title: SLX-14712.i727_i518

description: SLX-14712.i727_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14713.i704_i516

status: Public on May 27 2019

type: SRA

city: Dresden

first: Meritxell

last: Huch

address: Pfotenhauerstrasse 108

country: Germany

institute: Max Planck Institute of Molecular Cell Biology and Genetics

library_source: transcriptomic

data_processing:
Download ERCC sequences from Thermofisher (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt) and append them to mouse genome
Create star index using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49 --genomeFastaFiles /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/GRCm38.p6.all.ERCC.fa --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf --sjdbOverhang 49`
Perform alignment using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49/ --readFilesIn /scratch/rulands/Liver_Embryo_Meri_Huch/fastq --readFilesCommand zcat --outFileNamePrefix /scratch/rulands/Liver_Embryo_Meri_Huch/aligned_reads/ --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf`
Generate count matrix using subread 1.6.2. Command: `~/bin/subread-1.6.2-Linux-x86_64/bin/featureCounts -T 10 -t exon -g gene_id -a /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf -Q 30 -o counts.csv *.bam`; sed 1d counts.csv | cut -f1,7- | sed s/Geneid/id/ > counts_final_ercc.txt
Reading count matrix from `counts_final_ercc.txt` and metadata into scanpy 1.3.3 (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Quality control on cells (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Normalisation using scran (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Batch effect correction using mnn_correct (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Genome_build: Ensemble GRCm38, release 93
Supplementary_files_format_and_content: raw count and normalized counts

molecule: total RNA

organism: Mus musculus

extract_protocol:
E10.5 and E13.5 mouse livers were collected, digested into single cells and sorted by FACS to isolate Lgr5-GFP positive cells or bulk liver cells from each timepoint.
The Illumina Nextera XT DNA preparation kit (FC-131-1096) was used to prepare libraries.

tag: strain background

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

tag: cell type

value: liver hepatoblast cells

tag: sorting

value: Bulk


title: SLX-14712.i727_i521

description: SLX-14712.i727_i521.HWFHFBBXX.s_3.r_1.fq.gz

source_name: E13.5_liver_Lgr5GFP pos

value: Lgr5GFP pos


title: SLX-14712.i727_i517

description: SLX-14712.i727_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i727_i515

description: SLX-14712.i727_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i727_i516

description: SLX-14712.i727_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i727_i513

description: SLX-14712.i727_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i726_i522

description: SLX-14712.i726_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i726_i520

description: SLX-14712.i726_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i723_i521

description: SLX-14712.i723_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i724_i516

description: SLX-14712.i724_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i723_i518

description: SLX-14712.i723_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i726_i515

description: SLX-14712.i726_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i723_i516

description: SLX-14712.i723_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i723_i515

description: SLX-14712.i723_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i723_i513

description: SLX-14712.i723_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i522

description: SLX-14712.i722_i522.HWFHFBBXX.s_3.r_1.fq.gz

source_name: E10.5_liver_Lgr5GFP pos


title: SLX-14712.i728_i517

description: SLX-14712.i728_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i520

description: SLX-14712.i722_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i521

description: SLX-14712.i722_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i518

description: SLX-14712.i722_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i516

description: SLX-14712.i722_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i517

description: SLX-14712.i722_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i513

description: SLX-14712.i722_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i722_i515

description: SLX-14712.i722_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i520

description: SLX-14712.i721_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i517

description: SLX-14712.i721_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i522

description: SLX-14712.i721_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i518

description: SLX-14712.i721_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i516

description: SLX-14712.i721_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i515

description: SLX-14712.i721_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i726_i516

description: SLX-14712.i726_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i726_i517

description: SLX-14712.i726_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i522

description: SLX-14712.i720_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i521

description: SLX-14712.i720_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i520

description: SLX-14712.i720_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i518

description: SLX-14712.i720_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i721_i513

description: SLX-14712.i721_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i517

description: SLX-14712.i720_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i516

description: SLX-14712.i720_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i513

description: SLX-14712.i720_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i522

description: SLX-14712.i719_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i521

description: SLX-14712.i719_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i518

description: SLX-14712.i719_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i515

description: SLX-14712.i719_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i513

description: SLX-14712.i719_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i517

description: SLX-14712.i719_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i518

description: SLX-14712.i718_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i520

description: SLX-14712.i718_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i516

description: SLX-14712.i719_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i516

description: SLX-14712.i718_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i513

description: SLX-14712.i718_i513.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i522

description: SLX-14712.i716_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i517

description: SLX-14712.i718_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i521

description: SLX-14712.i718_i521.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i515

description: SLX-14712.i716_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i520

description: SLX-14712.i716_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i715_i508

description: SLX-14712.i715_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i516

description: SLX-14712.i716_i516.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i518

description: SLX-14712.i716_i518.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i716_i517

description: SLX-14712.i716_i517.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i715_i503

description: SLX-14712.i715_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i714_i507

description: SLX-14712.i714_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i720_i515

description: SLX-14712.i720_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i714_i506

description: SLX-14712.i714_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i719_i520

description: SLX-14712.i719_i520.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i714_i503

description: SLX-14712.i714_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i712_i508

description: SLX-14712.i712_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i712_i503

description: SLX-14712.i712_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i714_i505

description: SLX-14712.i714_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i522

description: SLX-14712.i718_i522.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i712_i502

description: SLX-14712.i712_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i508

description: SLX-14712.i711_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i718_i515

description: SLX-14712.i718_i515.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i505

description: SLX-14712.i711_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i503

description: SLX-14712.i711_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i506

description: SLX-14712.i711_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i502

description: SLX-14712.i711_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i710_i507

description: SLX-14712.i710_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i710_i510

description: SLX-14712.i710_i510.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i710_i506

description: SLX-14712.i710_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i710_i503

description: SLX-14712.i710_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i710_i505

description: SLX-14712.i710_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i714_i508

description: SLX-14712.i714_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i507

description: SLX-14712.i707_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i503

description: SLX-14712.i707_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i508

description: SLX-14712.i706_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i502

description: SLX-14712.i707_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i510

description: SLX-14712.i706_i510.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i505

description: SLX-14712.i707_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i507

description: SLX-14712.i706_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i506

description: SLX-14712.i707_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i511

description: SLX-14712.i706_i511.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i506

description: SLX-14712.i706_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i510

description: SLX-14712.i705_i510.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i511

description: SLX-14712.i705_i511.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i505

description: SLX-14712.i706_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i508

description: SLX-14712.i705_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i711_i507

description: SLX-14712.i711_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i505

description: SLX-14712.i705_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i507

description: SLX-14712.i705_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i503

description: SLX-14712.i705_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i706_i502

description: SLX-14712.i706_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i506

description: SLX-14712.i705_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i704_i508

description: SLX-14712.i704_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i704_i506

description: SLX-14712.i704_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i704_i507

description: SLX-14712.i704_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i705_i502

description: SLX-14712.i705_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i704_i503

description: SLX-14712.i704_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i707_i511

description: SLX-14712.i707_i511.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i703_i510

description: SLX-14712.i703_i510.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i703_i508

description: SLX-14712.i703_i508.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i702_i510

description: SLX-14712.i702_i510.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i703_i503

description: SLX-14712.i703_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i704_i505

description: SLX-14712.i704_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i703_i507

description: SLX-14712.i703_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i702_i506

description: SLX-14712.i702_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i702_i505

description: SLX-14712.i702_i505.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i702_i507

description: SLX-14712.i702_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i701_i507

description: SLX-14712.i701_i507.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i701_i511

description: SLX-14712.i701_i511.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i701_i506

description: SLX-14712.i701_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i702_i502

description: SLX-14712.i702_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i701_i503

description: SLX-14712.i701_i503.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14712.i703_i506

description: SLX-14712.i703_i506.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14711.i729_i521

description: SLX-14711.i729_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i729_i520

description: SLX-14711.i729_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14712.i704_i511

description: SLX-14712.i704_i511.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14711.i729_i516

description: SLX-14711.i729_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i729_i513

description: SLX-14711.i729_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i729_i515

description: SLX-14711.i729_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i521

description: SLX-14711.i728_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i520

description: SLX-14711.i728_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i518

description: SLX-14711.i728_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14712.i704_i502

description: SLX-14712.i704_i502.HWFHFBBXX.s_3.r_1.fq.gz


title: SLX-14711.i728_i513

description: SLX-14711.i728_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i520

description: SLX-14711.i727_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i515

description: SLX-14711.i728_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i517

description: SLX-14711.i727_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i515

description: SLX-14711.i727_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i516

description: SLX-14711.i727_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i518

description: SLX-14711.i727_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i522

description: SLX-14711.i726_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i521

description: SLX-14711.i726_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i520

description: SLX-14711.i726_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i727_i513

description: SLX-14711.i727_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i729_i517

description: SLX-14711.i729_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i513

description: SLX-14711.i726_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i515

description: SLX-14711.i726_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i516

description: SLX-14711.i726_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i517

description: SLX-14711.i726_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i521

description: SLX-14711.i724_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i520

description: SLX-14711.i724_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i522

description: SLX-14711.i724_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i518

description: SLX-14711.i724_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i517

description: SLX-14711.i728_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i728_i516

description: SLX-14711.i728_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i517

description: SLX-14711.i724_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_70kb-[Xite-Jpx]_VP:Xist_Clone#2_20E7

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Capture-C
L93F35_hicpro_nodup.bedgraph

library_source: genomic

data_processing:
Library strategy: Capture-C
Capture-C sequencing reads were trimmed using the Trim Galore! pipeline (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and then processed using the HiC-Pro pipeline 72 (v2.8.0).
genome build: mm9
Supplementary_files_format_and_content: Capture-C processed data are bedgraph files containing number of interactions per DpnII fragment generated by the makeViewpoint HiC-Pro utility. DpnII fragments without any observed interactions are omitted form the processed data file.

molecule: genomic DNA

source_name: mouse ES cells E14Tg2a

growth_protocol: Feeder-independent male mouse ESCs (E14Tg2a.4, Sanger) were grown on gelatin-coated flasks in Glasgow medium supplemented with 2 mM L-Glutamine, 0.1 mM NEAA and 1 mM sodium pyruvate (GIBCO) with 15% FBS (GIBCO), 10M b-mercaptoethanol (Sigma), 1000 U/ml of leukemia inhibitory factor (LIF, Chemicon). Cells were cultivated in 8% CO2, and passaged every 48h. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative. E14Tg2a.4 cells were transfected with CRISPR plasmids or TALENs to generate targeted inversions or deletions. Generated clones were validated by PCR and Sanger sequencing.

extract_protocol:
For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates and scraped off; For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate; For RAP cells were fixed and lysed.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using NEBNext kit; RNA-seq libraries were generated using the TruSeq Stranded mRNA kit (Illumina); RAP libraries were genrated using NEBNext kit.

