title: P2/CD23- ATAC-seq

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

country: France

institute: INSERM

data_processing:
Image analysis and base calling was performed using Illumina Real Time Analysis ( 2.7.7 ) with default parameters.
Sequencing quality was assessed by FastQC and reads were trimmed of adapter sequences with cutadapt.
Reads were aligned on the human hg19 genome with bowtie1 and duplicate reads were removed with PICARD.
Open chromatin regions were calld with MACS2 and no external background, an union of open regions was created with bedtools.
Read counts and densities were computed for each region and each sample with bedtools intersect, counts were analyzed with DESeq2 for determining differentially opened regions.
Genome_build: hg19
Supplementary_files_format_and_content: For each sample, a bigWig signal file, created with  bam2wig.py, is provided.

source_name: In vitro differentiated human B cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) from healthy volunteers were obtained from the Etablissement Français du Sang (Rennes, France) after Ficoll density centrifugation (Sigma-Aldrich, St Louis, MO). Subjects were recruited under institutional review board approval and informed consent according to the Declaration of Helsinki. Human naïve B cells were purified by negative selection using magnetic cell separation (Naive B Cell Isolation kit II, Miltenyi Biotech) following the manufacturer’s instructions, using the AutoMACS deplete-sensitive program. The purity of isolated CD19+/CD27- NBCs was routinely above 99%. Cell culture conditions, antibodies, as well as flow cytometry procedures, were as described in Le Gallou et al., 2012. All cultures were performed in complete medium consisting of RPMI 1640 (Invitrogen) supplemented with 10% FCS (Biowest) and antibiotics (Invitrogen). Briefly, purified human naive B cells were labeled with 1µM Violet Proliferation Dye 450 (VPD450, BD Biosciences) in PBS at 37oC for 10 min and washed in complete medium to follow cellular divisions, and enable cell sorting of VPD450hi/lo populations (D4hi/lo). Purified cells were cultured at 7.5.105 cells/ml in 24-well plates and stimulated during 4 days with cocktail 1 composed of 2.6 μg/ml F(ab’)2 fragment goat anti-human IgM (H+L) (Jackson ImmunoResearch Laboratories), 100 ng/ml recombinant human soluble CD40L (NCI), 1.0 mg/ml CpG oligodeoxynucleotide 2006 (Cayla Invivogen), and 50 U/ml recombinant IL-2 (SARL Pharmaxie). After 2 days, antigen-primed naive B cells received a 2-day 12.5 ng/ml IL-10 stimulation (R&D Systems). At day 4, activated B cells were washed, stained with surface markers and CaspGLOW kit (eBioscience) to exclude active caspase-3 cells according to the manufacturer’s instructions and sorted into D4hi/lo populations using FACsARIA cell sorter (BD Biosciences). D4lo cells were then cultured at 4 x 105 cells/ml for up to 3 days with cocktail 2 composed of 50 U/ml IL-2, 12.5 ng/ml IL-10, and 5 ng/ml IL-4 (R&D Systems).

extract_protocol:
Cells were stained with surface markers and CaspGLOW kit (eBioscience) and sorted at day 4 as D4lo cells and at day 5 as P2/CD23+ (VPDlo/CD38lo/CD23+), P2/CD23- VPDlo/CD38lo/CD23) and P1 (VPDlo/CD38hi) cells using a FACsARIA cell sorter (BD Biosciences).
50,000 live cells were manually counted immediately after sorting and ATAC-seq libraries were constructed according to the original ATAC-seq protocol (Buenrostro et al., 2013) with no further modification. No size selection was performed to keep a complete view the the open chromatin landscape. Quantity and quality of libraires were assessed by BioAnalyzer (Agilent) and qPCR (Kapa) analyses. Libraries were sequenced as a single equimolar pool on one lane of a paired end 2x100 bp run on the Illumina HiSeq4000 sequencer by an external provider (Integragen, Evry, France).

tag: days in culture

value: Day 5

tag: cell population


title: aipp2paipp2_rep1

status: Public on Nov 08 2020

type: SRA

city: shanghai

first: Yizhe

last: Zhang

address: No.300 Fenglin Road

country: China

institute: Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences

description:
Pp_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt

library_source: transcriptomic

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat software. The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions. Then the region of gene were expanded following depths of sites and the operon was obtained. In addition, the whole genome was split into multiple 15kb windows that share 5kb. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS 2.1.1
Genome_build: not provided
Supplementary_files_format_and_content: expression_value_FPKM.txt: Tab-delimited text file includes expression matrix.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: plant tissues

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark) photoperiod at 23 °C.

extract_protocol:
Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 (2×150bp read length).

tag: ecotype/background

tag: genotype/variation

tag: age

value: 12 days

tag: tissue

value: Seedling


title: lhp1_rep1

description:
Lhp1_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: circRNA of Control 1

city: Changsha

first: Hong

last: Liu

state: Hunan

address: Renmin Road 139#

department: Nephrology

institute: The Second Xiangya Hospital, Central South University

description: re-analysis of GSE145652

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Hisat to map reads to the genome of species.
Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion. All samples were generated unique circular RNAs.
The differentially expressed circRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package–edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Approximately 5 mg of total RNA was used to deplete ribosomal RNA according to the manuscript of the  Ribo-Zero™ rRNA Removal Kit  (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 following the vendor's recommended protocol.

tag: condition

value: Control


title: aipp2paipp2_rep2

description:
Pp_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: aipp2_rep1

description:
Phd_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: cpl2_rep2

description:
cpl2_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: ZM24 [sgCYLD-5-RFP + CC-122]

city: San Diego

first: Rajkumar

last: Balakrishnan

state: California

address: 10300 Campus Point Drive, Suite 100,

department: Informatics & Predictive Sciences

country: USA

institute: Bristol Myers Squibb

data_processing:
Raw fastq files were merged so that each sample had one R1 and one R2 files. The quality of the fastq files was evaluated using FastqQC (v 0.11.5). The fastq files were tested using bbmap reformat (v.37.24) for compliance with the fastq format and to convert the quality encoding to q33. Illumina adapters were trimmed using cutadapt (v1.15) and used for Salmon and any other downstream process.    In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option, STAR was also used to trim the reads on the fly using the clip3pAdapterSequence option. Salmon (v 0.7) was used to obtain pseudoalignments on genes on the trimmed fastq files.
Supplementary_files_format_and_content: Salmon Raw Counts

source_name: B lymphocyte

growth_protocol: SU-DHL-4 was maintained in RPMI 1640 medium (RPMI; #11875085, Thermo Fisher) supplemented with 10% fetal bovine serum, 1X sodium pyruvate, 1X non-essential amino acids, 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were cultured at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Duplicates of about 1 million freshly frozen, pelleted cells for each condition were shipped to GENEWIZ (South Plainfield, NJ). The RNA extraction was performed using QIAGEN RNeasy Plus Mini Kit and the mRNA was enriched through poly-A+ mRNA.
The RNA extraction, library preparation, and mRNAseq were performed by GENEWIZ using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (#7765, New England Biolabs). ERCC RNA spike-in mix (#4456653, invitrogen) was spiked into each sample after RNA extraction and universal human reference RNA (#14919, Thermal fisher) was included for quality control purpose.

treatment_protocol: SU-DHL-4 cells were transduced with a lentiviral vector expressing a sgRNA targeting either CYLD (sgCYLD-2, sgCYLD-5), NFKBIA (sgNFKBIA-5, sgNFKBIA-8 ), TRAF3 (sgTRAF3-4, sgTRAF3-7) or TRAF2 (sgTRAF2-3, sgTRAF2-4) and then selected by puromycin (2µg/mL) for three days.  Cells were then spin down and resuspended with fresh medium and seeded in 6 well plates at one million cells per mL and treated with either DMSO or 10 µM CC-122 for 24 hours. Cells were washed once by ice cold PBS and then the cell pellets were snap frozen and kept at -80 °C. One cell pellet from each condition was subjected to western blot to check the CRISPR editing of target genes and Ikaros degradation.

tag: cell line


title: paipp2_rep1

description:
Phdh_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: P2/CD23+ ATAC-seq

library_source: genomic

molecule: genomic DNA


title: aipp2_rep2

description:
Phd_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: clf_rep1

description:
Clf_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt

value: clf


title: paipp2_rep2

description:
Phdh_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: clf_rep2

description:
Clf_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: lhp1_rep2

description:
Lhp1_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: Col-0_rep2

description:
Col_0_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt

value: WT


title: Col-0_rep1

description:
Col_0_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: P1 ATAC-seq


title: D4lo ATAC-seq

value: Day 4


title: aipp3_rep2

description:
bah_2
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: aipp3_rep1

description:
bah_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt


title: MCF10A-D4_input

city: Washington

first: Ghada

last: Sharif

state: DC

address: 3970 Reservoir Rd NW NRB E311

institute: Georgetown University

data_processing:
ChIP-Seq data were aligned to hg19 using Rsubread.
The differential genomic binding was established using CSAW.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: *bed: Bed files that subtract each input from the ChIP-Seq data.

source_name: Mammary Epithelial Cells

growth_protocol: MCF10A and MCFDCIS cell lines were maintained in DMEM:F12 (Invitrogen, Carlsbad, CA) with 5% horse serum, 20ng/ml EGF, 0.5mg/ml Hydrocortisone, 100ng/ml Cholera Toxin, and 10mg/mL Insulin. All cell lines were grown at 37C with 5% CO2.

extract_protocol: ActiveMotif Low Cell ChIP-seq kit.

treatment_protocol: DNA was crosslinked used 1.2% formaldehyde, then sonicated and reverse crosslinked.

