maximum 2 mismatch per read.
Gene expression level was calculated by Cufflinks with default parameters and normalized by FPKM.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

extract_protocol:
Colons (0.5 cm in length, 0.5-1cm away from the anus) were removed, split open,  washed with PBS, immersed and homogeneized in 2 ml TRIzol, and toral RNA was harvested. Oligo dT was used to purify poly(A) mRNA which was subsequently reverse-transcibed into cDNA for libary construction and Illumina TruSeq.
Poly(A) mRNA was subsequently puriﬁed from 10 ng total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. The first strand cDNA was synthesized with NEBNext® RNA First Strand Synthesis Module. NEBNext® Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first strand cDNA. The resulted double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep Kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 100 bp paired-end reads strategy (Novogene Co. Ltd, Beijing).

treatment_protocol: Female Usp25+/+ and Usp25-/- mice were administered 2.5% DSS dissolved in sterile water for 5 days, followed by regular water for 2 days.

tag: strain background

value: female

tag: age

value: 8 weeks

value: 2.5% DSS treated for 5 days followed by two-day normal water

value: colon


title: KO 850

tag: genotype/variation


title: mut_CH12+N3mutant_ChIP-seq_with V5 Abs_Rep1

description: mut_CH12+N3mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz


title: CC001_lung_rna

tag: strain

value: lung


title: LFD_Hi-C_replicate1

value: male

value: low fat diet


title: mut_CH12+N3mutant_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+N3mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

tag: cell line


title: WT 140

value: wild type (Usp25+/+)


title: COAD.ct-109

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers using custom scripts (BamExtractor, D.Diep, K.Zhang)
methylation frequencies were calculated by binning data into 100bp regions and aggregating methylated and non-methylated cytosines within 100bp bins
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values for all samples at all analyzed 100bp genomic regions

tag: sample type

value: cell-free DNA


title: COAD.ct-108


title: WT 139

tag: treatment


title: mut_CH12+N3mutant_ChIP-seq_with RAD21 Abs_Rep2

tag: expressed vector

tag: chip antibody

value: Abcam RAD21 ABs (ab992)


title: COAD.ct-107


title: COAD.ct-111


title: mut_CH12+N3mutant_ChIP-seq_with RAD21 Abs_Rep1

tag: mutation


title: U12-3_nuc

city: Beijing

first: Yafei

last: Yin

state: Beijing

address: Zhongguancun North Street

department: Medical School

institute: Tsinghua University

description: Normalized abundance of lncRNAs in whole cell or subcellular fractions upon AMO treatment.txt

data_processing:
Basecalls performed using CASAVA version
Reads obtained from RNA-seq library sequencing were aligned to the mm10 genome assembly using tophat with uniq mapping parameters.
Gene expression (FPKM) were further calculated from mapped reads through Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: 46C mES cells

growth_protocol:
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
ESCs  were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). 293T cells  were maintained in medium supplemented with 10% heat-inactivated FCS, Penicillin-Streptomycin Solution (100 × stock, Life Technologies).

extract_protocol:
Subcellular fractionation was performed as previously described with following modifications45. Cytoplasmic buffer containing 0.05% or 0.15% NP-40 was used for isolating cytoplasmic fraction of mESC or 293T cells respectively. The whole sample of each subcellular fraction was spiked and mixed thoroughly with 5 µl 0.1 ng/µl spike-in RNA [contain two in vitro transcribed RNA: lacZ and mCherry, For polyA RNA-seq or SLAM-seq, ERCC spike-in (Thermo Fisher) was used].
For total RNA-seq, ribosomal RNAs were removed through Ribo-Zero rRNA Removal Kits (Epicentre), for polyA RNA-seq, polyA RNAs were isolated through Dynabeads mRNA Purification Kit (Thermo Fisher). RNA-seq libraries were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB).
Subcellular fractionation was performed as previously described with following modifications45. Cytoplasmic buffer containing 0.05% or 0.15% NP-40 was used for isolating cytoplasmic fraction of mESC or 293T cells respectively. The whole sample of each subcellular fraction was spiked and mixed thoroughly with 5 µl 0.1 ng/µl spike-in RNA [contain two in vitro transcribed RNA: lacZ and mCherry, For polyA RNA-seq or SLAM-seq, ERCC spike-in (Thermo Fisher) was used].
For total RNA-seq, ribosomal RNAs were removed through Ribo-Zero rRNA Removal Kits (Epicentre), for polyA RNA-seq, polyA RNAs were isolated through Dynabeads mRNA Purification Kit (Thermo Fisher). RNA-seq libraries were constructed through NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