tag: strain

value: 129/Ola, XY

tag: genotype

value: 70kb [Xite-Jpx]

tag: capture-c viewpoint

value: Xist


title: CapC_70kb-[Xite-Jpx]_VP:Xist_Clone#1_18C6

description:
Capture-C
L93F34_hicpro_nodup.bedgraph


title: SLX-14711.i724_i513

description: SLX-14711.i724_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i516

description: SLX-14711.i724_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i724_i515

description: SLX-14711.i724_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_70kb-[Xite-Jpx]_VP:Tsix_Clone#1_18C6

description:
Capture-C
L90F31_hicpro_nodup.bedgraph

value: Tsix


title: SLX-14711.i723_i522

description: SLX-14711.i723_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i726_i518

description: SLX-14711.i726_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Xist_rep3

description:
Capture-C
L93F33_hicpro_nodup.bedgraph

value: WT


title: SLX-14711.i723_i520

description: SLX-14711.i723_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Tsix_rep3

description:
Capture-C
L90F30_hicpro_nodup.bedgraph


title: SLX-14711.i723_i516

description: SLX-14711.i723_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i723_i517

description: SLX-14711.i723_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i723_i515

description: SLX-14711.i723_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i723_i521

description: SLX-14711.i723_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i722_i522

description: SLX-14711.i722_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: Apelin WT Rep 6

city: Vienna

first: Iris

last: Uribesalgo

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
Reads were trimmed using  trim-galore/0.5.0 and trimmed reads mapping to mouse rRNA transcripts were removed using bowtie2/2.3.4.1 alignment and samtools/1.9. Remaining reads were aligned to Mus musculus genome mm10 using star/2.6.0c (GTF annotation file mm10 RefSeq from UCSC, 2018/12). Reads in genes were counted with featureCounts (subread/1.6.2).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

source_name: Endothelial cells

extract_protocol:
100 Endothelial cells were sorted into 4 ul smart-seq2 lysis buffer from digested tumors based on CD31+ and CD105+ marker expression.
RNA libraries were prepared for sequencing using the Smart-Seq2 protocol

value: wild-type

tag: tissue

value: Endothelial cells

tag: treatment

value: shRenilla


title: SLX-14711.i723_i513

description: SLX-14711.i723_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: Apelin WT Rep 3


title: Apelin WT Rep 2


title: Apelin KO Rep 3

value: Apln-/-

value: shApln


title: SLX-14711.i722_i521

description: SLX-14711.i722_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_70kb-[Xite-Jpx]_VP:Tsix_Clone#2_20E7

description:
Capture-C
L90F32_hicpro_nodup.bedgraph


title: SLX-14711.i722_i520

description: SLX-14711.i722_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: Apelin WT Rep 4


title: Apelin WT Rep 1


title: CapC_WT_Jpx_rep2

description:
Capture-C
L127F2_hicpro_nodup.bedgraph

value: Jpx


title: SLX-14711.i722_i517

description: SLX-14711.i722_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: Apelin KO Rep 1


title: SLX-14711.i722_i516

description: SLX-14711.i722_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i723_i518

description: SLX-14711.i723_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i722_i515

description: SLX-14711.i722_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: Apelin WT Rep 5


title: Lytic BR3

city: Gainesville

first: Scott

last: Tibbetts

state: Florida

address: 1200 Newell Drive

department: Molecular Genetics and Microbiology

country: USA

institute: University of Florida

data_processing:
Adapter sequences were removed and low-quality reads were discarded using Trimmomatic.
Reads were analyzed using Hyb, a program which aligns reads to a transcript database and identifies RNA-RNA hybrids.
miRNA-mRNA hybrids were analyzed for the origin of the mRNA (5' UTR, CDS, or 3' UTR) using a custom script.
The binding characteristics of the miRNA portion of the hybrid with the mRNA portion were analyzed using a custom script.
Supplementary_files_format_and_content: .hyb files contain the read sequence, the energy of the hybrid folding, the read and genomic location of each RNA component of the hybrid, the alignment score of each  RNA component of the hybrid, and the identity of each RNA.

source_name: NIH 3T12 fibroblast cells

growth_protocol: NIH 3T12 murine fibroblasts were maintained in Dulbecco’s modified Eagle’s medium, DMEM, supplemented with 10% heat inactivated fetal bovine serum and 1X Penicillin/Streptomycin. HE2.1 cells were maintained in RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum, 1X Penicillin/Streptomycin,  50μM 2-mercaptoethanol and 300μg/mL hygromycin.

extract_protocol:
Protein G Dynabeads were coated with 2A8, a mouse monoclonal antibody against Argonaute (Ago).  Cells were lysed and treated with DNase and RNase T1.  The cell lysates were added to the antibody-coated beads and allowed to incubate overnight.  After immunoprecipitation, Ago-bound RNAs were phosphorylated.  Ago-RNA complexes were incubated overnight with RNA ligase.  This was followed by dephosphorylation and ligation of the miRCat-33 3’-linker (5’-TGGAATTCTCGGGTGCCAAGG-3’ ).  After the complexes were eluted from the beads, the samples were treated with proteinase K.  The RNA was phosphorylated and ligated to the Illumina TruSeq® Small RNA Sample Prep Kits RA5 5' adapter.
RNA was reverse-transcribed using Illumina TruSeq® Small RNA Sample Prep Kits RTP and then amplified through 19-24 PCR cycles with Illumina TruSeq® Small RNA Sample Prep Kits RP1 and one of the following barcoded primers: RPI1, RPI2, or RPI3.  WT_BR1, UI_BR1, and D11_BR1 received RPI1, WT_BR2, UI_BR2, and D11_BR2 received RPI2, and WT_BR3, UI_BR3, and D11_BR3 received RPI3.  PCR products were incubated with PEG-8000 and DNA was extracted from the supernatants.

treatment_protocol: 3T12 cells were infected with WT MHV68 at an MOI of 5 and incubated at 37°C. Lytically infected cells were harvested 16 hours post infection. For preparation of latent samples, HE2.1 cells, were collected in log phase growth.  For preparation  of reactivation samples, HE2.1 cells were treated with tetradecanoylphorbol acetate (TPA) at a concentration of 20ng/mL and incubated at 37°C and harvested 16 hours after TPA treatment. Cells were collected, washed twice in 1X PBS, resuspended in 10mL 1X PBS, and transferred to a cell culture dish on ice. Cells were UV-irradiated at a wavelength of 250nm, receiving a total energy of 600 joules/cm2. Cells were then pelleted at 4°C, supernatant removed, and cells frozen at -80°C.

value: Uninfected embryonic fibroblast

value: BALB/c


title: Lytic BR1


title: Lytic BR2


title: Reactivation BR3

source_name: HE2.1 B cells

value: B lymphocyte latently infected with MHV68


title: SLX-14711.i722_i513

description: SLX-14711.i722_i513.HWFHFBBXX.s_2.r_1.fq.gz

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

value: liver hepatoblast cells


title: SLX-14711.i721_i521

description: SLX-14711.i721_i521.HWFHFBBXX.s_2.r_1.fq.gz

value: Bulk


title: Reactivation BR2


title: Reactivation BR1


title: SLX-14711.i721_i518

description: SLX-14711.i721_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i721_i517

description: SLX-14711.i721_i517.HWFHFBBXX.s_2.r_1.fq.gz

value: Lgr5GFP pos


title: Latency Biological Replicate 1 (BR1)


title: Apelin KO Rep 2


title: SLX-14711.i722_i518

description: SLX-14711.i722_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: Latency BR3


title: Latency BR2


title: SLX-14711.i720_i522

description: SLX-14711.i720_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i721_i515

description: SLX-14711.i721_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i721_i513

description: SLX-14711.i721_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i720_i520

description: SLX-14711.i720_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i720_i518

description: SLX-14711.i720_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i721_i522

description: SLX-14711.i721_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i720_i521

description: SLX-14711.i720_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_WT #2

description:
5C
E14_B101_A836

data_processing:
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
Genome_build: mm9
Supplementary_files_format_and_content: 5C processed data files represent the contact counts between each pairs of 5C primers (reverse/forward)

extract_protocol:
 For Chromosome Conformation Capture (5C and Capture-C) cells were fixed in culture plates and scraped off; For RNA-seq cells were washed once with PBS and lysed in Trizol in the culture plate; For RAP cells were fixed and lysed.
5C libraries were generated based on a custom Illumina-compatible protocol (Nora et al 2017); Capture-C libraries were generated using NEBNext kit; RNA-seq libraries were generated using the TruSeq Stranded mRNA kit (Illumina); RAP libraries were genrated using NEBNext kit.
5C, Capture-C, RNA-seq, RAP

value: 129/Ola, XY


title: 5C_XiteC-inv #2

description:
5C
65_B100_A836

value: XiteC-inv


title: 5C_XiteC-inv #1

description:
5C
62_B100_A836


title: 5C_XiteC-del #2

description:
5C
E5_B100_A836

value: XiteC-del


title: SLX-14711.i720_i516

description: SLX-14711.i720_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_XiteE-inv #2

description:
5C
#4_B101_A836

value: XiteE-inv


title: 5C_XiteC-del #1

description:
5C
E2_B100_A836


title: 5C_WT #1

description:
5C
E14_B100_A836

value: WT


title: SLX-14711.i720_i515

description: SLX-14711.i720_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_XiteE-del #2

description:
5C
G11_B100_A836

value: XiteE-del


title: 5C_XiteE-del #1

description:
5C
F11_B100_A836


title: SLX-14711.i720_i517

description: SLX-14711.i720_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i721_i516

description: SLX-14711.i721_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i720_i513

description: SLX-14711.i720_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_XiteE-inv #1

description:
5C
#4_B100_A836


title: SLX-14711.i719_i521

description: SLX-14711.i719_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i719_i520

description: SLX-14711.i719_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i719_i522

description: SLX-14711.i719_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample9

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Basecalls performed using CASAVA version 1.8.2
The fastq were aligned to the mouse reference genome (version mm10) using STAR v2.3 (Dobin et al. 2013) aligner with default parameters
The alignment results were then evaluated through RNA-SeQC v1.17  (DeLuca et al., 2012) to ensure that all the samples had a consistent alignment rate, and no obvious 5’ or 3’ bias.
Aligned reads were then summarized through featureCounts (Liao et al., 2014) with the gene model from Ensemble (Mus_musculus.GRCm38.75.gtf) at gene level: specifically, the uniquely mapped reads (NH ‘tag’ in bam file) that overlapped with an exon (feature) by at least 1bp were counted and then the counts of all exons annotated to an Ensemble gene (meta features) were summed into a single number.
Only protein coding genes were used for the downstream analysis
Genome_build: mm9
Supplementary_files_format_and_content: raw counts matirx on coding ensembl genes (row) of all samples (column)

source_name: Oxycodone_Ventral Striatum

extract_protocol:
Total RNA were extracted using miRNeasy Mini kit (Qagen)
RNA-seq libraries were prepared using Illumina’s TruSeq® Stranded Total RNA LT kit (with Ribo-Zero™)

treatment_protocol: Mice self adminstered oxycodone (0.25mg/kg/infusion) 4 hours per day for 14 days, while yoked saline controls were infused with saline 4 hours per day for 14 days.

