title: CEMBA190305_11F_1_CEMBA190305_11F_2_C12_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C12_ad004

status: Public on Oct 10 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: DG

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C11_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C10_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B9_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad004


title: 12878-sample1

city: NanJing

first: Tu

last: Jing

state: JiangSu

address: Si Pailou

department: Biological Science and Medical Engineering

country: China

institute: South East University

data_processing:
Library strategy: DNA-seq
DNA-seq reads were aligned to hg19 human gennome by  BWA-MEM version 0.7.12-r12039
Mined G-quadruplexes (MG4s) were indentified by G4-miner.
Genome_build: hg19
Supplementary_files_format_and_content: OQs files

organism: Homo sapiens

growth_protocol: cultivated and passaged NA12878, and the number of passages was not more than three times

extract_protocol: sequencing the extracted DNA directly to avoid the impact of amplification

tag: cell type

value: primary human B lymphocytes


title: 12878-sample2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_C1_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad008


title: M2-chr

city: Paris

first: Violaine

last: Saint-Andre

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: chromatin-associated RNA

library_source: transcriptomic

data_processing:
Reads were mapped with tophat version 2.0.6, with a tolerance of 3 mismatches
Only unique mapped reads were kept for further analysis
read counts were calculated using htseq-count
differential expression analysis was performed in R using DEseq2
protein coding and non-coding transcripts were processed separately
Genome_build: hg19
Supplementary_files_format_and_content: filtered normalized read counts

molecule: total RNA

source_name: HEK-based cell line

growth_protocol: For each cell-line, cells were grown up to 90% confluence in 600 cm² square dishes in MEM-alpha medium supplemented with non-essential amino-acids and sodium pyruvate, at 37°C, 5% CO2.

extract_protocol:
Unless mentioned otherwise, everything should be performed on ice or at 4°C and all solutions should be ice-cold. As adapted from Gagnon et al 2014, cells were washed with 20ml PBS and first scraped in 30 ml PBS then in 15ml for a second time. Cells were pelleted for 3 min at 1500 rpm, washed in PBS and aliquoted at approx. 107 cells per microtube. Cells were pelleted again for 3 min at 800g and resuspended in 380µl HLB hypotonic lysis buffer (10mM TrisHCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.3% NP40, 10% glycerol) supplemented with 25µg/ml alpha-amanitin as well as RNase-inhibitor and proteinase inhibitor. Cells were lysed for 10 minutes and centrifuged for 3 min at 1000g. The cytoplasmic fraction was recovered and stored at -20°C after adding 1ml of RPS RNA precipitation solution (10 mM Na2Ac, 95% EtOH). The nuclei pellet was then washed 3 times by adding 1 ml HLB and centrifugating for 2 min at 300g. Then nuclei-pellet was lysed by resuspending in 380 µl of MWS Modified Wuarin Schibler buffer (10 mM Tris-HCl pH 7, 4 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) supplemented with 25µg/ml alpha-amanitin as well as RNase-inhibitor and proteinase inhibitor, vortexing for 30 sec on medium-speed, incubating on ice for 5 min , vortexing again for 30 sec and incubating once more for 10 min. Chromatin was pelleted for 3 min at 1000 g and nucleoplasmic fraction was recovered and stored in RPS at -20°C. Chromatin pellet was washed 3 times by adding 1 ml MWS, vortexing briefly on medium-speed and centrifugating for 2 min at 500g. Finally, 700µl of Qiazol was added to the pellet and stored at -20°C. The next day, cytoplasmic and nucleoplasmic fraction were centrifuged for 15 min at 14 000g, washed in 1 ml 70% EtOH and centrifuged again for 5 min at 14 000g. After air-drying the pellets, they were resuspended in Trizol. After unfreezing on ice, 10µl of 0.5M EDTA were added to the chromatin fraction. All fractions were incubated at 65°C for approx. 5 min and cooled at room temperature before proceeding to DNase treatment and RNA extraction using the QIAGEN miRNeasy Mini Kit according to the manufacturer’s instructions.
Total RNA-seq libraries were prepared with TruSeq Stranded Total RNA Sample Prep Kit (RS-122-2201, Illumina)

tag: cell line

value: Mes

tag: fraction

value: Chromatin


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad010


title: M1-chr

description: chromatin-associated RNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B7_ad002


title: E2-chr

description: chromatin-associated RNA

value: Epi


title: E1-chr

description: chromatin-associated RNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad012


title: M2-cyto

description: cytoplasmic RNA

value: Cytoplasm


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B6_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B8_ad004


title: E2-cyto

description: cytoplasmic RNA


title: E1-cyto

description: cytoplasmic RNA


title: M1-cyto

description: cytoplasmic RNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad008


title: MYCT58A+shTRIB3-1

city: bei jing

first: wang

last: feng

address: nan wei road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College,

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Raji cells

extract_protocol:
cells were collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B lymphocyte

tag: tissue

value: peripheral blood

tag: morphology

value: lymphoblast


title: MYCT58A+shCtrl-3


title: MYCT58A+shTRIB3-3


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad006


title: MYCT58A+shCtrl-2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad004


title: MYCWT+shTRIB3-1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B5_ad001


title: MYCWT+shTRIB3-3


title: MYCWT+shTRIB3-2


title: MYCT58A+shCtrl-1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B4_ad006


title: MYCWT+shCtrl-3


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B4_ad010


title: scramble-shRNA MiaPaCa-2 cells (F1)

city: Shanghai

first: Qingcai

last: Meng

address: No. 270 Dong'An Road

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8)software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(Solexa CHASTITY),then mapped to HG19 whole genome using Hisat2(v0.12.2)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown
Genome_build: HG19
Supplementary_files_format_and_content: bam files include RPKM values for each Sample

source_name: pancreatic carcinoma cells

growth_protocol: The scramble-shRNA and GPx1-shRNA pancreatic cancer cells were cultured in DMEM supplemented with 10% FBS and 2.5% horse serum

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) , KAPA Stranded RNA-Seq Library Prep Kit（Illumina） was used with 1-2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epithelial cell

value: pancreas

tag: transfection

value: scramble-shRNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B4_ad004


title: MYCWT+shCtrl-2


title: MYCWT+shCtrl-1


title: MYCT58A+shTRIB3-2


title: scramble-shRNA MiaPaCa-2 cells (E1)


title: GPx1-shRNA MiaPaCa-2 cells (E2)


title: GPx1-shRNA MiaPaCa-2 cells (D2)


title: scramble-shRNA MiaPaCa-2 cells (D1)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B4_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B4_ad012


title: P4_Leaf_eCO2_1930_rep3

type: RNA

city: Sendai

first: Yonghyun

last: Kim

state: Miyagi

address: Aramaki, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

description: Gene expression after 13.5hr at aCO2

hyb_protocol: cRNA flagmentation and hybridization to the rice oligo DNA microarray 4X44K RAP-DB (Agilent Technologies) and washing were conducted using gene expression hybridization kits (Agilent Technologies) according to manufacturer’s instruction.

scan_protocol: The hybridized slide was scanned immediately using the Agilent Microarray Scanner G2565BA (Agilent Technologies).

data_processing: The scanned images were analyzed with the Agilent Feature Extraction software 11.5.1.1 (Agilent Technologies) to obtain processed signal intensities.

organism: Oryza sativa

source_name: Developing leaf, 13.5hr,eCO2, replication 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 400 ng RNA using Quick Amp Labeling Kits (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Hilden, Germany). Cy3 incorporation and cRNA yield were checked with the NanoDrop ND-1000

growth_protocol: Rice plants were grown at high nitrogen (0.5g N/plant) and ambient CO2 condition (320-360 ppm) in two identical growth chambers up to eCO2 treatment (28/23°C, 14/10h, day/night, 60% humidity, light intensity: about 900 PPFD)

extract_protocol: Total RNA was isolated from the leaf samples using Plant RNeasy mini kit (QIAGEN, Hilden, Germany) according to manufacturer's instructions. RNA was quantified using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA). The total RNA integrity was analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: eCO2 (1000 ppm) begun at 6:00 am (beginning daytime) when plant age of leaf number was 7.1-7.3. 9th leaf was sampled for analysis 7 h and 13.5 h after elevated CO2 treatment.

value: Developing leaf

tag: cultivar

value: cv. Nipponbare


title: HL3

city: Qingdao

first: Yuanxiang

last: Li

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of sciences

data_processing:
The library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
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.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Gene function was annotated based on the following databases: Nr (NCBI non-redundant protein sequences); Nt (NCBI non-redundant nucleotide sequences); Pfam (Protein family); KOG/COG (Clusters of Orthologous Groups of proteins); Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database); GO (Gene Ontology).
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: tab-delimited files include RPKM values for each Sample

organism: Dunaliella salina

source_name: algal cells_HL

growth_protocol: Algal cells were cultivated at 22 ± 1°C with 150 ± 5 μmol photons·m−2s−1 provided by cold white fluorescent lamps with 16:8 h light-dark cycles.