treatment_protocol:
mESCs were transfected with 50 μM (U1+U2) AMO, and culture at 37℃ for 2 hours.
IAA, 4 hours

tag: cell type

value: embryonic stem cells

value: (U1 + U2) AMO nucleofection, 2 hours

tag: fraction

value: nucleoplasmic total RNA


title: mut_CH12+N4mutant_ChIP-seq_with CTCF Abs_Rep1

tag: genotype

value: mutant (mut)

value: mut_CH12 stably expressed N4mutant of CTCF(aa187-265), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: homozygous deletion of ZF9-11 in CTCF gene


title: CC001_kidney_rna

tag: tissue

value: kidney


title: CC068_lung_atac

data_processing:
Sequencing reads in FASTQ files were filtered (sequence quality score ≥ 20 for ≥ 90% of bases) and adapter contamination was removed using TagDust
Reads with >5 exact duplicates were filtered to only retain 5 of the reads
Reads were aligned to the appropriate pseudo-genome using GSNAP (parameter set: -k 15, -m 1, -i 5, –sampling=1, –trim-mismatch-score=0, –genome-unk-mismatch=1, –query-unk-mismatch=1)
Uniquely mapped reads were converted to mm9 (NCBI37) mouse reference genome coordinates using the associated MOD files (Build37, http://csbio.unc.edu/CCstatus/index.py?run=Pseudo) to allow comparison across strains.
Alignments overlapping regions in the mm9 blacklist (UCSC Genome Browser) were removed
Alignments were converted to BED format and shifted by +5 base pairs and -5 base pairs for the positive and negative strand alignments respectively
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing ATAC-seq read alignments to the mm9 mouse reference genome

extract_protocol:
Mice were euthanized by exsanguination following deep nembutal (100 mg/kg intraperitoneal injection) anesthesia. Lungs, livers, and kidneys were excised, snap-frozen in liquid nitrogen, and stored at –80°C. Flash frozen tissue samples were pulverized in liquid nitrogen using the BioPulverizer (Biospec) to break open cells and allow even exposure of intact chromatin to Tn5 transposase. Pulverized material was thawed in glycerol containing nuclear isolation buffer to stabilize nuclear structure and then filtered through Miracloth (Calbiochem) to remove large tissue debris. Nuclei were washed and directly used for treatment with Tn5 transposase
TruSeq libraries were constructed as per manufacturer's recommendations


title: COAD.ct-106

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads


title: COAD.ct-105


title: mut_CH12+N3mutant_ChIP-seq_with CTCF Abs_Rep2

description: mut_CH12+N3mutant_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N3mutant of CTCF(aa90-186), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: U12-3_chr

value: chromatin total RNA


title: COAD.ct-104


title: mut_CH12+N3mutant_ChIP-seq_with CTCF Abs_Rep1


title: U12-3_cell

value: total RNA


title: mut_CH12+N2mutant_ChIP-seq_with V5 Abs_Rep2

description: mut_CH12+N2mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N2mutant of CTCF(aa1-87), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-103


title: CC001_liver_rna

value: liver


title: CC068_liver_atac


title: CC062_lung_atac

value: lung


title: mut_CH12+N2mutant_ChIP-seq_with V5 Abs_Rep1


title: CC062_liver_atac


title: COAD.ct-102

value: cell-free DNA


title: mut_CH12+N2mutant_ChIP-seq_with RAD21 Abs_Rep2

description: mut_CH12+N2mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: RAD21 ABs Abcam (ab992)


title: CC061_lung_atac


title: U12-3_cyto

value: embryonic stem cells

value: cytoplasmic total RNA


title: CC068_kidney_atac


title: CC062_kidney_atac


title: COAD.ct-100


title: COAD.ct-101


title: CC061_liver_atac


title: mut_CH12+N2mutant_ChIP-seq_with RAD21 Abs_Rep1


title: CC061_kidney_atac


title: mut_CH12+N2mutant_ChIP-seq_with CTCF Abs

description: mut_CH12+N2mutant_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz


title: mut_CH12+N1mutant_ChIP-seq_with V5 Abs

description: mut_CH12+N1mutant_ChIP_seq_V5_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed N1mutant of CTCF(aa1-30), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: COAD.ct-98


title: U12-1_nuc

value: (U1 + U2) AMO nucleofection, 2 hours

value: nucleoplasmic total RNA


title: U12-1_cyto


title: mut_CH12+N1mutant_ChIP-seq_with RAD21 Abs_Rep2

description: mut_CH12+N1mutant_ChIP_seq_RAD21_ABs_treat_pileup.bdg.gz

value: mutant (mut)

value: homozygous deletion of ZF9-11 in CTCF gene


title: U12-2_cell


title: CC059_lung_atac


title: mut_CH12+N1mutant_ChIP-seq_with RAD21 Abs_Rep1


title: CC059_liver_atac


title: U12-1_chr


title: U12-2_cyto


title: CC059_kidney_atac

value: kidney


title: U12-2_nuc


title: U12-1_cell


title: COAD.ct-97


title: COAD.ct-96


title: CC057_lung_atac


title: COAD.ct-95


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_V5_Abs_Rep2

description: mut_CH12+(11ZFs+Cterm)_ChIP_seq_V5_ABs_Rep12_NoDup_treat_pileup.bdg.gz

value: mut_CH12 stably expressed truncated CTCF (11ZFs+C-terminus), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: COAD.ct-99


title: COAD.ct-94


title: U2-3_nuc

treatment_protocol:
mESCs were transfected with 75 μM U2 AMO, and culture at 37℃ for 2 hours.
IAA, 4 hours

value: U2 AMO nucleofection, 2 hours


title: U12-2_chr

value: chromatin total RNA


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_V5_Abs_Rep1


title: CC055_lung_atac


title: CC057_liver_atac


title: CC055_liver_atac


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_CTCF_Abs_Rep2

description: mut_CH12+(11ZFs+Cterm)_ChIP_seq_CTCF_ABs_Rep12_NoDup_treat_pileup.bdg.gz

value: CTCF Antibody (B-5):SantaCruz, sc-271514


title: CC057_kidney_atac


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_RAD21_Abs_Rep1

description: mut_CH12+(11ZFs+Cterm)_ChIP_seq_RAD21_ABs_Rep12_NoDup_treat_pileup.bdg.gz

value: Abcam RAD21 ABs (ab992)


title: COAD.ct-93


title: COAD.ct-90


title: COAD.ct-92


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_RAD21_Abs_Rep2


title: U2-3_chr


title: mut_CH12+(11ZFs+C-term)_ChIP-seq with_CTCF_Abs_Rep1


title: U2-3_cell

value: total RNA


title: U2-2_nuc


title: CC055_kidney_atac


title: CC053_lung_atac

value: lung


title: U2-2_cyto


title: COAD.ct-89

value: cell-free DNA


title: U2-2_cell


title: U2-2_chr


title: COAD.ct-88


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_V5_Abs_Rep1

description: mut_CH12+(Nterm+11ZFs)_ChIP_seq_V5_ABs_Rep12_NoDup_treat_pileup.bdg.gz

value: mut_CH12 stably expressed truncated CTCF (N-terminus+11ZFs), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: COAD.ct-87


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_V5_Abs_Rep2


title: CC053_liver_atac

value: liver


title: U2-3_cyto

value: embryonic stem cells

value: cytoplasmic total RNA


title: COAD.ct-91


title: U2-1_nuc

value: nucleoplasmic total RNA


title: mut_CH12+N1mutant_ChIP-seq_with CTCF Abs

description: mut_CH12+N1mutant_ChIP_seq_CTCF_ABs_treat_pileup.bdg.gz

value: mutant (mut)

value: mut_CH12 stably expressed N1mutant of CTCF(aa1-30), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: U2-1_cyto


title: COAD.ct-86


title: CC049_liver_atac


title: COAD.ct-84


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_RAD21_Abs_Rep1

description: mut_CH12+(Nterm+11ZFs)_ChIP_seq_RAD21_ABs_Rep12_NoDup_treat_pileup.bdg.gz

value: RAD21 ABs Abcam (ab992)