tag: cell type

value: Ductal carcino in situ MCF10A cells

tag: passages

tag: chip antibody


title: MCFDCIS_input

value: MCFDCIS

value: Ductal carcino in situ MCFDCIS cells


title: MCF10A-D4-3_AIB1

description: processed data file: clusters.MCFDCIS.AIB1.D4.Input.bed


title: Perennial_ryegrass heat treatment rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Library preparation for Transcriptome sequencing:A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing:The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000 platform and paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Transcriptome assembly: The left files (read1 files) from all libraries/samples were pooled into one big left.fq.gz file, and right files (read2 files) into one big right.fq.gz file. Transcriptome assembly was accomplished based on the left.fq.gz and right.fq.gz using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene functional annotation: Gene function was annotated based on the following databases: NR (NCBI non-redundant protein sequences)；Pfam (Protein family)；KOG/COG/eggNOG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KEGG (Kyoto Encyclopedia of Genes and Genomes)；GO (Gene Ontology).
Genome_build: Differential expression analysis: Gene expression levels were estimated by RSEM (Li et al, 2011) for each sample. Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Lolium perenne

source_name: leaf

growth_protocol: Seeds were sowed into plastic pots containing peat soil and vermiculite (1:1 of v/v) after 5 days of stratification at 4oC. The plants were maintained in growth chambers controlled at 22/18oC (day/night), 65% relative humidity, 16 h photoperiod and 150 μmol quanta m–2 s–1 photosynthetically active radiation. All plants were irrigated with nutrient solution twice each week before stress treatments.

extract_protocol:
The leaves of control and stress treated bermudagrass plants were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Arabidopsis plants were subjected to 42 oC for 12hs, or 4 oC for 6hs. For drought treatment, 14-day-old seedlings were withheld water for 2 weeks. All stress treated plants were recovered at control condition for 5 days.

value: leaf

tag: treatment

value: cold

tag: genotype


title: MCF10A-D4-2_AIB1


title: MCFDCIS-D4_input


title: MCF10A_input


title: Perennial_ryegrass cold treatment rep2

value: heat


title: MCF10A-2_AIB1

description: processed data file: clusters.MCFDCIS.AIB1.Input.bed


title: Perennial_ryegrass submergence treatment rep2

value: submergence


title: MCF10A-D4-1_AIB1


title: Perennial_ryegrass heat treatment rep1


title: Perennial_ryegrass submergence treatment rep1


title: Perennial_ryegrass drought treatment rep2

value: drought


title: MCF10A-1_AIB1


title: Perennial_ryegrass cold treatment rep1


title: MCFDCIS-D4-3_AIB1

description: processed data file: clusters.MCF10A.AIB1.D4.Input.bed


title: CD4ActivatedEffector_day13postvax_volunteer2

type: RNA

city: Sydney

first: C. Mee Ling

last: Munier

state: NSW

address: Level 5, Wallace Wurth Building, UNSW Sydney

department: Immunovirology and Pathogenesis Program

country: Australia

institute: The Kirby Institute, UNSW Sydney

hyb_protocol: The labelled cRNA underwent a clean up step, which was followed by quantification by spectrophetometer. 20μg of cRNA was then fragmented using the 5x fragmentation buffer in the clean up kit (Affymetrix) prior to hybridisation onto the microarrays. Hybridisation cocktails were made by adding fragmented and labelled cRNA, control cRNAs, grid alignment oligonucleotides and blocking reagents. These mixtures were hybridised overnight (~16 hrs) to the Affymetrix GeneChip® Human  Genome U133 Plus 2.0 Arrays at 45°C, under constant rotation at 60 rpm. Washing and staining of the hybridised arrays were performed on an Affymetrix Fluidics Station, according to the manufacturer’s protocols.

scan_protocol: Fluorescent signals were measured on the arrays using an Agilent GeneArray Laser Scanner and gene transcript levels were determined and scaled to 150 (i.e., high signal >500 and low signal <150) using algorithms in Microarray Analysis Suite Software 5.0 (Affymetrix). Hybridisation cocktails were required to satisfy the following criteria, background less than 150, the housekeeping genes Gapdh and β-actin 3’/5’ ratios less than 3 and similar scaling factors between samples.

data_processing:
The data were analysed initially using Microarray Analysis Suite software (MAS 5.0; Affymetrix). Signal value (in mat_MAS5.txt) represents the level of expression of a transcript. Scaling of gene expression intensity levels was performed using Microarray Analysis Suite Software 5.0 (Affymetrix).
The second analysis of the microarray data utilised the internet based bioinformatics program GenePattern (Broad Institute, Cambridge, MA, USA). Microarray data files were uploaded into GenePattern, normalised using the RMA method of normalisation, NormalizeAffymetrix3prime command that creates a .gct and .cls file, the .gct file was log2 transformed using the LogTransform function.

label: biotin

source_name: CD4 T cells, 13 days post vaccinia virus vaccination

label_protocol: A two-cycle cRNA synthesis method was performed to generate cRNA using  the Two-Cycle Target Labelling kit (Affymetrix) that included all reagents for synthesis, clean up and labelling. The method took three days. On the first day a poly A internal control was added to the RNA prior to cDNA synthesis followed by an in vitro transcription (IVT) reaction for synthesis and amplification of cRNA, samples were then run on a Bio-Rad PCR machine for 16 hrs. On day two the cRNA was cleaned up and quantified by spectrophetometer, 600ng of cRNA generated in the first cycle was then used for a second cycle of cDNA synthesis. The second cycle consisted of first and then second strand cDNA synthesis, clean up of cDNA followed by second cycle of IVT then biotin labelling of resulting cRNA.

extract_protocol: RNA extraction was performed using a modified small-scale method, linear polyacrylamide 5ng was added to 300μL of TRIzol and the mixture was used to lyse the cells. After vortexing for 10 sec, 60μL chloroform was added to the TRIzol mixture and vortexed. The aqueous phase was collected after centrifugation at 16000 x g at 4ºC for 5 min and RNA was precipitated overnight at 4ºC in 180μL Isopropanol. RNA was pelleted at 16000 x g at 4ºC for 30 min and washed with 500μL of 70% Ethanol. Pellets were air-dried after centrifugation at 16000 x g at 4ºC for 10 min. RNA was redissolved in 6.2μL RNAse-free water and stored at -80°C till required.

tag: subject status/id

value: healthy volunteer 2

value: Vaccinia Vaccination

tag: timepoint

value: 13 days following vaccinia virus vaccination

value: PBMC

tag: cell subtype

value: CD4 Activated Effector


title: CD4Naive_day13postvax_volunteer1

value: healthy volunteer 1

value: CD4 Naive


title: CD4RestingMemory_day13postvax_volunteer2

value: CD4 Resting Memory


title: CD4RestingMemory_day13postvax_volunteer1


title: CD4ActivatedEffector_day13postvax_volunteer1


title: Perennial_ryegrass control rep1

value: control

value: WT


title: CD8ActivatedEffector_day13postvax_volunteer2

source_name: CD8 T cells, 13 days post vaccinia virus vaccination

value: CD8 Activated Effector


title: CD4Naive_day13postvax_volunteer2


title: MCFDCIS-D4-2_AIB1

value: MCFDCIS

value: Ductal carcino in situ MCFDCIS cells


title: CD8ActivatedEffector_day13postvax_volunteer1


title: Perennial_ryegrass control rep2

value: leaf


title: MCF10A-3_AIB1

value: Ductal carcino in situ MCF10A cells


title: MCFDCIS-3_AIB1

description: processed data file: clusters.MCF10A.AIB1.Input.bed


title: HaCaT cells_passed for 50 passages without arsenic exposure_rep1

city: Chengdu

first: Zunzhen

address: West China School of Public Health and West China Fourth Hospital, Sichuan University

institute: Sichuan University

description: control human keratinocytes (HaCaT-T cells, passed for 50 passages without arsenic exposure)

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar Human mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing:
Data was extracted using Agilent Feature Extraction software. The probe signals passing "P" or "M" QC flags in at least 1 sample was retained for further analysis.
IP (Cy5-labelled) and Sup (Cy3-labelled) intensities were normalized by the RNA spike-in calibration controls. m6A methylation levels were calculated for the percentage of modified RNA of a transcript.
Processed data file includes normalized signal for each sample and channel.

source_name: IP_The modified RNAs were eluted from the m6A immunoprecipitated magnetic beads

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: The human keratinocyte line (HaCaT) was obtained from Jiangsu KeyGen BioTECH Corp. (China) and cultured in DMEM (High-glucose Dulbecco’s Modified Eagle’s Medium; Life Technologies, USA) containing serum (10%) and penicillin G, streptomycin.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: HaCaT cells were maintained in the medium with or without 1 μM sodium arsenite (NaAsO2, Sigma, USA, purity: 99.0%) continuously for 50 passages (72 h per passage, about 5 months). HaCaT cells with 1 μM arsenite treatment for 50 passages were termed HaCaT-Transformed (HaCaT-T) cells and the transformation phenotypes of HaCaT-T cells were characterized.

value: HaCaT

value: immortalized keratinocytes

value: 0 uM arsenite exposure for 50 passages

source_name: Sup_The m6A unmodified RNAs were recovered from the supernatant


title: MCFDCIS-D4-1_AIB1


title: MCFDCIS-2_AIB1


title: MCFDCIS-input

data_processing:
ChIP-Seq data were aligned to hg19 using Rsubread
the differential genomic binding was established using csaw
Genome_build: GRCh19
Supplementary_files_format_and_content: Bed files that subtract each input from the ChIP-Seq data

source_name: Mammary Epthelial Cells

growth_protocol: MCFDCIS cell lines were maintained in DMEM:F12 (Invitrogen, Carlsbad, CA) with 5% horse serum, 20ng/ml EGF, 0.5mg/ml Hydrocortisone, 100ng/ml Cholera Toxin, and 10mg/mL Insulin. All cell lines were grown at 37C with 5% CO2.

