title: Lung_Control GFP

status: Public on Mar 30 2019

city: Rochester

first: Stijn

last: De Langhe

state: Minnesota

address: 200 First street SW

department: Medicine

institute: Mayo Clinic Rochester Minnesota

data_processing:
CellRanger version 2.2.0 mkfastq tool was used for basecalling, which created 4 fastq files per sample from the 4 lanes of the flowcell. So, R1 has 4 fastq files; R2 has 4 fastq files; and I (index) has 4 fastq files.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98  nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
CellRanger version 2.2.0 count was used to create the matrix table for further processing.
Genome_build: mm10 plus eGFP and tdTomato sequences
Supplementary_files_format_and_content: tab-delimited text file containing gene symbols with their respective expression for each cell/barcode.

source_name: lung

extract_protocol:
The lung cells were dissociated in the digestion Buffer (10mM HEPES, 150mM NaCl, 5mM KCl, 1mM MgCl2, 1.8mM CaCl2,   2mg/ml Collagenase A, 1mg/ml Dispase II, 0.5mg/ml Elastase,  1mg/ml Dnase in PBS)  using gentleMACS Dissociator program mouse tumor implant program 01.01 and then incubated  in 37 ◦C incubator for 15 mins. After incubation, the digestion process were terminated by adding an equal volume of HBSS on ice. After straining the tissue digest through a 100-μm cell strainer, the cells were centrifuged at 300g for 10 minutes 4◦C. The cell pellets were re-suspended in 5-10 mL of RT 1X RBC lysis buffer (eBioscience 00-4333-57) for 5 minutes at RT and then diluted with an equal volume of HBSS and centrifuged again to pellets. Pellets were re-suspended in appropriate volume of FACS staining buffer (2%FBS in PBS). Each sample was added primary antibodies including Ter119-450 (Thermofisher, 48-5921-82), CD45-450 (Thermofisher, 48-0451-82) and LIVE/DEAD 450 (Thermofisher, L34963) for cell sorting and incubated for 20-30 min on ice. After washing 2 times, cells were counted and then sorted by fluorescence (antibody stainings and/or EGFP) on a BD FACS Aria II cell sorter (BD Biosciences), using FACS Diva software, into Eppendorf tube containing 20 µl of 2%FBS in PBS and stored on ice until proceeding to the GemCode Single Cell Platform.
Single cells were processed through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and Library Kits (V1) or single-cell suspensions were loaded onto 3′ library chips for the Chromium Single Cell 3′ Library (V2, PN-120267) according to the manufacturer’s recommendations (10X Genomics). In brief, single cells were partitioned into Gel Beads in Emulsion in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5′ adaptor and sample index attachment. An input of 1200 single cells was added to each channel with a recovery rate of roughly 300 cells. Libraries were sequenced on an Illumina Nextseq 500 at >190,000 reads per cell.
Libraries were sequenced on an Illumina Nextseq 500 at >190,000 reads per cell.

treatment_protocol: Sox2CreERT2;mTmG mice were placed on tamoxifen food for 3 weeks starting at 2 months of age, followed by a 2 month washout period prior to saline or bleomycin treatment. Whole lung tissues were collected, from lineage traced mice 6 weeks after saline or bleomycin treatment.

tag: strain

tag: developmental stage

value: adult

value: lung


title: A375 + FNG_RNA-seq

status: Public on Mar 31 2019

type: SRA

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

library_source: transcriptomic

data_processing:
RNA-seq aligned to reference transcript using bowtie2.
RNA-seq aligned to hg19 using HISAT(version 2.0.1-beta).
Gene expression level quantified by RSEM.
Bigwig generated after normalization.
Genome_build: Hg19
Supplementary_files_format_and_content: Bigwig

molecule: total RNA

organism: Homo sapiens

source_name: control cells treated with interferon gamma

extract_protocol:
RNA was harvested using RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard BGISEQ500 protocols

treatment_protocol: A375 cells were growth until 90% confluent, and then either treated with or without IFNG  (2000 U/ml)  for 24 hours.

tag: cell line

tag: cell type

value: Human melanoma cell line

tag: genotype/variation

value: control

tag: treatment

value: IFNG  (2000 U/ml)  for 24 h


title: A375 WTOE_RNA-seq

source_name: LNK overexpressing cells

value: overexpressing LNK


title: Lung_Injured GFP

country: USA

molecule: polyA RNA

organism: Mus musculus

value: bleomycin-mediated lung injury

tag: tissue


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_9

status: Public on Mar 13 2019

city: UTRECHT

first: Jop

last: Kind

state: utrecht

address: Upssalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_WT_Kdm5b_averOE_100kb_paternal.bedgraph

library_source: genomic

data_processing:
Library strategy: DamID-seq
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500. Sequenced reads were demultiplexed and trimmed for adaptor sequence using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}), then mapped to the mm10 genome assembly using bwa (version bwa-0.7.12) aln with default parameters. Reads aligning to the genome with quality score below 25 were discarded.
The identification of reads arising from the parental genome was carried out as follow:
The database of annotated SNPs between different mouse strains was obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/.
Hybrid C57BL/6 x CAST/EiJ or 129/Sv  x CAST/EiJ genomes were de novo compiled by nucleotide substitution of strain specific SNPs using SNPsplit_genome_preparation (version SNPsplit_v0.3.0/) in the original mm10 genome assembly. The reads were separately aligned to the parental (mm10 or hybrid) genomes using the above described parameters. The edit distance of the alignments of pre-filtered reads (quality score >= 25) was compared for the two genomes. The reads aligning with the lowest edit distance were assigned to the appropriate parental genome.The reads aligning with equal edit distance between the parental genomes were not assigned to the parental genomes but were kept for “non-allelic” profiles. The computation of Observed over Expected (OE) value per bin was carried out as described in Kind et. Al, 2015. Briefly, reads that precisely flanked an annotated GATC site were associated with GATC-fragments and kept for downstream analysis. In order to compare population samples to single cell samples, multiple reads aligning to the same position were counted as one and subsequently aggregated in genomic segments of 100kb in order to determine the experimentally Observed value. This was then divided by the Expected value per 100kb bin. The expected value was generated by in-silico determining potential DamID-seq reads of the same length as the experimental data (131 bp), aligning them to the mm10 genome assembly and selecting them based on the same filtering applied to the experimental data and aligned to GATC-fragments (see above).  The final OE value per 100 kb bins was computed by dividing the ratio of the two counts (Observed, Expected) by the total number of observed reads per bin. LAD domain calling was performed on the average population replicates for each stage in (parental or non-allelic) OE values calculated in 100kb bins using a using a two-state hidden Markov model (HMM).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for each population replicate and average of single cell experiments (both parental and non-allelic) showing the OE value per 100kb bins; bed files with LAD coordinates per stage (both parental and non-allelic)

molecule: genomic DNA

source_name: mechanically separated pronucleus

growth_protocol: Preimplantation embryos were collected from 5-8 weeks old F1 (CBAxC57BL/6J) females mated with CAST/EiJ males for hybrid crosses and with F1 males for non-hybrid crosses. Ovulation was induced by injecting 10 IU PMSG (IDT Biologika Gmbh) and then hCG (MSD Animal Health) 46-48 hours later. GV oocytes were collected 44-48 hours after PMSG injection. Reciprocal crosses (CAST/EiJ females mated with F1 males) were performed without inducing ovulation. Oocytes were cultured in IBMX containing M16 while embryos were cultured in KSOM drops under paraffin oil (Sigma). For DamID, an mRNA mixture containing 250 ng/μl TIR1, 50 ng/μl membrane-EGFP and embryonic stage dependent concentrations of AID-Dam-LaminB1 or AID-Dam-only were injected into the cytoplasm of oocytes and embryos. To methylate LADs only at the stages of interest we washed the embryos into auxin-free media for 6-8 hours at the late-S, G2 phases of the cell cycle. Oocytes (48 hours post PMSG) and zygotes (21 hours post hCG) were isolated and injected with 5 ng/μl AID-Dam-LaminB1 or 20 ng/μl AID-Dam-only and kept in auxin free KSOM for 6-8 hours to methylate LADs or accessible regions, respectively.  For DamID at 2-cell stage late-zygotes (27-28 hours post hCG) were isolated and injected with 10 ng/μl AID-Dam-LaminB1 or 40 ng/μl AID-Dam-only in auxin (500μM) containing media. Auxin was removed at 2-cell stage for 6-8 hours (from 42 to 48-50 hours post hCG). For DamID at 8-cell stage late-2-cell embryos (46-48 hours post hCG) were isolated and injected with 20 ng/μl AID-Dam-LaminB1 or 40 ng/μl AID-Dam-only in auxin containing media. Auxin was removed at 8-cell stage for 6-8 hours (from 66 to 72-74 hours post hCG). Afterwards, the zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C and the polar bodies were mechanically separated from the embryos and discarded. Either pools of 20 blastomeres or single blastomeres were placed into 2 μl of DamID buffer (10mM TRIS acetate pH 7.5, 10mM magnesium acetate, 50mM potassium acetate) and stored at -80 °C until downstream processing.