extract_protocol:
Algal cells were harvested by centrifugation for 4 min at 2,000 ×g at room temperature, fast frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells in mid-exponential growth phase were harvested by centrifugation for 4 min at 2,000 ×g at room temperature, and inoculated into fresh medium for light treatment. Irradiance was shifted in a single step from 150 μmol photons·m−2s−1  to 600 and 1500 μmol photons·m−2s−1

tag: growth phase

value: 7th, mid-exponential phase

tag: irradiance level

value: 1500 μmol photons•m−2s−1


title: P4_Leaf_eCO2_1930_rep4

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,eCO2, replication 4


title: HL2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad012

value: DG


title: P4_Leaf_eCO2_1930_rep2

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,eCO2, replication 2


title: HL1


title: GPx1-shRNA MiaPaCa-2 cells (F2)


title: ML2

source_name: algal cells_ML

value: 600 μmol photons•m−2s−1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad007

value: male


title: LL1

source_name: algal cells_LL

value: 150 μmol photons•m−2s−1


title: LL2


title: P4_Leaf_aCO2_1930_rep4

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,aCO2, replication 4


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad001


title: ATAC_PrimaryCells_Bcells_NIPBL_rep1_FK5062h_A23slow4h

first: Cornelis

last: Murre

address: 9500 Gilman Drive

department: Molecular Biology

institute: UCSD

description: Transposase-Accessible Chromatin DNA

data_processing:
HiC analysis. HiC reads were processed using HiC-Pro analysis pipeline (Servant et al., 2015). In brief, reads were aligned to mm9 with Bowtie2 with 'very sensitive' mode and reads with mapping quality (MAPQ) > 1 were kept for downstream analysis. Hi-C statistics was summarized (Wingett et al. 2015) (Supplemental Table S1). After stringent data filtering, including removal of PCR duplicates, self-ligation, restriction ends, continuous genomic fragments and re-ligation events, valid contacts file was converted to HIC files using the hicpro2juicebox.sh script. The balanced and normalized contact matrix was visualized by Juicebox (Durand et al., 2016b). PCA analysis by HOMER, applied to the normalized interaction matrix, and PC1 values for each 25-kb bin with positive and negative values, corresponding to A and B compartments, respectively. Genomic regions that displayed a continuum of either positive or negative PC1 values were defined as PC1 domains (PDs). PDs with minimum size of 100kb were identified by findHiCCompartments.pl using default settings. We consider the absolute difference in PC1 value (> 0.4) and the PC1 value change from positive to negative or vice versa to identify PDs that switch compartments.
ChIP-Seq and ATAC-Seq analysis. Reads were aligned to mm9 with Bowtie2 and reads non-uniquely mapped were discarded. Data were analyzed with HOMER. Tag directory was made by makeTagDirectory under the default setting, using option -tbp 1 -fragLength 150. Genome browser visualizing files were made by makeUCSCfile under the default setting, using option -fragLegth 150, -strand both. Bigwig files was created from bedgraph using UCSC utility bedGraphToBigWig. Meta-gene profile was made by makeMetaGeneProfile.pl under the default setting, using option -fraglength 150, -pc 1, -gbin 100 (small genes less than 3kb were excluded).  Average enrichment plot was made by annotatePeaks.pl under the default setting, using option -fraglength 150, -pc 1, -hist 100. Heatmaps were created by Deeptools package in 'reference-Point' mode, using option -bin size 100 -missingDataAsZero -skipZeros. ChIP-Seq peaks were identified by findPeaks in 'factor' mode under the default setting against the input directory, using option -fraglength 150, -size 200. Peaks from separate experiments were considered co-bound if their peak centers were located within 100_bp of each other. Peaks were merged by mergePeaks.pl. Differential peaks were identified by getDifferentialPeaks under the default setting, using option -size 200. Genomic annotations of peaks were computed with annotatePeaks.pl under the default setting. To identify motifs enriched in peak regions over the background, HOMER's motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used with option -mis 0 -len 10,12 -size 200 -mask -p 12 -cache 50000. The background sequences used for motif analysis either from random genome sequences of the same size and normalized GC content or from peaks in comparing condition were indicated in the figure legends. Scatterplots were used for direct comparison of two conditions, either the gene RPKM or normalized tag counts were used for ChIP-/ATAC-Seq respectively.
GRO-Seq analysis. Reads were trimmed 20-bp off the 3' end of the sequence to improve mappability. Reads were aligned to mm9 with Bowtie2 (Langmead and Salzberg, 2012) and reads non-uniquely mapped were discarded. Data were analyzed with HOMER (Heinz et al., 2010). Tag directory was made by makeTagDirectory under the default setting, using option -tbp 3 -fragLength 150, in order to effectively remove the super spikes but still allow genes with high RPKM to "express themselves" in the following analysis. Sequencing-depth normalized bedGraph files for visualization in the UCSC Genome Browser were made by makeUCSCfile under the default setting, using option -norm 1e7, -fragLegth 150, -strand + or -strand -, respectively. Strand-specific bigwig files was created from bedgraph using utility bedGraphToBigWig. The RefFlat gene expression values were quantified by analyzeRepeats under the default setting, using option -condenseGenes -count genes -rpkm -strand separate. Genes with RPKM value less than 0.5 in all conditions were defined as not expressed (8733 genes were expressed). Functional enrichment calculations were performed using PANTHER web portal (http://www.pantherdb.org) applying 'Overrepresentation Test' using the Fisher's exact test and FDR correction method. Meta-gene profile was made by makeMetaGeneProfile.pl under the default setting, using option -fraglength 150, -pc 3, -gbin 100. Average distribution histogram was made by annotatePeaks.pl under the default setting, using option -fraglength 150, -pc 3, -hist 100. Heatmaps were created by Deeptools package in scale-region mode, -bin size 100.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED files (ChIP-Seq peak file, Hi-C PC1 domain positions), RPKM CSV files (GRO-Seq expression data), Bedgraph and Bigwig (ChIP-Seq, GRO-Seq and ATAC-Seq tracks, principle component values along the genome for combined Hi-C data), and tab-delimited txt files, including HIC files (filtered read pairs from Hi-C data processed using HiC-Pro)

source_name: primary B cells

growth_protocol: GM-CSF-dependent ECOMG cells were grown in RPMI 1640 with 10% FBS and penicillin-streptomycin-glutamine, by the addition of 1:100 conditioned media (about 10 ng/mL GM-CSF) isolated from a B16 melanoma cell line stably transfected with a murine GM-CSF construct. b-estradiol where applicable, was added to the medium at a final concentration of 1 mM from a 10,000 × stock in 100% ethanol. Differentiation of ECOMG cells into granulocytes was induced by withdrawal β-estradiol for 5 days. Adult C57BL/6 mice were purchased from Jackson Laboratories and maintained in a specific pathogen-free facility at the University of California, San Diego. Mice were used between 8-12 weeks of age. Both male and female mice were used for study. Primary neutrophils were isolated from bone marrow as described (Zhu et. al. 2017). Primary B and T cells from spleens were isolated using negative-selection kits, Miltenyi Biotec 130-090-862 and 130-095-130 on MACS LS columns, respectively.

extract_protocol:
The ATAC-Seq experiments were performed similarly as described (M Ryan Corces, et al. 2017. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues)
ATAC-Seq libraries were prepared with custom ATAC PCR primer set and were selected by size by 8% PAGE and sequenced for 75 cycles on Illumina HiSeq 4000.

treatment_protocol: In vitro differentiated neutrophils from ECOMG cells were used as a model system to study nuclear architecture in response to calcium influx in neutrophils. ECOMG cells were cultured and differentiated as described (Zhu et. al. 2017). For inhibitors, neutrophils were treated with 10uM TRP or 100uM DRB for 30min, or 2uM FK506 for 2h before activation. Primary B cells were treated with 2uM FK506 for 2h before activation. Inhibitors were kept in culture during activation time course. Acute degradation was induced by treating the cells with a final concentration of 500 nM dTAG-13 molecule Tocris). dTAG-13 was kept in culture during activation time course. All the time series experiments were performed by inducing protein degradation at the beginning of the time course and harvest the samples at the different time points. RPMI-1640 contains 0.42mM calcium. Additional CaCl2 was supplied to the medium during activation to a final concentration of 1mM. Neutrophils were activated either in fast activation condition (20uM A23187 for 15min), or in slow activation condition (5uM A23187 for 4h). These two activation conditions were used throughout the manuscript unless otherwise mentioned. The time series activation experiments were performed by activation neutrophils at the beginning of the time course and harvest the samples at the different time points.

tag: genotype

value: wild type

value: primary B cells

tag: treatment

value: 2uM FK506 2h, slow_treated with 5uM A23187 for 4h

tag: chip antibody


title: P4_Leaf_aCO2_1930_rep3

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,aCO2, replication 3


title: GRO_Neu_rep1_UT_tbp3

description: nascent RNA

data_processing:
Library strategy: GRO-Seq
HiC analysis. HiC reads were processed using HiC-Pro analysis pipeline (Servant et al., 2015). In brief, reads were aligned to mm9 with Bowtie2 with 'very sensitive' mode and reads with mapping quality (MAPQ) > 1 were kept for downstream analysis. Hi-C statistics was summarized (Wingett et al. 2015) (Supplemental Table S1). After stringent data filtering, including removal of PCR duplicates, self-ligation, restriction ends, continuous genomic fragments and re-ligation events, valid contacts file was converted to HIC files using the hicpro2juicebox.sh script. The balanced and normalized contact matrix was visualized by Juicebox (Durand et al., 2016b). PCA analysis by HOMER, applied to the normalized interaction matrix, and PC1 values for each 25-kb bin with positive and negative values, corresponding to A and B compartments, respectively. Genomic regions that displayed a continuum of either positive or negative PC1 values were defined as PC1 domains (PDs). PDs with minimum size of 100kb were identified by findHiCCompartments.pl using default settings. We consider the absolute difference in PC1 value (> 0.4) and the PC1 value change from positive to negative or vice versa to identify PDs that switch compartments.
ChIP-Seq and ATAC-Seq analysis. Reads were aligned to mm9 with Bowtie2 and reads non-uniquely mapped were discarded. Data were analyzed with HOMER. Tag directory was made by makeTagDirectory under the default setting, using option -tbp 1 -fragLength 150. Genome browser visualizing files were made by makeUCSCfile under the default setting, using option -fragLegth 150, -strand both. Bigwig files was created from bedgraph using UCSC utility bedGraphToBigWig. Meta-gene profile was made by makeMetaGeneProfile.pl under the default setting, using option -fraglength 150, -pc 1, -gbin 100 (small genes less than 3kb were excluded).  Average enrichment plot was made by annotatePeaks.pl under the default setting, using option -fraglength 150, -pc 1, -hist 100. Heatmaps were created by Deeptools package in 'reference-Point' mode, using option -bin size 100 -missingDataAsZero -skipZeros. ChIP-Seq peaks were identified by findPeaks in 'factor' mode under the default setting against the input directory, using option -fraglength 150, -size 200. Peaks from separate experiments were considered co-bound if their peak centers were located within 100_bp of each other. Peaks were merged by mergePeaks.pl. Differential peaks were identified by getDifferentialPeaks under the default setting, using option -size 200. Genomic annotations of peaks were computed with annotatePeaks.pl under the default setting. To identify motifs enriched in peak regions over the background, HOMER's motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used with option -mis 0 -len 10,12 -size 200 -mask -p 12 -cache 50000. The background sequences used for motif analysis either from random genome sequences of the same size and normalized GC content or from peaks in comparing condition were indicated in the figure legends. Scatterplots were used for direct comparison of two conditions, either the gene RPKM or normalized tag counts were used for ChIP-/ATAC-Seq respectively.
GRO-Seq analysis. Reads were trimmed 20-bp off the 3' end of the sequence to improve mappability. Reads were aligned to mm9 with Bowtie2 (Langmead and Salzberg, 2012) and reads non-uniquely mapped were discarded. Data were analyzed with HOMER (Heinz et al., 2010). Tag directory was made by makeTagDirectory under the default setting, using option -tbp 3 -fragLength 150, in order to effectively remove the super spikes but still allow genes with high RPKM to "express themselves" in the following analysis. Sequencing-depth normalized bedGraph files for visualization in the UCSC Genome Browser were made by makeUCSCfile under the default setting, using option -norm 1e7, -fragLegth 150, -strand + or -strand -, respectively. Strand-specific bigwig files was created from bedgraph using utility bedGraphToBigWig. The RefFlat gene expression values were quantified by analyzeRepeats under the default setting, using option -condenseGenes -count genes -rpkm -strand separate. Genes with RPKM value less than 0.5 in all conditions were defined as not expressed (8733 genes were expressed). Functional enrichment calculations were performed using PANTHER web portal (http://www.pantherdb.org) applying 'Overrepresentation Test' using the Fisher's exact test and FDR correction method. Meta-gene profile was made by makeMetaGeneProfile.pl under the default setting, using option -fraglength 150, -pc 3, -gbin 100. Average distribution histogram was made by annotatePeaks.pl under the default setting, using option -fraglength 150, -pc 3, -hist 100. Heatmaps were created by Deeptools package in scale-region mode, -bin size 100.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED files (ChIP-Seq peak file, Hi-C PC1 domain positions), RPKM CSV files (GRO-Seq expression data), Bedgraph and Bigwig (ChIP-Seq, GRO-Seq and ATAC-Seq tracks, principle component values along the genome for combined Hi-C data), and tab-delimited txt files, including HIC files (filtered read pairs from Hi-C data processed using HiC-Pro)