extract_protocol:
De-cross-linked chromatin were subjected to RNAse and proteinase K treatment before isolating the DNA fragments. QIAquick PCR purification kit was used to isolate the DNA fragments
Kapa Hyper DNA library prep (Roche)

tag: passage

value: wildtype

value: none (input)


title: HaCaT-T cells_1 μM arsenite exposure for 50 passages_rep1

description: arsenite-transformed human keratinocytes (HaCaT-T cells, 1 μM arsenite exposure for 50 passages)

value: 1 uM arsenite exposure for 50 passages


title: MCFDCIS-1_AIB1


title: osteoblast D3

city: Zibo

first: Lianqing

last: Wang

state: Shandong

address: Gongqingtuan West Street 54#

department: Center of Translational Medicine

institute: Zibo Central Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files include counts, TPMs, FPKM values

source_name: osteoblast

extract_protocol: For constructing the library, 5 μg of RNA for each sample was prepared. Epicentre Ribo-Zero™ rRNA Removal Kit (Epicentre, USA) was used to remove rRNA, and ethanol precipitation was applied to clean up rRNA-free residue. In the library construction of mRNAs, the linear RNA was treated by RNase R (Epicentre, USA), which was not used in the library construction of circRNAs. The sequencing libraries were generated by using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to manufacturer’s protocol.

value: hFOB1.19 osteoblast cell line

tag: protocol

value: undergoing mineralization

tag: time

value: differentiation day 3


title: MCFDCIS-D4-input


title: ATAC-seq WT

city: Beijing

first: Mengfan

last: Li

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
Sequencing reads were aligned to hg19 reference genome using Bowtie2 with default parameters. Duplicate reads were removed using Picard’s MarkDuplicate algorithm. Reads numbers of the two samples were normalized to the same genome coverage.
Genome_build: hg19
Supplementary_files_format_and_content: bed (ChIP-seq), bw (ATAC-seq)

source_name: MDA-MB-231 breast cancer cells

growth_protocol: Human cell line MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle medium with high glucose (Lifetech). The medium contained 10% Fetal bovine serum (FBS) (Lifetech), and 1% of penicillin and streptomycin antibiotics (Lifetech). Cells were maintained at 37 °C and 5% CO2 in a humidified incubator.

extract_protocol: 5×10e4 cells were collected for each library and washed with PBS. Cells were lysed and DNA was digested by Tn5 transposase in 37℃ water bath for 30 min. Then DNA was purified using Qiagen MinElute PCR Purification Kit and PCR amplified. PCR products were purified using AMPure XP system and sequenced through XTen (Illumina).

value: mammary gland/breast

value: epithelial, breast cancer cell line

value: 51 years adult

tag: gender

value: female

value: wild type

value: lamin A antibody (ab26300, Abcam)


title: osteoblast D6

value: differentiation day 6


title: Perennial_ryegrass drought treatment rep1

value: leaf

value: drought

value: WT


title: MCFDCIS-D4-3_H3K27ac

value: Ductal carcino in situ MCFDCIS cells

value: H3K27ac (Active motif, #39135)


title: ATAC-seq LMNB1-KO

extract_protocol: 5×104 cells were collected for each library and washed with PBS. Cells were lysed and DNA was digested by Tn5 transposase in 37℃ water bath for 30 min. Then DNA was purified using Qiagen MinElute PCR Purification Kit and PCR amplified. PCR products were purified using AMPure XP system and sequenced through XTen (Illumina).


title: MCFDCIS-D4-2_H3K27ac


title: osteoblast D9

value: differentiation day 9


title: MCFDCIS-D4-1_H3K27ac


title: MCFDCIS-3_H3K27ac

value: wildtype


title: MCFDCIS-2_H3K27ac


title: RNA-seq LMNB1-KO rep2

data_processing:
RNA cleaned reads were aligned to the hg19 genome assembly using HISAT2. Transcripts assembly and gene expression quantification were using R package GenomicAlignments and DESeq2.
Genome_build: hg19

extract_protocol: Total RNA was collected using the TRIzol® Reagent (Life Technologies) following the manufacturer's instructions. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: MCFDCIS-1_H3K27ac


title: RNA-seq WT rep3


title: MCFDCIS-D4-3_H3K4me3

value: H3K4me3 (Active motif, #39159)


title: RNA-seq WT rep2


title: RNA-seq WT rep1


title: RNA-seq LMNB1-KO rep3


title: osteoblast D0

value: hFOB1.19 osteoblast cell line

value: control

value: differentiation day 0


title: MCFDCIS-D4-2_H3K4me3


title: Hi-C LMNB1-KO rep2

data_processing:
Library strategy: Hi-C
Hi-C data analysis was performed with HiC-Pro. Briefly, reads were first aligned on the hg19 reference genome. Uniquely mapped reads were assigned to restriction fragments. Then the invalid ligation products were filtered out, and eligible read pairs were counted to build Hi-C contact maps. At last, ICE normalization was used to normalize the raw counts data.
Genome_build: hg19

extract_protocol:
Cells were lysed and DNA was then cut with MboI and the overhangs were filled with a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
Sequencing libraries were generated using standard Illumina library construction protocol. Briefly, ends of sheared DNA were repaired and the blunt ends were added an “A” base to ligate with Illumina's adapters that have a single 'T' base overhang. Then DNA was PCR amplified for 8-12 cycles. At last, products were purified using AMPure XP system and sequenced through XTen (Illumina).

treatment_protocol: Cells were grown to about 70-80 % confluence, washed with PBS, crosslinked with 1%, v/v formaldehyde solution, and the reaction was quenched by 0.5M glycine solution.

value: mammary gland/breast

value: epithelial, breast cancer cell line


title: MCFDCIS-2_H3K4me3


title: MCFDCIS-D4-3_H3K4me1

value: H3K4me1 (Active motif, #39297)


title: MCFDCIS-D4-1_H3K4me3


title: MCFDCIS-1_H3K4me3


title: Hi-C LMNB1-KO rep1

treatment_protocol: Cells were grown to about 70-80 % confluence, washed with PBS, crosslinked with 1%, v/v formaldehyde solution, and the reaction was quenched by 0.4M glycine solution.

value: 51 years adult

value: female


title: microglia CBE_2

city: Rehovot

first: Yael

last: Pewzner-Jung

address: 234 Herzl St.

country: Israel

institute: Weiamann Institute of Science

description:
Acute nGD, in Deseq_Microglia_Acute_model.txt group: Acute
Deseq_Microglia_Acute_model.txt

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200)
Reads were mapped to genome
The pipeline quantifies the genes annotated in RefSeq
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Read count was performed with HTSeq-count
The proccesing was performed using UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 20, 154 (2019) doi:10.1186/s12859-019-2728-2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

organism: Mus musculus

source_name: Brain Microglia

extract_protocol:
Microglia was isolated from brain by FACS sorting  into lysis buffer & RNA was isolated using the RNeasy mini kit. RNA concentration (260/230 and 260/280 nm ratios)  were measured using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was evaluated using an RNA screen tape on a Tapestation 2200 (Agilent, Santa Clara, California, USA).
A bulk variation of MARSseq was used to construct RNAseq libraries: Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science. American Association for the Advancement of Science; 2014;343:776–9.

value: 3 weeks

tag: strain


title: MCFDCIS-D4-2_H3K4me1


title: microglia CBE_3

tag: age


title: MCFDCIS-2_H3K4me1

tag: tissue


title: MCFDCIS-1_H3K4me1


title: RNA-seq LMNB1-KO rep1


title: MCFDCIS-D4-1_H3K4me1


title: microglia PBS_3

description:
Control for Acute nGD, in Deseq_Microglia_Acute_model.txt group: Ctr OR in Deseq_Microglia_Age_effect.txt group: Ctr_3w
Deseq_Microglia_Acute_model.txt
Deseq_Microglia_Age_effect.txt


title: microglia CBE_1


title: Mix_T3_W5

description:
CPM_invivo.csv
Mix-T3-5W_S60_L006

data_processing:
Data was aligned to Hg19 by STAR; Gene Counts were generated with the following specifications: --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode TranscriptomeSAM GeneCounts
Count tables were merged with gawk (10A_Merged_reads, processed data files)
Counts per million were generated with EdgeR (CPM.csv, processed data files)
Genome_build: GRCh19
Supplementary_files_format_and_content: invitro_CPM.csv is a tab-separated values file containing the Counts Per Million of each cell line
Supplementary_files_format_and_content: invivo_CPM.csv is a tab-separated values file containing the Counts Per Million of each tumor pool

source_name: Mammary fat pad xenograft

growth_protocol: MCF10A  and MCFDCIS cell lines were maintained in DMEM:F12 (Invitrogen, Carlsbad, CA) with 5% horse serum, 20ng/ml EGF, 0.5mg/ml Hydrocortisone, 100ng/ml Cholera Toxin, and 10mg/mL Insulin. All cell lines were grown at 37C with 5% CO2.

extract_protocol:
RNA was isolated from cultured cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol and quantified by Nanodrop (Thermo Fisher, Waltham, MA).
RNA-sequencing used TruSeq total RNA with RiboZero Gold library preparation (Illumina, San Diego, CA, USA).