tag: Sex

value: male

value: oxycodone (0.25mg/kg/infusion) 4 hrs per day for 14 days

value: Ventral Striatum


title: Sample10

source_name: Saline_Ventral Striatum

value: saline 4 hrs per day for 14 days


title: Sample8


title: SLX-14711.i719_i516

description: SLX-14711.i719_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i719_i517

description: SLX-14711.i719_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample11


title: Sample12


title: Sample7


title: SLX-14711.i719_i513

description: SLX-14711.i719_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample6


title: SLX-14711.i719_i515

description: SLX-14711.i719_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i718_i522

description: SLX-14711.i718_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample4


title: SLX-14711.i718_i521

description: SLX-14711.i718_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample3


title: SLX-14711.i718_i518

description: SLX-14711.i718_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i718_i517

description: SLX-14711.i718_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i718_i520

description: SLX-14711.i718_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample5


title: Sample2


title: RAP_Xist_70kb-[Xite-Jpx]_Clone#1_18C6_Xist_rep1

description:
RAP
RAP_processed_data.txt
sample name in processed data file: 18C6.1

data_processing:
Library strategy: RAP-Seq
RAP sequencing reads were aligned using BWA version 0.5.9, and filtered using Picard.
genome build: mm9
Supplementary_files_format_and_content: RAP processed data is a text file containing raw and normalized enrichment ratios in 1Mb windows across the genome. Windows deemed "unmappable" are omitted (see Engreitz et al. 2013).

value: 70kb [Xite-Jpx]


title: RAP_Xist_70kb-[Xite-Jpx]_Clone#1_18C6_Xist_rep2

description:
RAP
RAP_processed_data.txt
sample name in processed data file: 18C6.2


title: SLX-14711.i718_i516

description: SLX-14711.i718_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: Sample1


title: RAP_70kb-[Xite-Jpx]_Clone#1_18C6_input

description:
RAP
RAP_processed_data.txt
sample name in processed data file: NA


title: SLX-14711.i716_i521

description: SLX-14711.i716_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: RAP_40kb-[Tsix-Xist]_Clone#1_2G1_Xist_rep2

description:
RAP
RAP_processed_data.txt
sample name in processed data file: 2G1.2

value: 40kb [Tsix-Xist]


title: RAP_40kb-[Tsix-Xist]_Clone#1_2G1_Xist_rep1

description:
RAP
RAP_processed_data.txt
sample name in processed data file: 2G1.1


title: SLX-14711.i716_i520

description: SLX-14711.i716_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: RAP_40kb-[Tsix-Xist]_Clone#1_2G1_input


title: SLX-14711.i718_i515

description: SLX-14711.i718_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i716_i517

description: SLX-14711.i716_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i716_i516

description: SLX-14711.i716_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i716_i518

description: SLX-14711.i716_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i719_i518

description: SLX-14711.i719_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_70kb-[Xite-Jpx]_Clone#2_20E7_rep2

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 20E7-d0-B14

data_processing:
RNA sequencing reads were aligned on the Mouse genome using the STAR mapper. Raw counts have been generated from the STAR mapper using the GENCODE annotation database vM1.
genome build: mm9
Supplementary_files_format_and_content: RNA-seq processed data is a text file containing CPM values (count-per-million) generated by the edgeR package. Gene counts were filtered for CPM>1 in at least two samples and normalized by the trimmed mean of M values (TMM).

molecule: polyA RNA


title: SLX-14711.i715_i520

description: SLX-14711.i715_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: RAP_WT_rep1

description:
RAP
RAP_processed_data.txt
sample name in processed data file: E14.1


title: RNA_70kb-[Xite-Jpx]_Clone#2_20E7_rep1

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 20E7-d0-B13


title: SLX-14711.i716_i513

description: SLX-14711.i716_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_70kb-[Xite-Jpx]_Clone#1_18C6_rep2

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 18C6-d0-B14


title: SLX-14711.i718_i513

description: SLX-14711.i718_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i715_i518

description: SLX-14711.i715_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_WT_rep1_(corresponding_to_70kb)

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: E14.2-d0-B13


title: RAP_input_corresponding_to_WT

description:
RAP
RAP_processed_data.txt
sample name in processed data file: NA


title: RNA_40kb-[Tsix-Xist]_Clone#2_3D5_rep2

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 3D5-d0-B6


title: SLX-14711.i714_i518

description: SLX-14711.i714_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i714_i517

description: SLX-14711.i714_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i714_i520

description: SLX-14711.i714_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: RAP_WT_rep2

description:
RAP
RAP_processed_data.txt
sample name in processed data file: E14.2


title: RNA_40kb-[Tsix-Xist]_Clone#1_2G1_rep1

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 2G1-d0-B1


title: RNA_40kb-[Tsix-Xist]_Clone#2_3D5_rep1

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 3D5-d0-B5


title: SLX-14711.i712_i521

description: SLX-14711.i712_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_40kb-[Tsix-Xist]_Clone#1_2G1_rep2

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 2G1-d0-B2


title: RNA_WT_rep2_(corresponding_to_40kb)

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: E14-d0-B6


title: SLX-14711.i712_i520

description: SLX-14711.i712_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_WT_rep2_(corresponding_to_70kb)

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: E14.2-d0-B14


title: SLX-14711.i712_i518

description: SLX-14711.i712_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_70kb-[Xite-Jpx]_VP:Jpx_Clone#2_20E7

description:
Capture-C
V280F38_hicpro_nodup.bedgraph

value: Jpx


title: SLX-14711.i715_i521

description: SLX-14711.i715_i521.HWFHFBBXX.s_2.r_1.fq.gz

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: SLX-14711.i714_i521

description: SLX-14711.i714_i521.HWFHFBBXX.s_2.r_1.fq.gz

value: liver hepatoblast cells


title: RNA_70kb-[Xite-Jpx]_Clone#1_18C6_rep1

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: 18C6-d0-B13


title: SLX-14711.i712_i516

description: SLX-14711.i712_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_70kb-[Xite-Jpx]_VP:Xite_Clone#2_20E7

description:
Capture-C
V278F29_hicpro_nodup.bedgraph

value: Xite


title: SLX-14711.i711_i521

description: SLX-14711.i711_i521.HWFHFBBXX.s_2.r_1.fq.gz

value: Bulk


title: CapC_70kb-[Xite-Jpx]_VP:Xite_Clone#1_18C6

description:
Capture-C
V278F28_hicpro_nodup.bedgraph

value: 129/Ola, XY


title: SLX-14711.i714_i516

description: SLX-14711.i714_i516.HWFHFBBXX.s_2.r_1.fq.gz

value: Lgr5GFP pos


title: SLX-14711.i712_i513

description: SLX-14711.i712_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_40kb-[Tsix-Xist]_VP:Xist_Clone#2_3D5

description:
Capture-C
V123F3_hicpro_nodup.bedgraph

value: Xist


title: SLX-14711.i712_i517

description: SLX-14711.i712_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_40kb-[Tsix-Xist]_VP:Xist_Clone#1_2G1

description:
Capture-C
V123F2_hicpro_nodup.bedgraph


title: SLX-14711.i711_i520

description: SLX-14711.i711_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i711_i517

description: SLX-14711.i711_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i711_i516

description: SLX-14711.i711_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i710_i522

description: SLX-14711.i710_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i711_i513

description: SLX-14711.i711_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_40kb-[Tsix-Xist]_VP:Tsix_Clone#2_3D5

description:
Capture-C
V125F7_hicpro_nodup.bedgraph

value: Tsix


title: CapC_40kb-[Tsix-Xist]_VP:Tsix_Clone#1_2G1

description:
Capture-C
V125F6_hicpro_nodup.bedgraph


title: CapC_WT_Jpx_rep1

description:
Capture-C
V280F36_hicpro_nodup.bedgraph

value: WT


title: CapC_WT_Xite_rep1

description:
Capture-C
V278F27_hicpro_nodup.bedgraph


title: SLX-14711.i710_i520

description: SLX-14711.i710_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Xite_rep2

description:
Capture-C
V206F18_hicpro_nodup.bedgraph


title: SLX-14711.i710_i517

description: SLX-14711.i710_i517.HWFHFBBXX.s_2.r_1.fq.gz


title: RNA_WT_rep1_(corresponding_to_40kb)

description:
RNAseq
counts_STAR_GENCODE.txt
sample name in processed data file: E14-d0-B2


title: SLX-14711.i712_i515

description: SLX-14711.i712_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Xist_rep2

description:
Capture-C
V123F4_hicpro_nodup.bedgraph


title: CapC_WT_Tsix_rep1

description:
Capture-C
V125F5_hicpro_nodup.bedgraph


title: SLX-14711.i710_i518

description: SLX-14711.i710_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i710_i515

description: SLX-14711.i710_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Tsix_rep2

description:
Capture-C
V125F8_hicpro_nodup.bedgraph


title: SLX-14711.i710_i513

description: SLX-14711.i710_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: CapC_WT_Xist_rep1

description:
Capture-C
V123F1_hicpro_nodup.bedgraph


title: SLX-14711.i707_i522

description: SLX-14711.i707_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i710_i516

description: SLX-14711.i710_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_Xite-del_Clone#2_C11_rep2

description:
5C
B51_C11_bwt2_rf.matrix.gz

data_processing:
Library strategy: 5C
5C sequencing reads were processed using 5C-Pro pipeline, available at https://github.com/bioinfo-pf-curie/5C-Pro. Single-end sequencing reads are trimmed and aligned using bowtie2. Quality controls were performed using the HiTC BioConductor package.
genome build: mm9
Supplementary_files_format_and_content: 5C processed data files represent the contact counts between each pairs of 5C primers (reverse/forward)

value: Xite-del


title: 5C_Xite-del_Clone#1_C3_rep2

description:
5C
B51_C3_bwt2_rf.matrix.gz


title: 5C_Xite-del_Clone#2_C11_rep1

description:
5C
B29_C11_bwt2_rf.matrix.gz


title: SLX-14711.i707_i518

description: SLX-14711.i707_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_Xite-del_Clone#1_C3_rep1

description:
5C
B29_C3_bwt2_rf.matrix.gz


title: 5C_Xite-inv_Clone#2_E12_rep1

description:
5C
B62-1_E12_bwt2_rf.matrix.gz

value: Xite-inv


title: 5C_Xite-inv_Clone#1_C10_rep2

description:
5C
B62-2_C10_bwt2_rf.matrix.gz


title: SLX-14711.i707_i515

description: SLX-14711.i707_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_CTCF-del_Clone#2_D7

description:
5C
B28_D7_bwt2_rf.matrix.gz

value: CTCF-del


title: 5C_Xite-inv_Clone#2_E12_rep2

description:
5C
B62-2_E12_bwt2_rf.matrix.gz


title: SLX-14711.i707_i513

description: SLX-14711.i707_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_Xite-inv_Clone#1_C10_rep1

description:
5C
B62-1_C10_bwt2_rf.matrix.gz


title: 5C_CTCF-del_Clone#1_13b

description:
5C
B28_13b_bwt2_rf.matrix.gz


title: SLX-14711.i706_i521

description: SLX-14711.i706_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i706_i520

description: SLX-14711.i706_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_70kb-[Xite-Jpx]_Clone#2_20E7_rep2

description:
5C
B51_20E7_bwt2_rf.matrix.gz


title: SLX-14711.i706_i516

description: SLX-14711.i706_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_70kb-[Xite-Jpx]_Clone#1_18C6_rep2

description:
5C
B51_18C6_bwt2_rf.matrix.gz


title: SLX-14711.i707_i521

description: SLX-14711.i707_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_70kb-[Xite-Jpx]_Clone#2_20E7_rep1

description:
5C
B20_20E7_bwt2_rf.matrix.gz


title: SLX-14711.i706_i513

description: SLX-14711.i706_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i706_i518

description: SLX-14711.i706_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_70kb-[Xite-Jpx]_Clone#1_18C6_rep1

description:
5C
B20_18C6_bwt2_rf.matrix.gz


title: 5C_40kb-[Tsix-Xist]_Clone#2_3D5_rep2

description:
5C
B51_3D5_bwt2_rf.matrix.gz


title: SLX-14711.i705_i521

description: SLX-14711.i705_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_40kb-[Tsix-Xist]_Clone#2_3D5_rep1

description:
5C
B28_3D5_bwt2_rf.matrix.gz


title: SLX-14711.i705_i520

description: SLX-14711.i705_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i707_i520

description: SLX-14711.i707_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i705_i515

description: SLX-14711.i705_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_40kb-[Tsix-Xist]_Clone#1_2G1_rep1

description:
5C
B28_2G1_bwt2_rf.matrix.gz


title: SLX-14711.i707_i516

description: SLX-14711.i707_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i706_i522

description: SLX-14711.i706_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i705_i513

description: SLX-14711.i705_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: 5C_WT_rep2

description:
5C
B29_E14R_bwt2_rf.matrix.gz


title: SLX-14711.i705_i518

description: SLX-14711.i705_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i704_i522

description: SLX-14711.i704_i522.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i704_i520

description: SLX-14711.i704_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i704_i521

description: SLX-14711.i704_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: AplnAntiSense.2