source_name: in-vitro differentiated neutrophils

extract_protocol:
The GRO-Seq experiments were performed as described (Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322: 1845-8).
GRO-Seq libraries were prepared with custom GRO-Seq PCR primers (in ordr to adapt to HiSeq4000) and were selected by size by 8% PAGE and sequenced for 75 cycles on Illumina HiSeq 4000.

value: human E2A_ER_Pbx1b, wild type

value: ECOMG derived neutrophils

value: untreated


title: ML1


title: P4_Leaf_aCO2_1930_rep2

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,aCO2, replication 2


title: P4_Leaf_aCO2_1930_rep1

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,aCO2, replication 1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad008


title: P4_Leaf_eCO2_1300_rep2

description: Gene expression after 7hr at eCO2

source_name: Developing leaf, 7hr,eCO2, replication 2


title: P4_Leaf_eCO2_1930_rep1

description: Gene expression after 13.5hr at aCO2

source_name: Developing leaf, 13.5hr,eCO2, replication 1


title: P4_Leaf_eCO2_1300_rep4

description: Gene expression after 7hr at eCO2

source_name: Developing leaf, 7hr,eCO2, replication 4


title: P4_Leaf_eCO2_1300_rep3

description: Gene expression after 7hr at eCO2

source_name: Developing leaf, 7hr,eCO2, replication 3


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: ATAC_Neu_rep1_UT

description: Transposase-Accessible Chromatin DNA


title: Input_Neu_rep3

description: Input DNA

extract_protocol:
The ChIP-Seq experiments were performed similarly as described (Lin YC, et al. 2012. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 13: 1196-1204).
ChIP-Seq libraries were prepared with the NEBNext primer set and were selected by size by 8% PAGE and sequenced for 75 or 100 cycles on Illumina HiSeq 4000.

value: slow_treated with 5uM A23187 for 4h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad010


title: ML3


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B3_ad002


title: P4_Leaf_aCO2_1300_rep4

description: Gene expression after 7hr at aCO2

source_name: Developing leaf, 7hr,aCO2, replication 4


title: Input_Neu_rep2

description: Input DNA

value: fast_treated with 20uM A23187 for 15min


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad012


title: Input_Neu_rep1

description: Input DNA


title: ATAC_PrimaryCells_Bcells_NIPBL_rep1_UT

description: Transposase-Accessible Chromatin DNA


title: ATAC_PrimaryCells_Bcells_NIPBL_rep1_DMSO2h_A23slow4h

description: Transposase-Accessible Chromatin DNA

value: DMSO 2h, slow_treated with 5uM A23187 for 4h


title: ChIP_PrimaryCells_Bcells_NIPBL_rep2_DMSO2h_A23slow4h

description: Immunoprecipitated DNA

value: NIPBL A301-779A  Bethyl Laboratries


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad007


title: P4_Leaf_eCO2_1300_rep1

description: Gene expression after 7hr at eCO2

source_name: Developing leaf, 7hr,eCO2, replication 1

value: Developing leaf

value: cv. Nipponbare


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad002


title: P4_Leaf_aCO2_1300_rep2

description: Gene expression after 7hr at aCO2

source_name: Developing leaf, 7hr,aCO2, replication 2


title: ChIP_PrimaryCells_Bcells_NIPBL_rep1_FK5062h_A23slow4h

description: Immunoprecipitated DNA


title: ChIP_PrimaryCells_Bcells_NIPBL_rep2_UT

description: Immunoprecipitated DNA


title: ChIP_PrimaryCells_Bcells_NIPBL_rep1_DMSO2h_A23slow4h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad008


title: P4_Leaf_aCO2_1300_rep3

description: Gene expression after 7hr at aCO2

source_name: Developing leaf, 7hr,aCO2, replication 3


title: ChIP_PrimaryCells_Bcells_NIPBL_rep1_UT

description: Immunoprecipitated DNA


title: ChIP_PrimaryCells_Tcells_NIPBL_rep1_A23slow4h

description: Immunoprecipitated DNA

source_name: primary T cells

value: primary T cells


title: P4_Leaf_aCO2_1300_rep1

description: Gene expression after 7hr at aCO2

source_name: Developing leaf, 7hr,aCO2, replication 1


title: ChIP_PrimaryCells_Tcells_NIPBL_rep1_UT

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad001

value: DG


title: ChIP_PrimaryCells_BMDN_NIPBL_rep1_A23slow4h

description: Immunoprecipitated DNA

source_name: primary bone-marrow derived neutrophils cells


title: P6_Leaf_eCO2_1930_rep1

description: Gene expression after 13.5hr at eCO2

source_name: Mature leaf, 13.5hr,eCO2, replication 1

treatment_protocol: eCO2 (1000 ppm) begun at 6:00 am (beginning daytime) when plant age of leaf number was 7.1-7.3. 7th leaf blade was sampled for analysis 7 h and 13.5 h after elevated CO2 treatment.

value: Mature leaf

value: Nipponbare


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B2_ad004

value: male


title: P6_Leaf_eCO2_1930_rep2

description: Gene expression after 13.5hr at eCO2

source_name: Mature leaf, 13.5hr,eCO2, replication 2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad010


title: ChIP_Degron_WAPL_Neu_RPB1_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA

source_name: in-vitro differentiated neutrophils

value: human E2A_ER_Pbx1b, WAPL degron

value: 0.5uM dTAG-13 6h, slow_treated with 5uM A23187 for 3h

value: RPB1 sc-899 Santa Cruz Biotechnology or 664912 Biolegend


title: ChIP_Degron_RAD21_Neu_RPB1_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, RAD21 degron


title: P6_Leaf_aCO2_1930_rep3

description: Gene expression after 13.5hr at aCO2

source_name: Mature leaf, 13.5hr,aCO2, replication 3


title: ChIP_PrimaryCells_BMDN_NIPBL_rep1_UT

description: Immunoprecipitated DNA

value: wild type

value: primary bone-marrow derived neutrophils cells


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad012


title: ChIP_Degron_RAD21_Neu_RPB1_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils

value: DMSO 6h, slow_treated with 5uM A23187 for 3h


title: ChIP_Degron_CTCF_Neu_RPB1_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, CTCF degron


title: P6_Leaf_eCO2_1930_rep3

description: Gene expression after 13.5hr at eCO2

source_name: Mature leaf, 13.5hr,eCO2, replication 3


title: ChIP_PrimaryCells_Bcells_NIPBL_rep2_FK5062h_A23slow4h

description: Immunoprecipitated DNA

source_name: primary B cells

value: primary B cells

value: 2uM FK506 2h, slow_treated with 5uM A23187 for 4h

value: NIPBL A301-779A  Bethyl Laboratries


title: ChIP_Degron_CTCF_Neu_RPB1_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA


title: P6_Leaf_aCO2_1930_rep1

description: Gene expression after 13.5hr at aCO2

source_name: Mature leaf, 13.5hr,aCO2, replication 1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad002


title: ChIP_Degron_SPT5_Neu_RPB1_rep1_dTAG4h_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, SPT5 degron

value: 0.5uM dTAG-13 4h, slow_treated with 5uM A23187 for 3h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad008

value: DG


title: GRO_Neu_rep1_A23slow4h_tbp3

description: nascent RNA

value: human E2A_ER_Pbx1b, wild type

value: slow_treated with 5uM A23187 for 4h


title: P6_Leaf_aCO2_1930_rep2

description: Gene expression after 13.5hr at aCO2

source_name: Mature leaf, 13.5hr,aCO2, replication 2

value: Mature leaf

value: Nipponbare


title: ChIP_Degron_SPT5_Neu_RPB1_rep1_DMSO4h_A23slow3h

description: Immunoprecipitated DNA

value: DMSO 4h, slow_treated with 5uM A23187 for 3h

value: RPB1 sc-899 Santa Cruz Biotechnology or 664912 Biolegend


title: ChIP_Degron_SPT5_Neu_NIPBL_rep1_dTAG4h_A23fast15min

description: Immunoprecipitated DNA

value: 0.5uM dTAG-13 4h, fast_treated with 20uM A23187 for 15min


title: P6_Leaf_eCO2_1300_rep3

description: Gene expression after 7hr at eCO2

source_name: Mature leaf, 7hr,eCO2, replication 3


title: P6_Leaf_eCO2_1300_rep1

description: Gene expression after 7hr at eCO2

source_name: Mature leaf, 7hr,eCO2, replication 1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad006

source_name: C57BL/6J Male P56 Mouse Brain

value: male


title: ChIP_Degron_WAPL_Neu_RPB1_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, WAPL degron

value: ECOMG derived neutrophils


title: P6_Leaf_eCO2_1300_rep2

description: Gene expression after 7hr at eCO2

source_name: Mature leaf, 7hr,eCO2, replication 2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad004