extract_protocol:
Embryos were captured by mouth pipetting and directly transferred into a PCR strip filled with 2ul DamID buffer (10mM TRIS acetate pH 7.5, 10mM magnesium acetate, 50mM potassium acetate) and stored at -80 °C until downstream processing.
Libraries were prepared in accordance with the Illumina TruSeq Nano DNA LT Library Prep Kit (#FC-121-4402). Briefly, 300ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit, (Epicentre #ER81050). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads (Beckman Coulter #A63881) with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation.

treatment_protocol:
For DamID in replication inhibited 2-cell embryos, late zygotes (26-28 hours post hCG) from hybrid crosses (CBAxC57BL/6J females mated with CAST/EiJ males) were injected with 10 ng/μl AID-Dam-LaminB1, 250 ng/μl TIR1 and 50 ng/μl membrane-EGFP coding mRNA and kept in auxin containing media to prevent Dam activity in the zygote. Embryos were washed into aphidicoline (3 μg/ml) containing media when reaching the first metaphase. Auxin was removed from 42 to 48-50 hours post hCG to allow methylation of LADs in the late 2-cell stage.
For DamID in Kdm5B overexpressing embryos, early zygotes (18 hours post hCG) were injected with 2 μg/μl wild-type or mutant Kdm5B, 5 ng/μl AID-Dam-LaminB1, 250 ng/μl TIR1 and 50 ng/μl membrane-EGFP coding mRNA. Zygotes were kept in auxin containing KSOM for 3 hours to prevent adenine methylation during pronucleus formation. At 21 hours post hCG auxin was removed for 6-8 hours to allow methylation. To separate pronuclei, the PN5 zygotes were transferred to M2 media containing 10 μg/ml cytochalasin B (Sigma-Aldrich). The zona pellucida was cut with a Piezo driven micromanipulator and one of the pronuclei was isolated into M2 drops. The pronuclei were distinguished based on their size and their relative position to the second polar body.

tag: damid profiling

tag: mrna injected

tag: treatments

tag: number of cells

value: mechanically separated pronucleus


title: DMC1 B6CASTF1 PRDM9hc

status: Public on Mar 18 2019

city: Oxford

first: Anjali

middle: Gupta

last: Hinch

address: Roosevelt Drive

department: WCHG

country: United Kingdom

institute: Oxford University

data_processing:
Alignment with a modified BWA mapper (Khil et al., 2012)
Peaks were called using an in-house algorithm R code available at https://github.com/anjali-hinch/hybrid-rescue
Alleles were called using an in-house algorithm (described in Hinch et al)
[Third-party reanalysis] H3K4me3 calls were made using an in-house algorithm (Hinch et al) using raw data from GSE119727
Filtering of false-positive hotspots and overlap with PRDM9-independent H3K4me3 were performed using in-house algorithm (Hinch et al)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with column descriptions in commented header; each line corresponds to one DMC1 peak

source_name: whole adult testis

growth_protocol: Data were generated from in vivo tissue samples from a 10 week old male mouse - no culturing was performed.

extract_protocol:
Testes samples were stripped of the tunica and processed as described in Khil et al, Genome Research, 2012). Single-stranded DNA sequencing and double-strand break detection were performed using a modified DMC1 ChIPseq protocol (Khil et al, as above). Full experimental procedures are reported in accompanying manuscript (Hinch et al).
Libraries were prepared according to Illumina's instructions

value: testis

tag: prdm9 genotype

value: HUM/CAST


title: 2cell-DMSO_LmnB1_pop_1

description:
2cell-DMSO_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
2cell-DMSO_LmnB1_pop_1_OE_100kb_maternal.bedgraph
2cell-DMSO_LmnB1_pop_1_OE_100kb_paternal.bedgraph

value: DMSO

value: C57BL/6 female x CAST/EiJ male


title: 2cell-aphidicolin_LmnB1_pop_2

description:
2cell-aphidicolin_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
2cell-aphidicolin_LmnB1_pop_2_OE_100kb_maternal.bedgraph
2cell-aphidicolin_LmnB1_pop_2_OE_100kb_paternal.bedgraph

value: aphidicolin


title: 2cell-aphidicolin_LmnB1_pop_4

description:
2cell-aphidicolin_LmnB1_pop_4_OE_100kb_non-allelic.bedgraph
2cell-aphidicolin_LmnB1_pop_4_OE_100kb_maternal.bedgraph
2cell-aphidicolin_LmnB1_pop_4_OE_100kb_paternal.bedgraph


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_6


title: 2cell-aphidicolin_LmnB1_pop_3

description:
2cell-aphidicolin_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph
2cell-aphidicolin_LmnB1_pop_3_OE_100kb_maternal.bedgraph
2cell-aphidicolin_LmnB1_pop_3_OE_100kb_paternal.bedgraph


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_4


title: 2cell-DMSO_LmnB1_pop_2

description:
2cell-DMSO_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
2cell-DMSO_LmnB1_pop_2_OE_100kb_maternal.bedgraph
2cell-DMSO_LmnB1_pop_2_OE_100kb_paternal.bedgraph


title: 2cell-aphidicolin_LmnB1_pop_1

description:
2cell-aphidicolin_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
2cell-aphidicolin_LmnB1_pop_1_OE_100kb_maternal.bedgraph
2cell-aphidicolin_LmnB1_pop_1_OE_100kb_paternal.bedgraph


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_8


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_5


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_19


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_3


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_2


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_18


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_16


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_7


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_15


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_14


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_13


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_17


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_12


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_11


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_5

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_MUTANT_Kdm5b_averOE_100kb_paternal.bedgraph


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_1


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_1


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_6


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_2


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_3


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_9

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_WT_Kdm5b_averOE_100kb_maternal.bedgraph


title: zygote_pat_pron_WT_Kdm5b_LmnB1_sc_10


title: zygote_pat_pron_MUTANT_Kdm5b_LmnB1_sc_4


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_7


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_6


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_8


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_2


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_19


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_18


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_17


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_13


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_4


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_5


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_15


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_14


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_3


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_12


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_10


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_11


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_9

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_MUTANT_Kdm5b_averOE_100kb_maternal.bedgraph


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_8


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_7


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_1


title: zygote_mat_pron_WT_Kdm5b_LmnB1_sc_16


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_6


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_4


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_3


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_10


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_1


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_11


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_5


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_12


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_2


title: zygote_mat_pron_MUTANT_Kdm5b_LmnB1_sc_13


title: zygote_pat_pron_LmnB1_sc_9

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_sc_averOE_100kb_paternal.bedgraph


title: zygote_pat_pron_LmnB1_sc_7


title: zygote_pat_pron_LmnB1_sc_8


title: zygote_pat_pron_LmnB1_sc_6


title: zygote_pat_pron_LmnB1_sc_5


title: zygote_pat_pron_LmnB1_sc_2


title: zygote_pat_pron_LmnB1_sc_4


title: zygote_pat_pron_LmnB1_sc_1


title: zygote_pat_pron_LmnB1_sc_11


title: zygote_pat_pron_LmnB1_sc_12


title: zygote_pat_pron_LmnB1_sc_13


title: zygote_pat_pron_LmnB1_sc_15


title: zygote_mat_pron_LmnB1_sc_9

description:
OE_all_sc_non-allelic.txt
zygote_pronuclei_LmnB1_sc_averOE_100kb_maternal.bedgraph