value: MCFDCIS+MCFDCIS-D4 mammary fat pad xenograft


title: microglia PBS_1


title: microglia Gba+/+_2

description:
Control for Chronic nGD,  in Deseq_Microglia_Chronic_model.txt group: WT3 OR in Deseq_Microglia_Age_effect.txt group: WT3_7m
Deseq_Microglia_Chronic_model.txt
Deseq_Microglia_Age_effect.txt

value: 7 months


title: microglia Gba+/+_1


title: Mix_T3_W2

description:
CPM_invivo.csv
Mix-T3-2W_S57_L006


title: Mix_T2_W5

description:
CPM_invivo.csv
Mix-T2-5W_S59_L006


title: Mix_T2_W2

description:
CPM_invivo.csv
Mix-T2-2W_S56_L006


title: microglia Gba+/-_3

description:
Control for Chronic nGD,  in Deseq_Microglia_Chronic_model.txt group: WT2
Deseq_Microglia_Chronic_model.txt


title: Mix_T1_W5

description:
CPM_invivo.csv
Mix-T1-5W_S58_L006


title: Hi-C WT rep2

treatment_protocol: Cells were grown to about 70-80 % confluence, washed with PBS, crosslinked with 1%, v/v formaldehyde solution, and the reaction was quenched by 0.3M glycine solution.

value: wild type


title: Mix_T1_W2

description:
CPM_invivo.csv
Mix-T1-2W_S55_L006


title: MCFDCIS-D4_T3_W5

description:
CPM_invivo.csv
D4-T3-5W_S63_L006

value: MCFDCIS-D4 mammary fat pad xenograft


title: MCFDCIS-D4_T2_W5

description:
CPM_invivo.csv
D4-T2-5W_S62_L006


title: microglia Gba+/-_2


title: microglia Gba+/-_1


title: microglia Gba+/-;Gbatg_3

description:
Control for Chronic nGD,  in Deseq_Microglia_Chronic_model.txt group: WT1
Deseq_Microglia_Chronic_model.txt


title: microglia Gba+/-;Gbatg_2


title: MCFDCIS-D4_T1_W5

description:
CPM_invivo.csv
D4-T1-5W_S61_L006


title: microglia PBS_2


title: MCFDCIS_T3_W5

description:
CPM_invivo.csv
DCIS-T3-5W_S54_L006

value: MCFDCIS mammary fat pad xenograft


title: microglia Gba-/-;Gbatg_4

description:
Chronic nGD, in Deseq_Microglia_Chronic_model.txt group: GD
Deseq_Microglia_Chronic_model.txt


title: MCFDCIS_T2_W5

description:
CPM_invivo.csv
DCIS-T2-5W_S53_L006


title: microglia Gba+/+_3


title: MCFDCIS_T3_W2

description:
CPM_invivo.csv
DCIS-T3-2W_S51_L006


title: microglia Gba-/-;Gbatg_3


title: Hi-C WT rep1

treatment_protocol: Cells were grown to about 70-80 % confluence, washed with PBS, crosslinked with 1%, v/v formaldehyde solution, and the reaction was quenched by 0.2M glycine solution.


title: microglia Gba-/-;Gbatg_1


title: MCFDCIS_T1_W5

description:
CPM_invivo.csv
DCIS-T1-5W_S52_L006


title: dC_a-EBF1_A-MuLV_input

city: Freiburg

first: Nikolay

last: Zolotarev

address: Stübeweg, 51

department: Cellular and Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: a-EBF1 ChIP-seq in EBF1 dC A-MuLV transformed pro-B cells

data_processing:
For quality control and reads mapping snakePipes – an automatic pipeline for analysis of deep sequencing data – was used.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2 (v2.3.3.1).
Reads were sorted and indexed using samtools (v1.9); duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.1) with RPGC normalization.
Peak calling was performed with MACS2 (v2.1.2) using input samples as control. Default MACS2 settings were used. For a-Brg1 ChIP-seq in fetal liver cells and a-EBF1 ChIP-seq in A-MuLV cells only peaks with -log10(qvalue) > 10 were selected.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were created using bamCoverage from deeptools (v3.3.1) with RPGC normalization. narrowPeak files were created using MACS2 (v2.1.2). narrowPeak is BED6+4 format file which contains for each peak: chromosome, start, end, name, integer score for display (-10*log10qvalue), strand, fold-change at peak summit, -log10pvalue, -log10qvalue, relative summit position to peak start.

source_name: fetal liver EBF1 fl/fl

growth_protocol: Production of A-MuLV transformed cells with the replacement of endogenous EBF1 by exogenous EBF1 wt and dC cells was described in Boller et al. 2016. A-MuLV transformed cells were cultured in the RPMI 1640 medium with 10% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol.

extract_protocol:
EBF1 ChIP was performed according to Boller et al. 2016 protocol with minor changes. Only crosslinking with formaldehyde was used. 4 µg rabbit a-EBF1 (1C) rabbit antibody per sample was used. Cells were harvested and washed with PBS. Cell pellet was resuspended in PBS with 2% FCS (4 mln cells per 1 ml buffer). Fresh formaldehyde mix (50mM HEPES-KOH pH8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 11% (v/v) formaldehyde) was added to the cell suspension to a final concentration of 1% FA. Tubes were incubated on rotator for 10 min at RT. Quenching was performed by adding 2 M Glycine to the final concentration 0.2 M. Cell pellet was resuspended in Lysis buffer (50mM Tris-HCl pH 8.0, 1% (w/v) SDS, 10mM EDTA; PIM) (4 mln cells per 100 μl buffer). Chromatin was sheared the chromatin with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). Fragment size and amount of chromatin was checked. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was mixed with 4 μg of EBF1 antibody or rabbit IgG and incubated on rotator ON at 4°C. Chromatin was incubated with 30 μl of Dynabeads Protein G (ThermoFisherScientific) suspension per sample on rotator for 4 hours at 4°C. Beads were washed 4 times with Wash buffer A (20mM Tris-HCl pH 8.0, 150mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA); once with Final wash buffer A (20mM Tris-HCl pH 8.0, 500mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2mM EDTA). Every wash was on rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were revese crosslinked, treated with RNase A and Proteinase K, and purified with QIAquick PCR Purification Kit.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol. No size selection was used. Amplification was performed using 10-12 PCR cycles. Deep sequencing was performed on a HiSeq 3000 system according to the standard Illumina protocol for 75 or 100 bp paired-end reads.

value: A-MuLV transformed pro-B cells

tag: transfection construct

tag: differentiation stage

value: pro-B


title: dC_a-EBF1_A-MuLV

tag: cell type

value: a-EBF1 (1C) rabbit antibody (Roessler et al. 2007)


title: wt_a-EBF1_A-MuLV_input

description: a-EBF1 ChIP-seq in EBF1 wt A-MuLV transformed pro-B cells


title: MCFDCIS_T2_W2

description:
CPM_invivo.csv
DCIS-T2-2W_S50_L006


title: dC_a-Brg1_A-MuLV

description: a-Brg1 ChIP-seq in EBF1 dC A-MuLV transformed pro-B cells

extract_protocol:
Brg1 ChIP was performed according to Bossen et al. 2015 protocol with minor changes. Double crosslinking with EGS and formaldehyde was used. 2.5 µg a-Brg1 antibody from Abcam (ab110641) per sample was used. Cells were harvested and washed with PBS. Cell pellet was resuspended in 10-20 ml PBS. 150 mM EGS stock solution in DMSO was added 1:100 to the cell suspenstion. Tubes were incubated on rotator for 15 min at RT. 37% formaldehyde stock solution was added to the final concentration 1%. Tubes were incubated on rotator for 15 min at RT. Quenching was performed by adding 2 M Glycine to the final concentration 0.2 M. Cells were resuspended in 4 ml buffer LB1 (50mM Hepes-KOH, pH 7.5; 140mM NaCl, 1mM EDTA; 10% glycerol; 0.5%NP-40; 0.25%Triton X-100; protease inhibitor mix (PIM) and incubated on ice for 10 minutes. Cells were resuspended LB3 buffer (10mM Tris-HCl, pH 8.0; 200mM NaCl; 1mM EDTA, pH 8.0; 0.5mM EGTA, pH 8.0; 0.1%Na-Deoxycholate; 0.5% N-lauroylsarcosine; PIM) about 1.5-3 mln cells per 100 μl buffer. Chromatin was sheared the chromatin with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). Fragment size and amount of chromatin was checked. 30 μl of Dynabeads Protein G (ThermoFisherScientific) suspension per sample was coupeled with 2.5 μg of Brg1 antibody or rabbit IgG in 200 μl of PBS with 0.5% BSA. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was added to beads and incubated on rotator ON at 4°C. Beads were washed with WB I (50 mM Tris-HCl, pH 8.0; 150 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); WB II (50 mM Tris-HCl, pH 8.0; 500 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); WB III (10 mM Tris-HCl, pH 8.0; 250 mM LiCl; 0.5 % NP-40; 0.5 % NaDOC; 1 mM EDTA pH 8.0) and TE. Every wash was on rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were revese crosslinked, treated with RNase A and Proteinase K, and purified with QIAquick PCR Purification Kit.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol. No size selection was used. Amplification was performed using 10-12 PCR cycles. Deep sequencing was performed on a HiSeq 3000 system according to the standard Illumina protocol for 75 or 100 bp paired-end reads.