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B12_ad007


title: ChIP_Degron_SPT5_Neu_NIPBL_rep1_DMSO4h_A23fast15min

description: Immunoprecipitated DNA

value: DMSO 4h, fast_treated with 20uM A23187 for 15min


title: ChIP_Degron_P300andCBP_Neu_NIPBL_rep1_dTAG2h_A23fast15min

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, P300andCBP degron

value: 0.5uM dTAG-13 2h, fast_treated with 20uM A23187 for 15min


title: ChIP_Degron_P300andCBP_Neu_RPB1_rep1_DMSO2h_A23slow3h

description: Immunoprecipitated DNA

value: DMSO 2h, slow_treated with 5uM A23187 for 3h


title: ChIP_Degron_P300andCBP_Neu_RPB1_rep1_dTAG2h_A23slow3h

description: Immunoprecipitated DNA

value: 0.5uM dTAG-13 2h, slow_treated with 5uM A23187 for 3h


title: ChIP_Degron_BRG1andBRM_Neu_RPB1_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, BRG1andBRM degron

value: 0.5uM dTAG-13 6h, slow_treated with 5uM A23187 for 3h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad012

value: DG


title: ChIP_Degron_BRG1andBRM_Neu_RPB1_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA

value: DMSO 6h, slow_treated with 5uM A23187 for 3h


title: ChIP_Degron_BRG1andBRM_Neu_P300_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA

value: P300 sc-585X Santa Cruz Biotechnology


title: ChIP_Degron_BRG1andBRM_Neu_SMC1_rep1_dTAG6h_A23fast15min

description: Immunoprecipitated DNA

value: 0.5uM dTAG-13 6h, fast_treated with 20uM A23187 for 15min

value: SMC1 A300-055A Bethyl Laboratries


title: ChIP_Degron_BRG1andBRM_Neu_P300_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad010


title: P6_Leaf_aCO2_1300_rep2

description: Gene expression after 7hr at aCO2

source_name: Mature leaf, 7hr,aCO2, replication 2

value: Mature leaf

value: Nipponbare


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad002

value: male


title: P6_Leaf_aCO2_1300_rep1

description: Gene expression after 7hr at aCO2

source_name: Mature leaf, 7hr,aCO2, replication 1


title: P6_Leaf_aCO2_1300_rep3

description: Gene expression after 7hr at aCO2

source_name: Mature leaf, 7hr,aCO2, replication 3


title: ChIP_Degron_BRG1andBRM_Neu_SMC1_rep1_DMSO6h_A23fast15min

description: Immunoprecipitated DNA

value: DMSO 6h, fast_treated with 20uM A23187 for 15min


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep2_dTAG6h_A23slow3h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils

value: NIPBL A301-779A  Bethyl Laboratries


title: ChIP_Degron_P300andCBP_Neu_NIPBL_rep1_DMSO2h_A23fast15min

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, P300andCBP degron

value: DMSO 2h, fast_treated with 20uM A23187 for 15min


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad001


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad008


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep1_DMSO6h_A23slow3h

description: Immunoprecipitated DNA


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep2_DMSO6h_A23slow3h

description: Immunoprecipitated DNA


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep1_dTAG6h_A23slow3h

description: Immunoprecipitated DNA


title: LL3

source_name: algal cells_LL

value: 7th, mid-exponential phase

value: 150 μmol photons•m−2s−1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad007


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep1_DMSO6h_A23fast15min

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, BRG1andBRM degron


title: ChIP_PU1KO_Neu_SMC1_rep1_UT

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, PU1KO

value: untreated


title: ChIP_PU1KO_Neu_NIPBL_rep1_A23fast15min

description: Immunoprecipitated DNA

value: fast_treated with 20uM A23187 for 15min


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad006

value: DG


title: Input_Neu_rep4

description: Input DNA

value: human E2A_ER_Pbx1b, wild type

value: slow_treated with 5uM A23187 for 4h


title: ChIP_PU1KO_Neu_NIPBL_rep1_UT

description: Immunoprecipitated DNA


title: ChIP_Degron_BRG1andBRM_Neu_NIPBL_rep1_dTAG6h_A23fast15min

description: Immunoprecipitated DNA

value: 0.5uM dTAG-13 6h, fast_treated with 20uM A23187 for 15min


title: ChIP_PU1KO_Neu_SMC1_rep1_A23fast15min

description: Immunoprecipitated DNA

value: SMC1 A300-055A Bethyl Laboratries


title: ChIP_WT_NFATInhibitors_Neu_NIPBL_rep1_DMSO2h_A23slow4h

description: Immunoprecipitated DNA

value: DMSO 2h, slow_treated with 5uM A23187 for 4h


title: ChIP_WT_NFATInhibitors_Neu_NIPBL_rep1_FK5062h_A23fast15min

description: Immunoprecipitated DNA

value: 2uM FK506 2h, fast_treated with 20uM A23187 for 15min


title: ChIP_WT_NFATInhibitors_Neu_NIPBL_rep1_FK5062h_A23slow4h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils

value: 2uM FK506 2h, slow_treated with 5uM A23187 for 4h


title: ChIP_WT_NFATInhibitors_Neu_NIPBL_rep1_DMSO2h_A23fast15min

description: Immunoprecipitated DNA

value: NIPBL A301-779A  Bethyl Laboratries


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B10_ad001

value: male


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B11_ad004


title: SEC (FITC-AGE+ CD31- B220-) rep 2

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

description:
Replicate 2
793

hyb_protocol: A total hybridisation volume of 30ul was prepared for each sample and 30ul loaded into a single array on the Ilumina MouseWG6V2 Expression Beadchip. The chip was then hybridised at 58C for 16 hours in an oven with a rocking platform.  After hybridisation, the chip was washed using the appropriate protocols as outlined in the Illumina manual.

scan_protocol: Upon completion of the washing, the chips were then coupled with Cy3 and scanned in the Illumina iScan Reader.  The scanner operating software, GenomeStudio, converts the signal on the array into a TXT file for analysis.

data_processing: The data were background corrected, log2 tranformed and quantile normalised using lumi (version 1.1.0)

label: biotin

source_name: HSC (FITC-AGE+ CD31- B220-)

label_protocol: The Standard Illumina Protocol, Illumina TotalPep RNA Amplification Kit p/n IL1791M Revision C, was used to label cRNA. A total of 500ng of total RNA was prepared for hybridisation to the Ilumina MouseWG6V2 Expression Beadchip by preparing a probe cocktail (cRNA @ 0.05ug/ul) that includes GEX-HYB Hybridisation Buffer (supplied with the beadchip).

extract_protocol: Total RNA were extracted from cells using Qiagen RNeasy Mini Kit according to manufacturer's instruction. Some RNA samples were pooled to get sufficent amount for labelling. The quality and quantity of mouse total RNA was ascertained on the Agilent Bioanalyser 2100 using the NanoChip protocol

tag: cell markers

value: FITC-AGE+ CD31- B220-

value: Scavenger endothelial cells (SEC)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B10_ad002

tag: brain region


title: ChIP_WT_TxInhibitors_Neu_NIPBL_rep1_TRP30min_A23slow2h

description: Immunoprecipitated DNA

value: 10 uM TRP 30min, slow_treated with 5uM A23187 for 2h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B10_ad008

tag: Sex


title: ChIP_WT_TxInhibitors_Neu_NIPBL_rep1_DRB30min_A23slow2h

description: Immunoprecipitated DNA

value: 100 uM DRB 30min, slow_treated with 5uM A23187 for 2h


title: ChIP_WT_TxInhibitors_Neu_NIPBL_rep1_FLAV30min_A23slow2h

description: Immunoprecipitated DNA

value: 10 uM FLAV 30min, slow_treated with 5uM A23187 for 2h


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep2_A23slow4h

description: Immunoprecipitated DNA

value: RNAPII Ser2 ab5095 Abcam


title: SEC (FITC-AGE+ CD31- B220-) rep 1

description:
Replicate 1
794


title: ChIP_WT_TxInhibitors_Neu_NIPBL_rep1_DMSO30min_A23slow2h

description: Immunoprecipitated DNA

value: DMSO 30min, slow_treated with 5uM A23187 for 2h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B10_ad012

value: DG

tag: age


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad004

tag: strain


title: SEC (FITC-AGE+ CD31+ B220-) rep 3

description:
Replicate 3
789

source_name: SEC (FITC-AGE+ CD31+ B220-)

value: FITC-AGE+ CD31+ B220-

tag: cell type


title: SEC (FITC-AGE+ CD31- B220-) rep 3

description:
Replicate 3
792


title: SEC (FITC-AGE+ CD31+ B220-) rep 2

description:
Replicate 2
790


title: SEC (FITC-AGE+ CD31+ B220+) rep 1

description:
Replicate 1
786

source_name: SEC (FITC-AGE+ CD31+ B220+)

value: FITC-AGE+ CD31+ B220+


title: HSC (LSK CD150+ CD48-) rep 2

description:
Replicate 2
430

source_name: HSC (LSK CD150+ CD48-)

value: LSK CD150+ CD48-

value: Bone marrow hemopoietic stem cell (HSC)


title: SEC (FITC-AGE+ CD31+ B220+) rep 2

description:
Replicate 2
788


title: SEC (FITC-AGE+ CD31+ B220-) rep 1

description:
Replicate 1
791


title: SEC (FITC-AGE+ CD31+ B220+) rep 3

description:
Replicate 3
787


title: HSC (LSK CD150+ CD48-) rep 1

description:
Replicate 1
456


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep2_A23slow2h

description: Immunoprecipitated DNA

source_name: in-vitro differentiated neutrophils

value: human E2A_ER_Pbx1b, wild type

value: slow_treated with 5uM A23187 for 2h


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep2_A23slow0h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils

value: untreated


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad010

value: male


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep2_A23slow3h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 3h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad012