title: zygote_pat_pron_LmnB1_sc_14


title: zygote_pat_pron_LmnB1_sc_3


title: zygote_mat_pron_LmnB1_sc_8


title: zygote_mat_pron_LmnB1_sc_6


title: zygote_mat_pron_LmnB1_sc_7


title: zygote_pat_pron_LmnB1_sc_10


title: zygote_mat_pron_LmnB1_sc_5


title: zygote_mat_pron_LmnB1_sc_4


title: zygote_mat_pron_LmnB1_sc_3


title: zygote_mat_pron_LmnB1_sc_1


title: zygote_mat_pron_LmnB1_sc_2


title: ES_LmnB1_sc_8

source_name: mES cells

value: mES cells

value: 129/Sv female x CAST/EiJ male


title: ES_LmnB1_sc_9


title: ES_LmnB1_sc_4


title: ES_LmnB1_sc_6


title: ES_LmnB1_sc_7


title: ES_LmnB1_sc_5


title: ES_LmnB1_sc_10


title: ES_LmnB1_sc_11


title: ES_LmnB1_sc_13


title: zygote_mat_pron_LmnB1_sc_10


title: 8cell_LmnB1_sc_5


title: ES_LmnB1_pop_2

description:
ES_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
ES_LmnB1_pop_2_OE_100kb_maternal.bedgraph
ES_LmnB1_pop_2_OE_100kb_paternal.bedgraph
ES_non-allelic_LAD_coordinates.bed
ES_maternal_LAD_coordinates.bed
ES_paternal_LAD_coordinates.bed


title: 8cell_LmnB1_sc_8


title: 8cell_LmnB1_sc_7


title: 8cell_LmnB1_sc_6


title: ES_Dam_pop_2

description:
ES_Dam_pop_2_OE_100kb_non-allelic.bedgraph
ES_Dam_pop_2_OE_100kb_maternal.bedgraph
ES_Dam_pop_2_OE_100kb_paternal.bedgraph

value: Dam


title: ES_Dam_pop_3

description:
ES_Dam_pop_3_OE_100kb_non-allelic.bedgraph
ES_Dam_pop_3_OE_100kb_maternal.bedgraph
ES_Dam_pop_3_OE_100kb_paternal.bedgraph


title: ES_LmnB1_pop_3

description:
ES_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph
ES_LmnB1_pop_3_OE_100kb_maternal.bedgraph
ES_LmnB1_pop_3_OE_100kb_paternal.bedgraph
ES_non-allelic_LAD_coordinates.bed
ES_maternal_LAD_coordinates.bed
ES_paternal_LAD_coordinates.bed


title: 8cell_LmnB1_sc_45


title: 8cell_LmnB1_sc_9


title: 8cell_LmnB1_sc_43


title: ES_Dam_pop_1

description:
ES_Dam_pop_1_OE_100kb_non-allelic.bedgraph
ES_Dam_pop_1_OE_100kb_maternal.bedgraph
ES_Dam_pop_1_OE_100kb_paternal.bedgraph


title: 8cell_LmnB1_sc_42


title: 8cell_LmnB1_sc_44


title: 8cell_LmnB1_sc_4


title: 8cell_LmnB1_sc_39


title: 8cell_LmnB1_sc_40


title: 8cell_LmnB1_sc_41


title: ES_LmnB1_pop_1

description:
ES_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
ES_LmnB1_pop_1_OE_100kb_maternal.bedgraph
ES_LmnB1_pop_1_OE_100kb_paternal.bedgraph
ES_non-allelic_LAD_coordinates.bed
ES_maternal_LAD_coordinates.bed
ES_paternal_LAD_coordinates.bed


title: 8cell_LmnB1_sc_37


title: 8cell_LmnB1_sc_38


title: 8cell_LmnB1_sc_36


title: ES_LmnB1_sc_12


title: 8cell_LmnB1_sc_30


title: 8cell_LmnB1_sc_34


title: 8cell_LmnB1_sc_31


title: 8cell_LmnB1_sc_32


title: 8cell_LmnB1_sc_33


title: 8cell_LmnB1_sc_29


title: 8cell_LmnB1_sc_35


title: 8cell_LmnB1_sc_28


title: 8cell_LmnB1_sc_25


title: 8cell_LmnB1_sc_27


title: 8cell_LmnB1_sc_22


title: 8cell_LmnB1_sc_24


title: 8cell_LmnB1_sc_23


title: 8cell_LmnB1_sc_26


title: 8cell_LmnB1_sc_19


title: 8cell_LmnB1_sc_18


title: 8cell_LmnB1_sc_16


title: 8cell_LmnB1_sc_15


title: 8cell_LmnB1_sc_17


title: 8cell_LmnB1_sc_14


title: 8cell_LmnB1_sc_13


title: 8cell_LmnB1_sc_10


title: 8cell_LmnB1_sc_11


title: 8cell_LmnB1_sc_12


title: 8cell_LmnB1_pop_3

description:
8cell_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph
8cell_LmnB1_pop_3_OE_100kb_maternal.bedgraph
8cell_LmnB1_pop_3_OE_100kb_paternal.bedgraph
8cell_non-allelic_LAD_coordinates.bed
8cell_maternal_LAD_coordinates.bed
8cell_paternal_LAD_coordinates.bed


title: 8cell_Dam_sc_6


title: 8cell_Dam_sc_5


title: 8cell_Dam_sc_7


title: 8cell_LmnB1_sc_20


title: 8cell_Dam_pop_3

description:
8cell_Dam_pop_3_OE_100kb_non-allelic.bedgraph
8cell_Dam_pop_3_OE_100kb_maternal.bedgraph
8cell_Dam_pop_3_OE_100kb_paternal.bedgraph


title: 8cell_Dam_pop_2

description:
8cell_Dam_pop_2_OE_100kb_non-allelic.bedgraph
8cell_Dam_pop_2_OE_100kb_maternal.bedgraph
8cell_Dam_pop_2_OE_100kb_paternal.bedgraph


title: 8cell_LmnB1_sc_21


title: 8cell_Dam_sc_4


title: 2cell_LmnB1_sc_9


title: 8cell_Dam_pop_1

description:
8cell_Dam_pop_1_OE_100kb_non-allelic.bedgraph
8cell_Dam_pop_1_OE_100kb_maternal.bedgraph
8cell_Dam_pop_1_OE_100kb_paternal.bedgraph


title: 2cell_LmnB1_sc_6


title: 2cell_LmnB1_sc_7


title: 2cell_LmnB1_sc_5


title: 2cell_LmnB1_sc_44


title: 2cell_LmnB1_sc_45


title: 2cell_LmnB1_sc_43


title: 2cell_LmnB1_sc_46


title: 2cell_LmnB1_sc_49


title: 2cell_LmnB1_sc_48


title: 8cell_LmnB1_pop_1

description:
8cell_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
8cell_LmnB1_pop_1_OE_100kb_maternal.bedgraph
8cell_LmnB1_pop_1_OE_100kb_paternal.bedgraph
8cell_non-allelic_LAD_coordinates.bed
8cell_maternal_LAD_coordinates.bed
8cell_paternal_LAD_coordinates.bed


title: 2cell_LmnB1_sc_50


title: 8cell_LmnB1_pop_2

description:
8cell_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
8cell_LmnB1_pop_2_OE_100kb_maternal.bedgraph
8cell_LmnB1_pop_2_OE_100kb_paternal.bedgraph
8cell_non-allelic_LAD_coordinates.bed
8cell_maternal_LAD_coordinates.bed
8cell_paternal_LAD_coordinates.bed


title: 2cell_LmnB1_sc_42


title: 2cell_LmnB1_sc_40


title: 2cell_LmnB1_sc_4


title: 2cell_LmnB1_sc_8


title: 2cell_LmnB1_sc_38


title: 2cell_LmnB1_sc_37


title: 2cell_LmnB1_sc_36


title: 2cell_LmnB1_sc_47


title: 2cell_LmnB1_sc_35


title: 2cell_LmnB1_sc_34


title: 2cell_LmnB1_sc_31


title: 2cell_LmnB1_sc_33


title: 2cell_LmnB1_sc_32


title: 2cell_LmnB1_sc_28


title: 2cell_LmnB1_sc_29


title: 2cell_LmnB1_sc_25


title: 2cell_LmnB1_sc_26


title: 2cell_LmnB1_sc_27


title: 2cell_LmnB1_sc_20


title: 2cell_LmnB1_sc_21


title: 2cell_LmnB1_sc_19


title: 2cell_LmnB1_sc_22


title: 2cell_LmnB1_sc_24


title: 2cell_LmnB1_sc_39


title: 2cell_LmnB1_sc_41


title: 2cell_LmnB1_sc_23


title: 2cell_LmnB1_sc_18


title: 2cell_LmnB1_sc_17


title: 2cell_LmnB1_sc_16


title: 2cell_LmnB1_sc_12


title: 2cell_LmnB1_sc_11


title: 2cell_LmnB1_sc_13


title: 2cell_LmnB1_sc_14


title: 2cell_LmnB1_pop_3

description:
2cell_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph
2cell_LmnB1_pop_3_OE_100kb_maternal.bedgraph
2cell_LmnB1_pop_3_OE_100kb_paternal.bedgraph
2cell_non-allelic_LAD_coordinates.bed
2cell_maternal_LAD_coordinates.bed
2cell_paternal_LAD_coordinates.bed