value: a-Brg1 (Abcam, ab110641)


title: MCFDCIS_T1_W2

description:
CPM_invivo.csv
DCIS-T1-2W_S49_L006


title: wt_a-Brg1_A-MuLV

description: a-Brg1 ChIP-seq in EBF1 wt A-MuLV transformed pro-B cells


title: wt_a-Brg1_A-MuLV_input


title: MCFDCIS-D4-3

description:
CPM_invitro.csv
D10-3_S44_L005

value: Ductal carcino in situ MCFDCIS cells


title: microglia Gba+/-;Gbatg_1


title: whole brain CBE_3

description:
group: Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: Acute_sick_CBE
Deseq_Whole_Brain_Acute_model.txt
53

data_processing:
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200)
Reads were mapped to genome
The pipeline quantifies the genes annotated in Gencode
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Read count was performed with HTSeq-count
The proccesing was performed using UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 20, 154 (2019) doi:10.1186/s12859-019-2728-2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: Whole brain

extract_protocol:
Brain tissue was homogenized using a GentleMACS dissociator and mRNA was isolated using the RNeasy mini kit. RNA concentration (260/230 and 260/280 nm ratios)  were measured using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was evaluated using an RNA screen tape on a Tapestation 2200 (Agilent, Santa Clara, California, USA).
A bulk variation of MARSseq was used to construct RNAseq libraries: Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science. American Association for the Advancement of Science; 2014;343:776–9.

value: 21 days


title: empty_a-Brg1_fetal_liver

description: a-Brg1 ChIP-seq in EBF1 -/- fetal liver cells

source_name: fetal liver EBF1 -/-

growth_protocol: 16-18 days EBF1 -/- mouse embryos were collected, and fetal livers were extracted. C-kit+ cells were sorted using standard MACS protocol. Cells were transduced with corresponding viruses using spin infection with 1:1000 poybrene reagent. Cells were cultured for 14-20 days on OP9 cells in the Opti-MEM medium with 4% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol, 5 ng/ml IL7, 10 ng/ml SCF, 10 ng/ml Flt3.

extract_protocol:
Brg1 ChIP was performed according to Bossen et al. 2015 protocol with minor changes. Double crosslinking with EGS and formaldehyde was used. 2.5 µg a-Brg1 antibody from Abcam (ab110641) per sample was used. Cells were harvested and washed with PBS. Cell pellet was resuspended in 10-20 ml PBS. 150 mM EGS stock solution in DMSO was added 1:100 to the cell suspenstion. Tubes were incubated on rotator for 15 min at RT. 37% formaldehyde stock solution was added to the final concentration 2%. Tubes were incubated on rotator for 15 min at RT. Quenching was performed by adding 2 M Glycine to the final concentration 0.2 M. Cells were resuspended in 4 ml buffer LB1 (50mM Hepes-KOH, pH 7.5; 140mM NaCl, 1mM EDTA; 10% glycerol; 0.5%NP-40; 0.25%Triton X-100; protease inhibitor mix (PIM) and incubated on ice for 10 minutes. Cells were resuspended LB3 buffer (10mM Tris-HCl, pH 8.0; 200mM NaCl; 1mM EDTA, pH 8.0; 0.5mM EGTA, pH 8.0; 0.1%Na-Deoxycholate; 0.5% N-lauroylsarcosine; PIM) about 1.5-3 mln cells per 100 μl buffer. Chromatin was sheared the chromatin with a Bioruptor (20-25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C). Fragment size and amount of chromatin was checked. 30 μl of Dynabeads Protein G (ThermoFisherScientific) suspension per sample was coupeled with 2.5 μg of Brg1 antibody or rabbit IgG in 200 μl of PBS with 0.5% BSA. 10-20 μg DNA was used for 1 ChIP reaction. Chromatin was added to beads and incubated on rotator ON at 4°C. Beads were washed with WB I (50 mM Tris-HCl, pH 8.0; 150 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); WB II (50 mM Tris-HCl, pH 8.0; 500 mM NaCl; 0.1% SDS; 0.1% NaDOC; 1 % Triton X-100; 1 mM EDTA pH 8.0); WB III (10 mM Tris-HCl, pH 8.0; 250 mM LiCl; 0.5 % NP-40; 0.5 % NaDOC; 1 mM EDTA pH 8.0) and TE. Every wash was on rotator for 5 minutes at 4°C. Chromatin was eluted with 100 μl Elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65°C for 30 min. Samples were revese crosslinked, treated with RNase A and Proteinase K, and purified with QIAquick PCR Purification Kit.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol. No size selection was used. Amplification was performed using 10-12 PCR cycles. Deep sequencing was performed on a HiSeq 3000 system according to the standard Illumina protocol for 75 or 100 bp paired-end reads.

value: fetal liver EBF1 -/- c-kit+ lymphocyte progenitors

value: blocked in B cell development before pro-B stage


title: MCFDCIS-D4-2

description:
CPM_invitro.csv
D10-2_S43_L005


title: whole brain CBE_2

description:
group: Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: Acute_sick_CBE
Deseq_Whole_Brain_Acute_model.txt
52


title: whole brain PBS_3

description:
group: Control for Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: CTR_acute_PBS OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_3w
Deseq_Whole_Brain_Acute_model.txt
Deseq_Whole_Brain_Age_effect.txt
50


title: whole brain CBE_1

description:
group: Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: Acute_sick_CBE
Deseq_Whole_Brain_Acute_model.txt
51


title: wt_a-EBF1_A-MuLV


title: whole brain PBS_2

description:
group: Control for Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: CTR_acute_PBS OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_3w
Deseq_Whole_Brain_Acute_model.txt
Deseq_Whole_Brain_Age_effect.txt
49


title: dPLD_a-Brg1_fetal_liver

description: a-Brg1 ChIP-seq in pro-B cells EBF1 with delition of PLD (480-520 aa)

value: partialy blocked in B cell development before pro-B stage


title: dC_a-Brg1_fetal_liver

description: a-Brg1 ChIP-seq in pro-B cells  EBF1 with delition of CTD


title: whole brain PBS_1

description:
group: Control for Acute nGD, in Deseq_Whole_Brain_Acute_model.txt group: CTR_acute_PBS OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_3w
Deseq_Whole_Brain_Acute_model.txt
Deseq_Whole_Brain_Age_effect.txt
48


title: wt_a-Brg1_fetal_liver

description: a-Brg1 ChIP-seq in pro-B cells EBF1 wt


title: MCFDCIS-3

description:
CPM_invitro.csv
DCIS-3_S41_L005


title: dC_a-Brg1_A-MuLV_input


title: MCFDCIS-2

description:
CPM_invitro.csv
DCIS-2_S40_L005


title: 10hpf rep2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
The reads were aligned to the zebrafish genome GRCz10 by Tophat2 (v2.1.1).
Read counting and adjusted fold change (GFOLD) quantification were performed using the GFOLD software (v1.1.4).
Genome_build: GRCz10
Supplementary_files_format_and_content: a tab-delimited text file containing GFOLD and RPKM values

organism: Danio rerio

source_name: whole organism

growth_protocol: Wild type zebrafish embryos obtained from a wild type cross were raised in a petridish containing emrbyo media at 28.5 degree until harvested

extract_protocol:
Embryos at 6 or 10 hours post fertilization were manually decorinated, stored in Trizol reagent at -80 degree unyil use. Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for deep sequencing using standard Illumina protocols

treatment_protocol: not treated

value: whole organism

tag: Stage

value: 10 hours post fertilization


title: whole brain Gba+/+_4

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_WT OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_7M
Deseq_Whole_Brain_Chronic_model.txt
Deseq_Whole_Brain_Age_effect.txt
29


title: 10hpf rep1


title: fetal_liver_input

description: input control for a-Brg1 ChIP-seq in pro-B cells EBF1 wt

tag: chip antibody


title: B46, bronchopulmonary dysplasia

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. BBDuk was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option. Next, alignment of the filtered reads to the human reference genome (GRCh38) was done using HISAT2 (version 2.1.0) applying --no-mixed and --no-discordant options. UMI specific workflow that was developed and distributed by NuGEN was used to extract reads that are free from PCR artifacts (i.e. deduplication). The resulting deduplicated reads were summarized to each gene using HTSeq by supplementing Ensembl gene annotation (GRCh38.78).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read count data

source_name: tracheal aspirate

extract_protocol:
Total RNA was extracted from 0.5ml of tracheal aspirate using the Plasma/Serum RNA Purification kit (Norgen Biotek) as per the manufacturer's instructions. Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using NuGEN’s Ovation® SoLo RNA-Seq System (Tecan Genomics, Inc.). This system offers a built-in Unique Molecular Identifier (UMI) application as well as a depletion of rRNA and other high-abundant transcripts using the proprietary InDA-C technology. UMIs are used to eliminate possible PCR duplicates in sequencing datasets and therefore facilitate unbiased gene expression profiling. The basic principle behind the UMI deduplication step is to collapse reads with identical mapping coordinates and UMI sequences. This step helps increase the accuracy of sequencing read counts for downstream analysis of gene expression levels. The processed libraries were assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies).
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions.