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using STAR 2.5.0a; reads in genes were counted with htseq-count (HTSeq version 0.6.1p1) ; differential expression analysis was performed with DESeq2 (v 1.10.1)
TPM estimation was performed with RSEM (v1.2.25)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including TPM estimates per gene (standard output RSEM); tab-delimited text files including read counts per gene (standard output htseq-count)

source_name: CD31+ endothelial cells

growth_protocol: Apelin sense and antisense mouse embryonic stem cells (mESCs) were cultured in DMEM with 15% fetal calf serum, penicillin/streptomycin (100U Pen/mL; 0.1mg Strep/mL), L-glutamine (2mM), non-essential amino acids, 1mM sodium pyruvate, 50mM b-Mercaptoethanol and leukaemia inhibitory factor (LIF). All cells were maintained at 37ºC and 5% CO2 conditions. Embryoid bodies (EBs) were generated as previously described (Jakobsson et al., 2010). Briefly, mESCs were trypsinized, depleted of LIF and left in low adhesion plates (day 0). On day 8, the formed EBs were transferred to a polymerized collagen I gel with addition of VEGFA164, Apelin or DMSO.

extract_protocol:
EBs in collagen were dissociated by treatment with Collagenase A and passed through a 70μm cell strainer. The cells were stained with APC-conjugated anti-CD31 antibodies including an anti-mouse CD16/CD32 Fc block and sorted. After sorting, RNA was harvested using Trizol reagent.
Library preparation and RNA sequencing were performed by the VBCF NGS facility using the TruSeq sample preparation kit and poly-A selection according to the manufacturers instructions (NEB, Illumina).

treatment_protocol: Apelin sense and antisense EBs were treated with 30ng/mL VEGFA164 from the day they were transferred to a polymerized collagen I gel. Apelin (Apelin Pyr13, 1000nM) or DMSO (control) were added just after sprouting initiation.

value: Apln anti-sense on C57BL/6x129

value: endothelial cell

tag: gender

value: female


title: AplnSense.2

value: Apln sense on C57BL/6x129


title: 5C_WT_rep1

description:
5C
B20_E14-2_bwt2_rf.matrix.gz


title: SLX-14711.i704_i516

description: SLX-14711.i704_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: E925_Hand2_KO1

city: San Francisco

first: Deepak

last: Srivastava

state: California

address: 1650 Owens Street

department: Cardiovascular Disease

institute: J. David Gladstone Institutes

description:
Single cell transcriptomes from looped heart and pharyngeal arch region from E9.25 Hand2-null mouse embryo
processed data file #2: E925_WTKO_10X.csv.gz

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger Suite (2.0.1) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v2.2 according to specifications in the tutorials (https://satijalab.org/seurat/pbmc3k_tutorial.html)
Each cell is identified by the barcode and gem.group ID at the end of the barcode in the processed data files (e.g. AAACCTGGTAAAGGAG-1). The gem.group ID for each sample and associated processed data file is provided in the characteristics fields above.
Genome_build: mm10
Supplementary_files_format_and_content: normalized gene-cellbarcode expression matrix in csv format

source_name: Embryonic mouse heart at E9.25

growth_protocol: Timed matings were set up between mice heterozygous for the Hand2 null allele. Morning of plug detection was considered E0.5 and embryos were harvested at embryonic day (E)7.75, E8.25 or E9.25

extract_protocol:
35ul of single cell suspensions were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237) and Chromium i7 Multiplex Kit (PN-120262).

treatment_protocol: Embryos were dissected in PBS and 1% FBS on ice. Cardiogenic tissue regions were microdissected and dissociated in 200ul TryplE for 5 minutes at 37C followed by brief trituration and incubation for an additional 5 minutes. TryplE was quenched with 600ul PBS/1% FBS and centrifuged at 150 rcf for 3 minutes and resuspended in 35ul of PBS/1% FBS

value: heart

tag: specific heart region

value: Looped heart, SHF and pharyngeal arch region

tag: additional cell lineages present in dataset

value: Non-cardiac mesoderm, ectoderm and endoderm

tag: gem.group in supplementary file # 2


title: E825_Hand2_KO2

description:
Single cell transcriptomes from heart tube region from E8.25 Hand2-null mouse embryo
processed data file #2: E775E825_WTKO_10X.csv.gz

source_name: Embryonic mouse heart at E8.25

value: Heart tube and SHF region


title: SLX-14711.i703_i518

description: SLX-14711.i703_i518.HWFHFBBXX.s_2.r_1.fq.gz

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

value: liver hepatoblast cells

value: Bulk


title: SLX-14711.i703_i521

description: SLX-14711.i703_i521.HWFHFBBXX.s_2.r_1.fq.gz


title: E825_Hand2_KO1


title: AplnSense.1


title: E925_WT2

description:
Single cell transcriptomes from looped heart and pharyngeal arch region from E9.25 WT mouse embryo
processed data file #1: AllTimePoints_WT_10X.csv.gz
processed data file #2: E925_WTKO_10X.csv.gz

value: Wild-Type

tag: gem.group id in supplementary file # 1


title: SLX-14711.i703_i516

description: SLX-14711.i703_i516.HWFHFBBXX.s_2.r_1.fq.gz

value: Lgr5GFP pos


title: SLX-14711.i703_i520

description: SLX-14711.i703_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: E925_WT1


title: SLX-14711.i702_i520

description: SLX-14711.i702_i520.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i703_i513

description: SLX-14711.i703_i513.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i702_i516

description: SLX-14711.i702_i516.HWFHFBBXX.s_2.r_1.fq.gz


title: E825_WT1

description:
Single cell transcriptomes from heart tube region from E8.25 WT mouse embryo
processed data file #1: AllTimePoints_WT_10X.csv.gz
processed data file #2: E775E825_WTKO_10X.csv.gz


title: SLX-14711.i703_i515

description: SLX-14711.i703_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: E825_WT2


title: SLX-14711.i704_i518

description: SLX-14711.i704_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: AplnAntiSense.1


title: SLX-14711.i701_i515

description: SLX-14711.i701_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14711.i701_i518

description: SLX-14711.i701_i518.HWFHFBBXX.s_2.r_1.fq.gz


title: A549 si-NC repeat2

city: nanjing

first: zhaoxia

last: wang

address: jiangjiayuan road 121

department: Cancer Medical Center

country: China

institute: The Second Affiliated Hospital of Nanjing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Homo sapiens

source_name: lung cancer cell line

growth_protocol: A549 cell lines were cultured in 1640 medium supplemented with 10 % fetal bovine serum (10 % FBS).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: RNA from A5493 cells with SNHG17 knockdown and control cells were isolated and quantified.

tag: cell line

value: lung cancer cell line

tag: genotype/variation

value: Control


title: A549 si-NC repeat3


title: SLX-14710.i729_i511

tag: strain background


title: A549 si-SNHG17 repeat3

value: SNHG17 knockdown


title: A549 si-SNHG17 repeat2


title: A549 si-SNHG17 repeat1


title: SLX-14710.i729_i510

tag: embryonic day


title: SLX-14710.i729_i507

tag: cell type


title: SLX-14710.i729_i503

tag: sorting


title: SLX-14711.i702_i515

description: SLX-14711.i702_i515.HWFHFBBXX.s_2.r_1.fq.gz


title: SLX-14710.i729_i508


title: SLX-14710.i729_i506


title: SLX-14710.i729_i505


title: E925_Hand2_KO2

tag: strain


title: SLX-14710.i728_i510


title: SLX-14710.i728_i508


title: WT-CFBE41o- miRseq [Urban_1_T6_S6]

city: Pittsburgh

first: Donald

middle: B.

last: DeFranco

state: PA

address: 7041 Biomedical Sciences Tower 3

department: Department of Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
The raw QIAseq miRNA sequencing files were uploaded to GeneGlobe Data Analysis Center (Qiagen) for quality control, alignment to the human reference genome (GRCh38) and expression quantification.
Briefly, 3’ adapter and low quality bases are trimmed off from reads first using cutadapt. Reads with less than 16bp insert sequences or with less than 10bp UMI sequences are discarded. The remaining reads were collapsed to UMI counts and aligned to miRBase (release v21) mature and hairpin databases sequentially using Bowtie v1.2.
All reads assigned to a particular miRNA or piRNA ID are counted, and the associated UMIs are clustered to count unique molecules. The primary analysis output file is downloaded from GeneGlobe.
EdgeR package is used for the differential analysis based on UMI counts for miRNA. miRNAs were filtered from the analysis if their count per million (as computed by edgeR's cpm function) was not greater than 2 in at least half of the samples.
The trimmed mean of M-values normalization method implemented in edgeR is used for normalization.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx, reads and UMI counts

source_name: WT-CFBE41o- Cells

growth_protocol: Immortalized human bronchial epithelial cell models: CFBE41o- (bronchial epithelial cells): stably expressing WT-CFTR were cultured Minimum Essential Media (MEM) containing 10% Fetal bovine serum (FBS), 50µg/mL streptomycin, 50U/mL Penicillin, 2mM L-Glutamine, 0.55 µg/mL Puromycin  (2.2 µg/mL Puromycin for F508del-CFBE41o- cells). Cells were split at 90% confluency  were seeded (~1 million/24mm insert)  on 24mm inserts (Corning) coated with 10% collagen (PureCol, Type I Bovine Collagen Solution, Advanced BioMatrix) in Opti-MEM (1X Opti-MEM Reduced Serum Medium, gibco, Life Technologies) and cultured in air liquid interface (ALI) for 7-8 days.