title: 2cell_LmnB1_pop_2

description:
2cell_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
2cell_LmnB1_pop_2_OE_100kb_maternal.bedgraph
2cell_LmnB1_pop_2_OE_100kb_paternal.bedgraph
2cell_non-allelic_LAD_coordinates.bed
2cell_maternal_LAD_coordinates.bed
2cell_paternal_LAD_coordinates.bed


title: 2cell_LmnB1_pop_1

description:
2cell_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
2cell_LmnB1_pop_1_OE_100kb_maternal.bedgraph
2cell_LmnB1_pop_1_OE_100kb_paternal.bedgraph
2cell_non-allelic_LAD_coordinates.bed
2cell_maternal_LAD_coordinates.bed
2cell_paternal_LAD_coordinates.bed


title: 2cell_Dam_sc_9


title: 2cell_LmnB1_sc_30


title: 2cell_Dam_sc_6


title: 2cell_Dam_sc_8


title: 2cell_Dam_sc_7


title: 2cell_Dam_sc_5


title: 2cell_Dam_sc_46


title: 2cell_Dam_sc_45


title: 2cell_Dam_sc_47


title: 2cell_Dam_sc_44


title: 2cell_LmnB1_sc_15


title: 2cell_Dam_sc_43


title: 2cell_Dam_sc_41


title: 2cell_Dam_sc_40


title: 2cell_Dam_sc_4


title: 2cell_Dam_sc_39


title: 2cell_Dam_sc_38


title: 2cell_Dam_sc_37


title: 2cell_Dam_sc_36


title: 2cell_LmnB1_sc_10


title: 2cell_Dam_sc_35


title: 2cell_Dam_sc_34


title: 2cell_Dam_sc_31


title: 2cell_Dam_sc_30


title: 2cell_Dam_sc_29


title: 2cell_Dam_sc_32


title: 2cell_Dam_sc_27


title: 2cell_Dam_sc_26


title: 2cell_Dam_sc_48


title: 2cell_Dam_sc_24


title: 2cell_Dam_sc_25


title: 2cell_Dam_sc_23


title: 2cell_Dam_sc_22


title: 2cell_Dam_sc_42


title: 2cell_Dam_sc_28


title: 2cell_Dam_sc_19


title: 2cell_Dam_sc_18


title: 2cell_Dam_sc_17


title: 2cell_Dam_sc_20


title: 2cell_Dam_sc_15


title: 2cell_Dam_sc_13


title: 2cell_Dam_sc_11


title: 2cell_Dam_sc_21


title: 2cell_Dam_sc_12


title: 2cell_Dam_sc_33


title: 2cell_Dam_sc_10


title: 2cell-recipr_LmnB1_pop_2

description:
2cell-recipr_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
2cell-recipr_LmnB1_pop_2_OE_100kb_maternal.bedgraph
2cell-recipr_LmnB1_pop_2_OE_100kb_paternal.bedgraph

value: CAST/EiJ female x C57BL/6 male


title: 2cell_Dam_pop_1

description:
2cell_Dam_pop_1_OE_100kb_non-allelic.bedgraph
2cell_Dam_pop_1_OE_100kb_maternal.bedgraph
2cell_Dam_pop_1_OE_100kb_paternal.bedgraph


title: 2cell_Dam_pop_2

description:
2cell_Dam_pop_2_OE_100kb_non-allelic.bedgraph
2cell_Dam_pop_2_OE_100kb_maternal.bedgraph
2cell_Dam_pop_2_OE_100kb_paternal.bedgraph


title: 2cell-recipr_LmnB1_pop_1

description:
2cell-recipr_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
2cell-recipr_LmnB1_pop_1_OE_100kb_maternal.bedgraph
2cell-recipr_LmnB1_pop_1_OE_100kb_paternal.bedgraph


title: zygote_LmnB1_sc_8

source_name: zygote

value: zygote


title: zygote_LmnB1_sc_5


title: zygote_LmnB1_sc_4


title: zygote_LmnB1_sc_22


title: zygote_LmnB1_sc_20


title: zygote_LmnB1_sc_6


title: 2cell_Dam_sc_14


title: 2cell_Dam_sc_16


title: zygote_LmnB1_sc_17


title: zygote_LmnB1_sc_18


title: zygote_LmnB1_sc_16


title: zygote_LmnB1_sc_15


title: zygote_LmnB1_sc_14


title: zygote_LmnB1_sc_13


title: 2cell_Dam_pop_3

description:
2cell_Dam_pop_3_OE_100kb_non-allelic.bedgraph
2cell_Dam_pop_3_OE_100kb_maternal.bedgraph
2cell_Dam_pop_3_OE_100kb_paternal.bedgraph


title: zygote_LmnB1_sc_11


title: zygote_LmnB1_sc_10


title: zygote_LmnB1_pop_1

description:
zygote_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph
zygote_LmnB1_pop_1_OE_100kb_maternal.bedgraph
zygote_LmnB1_pop_1_OE_100kb_paternal.bedgraph
zygote_non-allelic_LAD_coordinates.bed
zygote_maternal_LAD_coordinates.bed
zygote_paternal_LAD_coordinates.bed


title: zygote_LmnB1_pop_2

description:
zygote_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph
zygote_LmnB1_pop_2_OE_100kb_maternal.bedgraph
zygote_LmnB1_pop_2_OE_100kb_paternal.bedgraph
zygote_non-allelic_LAD_coordinates.bed
zygote_maternal_LAD_coordinates.bed
zygote_paternal_LAD_coordinates.bed


title: zygote_LmnB1_sc_9


title: zygote_Dam_sc_9


title: zygote_LmnB1_sc_7


title: zygote_Dam_sc_6


title: zygote_Dam_sc_4


title: zygote_Dam_sc_7


title: zygote_LmnB1_sc_21


title: zygote_Dam_sc_5


title: zygote_Dam_sc_8


title: zygote_LmnB1_sc_19


title: zygote_Dam_sc_49


title: zygote_Dam_sc_48


title: zygote_Dam_sc_47


title: zygote_LmnB1_sc_12


title: zygote_LmnB1_pop_3

description:
zygote_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph
zygote_LmnB1_pop_3_OE_100kb_maternal.bedgraph
zygote_LmnB1_pop_3_OE_100kb_paternal.bedgraph
zygote_non-allelic_LAD_coordinates.bed
zygote_maternal_LAD_coordinates.bed
zygote_paternal_LAD_coordinates.bed


title: zygote_Dam_sc_44


title: zygote_Dam_sc_45


title: zygote_Dam_sc_43


title: oocyte_LmnB1_sc_8

data_processing:
library strategy: DamID-seq
Basecalling and filtering were performed using standard software of the Illumina Illumina HiSeq 2500. Sequenced reads were demultiplexed and trimmed for adaptor sequence using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}), then mapped to the mm10 genome assembly using bwa (version bwa-0.7.12) aln with default parameters. Reads aligning to the genome with quality score below 25 were discarded.
The identification of reads arising from the parental genome was carried out as follow:
The database of annotated SNPs between different mouse strains was obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/.
Hybrid C57BL/6 x CAST/EiJ or 129/Sv  x CAST/EiJ genomes were de novo compiled by nucleotide substitution of strain specific SNPs using SNPsplit_genome_preparation (version SNPsplit_v0.3.0/) in the original mm10 genome assembly. The reads were separately aligned to the parental (mm10 or hybrid) genomes using the above described parameters. The edit distance of the alignments of pre-filtered reads (quality score >= 25) was compared for the two genomes. The reads aligning with the lowest edit distance were assigned to the appropriate parental genome.The reads aligning with equal edit distance between the parental genomes were not assigned to the parental genomes but were kept for “non-allelic” profiles. The computation of Observed over Expected (OE) value per bin was carried out as described in Kind et. Al, 2015. Briefly, reads that precisely flanked an annotated GATC site were associated with GATC-fragments and kept for downstream analysis. In order to compare population samples to single cell samples, multiple reads aligning to the same position were counted as one and subsequently aggregated in genomic segments of 100kb in order to determine the experimentally Observed value. This was then divided by the Expected value per 100kb bin. The expected value was generated by in-silico determining potential DamID-seq reads of the same length as the experimental data (131 bp), aligning them to the mm10 genome assembly and selecting them based on the same filtering applied to the experimental data and aligned to GATC-fragments (see above).  The final OE value per 100 kb bins was computed by dividing the ratio of the two counts (Observed, Expected) by the total number of observed reads per bin. LAD domain calling was performed on the average population replicates for each stage in (parental or non-allelic) OE values calculated in 100kb bins using a using a two-state hidden Markov model (HMM).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for each population replicate and average of single cell experiments (both parental and non-allelic) showing the OE value per 100kb bins; bed files with LAD coordinates per stage (both parental and non-allelic)
Supplementary_files_format_and_content: The 'OE_all_sc_non-allelic_resubmission.txt contains processed data for all the "sc" samples,  the bedgraph files have processed data for the  "pop" samples.