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep2_A23slow1h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 1h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad007


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep1_A23slow4h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 4h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad002


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep1_A23slow2h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep1_A23slow3h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep1_A23slow1h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_RPB1_rep1_A23slow4h

description: Immunoprecipitated DNA

value: RPB1 sc-899 Santa Cruz Biotechnology or 664912 Biolegend


title: ChIP_WT_SlowKinetics_Neu_RNAPIIS2_rep1_A23slow0h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_RPB1_rep1_A23slow2h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad001


title: ChIP_WT_SlowKinetics_Neu_RPB1_rep1_A23slow3h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_B1_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad010


title: ChIP_WT_SlowKinetics_Neu_RPB1_rep1_A23slow1h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_RPB1_rep1_A23slow0h

description: Immunoprecipitated DNA


title: CD34+GFP+shLuciferase_series B

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: cDNA is then hybridized to GeneChip® human U133 Plus 2.0 Array (Affymetrix). After overnight hybridization, chips are washed on the Fluidic Station FS450 following specific protocols (Affymetrix).

scan_protocol: Chips are scanned using the GCS3000 7G.

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V21 was used for annotation.

source_name: CD34+GFP+ cells upon shCtl-luciferase transduction

label_protocol: 1 ug of total RNA is reverse transcribed. The resulting double strand cDNA is used for in vitro transcription with T7 RNA pol (all these steps are included in the WT cDNA synthesis and amplification kit of Affymetrix). After fragmentation, cDNA is end labelled with biotin using Terminal Transferase (using the WT terminal labelling kit of Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Human cord bloods were collected and CD34+ cells were isolated by immunomagnetic beads (Miltenyi) and immediately frozen. CD34+CD38- were sorted from CD34+ thawed cells and cultured for one day in four-cytokine (IL3, 10 ng/ml; Flt3L, 100 ng/ml; SCF, 100 ng/ml; TPO, 20 nM) minimal cocktail medium before being transduced at multiplicity of infection of 20 with Control luciferase- or STAT5-shRNA encoding lentiviral vectors that co-express GFP marker. A few hours later, cells were seeded on MS5 stromal layer and allowed to grow for 5 days. CD34+/GFP+ cells were then sorted and RNA were prepared using Trizol reagent according to manufacturer’s instructions.

value: CD34+ hematopoietic stem progenitor cells

tag: shRNA

value: shCtl-luciferase


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad008


title: Input-TRIB3-Cas9_ChIPSeq

data_processing:
Illumina bcl2fq software was used for basecalling.
Low-quality reads (Q≤19 bases over 50%), Ns reads (N%>5%) and adapter polluted reads (adapter bases>5 bp) are filtered out.
ChIP-seq reads were aligned to the human genome assembly using Bowtie2.
Peaks were called using MACS2.
Genome_build: mm9

source_name: Raji cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

value: B lymphocyte

value: peripheral blood

value: lymphoblast


title: CD34+GFP+shSTAT5-102_series B

source_name: CD34+GFP+ cells upon shSTAT5 transduction


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep2_A23slow1h

description: Immunoprecipitated DNA

value: BRG1 ab110641 abcam or 07-478 Millipore


title: Ip-TRIB3-Cas9_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2630)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad004

value: DG


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep2_A23slow2h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type


title: Input-Ctrl-Cas9_ChIPSeq


title: CD34+GFP+shLuciferase_series A


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad006


title: CD34+GFP+shSTAT5-102_series A


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A9_ad002


title: INPUT-PCM4_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2629)


title: INPUT-PCON_ChIPSeq


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad008


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep1_A23slow3h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep1_A23slow4h

description: Immunoprecipitated DNA


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep2_A23slow0h

description: Immunoprecipitated DNA

value: untreated


title: FAPi rep4

first: Rui

last: Yue

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR
Aligned reads with high quality were quantified by HTSeq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids
Unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts by determined by UMI number to get rmdup.count file
To get the CPM value file of each sample, counts per million (CPM ) = gene counts/sample counts x 1,000,000
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm values and count files include raw count values for each sample

source_name: Bone Marrow Mesenchymal Stromal Cells

extract_protocol:
Seven thousand lived BMSCs (DAPI- Calcein-AM+ CD45- Ter119- Tie2- Pdgfra+) were sorted from limb bones of vehicle or FAPi-treated mice. Total RNA was extracted, digested with DNase I and purified using RNAclean Kit.
Libraries were constructed through a modified Smartseq2 method, and sequenced on a HiSeq X Ten system (Illumina) as paired-end 150-bp reads.

treatment_protocol: 8-week old male mice were divided into two groups: one group treated with 100 μl DPBS, and another group treated with 100 μl FAP inhibitor (500 ug/kg) daily for a total of 35 days

value: male

value: Bone Marrow Mesenchymal Stromal Cells

tag: sample type

value: primary

tag: injected

value: FAPi


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep1_A23slow2h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 2h


title: Ip-Ctrl-Cas9_ChIPSeq

tag: tissue

tag: morphology


title: HiC Progenitors replicate 2 [re-analysis]

description:
GSE93127_Pro_mapq1_allValidPairs.hic.bz2
GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.bedGraph.bz2
GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.txt.bz2

source_name: undifferentiated myeloid progenitor cells

extract_protocol:
Hi-C libraries were prepared with the NEBNext primer set and were selected by size by 6% PAGE and sequenced for 50 cycles on Illumina HiSeq 2500.
The in-situ Hi-C experiments were performed similarly as described (Rao SSP, et al. 2014. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159: 1665-1680).

value: Ecomg myeloid progenitor cell line


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad007


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep2_A23slow4h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 4h


title: FAPi rep3


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep1_A23slow1h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 1h


title: H7_b1

city: Toronto

first: Jean

last: Wang

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

hyb_protocol: Standard Illumina Hybridization protocol

scan_protocol: Scanned on a BeadArrayTM Reader using BeadScan software (v3.2)

data_processing: Data was normalized with variance stabilization and quantile normalization using the lumi (v2.16.0) package in R(v3.1.0)

source_name: peripheral blood

label_protocol: Biotin

extract_protocol: RNAeasy Mini Kit (Qiagen Inc)

tag: aml#


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: FAPi rep2


title: IP-PCON_ChIPSeq

value: B lymphocyte

value: peripheral blood


title: ChIP_WT_SlowKinetics_Neu_BRG1_rep1_A23slow0h

description: Immunoprecipitated DNA

value: BRG1 ab110641 abcam or 07-478 Millipore


title: INPUT-K427R_ChIPSeq

value: lymphoblast


title: FAPi rep1


title: ChIP_WT_SlowKinetics_Neu_P300_rep2_A23slow4h

description: Immunoprecipitated DNA

value: P300 sc-585X Santa Cruz Biotechnology


title: G3_b3


title: INPUT-c-Myc(WT)_ChIPSeq


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad004

value: DG


title: DPBS rep3

value: DPBS


title: IP-PCM4_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2629)


title: ChIP_WT_SlowKinetics_Neu_P300_rep2_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type

value: ECOMG derived neutrophils

value: slow_treated with 5uM A23187 for 3h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad002

value: male


title: IP-K427R_ChIPSeq

value: c-Myc antibody (CST, #9402)


title: ChIP_PrimaryCells_Bcells_NIPBL_rep1_A23slow4h

description: Immunoprecipitated DNA

source_name: primary B cells

value: wild type

value: primary B cells

value: NIPBL A301-779A  Bethyl Laboratries


title: DPBS rep2

value: Bone Marrow Mesenchymal Stromal Cells

value: primary


title: Input-Ad-UBE3B

value: B lymphocyte

value: peripheral blood


title: ChIP_WT_SlowKinetics_Neu_P300_rep1_A23slow4h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 4h


title: ChIP_WT_SlowKinetics_Neu_P300_rep2_A23slow1h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 1h

value: P300 sc-585X Santa Cruz Biotechnology


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad012

value: DG


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad008


title: IP-c-Myc(WT)_ChIPSeq

value: lymphoblast


title: Ip-Ad-UBE3B_ChIPSeq

value: Rpb1 CTD (4H8) (Cell Signaling Technology, #2629)


title: Input-Ad-CTRL


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad010


title: Ip-Ad-CTRL_ChIPSeq


title: ChIP_WT_SlowKinetics_Neu_P300_rep1_A23slow2h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type

value: ECOMG derived neutrophils

value: slow_treated with 5uM A23187 for 2h


title: DPBS rep1

value: male

value: DPBS


title: E12.5 Tal1cko R1

city: Helsinki

first: Kaia

last: Achim

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

description: 900 cells

data_processing:
Read 1: transcript
Read 2: BBBBBBBB[BBB]WWWWWWWWWWWWWWWWWWWWWWCCCCCCCCUUUUUUTTTTTTTTTT______________; B = Barcode1: 8, 9, 10 or 11 bases long. W = 'W1' sequence: GAGTGATTGCTTGTGACGCCTT. C = Barcode2, 8 bases. U = UMI, 6 bases. T = Beginning of polyT tail.
Previously published Python scripts were used to process the sequencing reads and to generate count matrices (Klein et al., 2015; Zilionis et al., 2017).
Briefly, raw transcript reads were trimmed with Trimmomatic 0.36 (Bolger et al., 2014), and barcode reads were filtered for expected structure (known cellular barcode, W1 sequence, poly-T tail).
Filtered reads were sorted based on barcodes, and barcodes having at least 12 000 reads were kept. The filtered reads were aligned with bowtie 1.1.1 (Langmead et al., 2009) to the Ensembl GRCm38 cDNA reference. A poly-A sequence of 125 bases was added to each transcript before building the bowtie index.
For UMI quantification, a minimum of 10 bases were required to overlap non-poly-A sequence in the aligned transcript reads. Only unambiguous UMI counts were kept.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Count matrices (gene x barcode) generated by preprocessing scripts. Columns 2-4 contain information on count sums, ambiguous count sums, and ambiguous counts, respectively.