extract_protocol:
Total RNA was isolated from cell lysate using the Quick-RNA Miniprep Kit (Zymo Research, R1054) according to the manufacturer’s instructions, with additional on-column DNase treatment with the RNase-free DNase Set (Zymo) to remove contaminating genomic DNA
100ng of total RNA was used with the QIAseqTM miRNA Library Kit ( Qiagen, Maryland, USA) following manufacturer’s instruction.
3’ and 5’ adapters were ligated to total input RNA. Reverse transcription, followed by PCR, was used to create cDNA constructs. PCR was performed with primers that anneal to the ends of the adapters. Quality was examined using Agilent Bioanalyzer Tapestation 2200 and Qubit 2.0 Fluorometer with miRNA library pre sequencing QC protocol mentioned in the QIAseqTM miRNA Library Kit. The cDNA libraries were pooled at a final concentration of 2.5pM. Cluster generation and 75 bp single read single-indexed sequencing was performed on Illumina NextSeq 500’s.

treatment_protocol: Human TGF-b1 (Sigma, St. Louis, MO) or vehicle control (4 mM HCl+1 mg/mL BSA) was used at concentration (15 ng/mL) for the treatment of cells on 24mm inserts (basolaterally) for 24 hour

value: WT-CFTR transfected immortalized  (CFBE) Cells

tag: passages


title: SLX-14710.i729_i502


title: WT-CFBE41o- miRseq [Urban_1_T5_S5]


title: WT-CFBE41o- miRseq [Urban_1_V1_S7]

value: HCL+BSA


title: WT-CFBE41o- miRseq [Urban_1_V3_S9]


title: A549 si-NC repeat1


title: WT-CFBE41o- miRseq [Urban_1_V2_S8]


title: WT-CFBE41o- miRseq [Urban_1_V4_S10]


title: SLX-14710.i728_i507


title: WT-CFBE41o- miRseq [Urban_1_T3_S3]


title: WT-CFBE41o- miRseq [Urban_1_V6_S12]


title: WT-CFBE41o- miRseq [Urban_1_T4_S4]


title: SLX-14710.i728_i506


title: SLX-14710.i728_i505


title: CapC_70kb-[Xite-Jpx]_VP:Jpx_Clone#1_18C6

description:
Capture-C
V280F37_hicpro_nodup.bedgraph

value: 129/Ola, XY

tag: genotype

value: 70kb [Xite-Jpx]

tag: capture-c viewpoint

value: Jpx


title: WT-CFBE41o- miRseq [Urban_1_V5_S11]

tag: treatment


title: WT-CFBE41o- miRseq [Urban_1_T2_S2]


title: WT-CFBE41o- miRseq [Urban_1_T1_S1]


title: SLX-14710.i728_i502


title: SLX-14710.i728_i511


title: SLX-14710.i728_i503


title: SLX-14710.i727_i508


title: ChIPseq_GRHL2_T47D_WT_Veh_45mins_rep2

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

data_processing:
RNA-seq: VIPER pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using STAR.
RNA-seq: Relative expression of transcripts were calculated by subjecting STAR output (BAM files) to Cufflinks package.
RNA-seq: Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
RNA-seq: The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
RNA-seq: Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
ChIP-seq: Chilin pipeline at CFCE, DFCI was used to perform ChIP-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
ChIP-seq: The output from Bowtie2 (BAM files) was subjected to MACS2 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
ChIP-seq: If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
ChIP-seq: Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets.
Supplementary_files_format_and_content: BED files

source_name: T47D cells

growth_protocol: Cells were cultured for 48 hours in charcoal-stripped serum media to deprive them of steroids.

extract_protocol:
RNA-seq: Hormone-treated cells were homogenized and total RNA was extracted using Qiagen RNAeasy kit
RNA-seq: Total RNA was isolated from the experimental cell populations and primary breast tumors using Trizol (Invitrogen). Poly-A selected, stranded RNA-seq libraries were constructed using the TruSeq Stranded mRNA kit (Illumina).
ChIP-seq: Hormone-treated were harvested and ChIP was performed as per the directions provided in materials and method of the paper
ChIP-seq libraries were prepared using Rubicon kits.

treatment_protocol: Steroid-deprived cell models were treated with 10 nM estradiol or Vehicle for 24 hours

value: T47D cells

tag: treatment duration

value: 45 minutes

value: Vehicle

tag: antibody

value: Anti-GRHL2 HPA004820 (Sigma)


title: SLX-14710.i727_i507

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: 5C_40kb-[Tsix-Xist]_Clone#1_2G1_rep2

description:
5C
B51_2G1_bwt2_rf.matrix.gz

value: 40kb [Tsix-Xist]


title: ChIPseq_INPUT_MCF7

source_name: MCF7 cells

value: MCF7 cells

value: Input sample


title: SLX-14710.i727_i506

value: liver hepatoblast cells

value: Lgr5GFP pos


title: SLX-14710.i727_i505


title: ChIPseq_GRHL2_MCF7_WT_Veh_45mins_rep2


title: ChIPseq_GRHL2_MCF7_WT_Veh_45mins_rep1


title: SLX-14710.i726_i508

value: Bulk


title: SLX-14710.i727_i503


title: SLX-14710.i726_i510


title: ChIPseq_ER_MCF7_CRISPR_GRHL2_E2_45min_rep2

source_name: MCF7 cells CRISPR_GRHL2

value: MCF7 cells CRISPR_GRHL2

value: 10 nM E2

value: Anti-ER HC-20 (Santa Cruz)


title: SLX-14710.i726_i511


title: ChIPseq_ER_MCF7_CRISPR_GRHL2_Veh_45min_rep1


title: ChIPseq_ER_MCF7_CRISPR_GRHL2_E2_45min_rep1


title: SLX-14710.i726_i507


title: ChIPseq_ER_MCF7_CRISPR_GRHL2_Veh_45min_rep2


title: SLX-14710.i726_i506


title: ChIPseq_ER_MCF7_WT_E2_45min_rep1


title: SLX-14710.i724_i511


title: SLX-14710.i726_i505


title: SLX-14710.i726_i503


title: ChIPseq_GRHL2_T47D_WT_Veh_45mins_rep1


title: ChIPseq_ER_MCF7_WT_E2_45min_rep2


title: SLX-14710.i724_i510


title: SLX-14710.i724_i508


title: MCF7_24h_RNAseq_WT_E2_rep3

value: 24 hours


title: MCF7_24h_RNAseq_WT_Veh_rep1


title: MCF7_24h_RNAseq_WT_Veh_rep3


title: ChIPseq_ER_MCF7_WT_Veh_45min_rep2


title: SLX-14710.i724_i505


title: MCF7_24h_RNAseq_WT_E2_rep2


title: ChIPseq_ER_MCF7_WT_Veh_45min_rep1


title: SLX-14710.i724_i503


title: MCF7_24h_RNAseq_WT_E2_rep1


title: MCF7_24h_RNAseq_CRISPR_GRHL2_Veh_rep1

source_name: MCF7 cells CRISPR_GRHL5

value: MCF7 cells CRISPR_GRHL5


title: MCF7_24h_RNAseq_CRISPR_GRHL2_E2_rep3

source_name: MCF7 cells CRISPR_GRHL4

value: MCF7 cells CRISPR_GRHL4


title: MCF7_24h_RNAseq_WT_Veh_rep2


title: SLX-14710.i723_i510


title: MCF7_24h_RNAseq_CRISPR_GRHL2_Veh_rep2

source_name: MCF7 cells CRISPR_GRHL6

value: MCF7 cells CRISPR_GRHL6


title: SLX-14710.i723_i506

source_name: E10.5_liver_Lgr5GFP pos


title: SLX-14710.i723_i511


title: SLX-14710.i724_i502


title: SLX-14710.i723_i505


title: SLX-14710.i724_i507


title: SLX-14710.i723_i507


title: A549 MUC1 -ve #3

city: Boston

first: Mehmet

middle: Kemal

last: Samur

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
VIPER-RNAseq pipeline
STAR aligner
Deseq
Genome_build: hg19

source_name: MUC1-C silenced Cells

extract_protocol:
Total RNA were isolated using RNAeasy Plus Kit (Qiagen) as directed. Briefly the RNA isolation was done using up to 5 million cells form each cell lines, Cells were first lysed and homogenized using QIAshredder columns (Qiagen). The cell lysates were passed through a gDNA Eliminator spin column supplied in the kit, ethanol is added to the gDNA column flow-through as instructed, and the ethanol mixed samples were applied to individual RNeasy spin columns. RNA binds to the membrane and contaminants are washed away using different wash buffer supplied in the kit. The high-quality RNA is finally eluted in 50µl water and stored in -70 degree Celsius till further use.
Illumina single end stranded

value: Kras mutant Non-small Cells Lung Cancer

value: shRNA against MUC1-C


title: MCF7_24h_RNAseq_CRISPR_GRHL2_E2_rep1


title: MCF7_24h_RNAseq_CRISPR_GRHL2_E2_rep2

source_name: MCF7 cells CRISPR_GRHL3

value: MCF7 cells CRISPR_GRHL3


title: A549 MUC1 +ve #3

source_name: MUC1-C +ve control cells

value: control


title: A549 MUC1 -ve #2


title: SLX-14710.i723_i502

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: A549 MUC1 +ve #2


title: SLX-14710.i722_i511


title: MCF7_24h_RNAseq_CRISPR_GRHL2_Veh_rep3

source_name: MCF7 cells CRISPR_GRHL7

value: MCF7 cells CRISPR_GRHL7

value: Vehicle


title: A549 MUC1 +ve #1


title: BT549 MUC1 -ve #3

value: TNBC Breast Cancer Cell line (ER -ve, PR -ve, HER2/neu -ve)


title: SLX-14710.i723_i508

value: liver hepatoblast cells


title: SLX-14710.i722_i510

value: Bulk


title: SLX-14710.i722_i508


title: A549 MUC1 -ve #1


title: BT549 MUC1 -ve #2


title: SLX-14710.i722_i507


title: SLX-14710.i722_i506

source_name: E13.5_liver_Lgr5GFP pos

value: Lgr5GFP pos


title: SLX-14710.i720_i511


title: BT549 MUC1 +ve #2


title: BT549 MUC1 -ve #1


title: BT549 MUC1 +ve #3


title: BT549 MUC1 +ve #1


title: SLX-14710.i721_i507


title: SLX-14710.i723_i503


title: SLX-14710.i720_i507


title: SLX-14710.i720_i503


title: N1_13-12ML_ER16_S6_ChIP-seq

description: ER ChIP-seq (SC HC20)

data_processing:
Chilin pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using Bowtie2
The output from Bowtie2 (BAM files) was subjected to MACS14 to call ChIP-seq peaks. Corresponding inputs for each of the treatment conditions were used as the background.
If needed, the ChIP-seq peaks thus obtained were filtered based on false discovery rates and height of the peaks.
Vehicle treated ChIP-peaksets were subtracted from the hormone-treated ChIP-peaksets.
Genome_build: HG19
Supplementary_files_format_and_content: BED files

source_name: Sorted mature luminal cells

growth_protocol:
Histologically confirmed normal breast samples were obtained from reduction mammoplasty specimens, where family history is generally not known, through the Pathology Departments of the Brigham and Women’s Hospital and Beth Israel Deaconess Medical Center. These breast specimens are in excess of normal diagnostic requirements, hence are normally discarded and are completely de-identified except for patient age. The tissue is collected under the Dana-Farber/Harvard Cancer Center (DF/HCC) institutional review board (IRB)-approved protocol 10-458.
Primary breast tumors were obtained from cancer surgery specimens through the Pathology Department of the Dana-Farber/Harvard Cancer Center. Any leftover remaining tumor tissue following clinical requirements was made available. The tissue is collected under the Dana-Farber/Harvard Cancer Center (DF/HCC) institutional review board (IRB)-approved protocol 10-458. These specimens are de-identified except for patient age, tumor type, grade/stage, and tumor receptor status (ER/PR/HER2).