source_name: oocyte

treatment_protocol:
For DamID in replication inhibited 2-cell embryos, late zygotes (26-28 hours post hCG) from hybrid crosses (CBAxC57BL/6J females mated with CAST/EiJ males) were injected with 10 ng/μl AID-Dam-LaminB1, 250 ng/μl TIR1 and 50 ng/μl membrane-EGFP coding mRNA and kept in auxin containing media to prevent Dam activity in the zygote. Embryos were washed into aphidicoline (3 μg/ml) containing media when reaching the first metaphase. Auxin was removed from 42 to 48-50 hours post hCG to allow methylation of LADs in the late 2-cell stage.
For the ICM/TE samples, 4-cell embryos were injected with 100ng/ul AID-Dam-lamin B1 or Dam-only mRNA at 60-62 hours post hCG injection. IAA was washed out at 90 hours post hCG when blastocysts started to cavitate. Embryos were treated with pronase at 96 hours and incubated in Fluorospheres (F8811 – Sigma) to mark TE cells for 2 minutes. Residual Fluorospheres were washed away and embryos were kept in Calcium-free M2 medium for 25 minutes followed by mechanical disaggregation. Fluorosphere positive TE cells were separated from  negative ICM cells under a fluorescent microscope and placed into DamID buffer.
For DamID in Kdm5B overexpressing embryos, early zygotes (18 hours post hCG) were injected with 2 μg/μl wild-type or mutant Kdm5B, 5 ng/μl AID-Dam-LaminB1, 250 ng/μl TIR1 and 50 ng/μl membrane-EGFP coding mRNA. Zygotes were kept in auxin containing KSOM for 3 hours to prevent adenine methylation during pronucleus formation. At 21 hours post hCG auxin was removed for 6-8 hours to allow methylation. To separate pronuclei, the PN5 zygotes were transferred to M2 media containing 10 μg/ml cytochalasin B (Sigma-Aldrich). The zona pellucida was cut with a Piezo driven micromanipulator and one of the pronuclei was isolated into M2 drops. The pronuclei were distinguished based on their size and their relative position to the second polar body.


title: oocyte_LmnB1_sc_5


title: oocyte_LmnB1_sc_56


title: oocyte_LmnB1_sc_53


title: oocyte_LmnB1_sc_57


title: oocyte_LmnB1_sc_52


title: oocyte_LmnB1_sc_55


title: oocyte_LmnB1_sc_58


title: oocyte_LmnB1_sc_49


title: oocyte_LmnB1_sc_47


title: oocyte_LmnB1_sc_51


title: oocyte_LmnB1_sc_48


title: oocyte_LmnB1_sc_50


title: oocyte_LmnB1_sc_46


title: zygote_Dam_sc_46


title: oocyte_LmnB1_sc_4


title: oocyte_LmnB1_sc_45


title: oocyte_LmnB1_sc_7


title: oocyte_LmnB1_sc_54


title: oocyte_LmnB1_sc_9


title: oocyte_LmnB1_sc_6


title: oocyte_LmnB1_sc_42


title: oocyte_LmnB1_sc_41


title: oocyte_LmnB1_sc_39


title: oocyte_LmnB1_sc_40


title: oocyte_LmnB1_sc_44


title: oocyte_LmnB1_sc_38


title: oocyte_LmnB1_sc_37


title: oocyte_LmnB1_sc_43


title: oocyte_LmnB1_sc_59


title: oocyte_LmnB1_sc_35


title: oocyte_LmnB1_sc_36


title: oocyte_LmnB1_sc_33


title: oocyte_LmnB1_sc_29


title: oocyte_LmnB1_sc_34


title: oocyte_LmnB1_sc_30


title: oocyte_LmnB1_sc_32


title: oocyte_LmnB1_sc_27


title: oocyte_LmnB1_sc_31


title: oocyte_LmnB1_sc_28


title: oocyte_LmnB1_sc_21


title: oocyte_LmnB1_sc_24


title: oocyte_LmnB1_sc_25


title: oocyte_LmnB1_sc_23


title: oocyte_LmnB1_sc_20


title: oocyte_LmnB1_sc_19


title: oocyte_LmnB1_sc_22


title: oocyte_LmnB1_sc_26


title: oocyte_LmnB1_sc_17


title: oocyte_LmnB1_sc_18


title: oocyte_LmnB1_sc_16


title: oocyte_LmnB1_sc_15


title: oocyte_LmnB1_sc_14


title: oocyte_LmnB1_sc_11


title: oocyte_LmnB1_sc_13


title: oocyte_LmnB1_sc_12


title: oocyte_Dam_sc_9


title: oocyte_LmnB1_sc_10


title: oocyte_Dam_sc_8


title: oocyte_Dam_sc_7


title: oocyte_Dam_sc_6


title: oocyte_Dam_sc_5


title: oocyte_Dam_sc_4


title: oocyte_Dam_sc_39


title: oocyte_Dam_sc_44


title: oocyte_Dam_sc_46


title: oocyte_Dam_sc_38


title: oocyte_Dam_sc_32


title: oocyte_Dam_sc_41


title: oocyte_Dam_sc_36


title: oocyte_Dam_sc_37


title: oocyte_Dam_sc_34


title: oocyte_Dam_sc_43


title: oocyte_Dam_sc_35


title: oocyte_Dam_sc_31


title: oocyte_Dam_sc_30


title: oocyte_Dam_sc_33


title: oocyte_Dam_sc_42


title: oocyte_Dam_sc_25


title: oocyte_Dam_sc_27


title: oocyte_Dam_sc_29


title: oocyte_Dam_sc_23


title: oocyte_Dam_sc_28


title: oocyte_Dam_sc_24


title: oocyte_Dam_sc_21


title: oocyte_Dam_sc_22


title: oocyte_Dam_sc_26


title: oocyte_Dam_sc_20


title: oocyte_Dam_sc_40


title: oocyte_Dam_sc_19


title: oocyte_Dam_sc_18


title: oocyte_Dam_sc_17


title: oocyte_Dam_sc_45


title: oocyte_Dam_sc_16


title: oocyte_Dam_sc_15


title: oocyte_Dam_sc_14


title: oocyte_Dam_sc_12


title: oocyte_Dam_sc_11


title: oocyte_Dam_sc_10


title: oocyte_Dam_sc_13


title: zygote_Kdm4d_WT_LmnB1_sc.6

description: processed data file: OE_all_sc_non-allelic_resubmission.txt

data_processing:
library strategy: DamID-seq
Basecalling and filtering were performed using standard software of the Illumina HiSeq 2500. Sequenced reads were demultiplexed and trimmed for adaptor sequence using custom scripts and cutadapt {Martin, 2011, http://dx.doi.org/10.14806/ej.17.1.200}), then mapped to the mm10 genome assembly using bwa (version bwa-0.7.12) aln with default parameters. Reads aligning to the genome with quality score below 25 were discarded.
The identification of reads arising from the parental genome was carried out as follow:
The database of annotated SNPs between different mouse strains was obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/.
Hybrid C57BL/6 x CAST/EiJ or 129/Sv  x CAST/EiJ genomes were de novo compiled by nucleotide substitution of strain specific SNPs using SNPsplit_genome_preparation (version SNPsplit_v0.3.0/) in the original mm10 genome assembly. The reads were separately aligned to the parental (mm10 or hybrid) genomes using the above described parameters. The edit distance of the alignments of pre-filtered reads (quality score >= 25) was compared for the two genomes. The reads aligning with the lowest edit distance were assigned to the appropriate parental genome.The reads aligning with equal edit distance between the parental genomes were not assigned to the parental genomes but were kept for “non-allelic” profiles. The computation of Observed over Expected (OE) value per bin was carried out as described in Kind et. Al, 2015. Briefly, reads that precisely flanked an annotated GATC site were associated with GATC-fragments and kept for downstream analysis. In order to compare population samples to single cell samples, multiple reads aligning to the same position were counted as one and subsequently aggregated in genomic segments of 100kb in order to determine the experimentally Observed value. This was then divided by the Expected value per 100kb bin. The expected value was generated by in-silico determining potential DamID-seq reads of the same length as the experimental data (131 bp), aligning them to the mm10 genome assembly and selecting them based on the same filtering applied to the experimental data and aligned to GATC-fragments (see above).  The final OE value per 100 kb bins was computed by dividing the ratio of the two counts (Observed, Expected) by the total number of observed reads per bin. LAD domain calling was performed on the average population replicates for each stage in (parental or non-allelic) OE values calculated in 100kb bins using a using a two-state hidden Markov model (HMM).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for each population replicate and average of single cell experiments (both parental and non-allelic) showing the OE value per 100kb bins; bed files with LAD coordinates per stage (both parental and non-allelic)
Supplementary_files_format_and_content: The 'OE_all_sc_non-allelic_resubmission.txt contains processed data for all the "sc" samples,  the bedgraph files have processed data for the  "pop" samples.