source_name: Brain cells

growth_protocol: The tissues and cells were extracted from freshly dissected mouse embryos. All the animal experiments  were approved by the Laboratory Animal Center, University of  Helsinki, and the National Animal Experiment Board in Finland.

extract_protocol:
Mice, their tissues and cells were untreated
Ventral r1 was dissected in the 5% FBS (fetal bovine serum; Millipore, Cat#ES-009-B) in L-15 (Gibco, Cat#11415-049). The ventral r1 was separated from the brain by using visible landmarks (such as the constriction of midbrain-hindbrain boundary). The pieces were washed 3 times with cold 500ul 1xPBS (Lonza, Cat#BE17-516Q) and dissociated using the Papain Dissociation System (Worthington, Cat#LK003150) according to the manufacturer's protocols. Post-dissociation, the cells were  washed 3 times in cold PBS and counted to determine the number of apoptotic cells (1-5%) before encapsulation.
InDrops E12.5 cDNA libraries were multiplexed and sequenced on NextSeq Illumina platform in paired-end mode using high-yield 75 cycle kit.

tag: Stage

value: brain

value: rhombomere 1

value: En1-cre, Tal1flox/flox

value: Female


title: ChIP_WT_SlowKinetics_Neu_P300_rep1_A23slow3h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 3h


title: ChIP_WT_SlowKinetics_Neu_P300_rep1_A23slow1h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad004

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: 06-CBPKD2

city: Nagasaki

first: Mitsuhiro

last: Yoneda

address: 1-12-4 Sakamoto

institute: Nagasaki University

data_processing:
Basecalls performed using Illumina MiSeq
RNA-seq reads were aligned to the Drosophila dm3 genome assembly using Illumina MiSeq
Genome_build: Drosophila dm3
Supplementary_files_format_and_content: RPKM

organism: Drosophila melanogaster

growth_protocol: S2 cells were grown in Schneider’s Drosophila media (Gibco) with 10% FBS.

extract_protocol:
S2 cells were collected.Total RNA was isolated using ISOGEN II reagent (NIPPON GENE), according to the manufacturer’s protocol.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit (Illumina)

tag: cell line

tag: genotype/variation

value: CBP-knockdown


title: E12.5 control R1

description: 458 cells

treatment_protocol: The tissues and cells were extracted from freshly dissected mouse embryos. All the animal experiments  were approved by the Laboratory Animal Center, University of  Helsinki, and the National Animal Experiment Board in Finland.

tag: genotype

value: WT


title: ChIP_WT_SlowKinetics_Neu_P300_rep2_A23slow0h

description: Immunoprecipitated DNA

tag: treatment

value: untreated

tag: chip antibody


title: E12.5 Tal1cko R1 6

data_processing:
Adapters were removed with Scythe 0.991.
Reads were mapped to the UCSC mm10 genome with STAR 2.4.
Gene counts were obtained from uniquely mapped reads using the featureCounts function of Rsubread 1.16.1, with the mm10 RefSeq gene annotation provided by Rsubread.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Count matrix (gene x sample) with 6 control (A001 – A006) and 6 knockout (A007 – A012) samples.

source_name: Brain tissue

growth_protocol: The RNA was extracted from freshly dissected mouse embryos. All the animal experiments  were approved by the Laboratory Animal Center, University of  Helsinki, and the National Animal Experiment Board in Finland.

extract_protocol:
Tissue from the E12.5 ventral r1 of 6 Ctrl and 6 Tal1cko embryos were dissected in DMEM. Total RNA was isolated by Trizol Reagent/chloroform extraction using Direct-zol™ RNA MiniPrep columns (Zymo research, catalog # R2051) followed by DNase I digestion, according to manufacturer's instructions. The RNA concentrations was measured spectrophotometrically using NanoDrop2000 (Thermo Scientific). RNA quality was assayed on RNA Nano Chips (Agilent) with Agilent Bioanalyzer 2100 according to manufacturer's instructions. All samples used for RNA-seq had RIN values of at least 9.4
Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit  (Illumina) with Ribo-Zero rRNA depletion. The libraries were sequenced in one run with the Illumina NextSeq500 sequencer producing 400 million single reads of 86 base pairs.

treatment_protocol: Mice, their tissues and cells were untreated. Samples were frozen in liquid nitrogen after dissection, in order to preserve RNA integrity, stored at -80C, and melted prior the RNA extraction.

tag: brain region

value: Rhombomere 1


title: 05-CBPKD1


title: 03-NAP1KD1

value: NAP-1 knockdown


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad007

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

value: DG

tag: Sex


title: 04-NAP1KD2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad001

tag: age


title: ChIP_WT_SlowKinetics_Neu_H3K27ac_rep1_A23slow2h

description: Immunoprecipitated DNA

tag: strain

value: H3K27ac ab4729  Abcam


title: ChIP_WT_SlowKinetics_Neu_P300_rep1_A23slow0h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type

tag: cell type

value: P300 sc-585X Santa Cruz Biotechnology


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad002


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad012


title: ChIP_WT_SlowKinetics_Neu_H3K27ac_rep1_A23slow4h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils

value: slow_treated with 5uM A23187 for 4h


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A7_ad006

value: male


title: E12.5 Tal1cko R1 5

value: brain


title: ChIP_WT_SlowKinetics_Neu_H3K27ac_rep1_A23slow3h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad010


title: E12.5 Tal1cko R1 4


title: ChIP_WT_SlowKinetics_Neu_H3K27ac_rep1_A23slow1h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 1h


title: 01-controlKD1

value: control


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad008


title: E12.5 Tal1cko R1 3

value: En1-cre, Tal1flox/flox


title: ChIP_WT_SlowKinetics_Neu_H3K27ac_rep1_A23slow0h

description: Immunoprecipitated DNA


title: E12.5 Tal1cko R1 2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad007


title: 02-controlKD2


title: E12.5 Tal1cko R1 1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad006


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep2_A23slow4h

description: Immunoprecipitated DNA

value: NIPBL A301-779A  Bethyl Laboratries


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad004


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep2_A23slow2h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 2h


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep2_A23slow1h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad002


title: E12.5 control R1 6

value: WT


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad006


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep2_A23slow0h

description: Immunoprecipitated DNA

value: untreated


title: E12.5 control R1 4

value: Rhombomere 1


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep1_A23slow4h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad012


title: E12.5 control R1 2


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep1_A23slow3h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 3h


title: JPR-R2_24h-H2O_vs_JPR-R2_24h-pyflubumide_3

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replicate 3 of 4 of (JPR-R2_24h-H2O) vs. (JPR-R2_24h-H2O)

hyb_protocol: Labeled cRNA were pooled and hybridized  on a custome-made Agilent 8x60k array using the Gene Expression Hybridization Kit (Agilent Technologies). Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: All arrays were scanned using an Agilent Microarray High Resolution Scanner (default settings for two-color GE micro-arrays).

data_processing: Raw data were extracted using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Data were transferred to limma (Smyth, 2004) for statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed using empirical Bayesian statistics.

organism: Tetranychus urticae

label_protocol: Cy5- and Cy3-labeled cRNA was synthesized from RNA following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Mites were reared and maintained in climatically controlled rooms at 25 °C, 60% RH and 16h:8h light:dark photoperiod.

extract_protocol: T. urticae RNA was isolated using the RNeasy minikit (Qiagen) using approximately 120-150 pooled female mites and was subsequently treated with DNase (Turbo DNA-free kit, Ambion).

tag: life stage

value: adult

tag: gender

value: female


title: JPR-R2_24h-H2O_vs_JPR-R2_24h-pyflubumide_4

description: Replicate 4 of 4 of (JPR-R2_24h-H2O) vs. (JPR-R2_24h-H2O)


title: JPR-R2_24h-H2O_vs_JPR-R2_24h-pyflubumide_2

description: Replicate 2 of 4 of (JPR-R2_24h-H2O) vs. (JPR-R2_24h-H2O)


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep2_A23slow3h

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type


title: E12.5 control R1 1


title: E12.5 control R1 5


title: JPR-R2_24h-H2O_vs_JPR-R2_24h-pyflubumide_1

description: Replicate 1 of 4 of (JPR-R2_24h-H2O) vs. (JPR-R2_24h-H2O)


title: JPR-R1_24h-H2O_vs_JPR-R1_24h-pyflubumide_4

description: Replicate 4 of 4 of (JPR-R1_24h-H2O) vs. (JPR-R1_24h-pyflubumide)


title: JPR-R1_24h-H2O_vs_JPR-R1_24h-pyflubumide_3

description: Replicate 3 of 4 of (JPR-R1_24h-H2O) vs. (JPR-R1_24h-pyflubumide)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad004

value: DG


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad008


title: JPR-R1_24h-H2O_vs_JPR-R1_24h-pyflubumide_2

description: Replicate 2 of 4 of (JPR-R1_24h-H2O) vs. (JPR-R1_24h-pyflubumide)


title: JPR-R1_24h-H2O_vs_JPR-R1_24h-pyflubumide_1

description: Replicate 1 of 4 of (JPR-R1_24h-H2O) vs. (JPR-R1_24h-pyflubumide)