extract_protocol:
The tissue was collected fresh and sterile from the operating room and transported on ice to the pathologist in the absence of formalin fixative. Following pathological examination, tissue in excess of diagnostic requirements was collected and subsequently de-identified at the tissue bank. The tissue was then transported on ice to the laboratory. Samples that were collected in the evening were stored in media at 4C overnight. The duration from surgery to the commencement of tissue dissociation did not exceed 24 hrs, the majority of the samples were processed on the same day as surgery.
Fragments of normal ER+ breast tissue were of insufficient cell number to utilize FACS after they were dissociated as described above, so epithelial cell enrichment was performed by utilizing magnetic EasySEP EpCAM beads (StemCell Technologies). Once the cells were washed in cold PBS, the appropriate amount of selection media and magnetic particles was added and incubated on ice for 15 minutes. Next, the tube was placed on the magnet at room temperature for five minutes and eluted with chilled media and this process was repeated for a total of four times to enrich for the ER+/EpCAM+ epithelial tumor cells.
Immuno-labelling of normal cells was performed at 4C using PBS as a buffer and wash solution. Incubating the cell pellet with 0.1 mg/ml DNase, 1 mg/ml rat immunoglobulin and a 1/10 dilution of anti-CD16/CD32 receptor antibody for 10 min. was sufficient to block non-specific antibody binding. The cell suspension was then made up to a final concentration of 106 cells /40 l with dilution buffer. For primary human breast tissue, antibodies directed against human lineage markers CD31 (endothelial cells), CD45 (leukocytes) and CD235a (red blood cells) were used to prepare a Lin- cell population, and these PE-linked antibodies were negatively selected against.  Primary antibodies were added at optimized dilutions and incubated for 25 min at 4C. The suspension was then washed, filtered using 40uM tube cap filters (Falcon) and centrifuged. Cells were resuspended in 0.5 g/ml propidium iodide (Sigma) before cell analysis and sorting to allow for only the selection of viable cells. Cell analysis and sorting was performed on either a FACS DIVA or FACS Aria (BD Biosciences) using a sheath pressure of 30 psi and nozzle size of 70 um. Cells were sorted into polystyrene FACS tubes (Westnet #352063) and collected into a mixture of 50% primary MEC media and 50% CDT. Reanalysis of the sorted populations routinely revealed a purity of more than 95%.

treatment_protocol: Freshly sorted cells were resuspended in cell culture media and treated with either vehicle or estradiol for 24 hours. Post treatment, cells were harvaested and ChIP was performed. Finer details are provided in the methods section of the paper.

tag: tissue type

value: Normal-MatureLuminal

tag: er status

value: ER+

tag: pr status

tag: her2 status

tag: age

tag: type

tag: grade

tag: protocol

value: ChIP-seq


title: SLX-14710.i719_i507

tag: strain background

tag: embryonic day

tag: cell type


title: SLX-14710.i719_i510

tag: sorting


title: N12_12-37ML_INPUT_16_S3_Control_INPUT

description: ChIP INPUT Control


title: N12_12-37ML_ER15_S1_ChIP-seq

description: ER ChIP-seq (SC HC20)


title: SLX-14710.i718_i506


title: SLX-14710.i718_i511


title: SLX-14710.i718_i503


title: SLX-14710.i716_i510


title: SLX-14710.i720_i508


title: SLX-14710.i720_i505


title: SLX-14710.i724_i506


title: SLX-14710.i716_i507


title: N7_20140909-13-89ML-E2-ER-DC1247_S1_R1_ChIP-seq

description: ER ChIP-seq (SC HC20)


title: N7_20140909-13-89ML-E2_INPUT_DC1247_S2_R1_Control_INPUT

description: ChIP INPUT Control


title: SLX-14710.i715_i507


title: SLX-14710.i715_i510


title: T15_JG14B_11.4.15-Control-INPUT

description: ChIP INPUT Control

source_name: ER+ breast tumor

value: ER+ breast tumor

value: negative

value: ductal

value: III


title: SLX-14710.i714_i511


title: SLX-14710.i715_i505


title: N11_12-31ML_ER_S7_ChIP-seq

description: ER ChIP-seq (SC HC20)


title: T8_JG8B-Control-INPUT

description: ChIP INPUT Control

value: positive

value: negative (0 or 1+)

value: lobular

value: II


title: T6_JG6B-1-Control-INPUT

description: ChIP INPUT Control

value: mixed


title: T13_JG13B-Control-INPUT

description: ChIP INPUT Control


title: SLX-14710.i714_i510

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: N3_12-36ML_ER_S2_ChIP-seq

description: ER ChIP-seq (SC HC20)


title: N11_12-31ML_INPUT_S9_Control_INPUT

description: ChIP INPUT Control


title: T3-rep1_11.4.15-Control-INPUT

description: ChIP INPUT Control


title: SLX-14710.i719_i505


title: SLX-14710.i714_i508


title: T14_JG7B-Control-INPUT

description: ChIP INPUT Control


title: SLX-14710.i714_i507


title: SLX-14710.i714_i505


title: SLX-14710.i714_i503


title: T11_JG11B-Control-INPUT

description: ChIP INPUT Control


title: T12_JG15B-Control-INPUT

description: ChIP INPUT Control

value: positive (3+)


title: SLX-14710.i712_i510

value: liver hepatoblast cells


title: SLX-14710.i712_i508

value: Bulk


title: T9_JG9B-Control-INPUT

description: ChIP INPUT Control


title: T10_JG10B-Control-INPUT

description: ChIP INPUT Control


title: T4_JG4B-2-Control-INPUT

description: ChIP INPUT Control


title: SLX-14710.i712_i503

value: Lgr5GFP pos


title: T5_JG5B-1-Control-INPUT

description: ChIP INPUT Control


title: T3_JG3B-2-Control-INPUT

description: ChIP INPUT Control


title: T2_JG2B-Control-INPUT

description: ChIP INPUT Control


title: SLX-14710.i712_i502


title: SLX-14710.i711_i510


title: SLX-14710.i711_i508


title: T15_IdxD1_JG14B_H3K27acChIP_11.4.15-ChIP-seq

description:
Input for H3K27: T15_JG14B_11.4.15-Control-INPUT
H3K27Ac ChIP-seq


title: SLX-14710.i711_i511


title: T13_JG13B_H3K27acChIP_IDX8-ChIP-seq

description:
Input for H3K27: T13_JG13B-Control-INPUT
H3K27Ac ChIP-seq


title: SLX-14710.i711_i507


title: T14_JG7B_H3K27acChIP_IDX22-ChIP-seq

description:
Input for H3K27: T14_JG7B-Control-INPUT
H3K27Ac ChIP-seq


title: SLX-14710.i710_i511


title: T12_JG15B_H3K27acChIP_IDX12-ChIP-seq

description:
Input for H3K27: T12_JG15B-Control-INPUT
H3K27Ac ChIP-seq


title: MCF7_LNA_antimiR-18a_rep3

type: RNA

city: Cartagena

first: Ginés

last: Luengo-Gil

address: C/ Mezquita s/n. 1ª planta

department: Department of Pathology

country: Spain

institute: UCAM

description: Gene expression data from MCF7 transfected with a LNA (AntimiR-18a), biological replicate 3

hyb_protocol: Following fragmentation, 3,5 ug of cRNA were hybridized for 20 hr at 48ºC on Affymetrix Human Gene 2.1 ST Array Strips using GeneAtlas Hybridization Station. Array Strips were washed and stained in the GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using  GeneAtlas Imaging Station.

data_processing:
Data were analyzed with RMA (Robust Multiarray Analysis) using Affymetrix default analysis settings and global scaling as normalization method.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label: Biotin

label_protocol: Biotinylated ss-cDNA was prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays,P/N 703174 Rev2, 2013, Affymetrix).

growth_protocol: DMEM 1g/l glucose supplemented with 10% FBS, 1% non-esential aminoacids, 1% pyruvate, +1% peniciline-streptomycin and without phenol-red. 37ºC in 5%CO2 incubator.

extract_protocol: RNAzol followed by Direct-zol™ RNA MiniPrep

treatment_protocol: Transfection using siPORT in OptiMEM following the supplier's protocol. Final concentration of oligonucleotides: 100 nM.

tag: cell line

value: breast cancer, immortalized cell line

tag: transfected with


title: N3_12-36ML_INPUT_S1_Control_INPUT

description: ChIP INPUT Control

value: Normal-MatureLuminal

value: ER+


title: SLX-14710.i710_i510

data_processing:
Download ERCC sequences from Thermofisher (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_095047.txt) and append them to mouse genome
Create star index using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49 --genomeFastaFiles /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/GRCm38.p6.all.ERCC.fa --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf --sjdbOverhang 49`
Perform alignment using STAR 2.6.0c. Command: `~/bin/STAR --runThreadN 10 --genomeDir /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/star_index_overhang49/ --readFilesIn /scratch/rulands/Liver_Embryo_Meri_Huch/fastq --readFilesCommand zcat --outFileNamePrefix /scratch/rulands/Liver_Embryo_Meri_Huch/aligned_reads/ --outSAMtype BAM SortedByCoordinate --sjdbGTFfile /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf`
Generate count matrix using subread 1.6.2. Command: `~/bin/subread-1.6.2-Linux-x86_64/bin/featureCounts -T 10 -t exon -g gene_id -a /ssd/rulands/Genomes/Mouse/GRCm38_ERCC/Mus_musculus.GRCm38.93.ERCC.gtf -Q 30 -o counts.csv *.bam`; sed 1d counts.csv | cut -f1,7- | sed s/Geneid/id/ > counts_final_ercc.txt
Reading count matrix from `counts_final_ercc.txt` and metadata into scanpy 1.3.3 (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Quality control on cells (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Normalisation using scran (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Batch effect correction using mnn_correct (code will be available on https://github.com/fabianrost84/prior_et_al_2019.git upon publication)
Genome_build: Ensemble GRCm38, release 93
Supplementary_files_format_and_content: raw count and normalized counts


title: SLX-14710.i712_i507


title: MCF7_LNA_antimiR-18a_rep2

description: Gene expression data from MCF7 transfected with a LNA (AntimiR-18a), biological replicate 2


title: MCF7_LNA_antimiR-18a_rep1

description: Gene expression data from MCF7 transfected with a LNA (AntimiR-18a), biological replicate 1


title: T11_JG11B_H3K27acChIP_IDX5-ChIP-seq

description:
Input for H3K27: T11_JG11B-Control-INPUT
H3K27Ac ChIP-seq

value: ER+ breast tumor

value: ChIP-seq


title: MCF7_LNA_control_rep3

description: Gene expression data from MCF7 transfected with a LNA (AntimiR, negative control), biological replicate 3

value: LNA negative control


title: T7_JG10A-Control-INPUT

description: ChIP INPUT Control

value: negative

value: III


title: MCF7_LNA_control_rep2

description: Gene expression data from MCF7 transfected with a LNA (AntimiR, negative control), biological replicate 2