tag: lung disease

value: bronchopulmonary dysplasia

tag: Sex

value: Female

tag: premature birth

value: yes


title: MCFDCIS-1

description:
CPM_invitro.csv
DCIS-1_S39_L005


title: B45, bronchopulmonary dysplasia

value: Male


title: whole brain Gba+/+_3

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_WT OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_7M
Deseq_Whole_Brain_Chronic_model.txt
Deseq_Whole_Brain_Age_effect.txt
28

value: 6 months


title: F-GATA3_a-Brg1_fetal_liver

description: a-Brg1 ChIP-seq in pro-B cells EBF1 with CTD substituted with TA1 domain of GATA3


title: C43, no lung disease

value: no


title: C41, no lung disease


title: C40, no lung disease


title: whole brain Gba+/+_2

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_WT OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_7M
Deseq_Whole_Brain_Chronic_model.txt
Deseq_Whole_Brain_Age_effect.txt
27

value: 9 months


title: C38, no lung disease


title: MCFDCIS-D4-1

description:
CPM_invitro.csv
D10-1_S42_L005


title: B44, bronchopulmonary dysplasia


title: B35, bronchopulmonary dysplasia


title: whole brain Gba+/-;Gbatg_3

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_Het_TG
Deseq_Whole_Brain_Chronic_model.txt
25

value: 6.75 months


title: C39, no lung disease


title: B36, bronchopulmonary dysplasia


title: C34, no lung disease


title: whole brain Gba+/-;Gbatg_1

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_Het_TG
Deseq_Whole_Brain_Chronic_model.txt
22

value: 7.5 months


title: C33, no lung disease


title: C47, no lung disease


title: C32, no lung disease


title: C31, no lung disease


title: B30, bronchopulmonary dysplasia


title: whole brain Gba-/-;Gbatg_4

description:
group: Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: ChronicGD_KO
Deseq_Whole_Brain_Chronic_model.txt
21


title: B29, bronchopulmonary dysplasia


title: B26, bronchopulmonary dysplasia


title: SYK-KO EGF rep1

city: Baltimore

first: Yu

last: Yu

state: MD

address: CRB-2, Rm 376, 1550 Orleans St

department: Department of Pathology

institute: Johns Hopkins School of Medicine

data_processing:
Bioinformatics analysis was performed using Galaxy, an open access web-based program that contains a variety of next-generation sequencing analysis tools. Reads were processed and aligned to Homo sapiens reference genome build hg19 using Tophat gapped-read mapper (ver. 2.1.0). The aligned reads were processed with Cufflinks transcript assembly (ver. 2.2.1.0), and the resulting GTF files were amalgamated to UCSC hg19 RefSeq genes annotation file using Cuffmerge (ver. 2.2.1.0). Differential expression analysis was performed using Cuffdiff (ver. 2.2.1.3) to curate a list of gene whose changes were statistically significant (q-val<0.05) between the genotypes tested.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff output

source_name: OVISE ovarian carcinoma cells

extract_protocol:
Isogenic OVISE cell lines with SYK knockout was treated with EGF (BD) at 50 ng/mL for 24 h. RNA was isolated and purified using the RNeasy Plus Mini Kit (Qiagen). The RNA quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer RNA Nano Chip; RIN values ranged between 9.4 and 10.0.
Paired-end index libraries were constructed using a standard protocol provided by Illumina.

treatment_protocol: Ovarian carcinoma OVISE cell lines with detectable total SYK expression were obtained from the Japanese Health Science Research Resources Bank (Osaka, Japan). The pSpCas9n(BB)-2A-Puro (PX462) CRISPR/Cas9 vector from Addgene (plasmid no. 48141) was used in this study. Cloning was performed using a pair of CRISPR single-guide RNA (sgRNA) specifically targeting exon 2 of SYK: top strand-nicking sgRNA (CGGACAGGGCGAAGCCACCC) and bottom strand-nicking sgRNA (CACACCACTACACCATCGAG), which were designed and cloned as previously described [Ran FA, Hsu PD, Wright J, et al. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013;8(11):2281-308.]. OVISE cells were transfected using Lipofectamine® 3000 (Life Technologies), and positive cells were selected in the presence of 2 μg/ml puromycin. Two to three weeks after transfection, single cell clones were isolated and screened for Cas9 expression. The knockout was verified by immunoblotting.

tag: cell line

value: OVISE

value: ovarian carcinoma

tag: genotype

value: SYK-KO

tag: treatment

value: EGF (50 ng/ml, 24h)


title: whole brain Gba-/-;Gbatg_2

description:
group: Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: ChronicGD_KO
Deseq_Whole_Brain_Chronic_model.txt
18


title: SYK-KO EGF rep2


title: whole brain Gba+/+_1

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_WT OR in Deseq_Whole_Brain_Age_effect.txt group: Brain_WT_7M
Deseq_Whole_Brain_Chronic_model.txt
Deseq_Whole_Brain_Age_effect.txt
26

value: 7.2 months


title: SYK-WT EGF rep2

value: SYK-WT


title: whole brain Gba-/-;Gbatg_1

description:
group: Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: ChronicGD_KO
Deseq_Whole_Brain_Chronic_model.txt
17


title: SYK-WT EGF rep1


title: C22, no lung disease


title: B25, bronchopulmonary dysplasia


title: B21, bronchopulmonary dysplasia


title: whole brain Gba+/-;Gbatg_2

description:
group: Control for Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: CTR_Het_TG
Deseq_Whole_Brain_Chronic_model.txt
23

value: 8.3 months


title: crypt cell: Input

first: Liu

last: Yang

address: Qinghuayuan street

institute: Tsinghua University

description: contol sample

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then clean reads were obtained.
Clean reads were mapped to GCF_000001635.26_GRCm38.p6 genome sequence from NCBI using SOAPaligner/soap2.
Based on analysis model from BGISEQ (BGI genomics), perform Peak (ChIP Sequencing enrichment area) scan in the whole genome to obtain the position information of Peak on the genome and the sequence information of the Peak region.
Genome_build: GRCm38.p6 C57BL/6J
Supplementary_files_format_and_content: Peak results are stored in wiggle file format

source_name: intestinal crypt

extract_protocol:
The crypt cells were crosslinked with 1% formaldehyde for 10 min at 37℃, and the nuclei were extracted according to the manufacturer’s instructions (CST, 9004). The DNA was sheared to length of approximately 100-300 bp by sonicating the samples with 20 pulses. Samples were incubated on ice between each pulse. ChIP assays were then carried out with the manufacturer’s instructions, using anti-CREPT antibody.
The input and CREPT antibody enriched DNA were added by A at 3', and ligated by adaptors. The DNA were amplified by PCR.

value: intestine

value: crypt


title: LAMP2A+DM-αKG rep3

city: Philadelphia

first: Xiaolu

address: BRB2/3,421 curie blvd

institute: University of Pennsylvania

description:
LAMP2A_htseqcount_gene.txt
LAMP2A_DM_KG_vs_LAMP2A_full_DESeq2_results.txt

data_processing:
STAR (v.2.7.1) was used to align sequencing reads to the mm10 mouse reference genome.
HTSeq (v.0.11.2) was used to quantify gene-level abundance corresponding to the mm10 reference genome.
DESeq2 ((v.1.22.2) was used to perform differential expression analysis to compare transcriptomic changes in (1) LAMP2A versus VT control and (2) LAMP2A+ DM-αKG versus LAMP2A.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include mapped read values per gene for each sample that passed QC (LAMP2A_htseqcount_gene.txt) and gene level-based differential expression results for the (1) LAMP2A versus VT control (LAMP2A_vs_VT_full_DESeq2_results.txt) and (2) LAMP2A+ DM-αKG versus LAMP2A (LAMP2A_DM_KG_vs_LAMP2A_full_DESeq2_results.txt).

source_name: Embryonic stem cell

growth_protocol: D3 mouse ES cells were cultured in feeder-free condition on 0.1% gelatin-coated disheswere with Knockout DMEM (Thermo Fisher Scientific) supplemented with 15% Stem cell qualified fetal bovine serum (Gemini), 1% (v/v) penicillin/streptomycin (Thermo Fisher Scientific), 0.1 mM 2-mercaptoethanol (Gibco), 2 mM L-glutamine (Gibco), 1% (v/v) non-essential amino acid (Gibco), and 1000 U/mL ESGRO (Millipore).

extract_protocol:
RNA was isolated with miRNAeasy Mini Kit (Qiagen, 74106). Illumina TruSeq stranded mRNA Sample Prep Kit (A Cat#FC-122-2101, B Cat#FC-122-2102) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared using TruSeq Stranded mRNA Sample Preparation Kit v2

treatment_protocol: Cells stably expressed pCDH-control vector (VT),LAMP2A-overexpressed cells without (LAMP2A), and with DM-αKG treatment (4 mM, 72 hrs) (LAMP2A+ DM-αKG).

tag: index

value: CTTGTA


title: SYK-KO rep2

value: No treatment


title: B19, bronchopulmonary dysplasia

value: bronchopulmonary dysplasia

value: Male

value: yes


title: LAMP2A+DM-αKG rep2

value: GGCTAC


title: B18, bronchopulmonary dysplasia


title: whole brain Gba-/-;Gbatg_3

description:
group: Chronic nGD, in Deseq_Whole_Brain_Chronic_model.txt, group: ChronicGD_KO
Deseq_Whole_Brain_Chronic_model.txt
20

value: 6 months


title: SYK-WT rep2


title: Vil_WT1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then clean reads were obtained.
Clean reads were mapped to mm10 genome sequence from UCSC using HISAT.
Clean reads were mapped to reference gene sequence by Bowtie2. Gene expression level for each sample was caculated with RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file includes FPKM for all 4 samples

source_name: Intestine

extract_protocol:
WT and Vil-CREPTKO mice were irradiated by X-ray (10Gy) and allowed regenerating for 3 days. Then, the intestines were harvested and total RNAs were extracted by TriZol (Invitrogen) according to manufacturers’ recommendations.
RNA libraries were prepared for sequencing using standard BGI protocols

value: Intestine

value: wildtype


title: Vil_KO2

value: Vil-CREPTKO


title: C16, no lung disease

value: Female

value: no


title: SYK-WT rep1

value: OVISE

value: ovarian carcinoma


title: Vil_KO1


title: crypt cell: CREPT ChIP

description: experimental sample


title: LAMP2A rep2

description:
LAMP2A_htseqcount_gene.txt
LAMP2A_vs_VT_full_DESeq2_results.txt
LAMP2A_DM_KG_vs_LAMP2A_full_DESeq2_results.txt

value: ACAGTG


title: C15, no lung disease


title: low5

city: Milwaukee

first: Rebecca

middle: D

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin Milwaukee

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed for adapters with Ctuadapt v. 1.1.18, and a reference transcriptome assembled with Trinity v. 2.8.3 using standard parameters
Estimated counts were determined by mapping reads to the reference transcriptome assembly with Kalisto 0.45.0 using parameters --rf-stranded -t 4
Genome_build: assembled transcriptome
Supplementary_files_format_and_content: estimated counts, tsv text

organism: Chironomus riparius

source_name: larvae

growth_protocol: Larvae were fed once daily with 0.5 mL of the supernatant of finely ground TetraMin Tropical Flake fish food at 20 mg/mL for 2 d and the full TetraMin suspension for another 3 d.