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep1_A23slow2h

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A6_ad001


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep1_A23slow1h

description: Immunoprecipitated DNA


title: E12.5 control R1 3


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A5_ad001


title: ChIP_WT_SlowKinetics_Neu_NIPBL_rep1_A23slow0h

description: Immunoprecipitated DNA


title: ChIP_WT_FastAndSlow_Neu_RNAPIIS2_rep2_UT

description: Immunoprecipitated DNA

value: RNAPII Ser2 ab5095 Abcam


title: ChIP_WT_FastAndSlow_Neu_RNAPIIS2_rep2_A23fast15min

description: Immunoprecipitated DNA

value: fast_treated with 20uM A23187 for 15min


title: ChIP_WT_FastAndSlow_Neu_RNAPIIS2_rep1_UT

description: Immunoprecipitated DNA


title: JPR_9h-H2O_vs_JPR_9h-pyflubumide_4

description: Replicate 4 of 4 of (JPR_9h-H2O) vs. (JPR_9h-pyflubumide)

value: JPR


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 5

city: Fougères

first: Antoine

last: Huguet

address: 10B rue Claude Bourgelat

institute: Anses

description: Gene expression after 24hr in 27.7 nM DTX2 exposed Caco-2 cells

hyb_protocol: For the experiments we used 4 X 44K Whole Human Genome 70-mer oligo-chips (G4112F; Agilent Technologies). Hybridisation of Cyanine-labeled cRNA samples was performed onto each microarray for 17 hrs at 65°C with an HSPro4800 hybridisation automatic station (Tecan) and using the Gene Expression Wash Pack kit (Agilent Technologies) and the “Stabilization and Drying Solution” kit (Agilent Technologies) according to the manufacturers’ protocols.

scan_protocol: The absorbance was measured at 532 nm (for cyanine-3-labeled cRNA samples) or 635 nm (for cyanine-5-labeled cRNA samples) with an Innoscan 900AL scanner (Innopsys, Carbonne, France).

data_processing: Raw data, corresponding to the median pixel intensity for each probe, were extracted with Mapix software, version 5.0. The quality of the extracted raw data was checked for signal homogeneity using the Pearson correlation. A Lowess normalisation was performed on the raw data with R software using the Linear Model for Microarray Data Bioconductor package. A background signal was calculated from the mean of the one hundred lowest values of each sample. Following this, the normalised data were filtered on threshold intensity (3 times the background signal): for each probe, values were selected if the median value for at least one experimental condition was higher than the threshold intensity. This dataset, including the 26 960 post-filtering probes, was labelled “filtered data”.

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 5

label_protocol: For probe preparation, 200 ng of total RNA were reverse transcribed into double strand cDNA and then amplified and labelled into cRNA with either cyanine-3 CTP or cyanine-5 CTP using the “Low Input QuickAmp Labeling” kit according to the manufacturer’s protocol (Agilent Technologies, Massy, France). Cyanine-labeled cRNA was purified using the “RNeasy Mini” kit according to the manufacturer’s instructions (Qiagen, Courtaboeuf, France), cyanine incorporation was monitored with a NanoPhotometer (Implen, Munich, Germany), and cyanine-labeled cRNA was fragmented for 30 min at 60°C.

growth_protocol: Caco-2 cells were seeded at 5 x 104 cells/cm2 in 6-well plates and grown in Minimum Essential Medium containing 5.5 mM D-glucose, Earle’s salts and 2 mM L-alanyl-glutamine, supplemented with 1% non-essential amino acids, 50 IU/mL penicillin, 50 μg/mL streptomycin, and 20% foetal calf serum for 24 hours.

extract_protocol: Following cell treatments, total RNA was isolated using the NucleoSpin® RNA II kit according to the manufacturer’s instructions with a final elution volume of 10 µL of RNase free water (Macherey-Nagel, Hoerd, France). RNA was quantified with the BioSpec-Nano (Shimadzu, Marne la Vallée, France), and RNA integrity was assessed with the “Experion RNA StdSens analysis” kit using the Experion automated electrophoresis system (Bio-Rad, Marnes-la-Coquette, France). Only RNA with an RNA quality indicator ≥ 9 was used for further experiments (Experion software 3.0; Bio-Rad).

treatment_protocol: Undifferentiated Caco-2 cells were exposed for 24 hrs to 13.8 nM of okadaic acid, 6.9 nM of dinophysistoxin-1, and 27.7 nM of dinophysistoxin-2 in medium at 37°C in an atmosphere containing 5% CO2. A vehicle control (0.31% methanol) was also included for each experiment. Six independent experiments were performed.

value: undifferentiated Caco-2 cells


title: JPR_9h-H2O_vs_JPR_9h-pyflubumide_1

description: Replicate 1 of 4 of (JPR_9h-H2O) vs. (JPR_9h-pyflubumide)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad007

value: male


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 4

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 4


title: JPR_9h-H2O_vs_JPR_9h-pyflubumide_2

description: Replicate 2 of 4 of (JPR_9h-H2O) vs. (JPR_9h-pyflubumide)


title: JPR_9h-H2O_vs_JPR_9h-pyflubumide_3

description: Replicate 3 of 4 of (JPR_9h-H2O) vs. (JPR_9h-pyflubumide)


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 6

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 6


title: JPR-R1_9h-H2O_vs_JPR-R1_9h-pyflubumide_4

description: Replicate 4 of 4 of (JPR-R1_9h-H2O) vs. (JPR-R1_9h-pyflubumide)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad004


title: ChIP_WT_FastAndSlow_Neu_RPB2_rep1_A23slow4h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 4h

value: RPB2 GTX102535 GeneTex


title: JPR-R2_vs_JPR_4

description: Replicate 4 of 4 of (JPR-R2_non-induced) vs. (JPR_non-induced)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad002


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 6

description: Gene expression after 24hr in 6.9 nM DTX1 exposed Caco-2 cells

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 6


title: ChIP_WT_FastAndSlow_Neu_RNAPIIS2_rep1_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad010


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 5

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 5


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 2

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 2


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 4

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 4


title: JPR-R1_9h-H2O_vs_JPR-R1_9h-pyflubumide_3

description: Replicate 3 of 4 of (JPR-R1_9h-H2O) vs. (JPR-R1_9h-pyflubumide)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad008


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 3

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 3


title: Caco-2 cells_27.7 nM DTX2_24 hr_rep 1

source_name: Caco-2 cells, 27.7 nM DTX2, 24 hours, biological replicate 1


title: JPR-R1_9h-H2O_vs_JPR-R1_9h-pyflubumide_1

description: Replicate 1 of 4 of (JPR-R1_9h-H2O) vs. (JPR-R1_9h-pyflubumide)


title: JPR-R1_9h-H2O_vs_JPR-R1_9h-pyflubumide_2

description: Replicate 2 of 4 of (JPR-R1_9h-H2O) vs. (JPR-R1_9h-pyflubumide)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A8_ad001


title: JPR-R2_vs_JPR_3

description: Replicate 3 of 4 of (JPR-R2_non-induced) vs. (JPR_non-induced)


title: JPR-R2_vs_JPR_2

description: Replicate 2 of 4 of (JPR-R2_non-induced) vs. (JPR_non-induced)


title: JPR-R1_vs_JPO_4

description: Replicate 4 of 4 of (JPR-R1_non-induced) vs. (JPO_non-induced)

value: JPO


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 2

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A4_ad001


title: ChIP_WT_FastAndSlow_Neu_RPB2_rep1_UT

description: Immunoprecipitated DNA

source_name: in-vitro differentiated neutrophils


title: ChIP_WT_FastAndSlow_Neu_RPB2_rep1_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad007


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad012


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep3_A23fast15min

description: Immunoprecipitated DNA

value: BRG1 ab110641 abcam or 07-478 Millipore


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 3

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 3


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep2_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad008


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep1_A23slow4h

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad004


title: JPR-R2_vs_JPR_1

description: Replicate 1 of 4 of (JPR-R2_non-induced) vs. (JPR_non-induced)


title: AML21_bulk

data_processing:
Quality of the reads assessed by FASTQC
Alignment was performed using human genome 19 and STAR 2.4.1 using default parameters
Gene raw counts were generated using featureCounts with default parameters
raw counts were TMM normalized in edgeR and log2 counts per million were generated

source_name: Peripheral blood

extract_protocol:
RNAeasy Mini kit (Qiagen Inc.)
Libraries were prepared using 150ng of RNA input and NEBNext® Ultra™ II Directional RNA Library Prep Kit (Illumina), following manufacturers’ protocols.
Sequencing of libraries was performed on an Illumina HiSeq 2500, high output flow cell (PE126bp) and targeted a final coverage of 30M paired reads per library.


title: JPR-R1_vs_JPO_3

description: Replicate 3 of 4 of (JPR-R1_non-induced) vs. (JPO_non-induced)


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep1_UT

description: Immunoprecipitated DNA

value: untreated


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep2_UT

description: Immunoprecipitated DNA


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep3_UT

description: Immunoprecipitated DNA


title: Caco-2 cells_6.9 nM DTX1_24 hr_rep 1

source_name: Caco-2 cells, 6.9 nM DTX1, 24 hours, biological replicate 1


title: ChIP_WT_FastAndSlow_Neu_P300_rep1_A23slow4h

description: Immunoprecipitated DNA

value: P300 sc-585X Santa Cruz Biotechnology


title: Caco-2 cells_13.8 nM OA_24 hr_rep 6

description: Gene expression after 24hr in 13.8 nM OA exposed Caco-2 cells

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 6


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A2_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: LSCR_0013_MR_1

data_processing:
Quality of the reads assessed by FASTQC
Alignment was performed using human genome 19 and STAR 2.4.1 using default parameters
Gene raw counts were generated using Tuxedo Suite with default parameters

extract_protocol:
RNAeasy Mini/Micro kit (Qiagen Inc.)
Whole transcriptome libraries were prepared using 100ng of RNA input and the KAPA RNA Hyper Prep Library Kit (Roche), following manufacturers’ protocols
Sequencing of whole transcriptome libraries was performed on an Illumina NovaSeq6000 system to generate 2x100 paired reads, targeting a final coverage of 50M clusters per library.