value: homozygous deletion of ZF9-11 in CTCF gene


title: COAD.ct-85


title: CC053_kidney_atac

value: kidney


title: CC049_lung_atac


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_CTCF_Abs_Rep3

description: mut_CH12+(Nterm+11ZFs)_ChIP_seq_CTCF_ABs_Rep12_NoDup_treat_pileup.bdg.gz


title: U2-1_chr

value: U2 AMO nucleofection, 2 hours

value: chromatin total RNA


title: CC046_lung_atac


title: CC049_kidney_atac


title: COAD.ct-83


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_CTCF_Abs_Rep1


title: COAD.ct-82


title: U1-3_nuc

treatment_protocol:
mESCs were transfected with 75 μM U1 AMO, and culture at 37℃ for 2 hours.
IAA, 4 hours

value: U1 AMO nucleofection, 2 hours


title: U1-3_cyto


title: mut_CH12+FL-CTCF_ChIP-seq_with V5-Tag Abs_Rep3

description: mut_CH12+FL-CTCF_ChIP_seq_V5_ABs_Rep12_treat_pileup.bdg.gz

value: mut_CH12 stably expressed Fl-CTCF (Full-Length CTCF, tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC046_liver_atac


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_CTCF_Abs_Rep2


title: CC046_kidney_atac


title: mut_CH12+FL-CTCF_ChIP-seq_with V5-Tag Abs_Rep2


title: U1-3_cell

value: total RNA


title: COAD.ct-80

value: cell-free DNA


title: U1-3_chr


title: mut_CH12+(Nterm+11ZFs)_ChIP-seq with_RAD21_Abs_Rep2

value: mut_CH12 stably expressed truncated CTCF (N-terminus+11ZFs), tagged with V5 Tag at the C-terminus) from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)


title: CC045_lung_atac

value: lung


title: COAD.ct-79


title: U2-1_cell

value: embryonic stem cells


title: mut_CH12+FL-CTCF_ChIP-seq_with RAD21 Abs_Rep3

description: mut_CH12+FL-CTCF_ChIP_seq_RAD21_ABs_Rep12_treat_pileup.bdg.gz


title: CC045_liver_atac

value: liver


title: mut_CH12+FL-CTCF_ChIP-seq_with V5-Tag Abs_Rep1

value: V5 Tag Monoclonal Antibody, ThermoFisher (Catalog # R960-25)


title: CC045_kidney_atac


title: U1-2_cyto

value: cytoplasmic total RNA


title: U1-2_nuc

value: nucleoplasmic total RNA


title: mut_CH12+FL-CTCF_ChIP-seq_with RAD21 Abs_Rep2

value: mutant (mut)


title: COAD.ct-77


title: CC044_lung_atac


title: COAD.ct-75


title: U1-2_chr


title: COAD.ct-76


title: U1-2_cell


title: mut_CH12+FL-CTCF_ChIP-seq_with CTCF Abs_Rep2

description: mut_CH12+FL-CTCF_ChIP_seq_CTCF_ABs_Rep12_treat_pileup.bdg.gz

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: COAD.ct-81


title: CC044_liver_atac


title: mut_CH12+FL-CTCF_ChIP-seq_with CTCF Abs_Rep1

value: homozygous deletion of ZF9-11 in CTCF gene


title: mut_CH12+FL-CTCF_ChIP-seq_with RAD21 Abs_Rep1

value: RAD21 ABs Abcam (ab992)


title: CC044_kidney_atac

value: kidney


title: U1-1_nuc

description: Normalized abundance of lncRNAs in whole cell or subcellular fractions upon AMO treatment.txt


title: mut_CH12+BORIS_ChIP-seq_with BORIS Abs

description: mut_CH12+BORIS_ChIP_seq_BORIS_ABs_treat_pileup.bdg.gz

value: mut_CH12 stably expressed BORIS from vector (of pMy-MouseCTCFbiotag-T2A-mOrange)

value: custom mouse monoclonal BORIS  (characterized in PMID:21659515)


title: U1-1_cyto

value: U1 AMO nucleofection, 2 hours


title: COAD.ct-74


title: CC043_lung_atac


title: U1-1_chr

value: chromatin total RNA


title: CC043_liver_atac


title: COAD.ct-78

value: cell-free DNA