extract_protocol:
Flash-frozen larvae were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 48 h exposure in 1 or 10 mg/L LCO, or 150 μg/L LiCl respectively

value: wild type

value: whole larvae

value: LCO 1 mg/L

value: 5 days

tag: exposure


title: Lgr5KO_2

extract_protocol:
Intestinal Crypts were collected from Lgr5-WT and Lgr5-CREPTKO mice by pre-cold PBS with 2 mM EDTA and then suspended in TryPLE (Gibco, 12604) to be disaggregated into single cells. Lgr5+ cells were sorted by flow cytometry (BD Arial Ⅲ) based on the fluorescent signals of GFP proteins. Total RNAs were extracted by TriZol (Invitrogen) according to manufacturers’ recommendations.
RNA libraries were prepared for sequencing using standard BGI protocols


title: C20, no lung disease


title: B14, bronchopulmonary dysplasia

value: bronchopulmonary dysplasia


title: low4


title: Vil_WT2


title: LAMP2A rep1

value: TGACCA


title: B13, bronchopulmonary dysplasia

value: yes


title: VT rep3

description:
LAMP2A_htseqcount_gene.txt
LAMP2A_vs_VT_full_DESeq2_results.txt

value: VT

value: TTAGGC


title: SYK-KO rep1

value: SYK-KO

value: No treatment


title: Lgr5KO_1

value: Intestine


title: low3


title: B11, bronchopulmonary dysplasia

value: Female


title: Lgr5_2


title: VT rep2

value: CGATGT


title: low2


title: C10, no lung disease

value: Male

value: no


title: Lgr5_1


title: LAMP2A rep3

value: GCCAAT


title: VT rep1

value: ATCACG


title: B9, bronchopulmonary dysplasia


title: P1 RNA-seq, replicate 3

city: Oullins

first: Fabrice

address: 165 Chemin du Grand Revoyet

institute: INSERM

data_processing:
Quality of sequencing data was monitored by FastQC. If needed, residual adapters from sequencing were trimmed using cutadapt
Reads were then aligned on the hg19 human genome using tophat2, accepting only reads with a single alignment. Reads with MAPQ < 20 were removed by SAMtools.
Raw counts by samples were obtained with HTSeq-counts. Differential expression on filtered genes (HTSfilter 1.7.1), were performed using DESeq2 in R v.3.3.1. Genes were declared differentially expressed with a false discovery rate < 5%.
Genome_build: hg19
Supplementary_files_format_and_content: Raw and normalized counts matrices after DESeq2 analysis, in txt.

molecule: polyA RNA

source_name: In vitro differentiated human B cells

extract_protocol:
Cells were stained with surface markers and CaspGLOW kit (eBioscience) and sorted at day 4 as D4lo cells and at day 5 as P2/CD23+ (VPDlo/CD38lo/CD23+), P2/CD23- VPDlo/CD38lo/CD23) and P1 (VPDlo/CD38hi) cells using a FACsARIA cell sorter (BD Biosciences). RNA extractions were performed with the NucleoSpin® RNA XS (Macherey-Nagel).
QC, library preparation and sequencing were performed by Helixio Company (Clermont-Ferrand, France). After QC by BioAnalyzer, Nanodrop and Qubit, libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina).  Librairies were sequenced on an Illumina NextSeq 500 using 75-bp single-end reads (NextSeq 500 High Output v2, Illumina).

tag: days in culture

value: Day 5

tag: cell population


title: low1

value: wild type

value: whole larvae

value: LCO 1 mg/L

tag: age


title: Vil_KO_2

data_processing:
Illumina Casava 1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GCF_000001635.26_GRCm38.p6 genome sequence from NCBI using bowtie2.
Gene expression level for each sample was caculated with RSEM.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Processed data file includes readcount for all 4 samples

extract_protocol:
Intestinal crypts were disaggregated by pre-cold PBS with 2 mM EDTA. Total RNAs were extracted by TriZol (Invitrogen) according to manufacturers’ recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Vil-CREPTKO


title: Ion5

value: Ion

value: 5 days


title: Vil_KO_1


title: B8, bronchopulmonary dysplasia

value: bronchopulmonary dysplasia

value: yes


title: Ion4


title: LAMP2A+DM-αKG rep1

value: TAGCTT


title: P1 RNA-seq, replicate 2


title: Vil_WT_2

value: Intestine

value: wildtype


title: C7, no lung disease


title: P1 RNA-seq, replicate 1


title: Ion3


title: Vil_WT_1


title: B6, bronchopulmonary dysplasia


title: Ion2


title: P2/CD23- RNA-seq, replicate 3


title: Tp53-Pten-Nf1-08

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: Tumor from orthotopic injection of Tp53-/-;Pten-/-;Nf1-/- organoids

extract_protocol:
Tumors were from four of each genotyped organoid implants, all at 2 months post-injection. RNA was extracted by using the miRNeasy mini Kit (Qiagen), following the manufacturer’s instruction.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.

tag: tumor


title: P2/CD23- RNA-seq, replicate 2

last: Chatonnet


title: B5, bronchopulmonary dysplasia

value: Female


title: Tp53-Pten-Nf1-07


title: Ion1


title: B4, bronchopulmonary dysplasia

value: Male


title: high5

value: LCO 10 mg/L


title: Tp53-Pten-Nf1-06


title: P2/CD23- RNA-seq, replicate 1


title: C3, no lung disease

value: no


title: Tp53-Pten-Nf1-05


title: high4


title: P2/CD23+ RNA-seq, replicate 2


title: P2/CD23+ RNA-seq, replicate 1


title: ChIP-seq LMNB1-KO input

data_processing:
Sequencing reads were aligned to hg19 reference genome using Bowtie2 with default parameters. Duplicate reads were removed using Picard’s MarkDuplicate algorithm. LADs were called using enriched domain detector (EDD) peak-calling algorithm with parameters of 11 Kb bin size and a gap penalty of 5.
Genome_build: hg19
Supplementary_files_format_and_content: bed (ChIP-seq), bw (ATAC-seq)

extract_protocol: Cells were collected and fixed with 1% formaldehyde (Sigma) at room temperature for 3 min, followed by 125 mM glycine (Amresco) quenching. About 0.8 M fixed cells for each replicate were resuspended with 1 ml hypotonic buffer (20 mM Hepes pH 7.9, 10 mM KCl, 1 mM EDTA, 10% Glycerol, 0.2% NP-40) and incubated in ice for 20 min. After centrifugation at 3000 rpm for 5 min at 4°C, the supernatant was discarded and the nuclei pellets were resuspended with 30 μl nuclei lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0). After lysis at 4°C for 30 min, add 70 μl dilution buffer ((0.01% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8.0, 200 mM NaCl) to totally 100 μl with 0.3% SDS. The sample is transferred t 200 μl PCR tubes at this step. Chromatin was sheared into mainly 200-800 bp fragments with Q800R sonicator, at 80% power for 4 min, with 15 s ON and 30 s OFF. After sonication, the Triton X-100 in system was added to finally 1%. The chromatin was centrifuged at 20,000 g for 15 min at 4°C. The supernatant was saved to new PCR tubes and precleared with 8 μl protein A dynabeads (Invitrogen) at 4°C for 1 h, followed by adding lamin A antibody (ab26300, Abcam). About 1/50 of chromatin was taken out as the input. The chromatin-antibody mixture was incubated overnight at 4°C. Each 15 μl Protein A dynabeads blocked by 1% BSA/PBS were added into chromatin-antibody mixture and rotated together for 4 h at 4°C. Beads were washed with 150 μl low salt buffer for 3 min × 3 times, then for 1 min with 150 μl high salt buffer, and finally transferred into new tubes with 150 μl low salt buffer. Then ChIPmentation method was applied to add adaptors to ChIPed fragments and input fragments. After pheno-chloroform purification, the adaptor-ligated fragments were amplified by Q5 polymerase (NEB) to make libraries with Illumina Nextera index primers. Cycles were determined in advance. ChIPed groups were amplified for 10 cycles and input groups were amplified for 8 cycles. After size selection for 200-1000 bp fragments, the libraries were quantified with Qubit for concentrations and sequenced with paired-end 150 bp reads on Nova 6000 platform (Illumina).