tag: cd200 expression

value: positive

tag: lsc activity


title: LSCR_0012_MR_2

value: negative


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A2_ad004


title: ChIP_WT_FastAndSlow_Neu_BRG1_rep1_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A2_ad002


title: LSCR_0012_MR_1


title: LSCR_0013_MR_2


title: ChIP_WT_FastAndSlow_Neu_PU1_rep1_A23slow4h

description: Immunoprecipitated DNA

value: PU.1 sc-352 Santa Cruz Biotechnology


title: LSCR_0011_MR_1


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad002


title: ChIP_WT_FastAndSlow_Neu_PU1_rep1_UT

description: Immunoprecipitated DNA

value: human E2A_ER_Pbx1b, wild type


title: ChIP_WT_FastAndSlow_Neu_P300_rep1_A23fast15min

description: Immunoprecipitated DNA


title: JPR-R1_vs_JPO_1

description: Replicate 1 of 4 of (JPR-R1_non-induced) vs. (JPO_non-induced)

value: adult

value: female


title: Caco-2 cells_0 nM_24 hr_rep 6

description: Gene expression after 24hr in 0 nM exposed Caco-2 cells

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 6


title: Caco-2 cells_13.8 nM OA_24 hr_rep 2

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 2


title: JPR-R1_vs_JPO_2

description: Replicate 2 of 4 of (JPR-R1_non-induced) vs. (JPO_non-induced)


title: Caco-2 cells_13.8 nM OA_24 hr_rep 1

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 1


title: Caco-2 cells_13.8 nM OA_24 hr_rep 4

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 4


title: Caco-2 cells_0 nM_24 hr_rep 2

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 2


title: Caco-2 cells_13.8 nM OA_24 hr_rep 5

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 5


title: Caco-2 cells_13.8 nM OA_24 hr_rep 3

source_name: Caco-2 cells, 13.8 nM OA, 24 hours, biological replicate 3


title: ChIP_WT_FastAndSlow_Neu_P300_rep1_UT

description: Immunoprecipitated DNA

value: ECOMG derived neutrophils


title: HiC Progenitors replicate 7 [re-analysis]

description:
GSE93127_Pro_mapq1_allValidPairs.hic.bz2
GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.bedGraph.bz2
GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.txt.bz2

source_name: undifferentiated myeloid progenitor cells

value: Ecomg myeloid progenitor cell line


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A3_ad002

value: DG


title: LSCR_0011_MR_2


title: ChIP_WT_FastAndSlow_Neu_CTCF_rep1_A23slow4h

description: Immunoprecipitated DNA

value: CTCF 07-729 Millipore


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad010

value: male


title: HiC Neutrophils replicate 7 PCR replicate 2 [re-analysis]

description:
GSE93127_NeuUT_mapq1_allValidPairs.hic.bz2
GSE93127_NeuUT_mapq1_hicpro2homer.25x50kb.PC1.bedGraph.bz2
GSE93127_NeuUT_mapq1_hicpro2homer.25x50kb.PC1.txt.bz2
GSE93127_NeuUT_mapq1_negativeDomain.new.txt.bz2
GSE93127_NeuUT_mapq1_positiveDomain.new.txt.bz2
GSE93127_NeuUT_mapq1_negativeDomain.new.txt.bz2
GSE93127_NeuUT_mapq1_positiveDomain.new.txt.bz2

value: Ecomg derived neutrophils


title: Caco-2 cells_0 nM_24 hr_rep 1

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 1

value: undifferentiated Caco-2 cells


title: Caco-2 cells_0 nM_24 hr_rep 5

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 5


title: LSCR_0007_MR_2


title: Caco-2 cells_0 nM_24 hr_rep 4

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 4


title: LSCR_0008_MR_2


title: Caco-2 cells_0 nM_24 hr_rep 3

source_name: Caco-2 cells, 0 nM, 24 hours, biological replicate 3


title: LSCR_0007_MR_1


title: LSCR_0010_MR_2


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad008


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad012


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad012


title: ChIP_WT_FastAndSlow_Neu_PU1_rep1_A23fast15min

description: Immunoprecipitated DNA

source_name: in-vitro differentiated neutrophils

value: fast_treated with 20uM A23187 for 15min


title: LSCR_0010_MR_1

source_name: Peripheral blood


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad001


title: ChIP_WT_FastAndSlow_Neu_CTCF_rep1_A23fast15min

description: Immunoprecipitated DNA


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep1_A23slow4h

description: Immunoprecipitated DNA

value: slow_treated with 5uM A23187 for 4h

value: SMC1 A300-055A Bethyl Laboratries


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep1_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad002


title: HiC Neutrophils replicate 5 [re-analysis]

value: untreated


title: ChIP_WT_FastAndSlow_Neu_CTCF_rep1_UT

description: Immunoprecipitated DNA


title: LSCR_0008_MR_1

value: positive


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep2_A23slow4h

description: Immunoprecipitated DNA


title: HiC Neutrophils replicate 7 PCR replicate 1 [re-analysis]


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep2_A23fast15min

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad004


title: HiC Progenitors replicate 6 [re-analysis]


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A12_ad007


title: HiC Neutrophils replicate 6 [re-analysis]


title: LSCR_0003_MR_2

value: negative


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep2_UT

description: Immunoprecipitated DNA


title: HiC Neutrophils replicate 4 [re-analysis]


title: LSCR_0003_MR_1


title: ChIP_WT_FastAndSlow_Neu_NIPBL_rep4_A23fast15min

description: Immunoprecipitated DNA

value: NIPBL A301-779A  Bethyl Laboratries


title: HiC Progenitors replicate 5 [re-analysis]

value: human E2A_ER_Pbx1b, wild type


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad010


title: HiC Progenitors replicate 4 [re-analysis]


title: ChIP_WT_FastAndSlow_Neu_SMC1_rep1_UT

description: Immunoprecipitated DNA


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad008


title: LSCR_0002_MR_2


title: HiC Neutrophils replicate 3 [re-analysis]


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad006


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad007


title: ChIP_WT_FastAndSlow_Neu_NIPBL_rep3_A23slow4h

description: Immunoprecipitated DNA


title: HiC Progenitors replicate 3 [re-analysis]


title: ChIP_WT_FastAndSlow_Neu_NIPBL_rep4_A23slow4h

description: Immunoprecipitated DNA


title: LSCR_0002_MR_1


title: siCTRL_n3_HEK

first: Alexandre

last: Houy

data_processing:
fastq files were mapped on Human genome (hg19) using STAR (v2.5.3a) with default parameters and with –quandMode GeneCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files containing the number of reads per gene (_ReadsPerGene.out.tab). _ReadsPerGene.out.tab format: column 1: gene ID;column 2: counts for unstranded RNA-seq;column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes);column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).
Supplementary_files_format_and_content: tab delimited text files containing the number of reads per splice junction (_SJ.out.tab).  _SJ.out.tab format: column 1: chromosome column 2: first base of the intron (1-based) column 3: last base of the intron (1-based) column 4: strand (0: undefined, 1: +, 2: -) column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT column 6: 0: unannotated, 1: annotated (only if splice junctions database is used) column 7: number of uniquely mapping reads crossing the junction column 8: number of multi-mapping reads crossing the junction column 9: maximum spliced alignment overhang.

source_name: HEK293T cells transfected with siRNA Control (replicate n=3)

growth_protocol: HEK293T and HAP1 cell lines were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted with NucleoSpin RNA kit (Macherey-Nagel). The quantity and quality of RNA was determined by spectrophotometry (NanoDrop Technologies). Five hundred nanograms of RNA was used as a template for cDNA synthesis with the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform using a 100-bp paired-end sequencing strategy.

treatment_protocol: A point mutation in SUGP1 resulting in P636L amino-acid substitution was introduced using CRISPR/cas9-stimulated homology-directed repair to generate isogenic HAP1 cell lines. A second point mutation in ATP1A1 was simultaneously introduced conferring ouabain resistance. Cells were transfected with preformed Cas9 ribonucleoprotein complexes (RNPs) containing synthetic crRNAs specific for ATP1A1 and SUGP1 along with ssODNs-specified mutation at a 3:1 ratio (Integrated DNA Technologies, Inc, IDT). Sequence of gRNA: TGGTACGCATGTCCTCCTGG; donor sequence: TCCTACCACCACCCTCTCCTGTCGACTGAGCAAAGGCAGCCCAGGAGGACATGCGTACCAGGAGGTTGGGCCGGAAGCGGTAGGCCAGCATCATCCTCTTGCGGAACGCCTCATACTCGTCGTCCTCC. Cells were selected and expanded in the presence of ouabain (0.5µM) and verified by Sanger sequencing.  Plasmid transfections were carried out in cell lines using 500 ng of plasmid construct and Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s instructions. For siRNA-mediated knockdown, cells were transfected with 50nM of siRNA using lipofectamine RNAiMAX (Invitrogen) and the following siRNA: siSUGP1 (Cat.No. s33721, Ambion; and GeneSolution Cat.No. 1027416, Qiagen), or control siRNA (Cat.No. S103650318).

tag: transfection

value: transfected with siRNA Control


title: SF3B1WT_n3_HEK

source_name: HEK293T cells transfected with Wildtype SF3B1 expression vector (replicate n=3)


title: SF3B1mut_n3_HEK

source_name: HEK293T cells transfected with SF3B1-K700E expression vector (replicate n=3)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad001

first: Joseph

last: Ecker

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A10_ad012


title: HiC Progenitors replicate 1 [re-analysis]


title: HiC Neutrophils replicate 1 [re-analysis]


title: ChIP_WT_FastAndSlow_Neu_NIPBL_rep4_UT

description: Immunoprecipitated DNA


title: siSUGP1_n3_HEK

source_name: HEK293T cells transfected with siSUGP1 (replicate n=3)

value: transfected with siSUGP1


title: siCTRL_n2_HEK

source_name: HEK293T cells transfected with siRNA Control (replicate n=2)


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A11_ad004


title: siSUGP1_n2_HEK

source_name: HEK293T cells transfected with siSUGP1 (replicate n=2)


title: SF3B1mut_n2_HEK

source_name: HEK293T cells transfected with SF3B1-K700E expression vector (replicate n=2)


title: HiC Neutrophils replicate 2 [re-analysis]


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A10_ad010


title: CEMBA190305_11F_1_CEMBA190305_11F_2_A10_ad001