title: T10_JG10B_H3K27acChIP_IDX4-ChIP-seq

description:
Input for H3K27: T10_JG10B-Control-INPUT
H3K27Ac ChIP-seq

value: positive

value: negative (0 or 1+)


title: SLX-14710.i710_i508


title: MCF7_LNA_control_rep1

description: Gene expression data from MCF7 transfected with a LNA (AntimiR, negative control), biological replicate 1


title: T9_JG9B_H3K27acChIP_IDX2-ChIP-seq

description:
Input for H3K27: T9_JG9B-Control-INPUT
H3K27Ac ChIP-seq

value: ductal

value: II


title: SLX-14710.i710_i507

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: T6_JG6B-1_H3K27acChIP_IDX20-ChIP-seq

description:
Input for H3K27: T6_JG6B-1-Control-INPUT
H3K27Ac ChIP-seq

value: mixed


title: MCF7_miRNA_miR-18a_rep1

description: Gene expression data from MCF7 transfected with a miRNA mimic (miR-18a), biological replicate 1

value: miR-18a mimic


title: MCF7_miRNA_miR-18a_rep3

description: Gene expression data from MCF7 transfected with a miRNA mimic (miR-18a), biological replicate 3


title: MCF7_miRNA_control_rep2

description: Gene expression data from MCF7 transfected with a miRNA mimic (negative control), biological replicate 2

value: miRNA mimic negative control


title: MCF7_miRNA_control_rep1

description: Gene expression data from MCF7 transfected with a miRNA mimic (negative control), biological replicate 1


title: MCF7_miRNA_control_rep3

description: Gene expression data from MCF7 transfected with a miRNA mimic (negative control), biological replicate 3


title: SLX-14710.i707_i510

value: liver hepatoblast cells

value: Bulk


title: SLX-14710.i707_i511


title: T5_JG5B-1_H3K27acChIP_IDX18-ChIP-seq

description:
Input for H3K27: T5_JG5B-1-Control-INPUT
H3K27Ac ChIP-seq


title: T8_JG8B_H3K27acChIP_IDX24-ChIP-seq

description:
Input for H3K27: T8_JG8B-Control-INPUT
H3K27Ac ChIP-seq

value: lobular


title: SLX-14710.i707_i508


title: SLX-14710.i707_i507


title: T4_JG4B-2_H3K27acChIP_IDX16-ChIP-seq

description:
Input for H3K27: T4_JG4B-2-Control-INPUT
H3K27Ac ChIP-seq


title: T3-rep1_IdxC1_JG3B_H3K27acChIP_11.4.15-ChIP-seq

description:
Input for H3K27: T3-rep1_11.4.15-Control-INPUT
H3K27Ac ChIP-seq


title: SLX-14710.i707_i506

value: Lgr5GFP pos


title: islet NZO_667

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

description: RMA expression value derived from Expression Console software

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

label: biotin

source_name: pancreatic island

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

growth_protocol: Diabetes-prone NZO/Hl  and C3HeB/FeJ  mice were housed at three to six mice per cage (Macrolon type III) at a constant temperature of 22°C and a 12-h light-dark cycle (lights on at 6 a.m.).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: After weaning at the age of 21 days, all experimental animals received a high-fat diet (HFD) containing 45 kcal% fat,  20 kcal% protein and 35 kcal% carbohydrates with 4.73 kcal/gm energy (D12451 Research Diets Inc., New Jersey, USA). At the age of 6 weeks, mice were sacrificed by cervical dislocation and the pancreatic islets were isolated by ductal collagenase perfusion of the pancreas, as previously described (PMID: 21099271 ). Subsequently, the islets were allowed to regenerate overnight at 37°C with 5% CO2 in CMRL (Connaught Medical Research Laboratories) medium containing 15% fetal calf serum, 0.05 mM β-mercaptoethanol , 1 % penicillin/streptomycin, 10 mM glucose and 39.2 mM NaHCO3.

tag: strain

value: NZO/Hl (NZO; German Diabetes Centre Düsseldorf (HERBERG and COLEMAN 1977))

tag: gender

value: male

value: 6 weeks


title: islet NZO_636_637


title: islet NZO_648_651


title: MCF7_miRNA_miR-18a_rep2

description: Gene expression data from MCF7 transfected with a miRNA mimic (miR-18a), biological replicate 2

value: breast cancer, immortalized cell line


title: islet NZO_668-670


title: islet C3H_136_139

value: C3H (000658, Jackson Lab)


title: islet C3H_135_140


title: islet C3H_133_134


title: islet NZO_649_652


title: T14_JG7B_ERChIP_IDX14-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: ER+ breast tumor

value: positive

value: negative

value: III

value: ChIP-seq


title: islet C3H_129_130


title: T3-rep2_IdxA2_JG3B_Breast_H3K27ac_11.24.15-ChIP-seq

value: ductal

value: II


title: islet C3H_131_132


title: SLX-14710.i706_i510

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: T3-rep2-Control-INPUT

description: ChIP INPUT Control


title: E6Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (gene-level)

description: RNA expression value derived from Expression Console software; core-gene analysis

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RNA analyses  for  gene default and exon default .CHP files.

growth_protocol: Ba/F3 cell lines were cultured in DMEM with 1% PenStrep and 10%FCS with recombinant Hyper-IL-6 (10 ng/ml cell culture supernatant) in 10 cm cell culture plattes  and were splitted in a ratio from 1:10000 to 1:5

treatment_protocol: Ba/F3-gp130 cell lines were washed four times with sterile PBS and incubated in serum-free DMEM for 3 h. Equal numbers of cells (2 x 10^6) were stimulated  for 1h at 37°C with 50µl GFP-PFC emulsion in 1ml serum free DMEM medium (1 h at 37°C). As a positive stimulation control Ba/F3-gp130 cells were incubated for 1h at 37°C with 100ng/ml Hyper IL-6 in serum free medium (Samples E2, E4, E6)

tag: cell line vendor

value: Ba/F3 (DSMZ no.:ACC 300)

tag: transfection

value: untransfected

tag: stimulation

value: 100ng/ml Hyper IL-6


title: SLX-14710.i707_i503

value: liver hepatoblast cells

value: Lgr5GFP pos


title: E2Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (gene-level)


title: T3-rep3_JG3B-2_H3K27acChIP_IDX14-ChIP-seq

description:
Input for H3K27: T3-rep2-Control-INPUT
H3K27Ac ChIP-seq

tag: tissue type

tag: er status

tag: pr status


title: SLX-14710.i706_i511

value: Bulk


title: SLX-14710.i706_i508


title: T12_JG15B_ERChIP_IDX6-ChIP-seq

description: ER ChIP-seq (SC HC20)

tag: her2 status

value: positive (3+)

tag: age

tag: type


title: E4Ba/F3-gp130 cells stimulated with 100ng/ml Hyper IL-6 (gene-level)


title: T10_JG10B_ERChIP_IDX20-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: negative (0 or 1+)

value: mixed

tag: grade

tag: protocol


title: T11_JG11B_ERChIP_IDX22-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: ER+ breast tumor


title: SLX-14710.i706_i505

tag: strain background

tag: embryonic day

tag: cell type


title: SLX-14710.i706_i507

tag: sorting


title: T7_JG10A_ERChIP_IDX19-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: positive


title: D3Ba/F3-gp130-CIR3 (gene-level)

tag: cell line

value: unstimulated


title: D4Ba/F3-gp130-CIR3 stimulated with GFP-PFC (gene-level)

value: GFP-PFC (50µl/ml)


title: SLX-14710.i706_i506


title: D5Ba/F3-gp130-CIR3 (gene-level)


title: SLX-14710.i706_i502


title: D6Ba/F3-gp130-CIR3 stimulated with GFP-PFC (gene-level)


title: D2Ba/F3-gp130-CIR3 stimulated with GFP-PFC (gene-level)


title: D1Ba/F3-gp130-CIR3 (gene-level)


title: T9_JG9B_ERChIP_IDX18-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: negative

value: ChIP-seq


title: SLX-14710.i705_i511


title: T5_JG5B-1_ERChIP_IDX10-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: ductal

value: II


title: T4_JG4B-2_ERChIP_IDX8-ChIP-seq

description: ER ChIP-seq (SC HC20)


title: SLX-14710.i706_i503

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female


title: T3_JG3B-2_ERChIP_IDX6-ChIP-seq

description: ER ChIP-seq (SC HC20)


title: C6Ba/F3-gp130-CIR2 stimulated with GFP-PFC (gene-level)

value: Ba/F3 (DSMZ no.:ACC 300)


title: B3Ba/F3-gp130-CIR1 (gene-level)


title: C1Ba/F3-gp130-CIR2 (gene-level)


title: C2Ba/F3-gp130-CIR2 stimulated with GFP-PFC (gene-level)


title: C4Ba/F3-gp130-CIR2 stimulated with GFP-PFC (gene-level)


title: C3Ba/F3-gp130-CIR2 (gene-level)


title: T2_JG2B_ERChIP_IDX4-ChIP-seq

description: ER ChIP-seq (SC HC20)

value: III


title: B5Ba/F3-gp130-CIR1 (gene-level)


title: SLX-14710.i705_i508

value: liver hepatoblast cells


title: SLX-14710.i705_i507


title: A6Ba/F3-gp130 cells stimulated with GFP-PFC (gene-level)

value: untransfected


title: C5Ba/F3-gp130-CIR2 (gene-level)


title: B1Ba/F3-gp130-CIR1 (gene-level)


title: B6Ba/F3-gp130-CIR1 stimulated with GFP-PFC (gene-level)


title: B2Ba/F3-gp130-CIR1 stimulated with GFP-PFC (gene-level)


title: T13_JG13B-20151001-IDX4_RNAseq

description: mRNA-seq

data_processing:
VIPER pipeline at CFCE, DFCI was used to perform RNA-seq analyses. The FASTQ files were filtered and good quality reads were groomed and subsequently aligned to HG19 genome build using STAR.
Relative expression of transcripts were calculated by subjecting STAR output (BAM files) to Cufflinks package.
Cufflinks assemblies obtained from Cufflinks package were merged using cuffmerge. For every model system, cufflink assemblies of each of the treatments were merged with the cufflinks assemblies of the respective vehicle-treated samples.
The output from Cuffmerge along with the corresponding TopHat output (BAM files) were subjected to Cuffdiff to calculate transcript expression.
Genes that were up or down regulated by at least two fold were used for downstream analyses.
Genome_build: HG19
Supplementary_files_format_and_content: Readcount matrix containing expression levels of genes in each of the samples is provided

extract_protocol:
The tissue was collected fresh and sterile from the operating room and transported on ice to the pathologist in the absence of formalin fixative. Following pathological examination, tissue in excess of diagnostic requirements was collected and subsequently de-identified at the tissue bank. The tissue was then transported on ice to the laboratory. Samples that were collected in the evening were stored in media at 4C overnight. The duration from surgery to the commencement of tissue dissociation did not exceed 24 hrs, the majority of the samples were processed on the same day as surgery.
Fragments of normal ER+ breast tissue were of insufficient cell number to utilize FACS after they were dissociated as described above, so epithelial cell enrichment was performed by utilizing magnetic EasySEP EpCAM beads (StemCell Technologies). Once the cells were washed in cold PBS, the appropriate amount of selection media and magnetic particles was added and incubated on ice for 15 minutes. Next, the tube was placed on the magnet at room temperature for five minutes and eluted with chilled media and this process was repeated for a total of four times to enrich for the ER+/EpCAM+ epithelial tumor cells.
Immuno-labelling of normal cells was performed at 4C using PBS as a buffer and wash solution. Incubating the cell pellet with 0.1 mg/ml DNase, 1 mg/ml rat immunoglobulin and a 1/10 dilution of anti-CD16/CD32 receptor antibody for 10 min. was sufficient to block non-specific antibody binding. The cell suspension was then made up to a final concentration of 106 cells /40 l with dilution buffer. For primary human breast tissue, antibodies directed against human lineage markers CD31 (endothelial cells), CD45 (leukocytes) and CD235a (red blood cells) were used to prepare a Lin- cell population, and these PE-linked antibodies were negatively selected against.
Primary antibodies were added at optimized dilutions and incubated for 25 min at 4C. The suspension was then washed, filtered using 40uM tube cap filters (Falcon) and centrifuged. Cells were resuspended in 0.5 g/ml propidium iodide (Sigma) before cell analysis and sorting to allow for only the selection of viable cells. Cell analysis and sorting was performed on either a FACS DIVA or FACS Aria (BD Biosciences) using a sheath pressure of 30 psi and nozzle size of 70 um. Cells were sorted into polystyrene FACS tubes (Westnet #352063) and collected into a mixture of 50% primary MEC media and 50% CDT. Reanalysis of the sorted populations routinely revealed a purity of more than 95%.