value: mammary gland/breast

tag: cell type

value: epithelial, breast cancer cell line

value: 51 years adult

tag: gender

value: female

value: lamin A antibody (Abcam, catalog# ab26300, lot# GR3222248-1)


title: Tp53-Ccne1-Akt2-Kras-04

source_name: Tumor from orthotopic injection of Tp53-/-;Ccne1OE;Akt2OE;KrasOE organoids


title: D4lo RNA-seq, replicate 3

value: Day 4


title: Tp53-Ccne1-Akt2-Kras-03


title: high2

value: wild type

value: whole larvae


title: Tp53-Ccne1-Akt2-Kras-02


title: D4lo RNA-seq, replicate 2


title: control5

value: untreated

value: 5 days


title: D4lo RNA-seq, replicate 1


title: Tp53-Brca1-Myc-12

source_name: Tumor from orthotopic injection of Tp53-/-;Brca1-/-;MycOE organoids


title: control4


title: 6hpf

value: whole organism

tag: Stage

value: 6 hours post fertilization


title: P2/CD23+ RNA-seq, replicate 3

value: Day 5


title: B1, bronchopulmonary dysplasia

tag: lung disease

value: bronchopulmonary dysplasia

value: yes


title: Tp53-Brca1-Myc-11


title: ChIP-seq LMNB1-KO laminA rep1

source_name: MDA-MB-231 breast cancer cells

tag: chip antibody


title: ChIP-seq WT input


title: ChIP-seq LMNB1-KO laminA rep2


title: control2


title: control3


title: high3

value: LCO 10 mg/L


title: Tp53-Brca1-Myc-10


title: ChIP-seq WT laminA rep3


title: IP_AIPP3_rep2

city: shanghai

first: Yizhe

last: Zhang

address: No.300 Fenglin Road

institute: Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences

data_processing:
We cleaned the paired-end reads by Trimimomatic. After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
Clean reads were mapped to the Arabidopsis thaliana genome (TAIR10) by Bowtie2 (version 2.2.8) with default parameters.
Enriched peaks were identified by MACS (version 1.4) with default parameters.
We defined the region of a target gene as the range from 1kb upstream of transcription start site (TSS) to transcription end site (TES). The target genes of each peak were annotated by annotatePeak function in ChIPseeker package.
The visualization of the average read coverage over gene body and additional 1kb up- and down-stream of the TSS and TES was performed by deepTools (version 2.4.1).
Supplementary_files_format_and_content: .bed file include  peak information

source_name: plant tissues

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark)  photoperiod at 23 °C.

extract_protocol: Lysates were clarified from sonicated nuclei and AIPP3-DNA complexes were isolated with antibody.

tag: ecotype

value: 13-day-old seedlings

tag: antibody

value: Myc(millipore)


title: IP_AIPP3_rep1


title: ChIP-seq LMNB1-KO laminA rep3

tag: cell line

value: mammary gland/breast

value: epithelial, breast cancer cell line

tag: genotype


title: ChIP-seq WT laminA rep2

value: 51 years adult

value: female


title: control1

tag: treatment


title: Tp53-Brca1-Myc-09


title: IP_Col0


title: ChIP-seq WT laminA rep1

value: lamin A antibody (Abcam, catalog# ab26300, lot# GR3222248-1)


title: JH1-4_Wapl-degron_single igh_IAADox_rep2

status: Public on Nov 07 2020

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplification PCR-mediated HTGTS
Standard basecalling formats for Miseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: v-Abl transformed pro-B cell line

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
LAM-HTGTS V(D)J-Seq libraries were prepared using linear-amplification PCR-mediated HTGTS.

treatment_protocol:
RAG1/2 retrovirus infected, 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 mg/mL Dox treated for 3 days
3 uM STI-571 treated for 4 days

value: Wapl-degron, OsTIR1, Single Igh, Emu-Bcl2, RAG1 deficient


title: JH1-4_Wapl-degron_single igh_IAADox_rep3

description: aligned to mm9 genome


title: JH1-4_Wapl-degron_single igh_IAADox_rep1

description: aligned to mm9 genome


title: Tp53-Ccne1-Akt2-Kras-01


title: BM_INV_3C_3CBEbait_rep3

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Nextseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to inditated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome
Supplementary_files_format_and_content: bedgraph files

source_name: CB7BL/6 mouse  BM pro-B cell

growth_protocol:
Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days
RPMI1640+15% FBS

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.

treatment_protocol:
Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)
3 uM STI-571 treated for 4 days

value: Igh Inversion,RAG1 deficient


title: BM_INV_3C_3CBEbait_rep4

description: aligned to mm9 genome


title: BM_INV_3C_3CBEbait_rep2

description: aligned to mm9 genome


title: BM_WT_3C_RCbait_rep3

description: aligned to mm9 genome

data_processing:
Library strategy: Linear-amplificate PCR-mediated HTGTS
Standard basecalling formats for Nextseq reads
Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome
Supplementary_files_format_and_content: bedgraph files

source_name: CB7BL/6 mouse BM pro-B cell

value: RAG1 deficient


title: BM_INV_3C_3CBEbait_rep1

description: aligned to mm9 genome


title: high1

value: wild type

value: whole larvae

value: untreated

value: 5 days

tag: exposure


title: BM_WT_3C_3CBEbait_rep3

description: aligned to mm9 genome


title: BM_WT_3C_3CBEbait_rep2

description: aligned to mm9 genome


title: BM_WT_3C_3CBEbait_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_Input_rep4

description: aligned to mm9 genome

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
bigwig files were produced using RseqQ package
Genome_build: mm9 genome
Supplementary_files_format_and_content: bigwig files contain peak information for samples

source_name: v-Abl transformed B6 pro-B cell line

extract_protocol:
Crosslinked cells were treated with cell lysis buffer (5mM PIPES pH 8, 85mM KCl, 0.5% NP-40) and nuclei lysis buffer (50mM TrisCl pH 8.1, 10mM EDTA, 1% SDS) and subjected to sonication. IP and Input DNA were de-crosslinked at 65o overnight and purified via Qiagen PCR purification columns.
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645)

treatment_protocol:
3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 mg/mL Dox treated for 3 days
3 uM STI-571 treated for 4 days

value: Wapl degron, Emu-Bcl2, RAG1 deficient


title: VAblRad21ChIPDOXIAA_rep4

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_rep4

description: aligned to mm9 genome

treatment_protocol:
3 uM STI 4 days
3 uM STI-571 treated for 4 days


title: BMINVRad21ChIP_Input_rep3

description: aligned to mm9 genome

source_name: B6 mouse BM pro-B cell


title: VAblRad21ChIPUntreated_Input_rep4

description: aligned to mm9 genome


title: BMINVCTCFChIP_rep3

description: aligned to mm9 genome


title: BMINVRad21ChIP_rep3

description: aligned to mm9 genome


title: BMINVCTCFChIP_Input_rep23

description: aligned to mm9 genome


title: BMINVCTCFChIP_Input_rep1

description: aligned to mm9 genome


title: BMINVCTCFChIP_rep2

description: aligned to mm9 genome


title: BMWTCTCFChIP_Input_rep23

description: aligned to mm9 genome


title: BMINVCTCFChIP_rep1

description: aligned to mm9 genome


title: BMWTCTCFChIP_rep3

description: aligned to mm9 genome


title: BMWTCTCFChIP_rep1

description: aligned to mm9 genome


title: VAbl3CRCbaitDOXIAA-RC_rep2

description: aligned to mm9 genome

data_processing:
Standard basecalling formats for Miseq reads
Miseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to inditated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
Genome_build: mm9 genome
Supplementary_files_format_and_content: bedgraph files

extract_protocol:
DNA was lysed overnight at 56degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, precipitated by isopropanol and dissolved in buffer containing 10mM Tris-HCl pH7.5, 0.1mM EDTA
3C-HTGTS libraries were prepared using linear-amplification PCR-mediated HTGTS.
Linear-amplificate PCR-mediated HTGTS


title: VAbl3CRCbaitUntreated-RC_rep3

description: aligned to mm9 genome


title: VAbl3CRCbaitDOXIAA-RC_rep3

description: aligned to mm9 genome


title: BMWTCTCFChIP_Input_rep1

description: aligned to mm9 genome

source_name: B6 mouse BM pro-B  cell


title: VAbl3CRCbaitUntreated-RC_rep1

description: aligned to mm9 genome


title: BM_INV_3C_RCbait_rep3

description: aligned to mm9 genome


title: BM_INV_3C_RCbait_rep1

description: aligned to mm9 genome


title: BM_WT_3C_RCbait_rep2

description: aligned to mm9 genome


title: VAbl3CRCbaitUntreated-RC_rep2

description: aligned to mm9 genome


title: BM_WT_3C_RCbait_rep1

description: aligned to mm9 genome


title: VAblCTCF13WAPL13ChIPDOXIAA_Input_rep1

description: aligned to mm9 genome


title: VAblCTCF2WAPL2Rad213ChIPDOXIAA_Input_rep2

description: aligned to mm9 genome


title: VAblCTCFChIPDOXIAA_rep3

description: aligned to mm9 genome


title: VAblCTCF2WAPL2Rad213ChIPUntreated_Input_rep2

description: aligned to mm9 genome


title: VAblCTCFChIPDOXIAA_rep2

description: aligned to mm9 genome


title: BMWTCTCFChIP_rep2

description: aligned to mm9 genome


title: VAblCTCFChIPDOXIAA_rep1

description: aligned to mm9 genome


title: VAblWAPLChIPDOXIAA_rep3

description: aligned to mm9 genome


title: VAblCTCFChIPUntreated_rep1

description: aligned to mm9 genome


title: VAblCTCFChIPUntreated_rep3

description: aligned to mm9 genome


title: VAblCTCFChIPUntreated_rep2

description: aligned to mm9 genome


title: VAbl3CRCbaitDOXIAA-RC_rep1

description: aligned to mm9 genome


title: VAblWAPLChIPUntreated_rep2

description: aligned to mm9 genome


title: VAblWAPLChIPDOXIAA_rep2

description: aligned to mm9 genome


title: VAblWAPLChIPDOXIAA_rep1

description: aligned to mm9 genome


title: VAblWAPLChIPUntreated_rep3

description: aligned to mm9 genome


title: VAblWAPLChIPUntreated_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_Input_rep2

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_rep3

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_rep2

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_Input_rep1

description: aligned to mm9 genome


title: BM_INV_3C_RCbait_rep2

description: aligned to mm9 genome


title: VAblRad21ChIPDOXIAA_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_Input_rep2

description: aligned to mm9 genome


title: VAblCTCF13WAPL13ChIPUntreated_Input_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_rep3

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_Input_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_rep1

description: aligned to mm9 genome


title: VAblRad21ChIPUntreated_rep2

description: aligned to mm9 genome