title: zygote_Kdm4d_MUT_LmnB1_sc.8


title: zygote_Kdm4d_MUT_LmnB1_sc.6


title: zygote_Kdm4d_MUT_LmnB1_sc.5


title: zygote_Kdm4d_WT_LmnB1_sc.8


title: zygote_Kdm4d_MUT_LmnB1_sc.4


title: zygote_Kdm4d_WT_LmnB1_sc.10


title: zygote_Kdm4d_WT_LmnB1_sc.12


title: zygote_Kdm4d_WT_LmnB1_sc.9


title: zygote_Kdm4d_WT_LmnB1_sc.11


title: zygote_Kdm4d_MUT_LmnB1_sc.7


title: zygote_Kdm4d_MUT_LmnB1_sc.1


title: zygote_Kdm4d_WT_LmnB1_sc.7


title: zygote_Kdm4d_MUT_LmnB1_sc.3


title: zygote_Kdm4d_WT_LmnB1_sc.5


title: zygote_Kdm4d_WT_LmnB1_sc.2


title: zygote_Kdm4d_MUT_LmnB1_sc.10


title: zygote_Kdm4d_WT_LmnB1_sc.1


title: zygote_Kdm4d_MUT_LmnB1_sc.9


title: zygote_Kdm4d_MUT_LmnB1_sc.2


title: zygote_Kdm4d_WT_LmnB1_sc.3


title: zygote_Kdm4d_WT_LmnB1_sc.4


title: ICM_LmnB1_pop.3

description: processed data file: ICM_non-allelic_LAD_coordinates.bed

source_name: ICM

value: whole ICM


title: ICM_LmnB1_pop.2


title: oocyte_50ng_LmnB1_sc.27

value: Dam_LmnB1 50ng


title: TE_LmnB1_pop.1

description: processed data file: TE_non-allelic_LAD_coordinates.bed

source_name: TE

value: whole TE


title: TE_LmnB1_pop.2


title: ICM_LmnB1_pop.1


title: oocyte_50ng_LmnB1_sc.23


title: oocyte_20ng_LmnB1_sc.26


title: oocyte_20ng_LmnB1_sc.18


title: oocyte_20ng_LmnB1_sc.19


title: oocyte_20ng_LmnB1_sc.20


title: oocyte_50ng_LmnB1_sc.21


title: TE_LmnB1_pop.3


title: oocyte_20ng_LmnB1_sc.25


title: oocyte_50ng_LmnB1_sc.26


title: oocyte_20ng_LmnB1_sc.22


title: oocyte_20ng_LmnB1_sc.24


title: oocyte_50ng_LmnB1_sc.25


title: oocyte_50ng_LmnB1_sc.22


title: oocyte_50ng_LmnB1_sc.19


title: oocyte_50ng_LmnB1_sc.24


title: oocyte_20ng_LmnB1_sc.21


title: oocyte_50ng_LmnB1_sc.20


title: oocyte_50ng_LmnB1_sc.17


title: oocyte_50ng_LmnB1_sc.18


title: oocyte_50ng_LmnB1_sc.16


title: oocyte_50ng_LmnB1_sc.15


title: oocyte_50ng_LmnB1_sc.14


title: oocyte_50ng_LmnB1_sc.13


title: oocyte_20ng_LmnB1_sc.23


title: oocyte_50ng_LmnB1_sc.12


title: oocyte_50ng_LmnB1_sc.11


title: oocyte_50ng_LmnB1_sc.10


title: oocyte_50ng_LmnB1_sc.9


title: oocyte_50ng_LmnB1_sc.8


title: oocyte_50ng_LmnB1_sc.7


title: oocyte_50ng_LmnB1_sc.5


title: oocyte_50ng_LmnB1_sc.6


title: oocyte_20ng_LmnB1_sc.17

value: Dam_LmnB1 20ng


title: oocyte_20ng_LmnB1_sc.16


title: oocyte_20ng_LmnB1_sc.13


title: oocyte_20ng_LmnB1_sc.14


title: oocyte_20ng_LmnB1_sc.15


title: oocyte_20ng_LmnB1_sc.11


title: oocyte_20ng_LmnB1_sc.10


title: oocyte_50ng_LmnB1_sc.4


title: oocyte_20ng_LmnB1_sc.12


title: oocyte_50ng_LmnB1_sc.1


title: oocyte_50ng_LmnB1_sc.2


title: oocyte_20ng_LmnB1_sc.8


title: oocyte_50ng_LmnB1_sc.3


title: oocyte_20ng_LmnB1_sc.5


title: oocyte_20ng_LmnB1_sc.4


title: oocyte_20ng_LmnB1_sc.6


title: oocyte_20ng_LmnB1_sc.2


title: zygote_aphidicolin_Lmnb1_sc.9


title: zygote_aphidicolin_Lmnb1_sc.8


title: oocyte_20ng_LmnB1_sc.1


title: oocyte_20ng_LmnB1_sc.9


title: oocyte_20ng_LmnB1_sc.7


title: zygote_aphidicolin_Lmnb1_sc.3


title: zygote_aphidicolin_Lmnb1_sc.4


title: zygote_aphidicolin_Lmnb1_sc.2


title: oocyte_20ng_LmnB1_sc.3


title: zygote_aphidicolin_Lmnb1_sc.1


title: zygote_DMSO_Lmnb1_sc.9


title: zygote_DMSO_Lmnb1_sc.8


title: zygote_DMSO_Lmnb1_sc.6


title: zygote_DMSO_Lmnb1_sc.11


title: zygote_DMSO_Lmnb1_sc.10


title: zygote_DMSO_Lmnb1_sc.4


title: zygote_DMSO_Lmnb1_sc.5


title: zygote_DMSO_Lmnb1_sc.7


title: zygote_DMSO_Lmnb1_sc.1


title: zygote_Kdm5b_WT_Lmnb1_sc.10


title: zygote_Kdm5b_WT_Lmnb1_sc.12


title: zygote_DMSO_Lmnb1_sc.3


title: zygote_Kdm5b_WT_Lmnb1_sc.14


title: zygote_Kdm5b_WT_Lmnb1_sc.11


title: zygote_DMSO_Lmnb1_sc.2


title: zygote_Kdm5b_WT_Lmnb1_sc.13


title: zygote_aphidicolin_Lmnb1_sc.5


title: zygote_aphidicolin_Lmnb1_sc.7


title: zygote_aphidicolin_Lmnb1_sc.6


title: zygote_Kdm5b_WT_Lmnb1_sc.7


title: zygote_Kdm5b_WT_Lmnb1_sc.9


title: zygote_Kdm5b_WT_Lmnb1_sc.4


title: zygote_Kdm5b_WT_Lmnb1_sc.8


title: zygote_Kdm5b_WT_Lmnb1_sc.5


title: zygote_Kdm5b_WT_Lmnb1_sc.1


title: zygote_Kdm5b_WT_Lmnb1_sc.3


title: zygote_Kdm5b_MUT_Lmnb1_sc.9


title: zygote_Kdm5b_WT_Lmnb1_sc.2


title: zygote_Kdm5b_MUT_Lmnb1_sc.8


title: zygote_Kdm5b_MUT_Lmnb1_sc.7


title: zygote_Kdm5b_MUT_Lmnb1_sc.6


title: zygote_Kdm5b_MUT_Lmnb1_sc.5


title: zygote_Kdm5b_MUT_Lmnb1_sc.3


title: zygote_Kdm5b_MUT_Lmnb1_sc.2


title: zygote_Kdm5b_MUT_Lmnb1_sc.4


title: zygote_Kdm5b_WT_Lmnb1_sc.6


title: zygote_Dam_sc_35


title: zygote_Dam_sc_37


title: zygote_Dam_sc_38


title: zygote_Dam_sc_39


title: zygote_Dam_sc_32


title: zygote_Dam_sc_41


title: zygote_Dam_sc_40


title: zygote_Dam_sc_36


title: zygote_Dam_sc_33


title: zygote_Dam_sc_31


title: zygote_Dam_sc_30


title: zygote_Dam_sc_27


title: zygote_Dam_sc_24


title: zygote_Dam_sc_23


title: zygote_Dam_sc_25


title: zygote_Dam_sc_22


title: zygote_Dam_sc_28


title: zygote_Kdm5b_MUT_Lmnb1_sc.1


title: zygote_Dam_sc_26


title: zygote_Dam_sc_20


title: zygote_Dam_sc_19


title: zygote_Dam_sc_42


title: zygote_Dam_sc_21


title: zygote_Dam_sc_34


title: zygote_Dam_sc_17


title: zygote_Dam_sc_12


title: zygote_Dam_sc_11


title: zygote_Dam_pop_1

description:
zygote_Dam_pop_1_OE_100kb_non-allelic.bedgraph
zygote_Dam_pop_1_OE_100kb_maternal.bedgraph
zygote_Dam_pop_1_OE_100kb_paternal.bedgraph