treatment_protocol: Freshly sorted cells were resuspended in cell culture media and treated with either vehicle or estradiol for 24 hours. Post treatment, cells were harvaested and RNA was extracted for further downstream analyses. Finer details are provided in the methods section of the paper.

tag: drug treatment

tag: hormone exposure time


title: B4Ba/F3-gp130-CIR1 stimulated with GFP-PFC (gene-level)

tag: cell line vendor

tag: transfection


title: iCLIP_SRSF3_2

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

data_processing:
libraries sequenced usign Illumina HiSeq 2000 single end 75nt
Adapters and barcodes were removed from all iCLIP reads before mapping to the mouse mm9 genome assembly (Ensembl59 annotation) using Bowtie software (version 0.10.1).
statistically significant cross-link events (X-links), all uniquely mapping reads were used, PCR duplicates were removed using the random barcodes within the 3’adapter, X-link sites were extracted (1st nucleotide of the read) and randomized within co-transcribed regions.
Significant X-links (false discovery rate [FDR] <0.05) were calculated using normalized numbers of input X-links
Genome_build: mm9
Supplementary_files_format_and_content: Significant X-links (false discovery rate [FDR] <0.05) in BED format

source_name: Neonatal cardiomyocytes

growth_protocol: Neonatal cardiomyocytes were extracted from C57BL/6 mice at P0 or P1.23 A total of 8 million cells were plated in 10 cm2 plates

extract_protocol:
Mice were sacrificed with carbon dioxide, hearts were extracted, perfused with PBS and tissue was inmediatly freezed in liquid nitrogen. Total RNA was purified using RNeasy Mini Kit (Qiagen).
Briefly, crosslinked RNA was digested to lengths of 80-200 nucleotides using RNaseI (Ambion) and RNA-protein complexes were immunopurified using Protein G Dynabeads® (ThermoFisher Scientific) coupled with a goat anti-GFP antibody (D. Drechsel, MPI-CBG, Dresden). Isolated and purified RNA fragments were ligated to pre-adenylated DNA 3’ adapters (IDT) and reverse-transcribed using barcoded RT-primers and SuperscriptIV (ThermoFisher Scientific). cDNA fragments were size-selected, circularized using CircLigaseTM (Epicentre) and re-linearized by BamHI (NEB). The final cDNA libraries now containing 5’ and 3’ adapters were amplified using AccuPrime (ThermoFisher Scientific)
iCLIP

treatment_protocol: The following day, cells were transfected with 15 μg of SRSF3-GFP modRNA using 21 μL Lipofectamine 2000. At 48 h post-transfection, cells were irradiated once with 100 mJ UV light (254 nm)

tag: strain

tag: Stage

tag: tissue

value: Neonatal cardiomyocytes


title: T12_JG15B-20151001-IDX9_RNAseq

description: mRNA-seq

tag: tissue type

tag: er status

tag: pr status

tag: her2 status

value: positive (3+)


title: SLX-14710.i705_i510

extract_protocol:
E10.5 and E13.5 mouse livers were collected, digested into single cells and sorted by FACS to isolate Lgr5-GFP positive cells or bulk liver cells from each timepoint.
The Illumina Nextera XT DNA preparation kit (FC-131-1096) was used to prepare libraries.

value: Bulk


title: A3Ba/F3-gp130 cells (gene-level)

source_name: A3Ba/F3-gp130 cells

tag: stimulation


title: SLX-14710.i705_i506

tag: strain background

value: Lgr5GFP pos


title: A5Ba/F3-gp130 cells (gene-level)

source_name: A5Ba/F3-gp130 cells


title: T11_JG11B-20151001-IDX1_RNAseq

description: mRNA-seq

value: ER+ breast tumor

value: negative (0 or 1+)

tag: age

tag: type

tag: grade


title: A4Ba/F3-gp130 cells stimulated with GFP-PFC (gene-level)

tag: cell line

tag: cell type


title: SLX-14710.i705_i505

tag: embryonic day

tag: sorting


title: SLX-14710.i705_i503


title: T10_JG10B-20151001-IDX27_RNAseq

description: mRNA-seq

value: positive

value: mixed

tag: drug treatment

tag: hormone exposure time


title: SRSF3_KO_2

description:
SRSF3flox/flox;αMHC-CreERT2
LMG_302

data_processing:
libraries sequenced usign Illumina HiSeq 2000 pair end 125nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using TMM option from edgeR package
Genome_build: GRCm38 v84
Supplementary_files_format_and_content: RSEM estimated counts per sample per gene. Samples in columns, Genes in rows

source_name: Heart

extract_protocol:
Mice were sacrificed with carbon dioxide, hearts were extracted, perfused with PBS and tissue was inmediatly freezed in liquid nitrogen. Total RNA was purified using RNeasy Mini Kit (Qiagen).
A cDNA library was prepared with polyA positive selection according to Illumina protocol

treatment_protocol: Mice were treated with 3 inyections of 1 mg 4-hydroxytamoxifen in non-consequtive days.

tag: strain

tag: genotype

tag: Stage

value: Adult

value: Heart


title: SRSF3_KO_3

description:
SRSF3flox/flox;αMHC-CreERT2
LMG_303

tag: tissue


title: Control_2

description:
αMHC-CreERT2
MER_148


title: T9_JG9B-20151001-IDX23_RNAseq

description: mRNA-seq

tag: tissue type

tag: er status

tag: pr status

value: negative

value: ductal


title: A2Ba/F3-gp130 cells stimulated with GFP-PFC (gene-level)

tag: cell line vendor

tag: transfection

tag: stimulation

value: GFP-PFC (50µl/ml)


title: A1Ba/F3-gp130 cells (gene-level)

source_name: A1Ba/F3-gp130 cells

value: Ba/F3 (DSMZ no.:ACC 300)

value: unstimulated


title: SRSF3_KO_1

description:
SRSF3flox/flox;αMHC-CreERT2
LMG_299


title: T8_JG8B-20151001-IDX21_RNAseq

description: mRNA-seq

tag: her2 status

tag: age

tag: type

value: lobular

tag: grade

value: II


title: CPU10

data_processing:
Basecalls performed using CASAVA version 1.8.2
The fastq were aligned to the mouse reference genome (version mm10) using STAR v2.3 (Dobin et al. 2013) aligner with default parameters
The alignment results were then evaluated through RNA-SeQC v1.17  (DeLuca et al., 2012) to ensure that all the samples had a consistent alignment rate, and no obvious 5’ or 3’ bias.
Aligned reads were then summarized through featureCounts (Liao et al., 2014) with the gene model from Ensemble (Mus_musculus.GRCm38.75.gtf) at gene level: specifically, the uniquely mapped reads (NH ‘tag’ in bam file) that overlapped with an exon (feature) by at least 1bp were counted and then the counts of all exons annotated to an Ensemble gene (meta features) were summed into a single number.
Only protein coding genes were used for the downstream analysis
Genome_build: mm9
Supplementary_files_format_and_content: raw counts matirx on coding ensembl genes (row) of all samples (column)

source_name: Saline_Dorsal Striatum

tag: Sex

value: male

tag: treatment

value: saline 4 hrs per day for 14 days

value: Dorsal Striatum


title: Control_3

description:
αMHC-CreERT2
MER_149


title: SLX-14710.i704_i511

tag: strain background

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

tag: cell type

value: liver hepatoblast cells

tag: sorting

value: Bulk


title: CPU6P

tag: strain

tag: tissue


title: CPU5P

source_name: Oxycodone_Dorsal Striatum

value: oxycodone (0.25mg/kg/infusion) 4 hrs per day for 14 days


title: SLX-14710.i705_i502

value: Lgr5GFP pos


title: iCLIP_SRSF3_1

tag: Stage

value: Neonatal cardiomyocytes


title: T6-2_JG6B-2-20151001-IDX16_RNAseq

description: mRNA-seq

tag: tissue type

value: ER+ breast tumor

tag: er status

value: positive

tag: pr status

value: negative (0 or 1+)

value: mixed

value: III

tag: drug treatment

tag: hormone exposure time


title: CPU4P


title: SLX-14710.i704_i507


title: CPU4


title: CPU3P


title: T7_JG10A-20151001-IDX25_RNAseq

description: mRNA-seq

tag: her2 status

value: negative

tag: age


title: SLX-14710.i704_i508


title: T6-1_JG6B-1-20151001-IDX15_RNAseq

description: mRNA-seq

tag: type

tag: grade


title: SLX-14710.i704_i506


title: Control_1

description:
αMHC-CreERT2
MER_147

tag: genotype

value: Adult

value: Heart


title: CPU3

tag: Sex

value: male

tag: treatment


title: T5_JG5B-1-20151001-IDX13_RNAseq

description: mRNA-seq

value: ductal

value: II


title: CPU2

value: saline 4 hrs per day for 14 days

value: Dorsal Striatum


title: SLX-14710.i704_i505

tag: strain background

value: male Lgr5-EGFP-IRES-creERT2 mice maintained on a C57BL/6 background, mated with MF1 female

tag: embryonic day

tag: cell type

value: liver hepatoblast cells


title: CPU1

tag: strain

value: oxycodone (0.25mg/kg/infusion) 4 hrs per day for 14 days

tag: tissue


title: T4_JG4B-2-20151001-IDX11_RNAseq

description: mRNA-seq

tag: tissue type


title: CPU7P


title: SLX-14710.i704_i503

tag: sorting

value: Lgr5GFP pos


title: SLX-14710.i703_i511

value: Bulk


title: T2_JG2B-20151001-IDX5_RNAseq

description: mRNA-seq

value: ER+ breast tumor

tag: er status

value: positive

tag: pr status


title: T1_JG1B-20151001-IDX2_RNAseq

description: mRNA-seq

value: positive (3+)

tag: drug treatment

tag: hormone exposure time