title: zygote_Dam_sc_10


title: zygote_Dam_pop_2

description:
zygote_Dam_pop_2_OE_100kb_non-allelic.bedgraph
zygote_Dam_pop_2_OE_100kb_maternal.bedgraph
zygote_Dam_pop_2_OE_100kb_paternal.bedgraph


title: oocyte_LmnB1_pop_2

description: oocyte_LmnB1_pop_2_OE_100kb_non-allelic.bedgraph

value: oocyte


title: zygote_Dam_sc_13


title: zygote_Dam_sc_14


title: oocyte_LmnB1_pop_1

description: oocyte_LmnB1_pop_1_OE_100kb_non-allelic.bedgraph


title: oocyte_LmnB1_pop_3

description: oocyte_LmnB1_pop_3_OE_100kb_non-allelic.bedgraph


title: zygote_Dam_pop_3

description:
zygote_Dam_pop_3_OE_100kb_non-allelic.bedgraph
zygote_Dam_pop_3_OE_100kb_maternal.bedgraph
zygote_Dam_pop_3_OE_100kb_paternal.bedgraph


title: zygote_Dam_sc_29


title: oocyte_Dam_pop_3

description: oocyte_Dam_pop_3_OE_100kb_non-allelic.bedgraph


title: zygote_Dam_sc_18


title: ChIP-seq from GM12878 (ENCLB720WTE)

status: Public on Mar 02 2019

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR439WAF/
***************
biological replicate number: 2
technical replicate number: 1
description: E4F1 ChIP-seq on human GM12878
experiment encode accession: ENCSR439WAF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB720WTE
size range: 450-650

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens GM12878 immortalized cell line

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: unknown

tag: health state

tag: lab

value: Michael Snyder, Stanford

tag: link

value: ENCBS339VHO at ENCODE; https://www.encodeproject.org/ENCBS339VHO/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: oocyte_Dam_pop_2

description: oocyte_Dam_pop_2_OE_100kb_non-allelic.bedgraph

tag: developmental stage

tag: strain


title: ChIP-seq from GM12878 (ENCLB473OXT)

description:
https://www.encodeproject.org/experiments/ENCSR974OFJ/
***************
biological replicate number: 2
technical replicate number: 1
description: KLF5 ChIP-seq on human GM12878
experiment encode accession: ENCSR974OFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB473OXT
size range: 450-650

tag: description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: ENCBS594YOH at ENCODE; https://www.encodeproject.org/ENCBS594YOH/

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from GM12878 (ENCLB047NYH)

description:
https://www.encodeproject.org/experiments/ENCSR436QMA/
***************
biological replicate number: 13
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human GM12878 (fragmentation date 01-30-14)
experiment encode accession: ENCSR436QMA
assay title: ChIP-seq
assembly: GRCh38, hg19
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB047NYH
size range: 100-500

value: Control

value: GM12878, B-lymphocyte, lymphoblastoid

tag: passage number

value: Richard Myers, HAIB

value: ENCBS057BBL at ENCODE; https://www.encodeproject.org/ENCBS057BBL/

value: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from GM12878 (ENCLB597PSK)

description:
https://www.encodeproject.org/experiments/ENCSR974OFJ/
***************
biological replicate number: 1
technical replicate number: 1
description: KLF5 ChIP-seq on human GM12878
experiment encode accession: ENCSR974OFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB597PSK
size range: 450-650

value: ENCBS260WJQ at ENCODE; https://www.encodeproject.org/ENCBS260WJQ/


title: ChIP-seq from GM23338 (ENCLB663MRT)

description:
https://www.encodeproject.org/experiments/ENCSR917MAH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR917MAH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR655HDE
encode release date: 2016-03-05
lab: Richard Myers, HAIB
library encode accession: ENCLB663MRT

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

value: JUNB

value: cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: zygote_Dam_sc_15

tag: damid profiling

value: Dam

tag: mrna injected

value: zygote

value: C57BL/6 female x CAST/EiJ male


title: zygote_Dam_sc_16

tag: treatments

tag: number of cells


title: ChIP-seq from GM23338 (ENCLB284CPG)

description:
https://www.encodeproject.org/experiments/ENCSR871KYB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR871KYB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR655HDE
encode release date: 2018-03-06
lab: Richard Myers, HAIB
library encode accession: ENCLB284CPG

tag: antibody

value: REST

value: adult


title: ChIP-seq from GM12878 (ENCLB934BCL)

description:
https://www.encodeproject.org/experiments/ENCSR212YKD/
***************
biological replicate number: 2
technical replicate number: 1
description: SKIL ChIP-seq on human GM12878
experiment encode accession: ENCSR212YKD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO, ENCSR398JTO
encode release date: 2017-07-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB934BCL
size range: 450-650

value: SKIL

tag: line

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS965YSG at ENCODE; https://www.encodeproject.org/ENCBS965YSG/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from GM23338 (ENCLB457FOF)

description:
https://www.encodeproject.org/experiments/ENCSR061DGF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR061DGF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB457FOF

value: NANOG

value: cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

tag: biosample encode accession

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: ChIP-seq from GM12878 (ENCLB587UUM)

description:
https://www.encodeproject.org/experiments/ENCSR439WAF/
***************
biological replicate number: 1
technical replicate number: 1
description: E4F1 ChIP-seq on human GM12878
experiment encode accession: ENCSR439WAF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB587UUM
size range: 450-650

tag: dev stage

value: adult

value: ENCBS276RPG at ENCODE; https://www.encodeproject.org/ENCBS276RPG/


title: ChIP-seq from GM12878 (ENCLB319THK)

description:
https://www.encodeproject.org/experiments/ENCSR212YKD/
***************
biological replicate number: 1
technical replicate number: 1
description: SKIL ChIP-seq on human GM12878
experiment encode accession: ENCSR212YKD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO, ENCSR398JTO
encode release date: 2017-07-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB319THK
size range: 450-650

value: SKIL

value: unknown

tag: Sex

value: ENCBS488GLI at ENCODE; https://www.encodeproject.org/ENCBS488GLI/


title: ChIP-seq from GM12878 (ENCLB417QRW)

description:
https://www.encodeproject.org/experiments/ENCSR177VFS/
***************
biological replicate number: 2
technical replicate number: 1
description: MEF2B ChIP-seq on human GM12878
experiment encode accession: ENCSR177VFS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2018-02-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB417QRW
size range: 450-650

tag: age

value: female

value: Michael Snyder, Stanford

value: ENCBS421UOG at ENCODE; https://www.encodeproject.org/ENCBS421UOG/


title: ChIP-seq from GM12878 (ENCLB855XBW)

description:
https://www.encodeproject.org/experiments/ENCSR177VFS/
***************
biological replicate number: 1
technical replicate number: 1
description: MEF2B ChIP-seq on human GM12878
experiment encode accession: ENCSR177VFS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2018-02-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB855XBW
size range: 450-650

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: health state

value: ENCBS803QIM at ENCODE; https://www.encodeproject.org/ENCBS803QIM/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from GM12878 (ENCLB094VWJ)

description:
https://www.encodeproject.org/experiments/ENCSR041XML/
***************
biological replicate number: 2
technical replicate number: 1
description: SRF ChIP-seq on human GM12878
experiment encode accession: ENCSR041XML
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB094VWJ
size range: 450-650

value: SRF

value: cell line

tag: lab

value: ENCBS594YOH at ENCODE; https://www.encodeproject.org/ENCBS594YOH/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: WGBS from GM23248 (ENCLB777FMV)

description:
https://www.encodeproject.org/experiments/ENCSR625HZA/
***************
biological replicate number: 1
technical replicate number: 1
description: The libraries contained in this Experiment come from whole genome bisulfite sequencing of primary cell skin fibroblasts from the PGP1 donor.
experiment encode accession: ENCSR625HZA
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB777FMV

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

tag: link

value: ENCBS367AAA at ENCODE; https://www.encodeproject.org/ENCBS367AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166


title: WGBS from GM23248 (ENCLB436YZI)

description:
https://www.encodeproject.org/experiments/ENCSR625HZA/
***************
biological replicate number: 2
technical replicate number: 1
description: The libraries contained in this Experiment come from whole genome bisulfite sequencing of primary cell skin fibroblasts from the PGP1 donor.
experiment encode accession: ENCSR625HZA
assay title: WGBS
assembly: GRCh38
encode release date: 2017-12-04
lab: Richard Myers, HAIB
library encode accession: ENCLB436YZI

value: adult

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/


title: 11 HCT116-SMC1A2027 17-090 RNA-seq

status: Public on Feb 21 2019

city: Udine

first: Simone

last: Scalabrin

state: UD

address: via Jacopo Linussio 51

country: Italy

institute: IGA Technology Services

description: R2 files contain 8 nucleotides per read to perform deduplication (NuGEN SoLo protocol)

data_processing:
Basecalls performed using CASAVA version 1.4
Adapter removal with cutadapt v1.1
quality trimming with erne-filter v1.4.6
alignment with STAR v2.5
read count with StringTie v 1.3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: human colon

extract_protocol: Libraries were prepard by using NuGEN Ovation® SoLo RNA-Seq System

tag: tumor stage

value: Tumour induced by HCT116 SMC1A c.A2027G

tag: host organism

value: Nude mice


title: ChIP-seq from GM12878 (ENCLB397QCK)

description:
https://www.encodeproject.org/experiments/ENCSR542FLV/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB33 ChIP-seq on human GM12878
experiment encode accession: ENCSR542FLV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2017-11-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB397QCK
size range: 450-650

tag: description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: female

value: Michael Snyder, Stanford

value: unknown

value: ENCBS519VWT at ENCODE; https://www.encodeproject.org/ENCBS519VWT/

value: derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from GM12878 (ENCLB278BBE)

description:
https://www.encodeproject.org/experiments/ENCSR041XML/
***************
biological replicate number: 1
technical replicate number: 1
description: SRF ChIP-seq on human GM12878
experiment encode accession: ENCSR041XML
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2018-01-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB278BBE
size range: 450-650

value: SRF

value: cell line


title: ChIP-seq from GM12878 (ENCLB012KKL)

description:
https://www.encodeproject.org/experiments/ENCSR900XDB/
***************
biological replicate number: 5
technical replicate number: 1
description: ZFP36 ChIP-seq on human GM12878
experiment encode accession: ENCSR900XDB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR553NUG
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB012KKL
size range: 150-350

value: ENCBS802GDX at ENCODE; https://www.encodeproject.org/ENCBS802GDX/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526


title: 9 HCT116-SMC1A2027 17-084 RNA-seq


title: ChIP-seq from GM12878 (ENCLB827EFP)

description:
https://www.encodeproject.org/experiments/ENCSR900XDB/
***************
biological replicate number: 4
technical replicate number: 1
description: ZFP36 ChIP-seq on human GM12878
experiment encode accession: ENCSR900XDB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR553NUG
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB827EFP
size range: 150-350

source_name: Homo sapiens GM12878 cell line

value: ENCBS361VFY at ENCODE; https://www.encodeproject.org/ENCBS361VFY/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; https://web.expasy.org/cellosaurus/CVCL_7526


title: oocyte_Dam_pop_1

description: oocyte_Dam_pop_1_OE_100kb_non-allelic.bedgraph

value: Dam

tag: developmental stage

value: oocyte

tag: strain


title: 10 HCT116-SMC1A2027 17-085 RNA-seq

value: Tumour induced by HCT116 SMC1A c.A2027G

value: Nude mice


title: ChIP-seq from GM23338 (ENCLB865GUA)

description:
https://www.encodeproject.org/experiments/ENCSR071NFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR071NFQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR655HDE
encode release date: 2016-08-09
lab: Richard Myers, HAIB
library encode accession: ENCLB865GUA

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: 7 HCT116-SMC1AWT 17-089 RNA-seq

value: Tumour induced by HCT116 SMC1A wild-type


title: 3 HCT116 17-080 RNA-seq

value: Tumour induced by HCT116


title: 2 HCT116 17-087 RNA-seq


title: 6 HHCT116-SMC1AWT 17-088 RNA-seq


title: 8 HCT116-SMC1A2027 17-083 RNA-seq


title: 1 HCT116 17-079 RNA-seq


title: 4 HCT116-SMC1AWT 17-077 RNA-seq


title: ChIP-seq from GM23338 (ENCLB249NXV)

description:
https://www.encodeproject.org/experiments/ENCSR061DGF/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on PGP1 iPSC
experiment encode accession: ENCSR061DGF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR447FVP, ENCSR655HDE
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB249NXV

value: NANOG

value: cell line

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/


title: ChIP-seq from GM12878 (ENCLB917LXI)

description:
https://www.encodeproject.org/experiments/ENCSR542FLV/
***************
biological replicate number: 4
technical replicate number: 1
description: ZBTB33 ChIP-seq on human GM12878
experiment encode accession: ENCSR542FLV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR398JTO
encode release date: 2017-11-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB917LXI

value: unknown

value: female

value: Michael Snyder, Stanford

value: ENCBS607NAA at ENCODE; https://www.encodeproject.org/ENCBS607NAA/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/


title: placenta-input-6

status: Public on Feb 19 2019

city: Guangzhou

first: Shan

last: Xiao

address: Southern Shatai Road

department: Developmental Biology

country: China

institute: Southern Medical University

description: Stomach.bed

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
For RIP seq, after removal of rRNA and tRNA, sequenced reads were mapped to GRCh38 using hisat2-align-s (v2.0.5). PCR duplicates were further removed with Picard (v2.16.0) and high quality mapped reads were extracted by samtools view (v0.1.09) “-q 30”. Regions enriched in the RIP RNA samples over input RNA samples were identified as m6A peaks using MACS2 peak-caller, MeTPeak and moving-window..
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files were generated using MACS2, MeTPeak and moving-window.

source_name: placenta

extract_protocol: For RIP-seq, the tissues were isolated after a mechanical dissection, and all the samples were serially washed and immediately frozen in liquid nitrogen. Total RNA of tissue or cells was isolated using TRIzol and treated with DNase. RNA were then chemically fragmented, and subjected to immunoprecipitation with anti-m6A antibody. After stringent washing, bound RNA was eluted by competition with N6-methyladenosine, and used for library construction as IP samples. After removal of ribosomal RNA from total RNA, the input RNA samples was subsequently fragmented and subjected to library construction. The libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

tag: tissue

value: placenta

value: 25 weeks

tag: rip antibody

tag: data type


title: placenta-input-2

description: Placenta.bed

value: 24 weeks


title: stomach-input-5

description: Placenta.bed

source_name: stomach

value: stomach

value: 23 weeks


title: heart-input-1

description: Heart.bed

source_name: heart

value: heart

value: 22 weeks


title: 5 HCT116-SMC1AWT 17-078 RNA-seq

value: Tumour induced by HCT116 SMC1A wild-type

value: Nude mice


title: brain-input-3

description: Brain.bed

source_name: brain

value: brain

value: 19 weeks


title: brain-input-2

description: Brain.bed


title: heart-input-3

description: Heart.bed


title: heart-input-2

description: Heart.bed


title: kidney-input-2

description: Kidney.bed

source_name: kidney

value: kidney


title: lung-input-5

description: Lung.bed

source_name: lung

value: lung


title: liver-input-2

description: Liver.bed

source_name: liver

value: liver


title: liver-input-1

description: Liver.bed


title: liver-input-3

description: Liver.bed


title: placenta-IP-4

description: Stomach.bed


title: placenta-IP-6

description: Stomach.bed


title: placenta-IP-2

description: Placenta.bed


title: muscle-input-4

description: Muscle.bed

source_name: muscle

value: skeletal muscle


title: input-m3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Sequenced reads were mapped to GRCh38 using bowtie. PCR duplicates were further removed with Picard (v2.16.0) and high quality mapped reads were extracted by samtools view (v0.1.09) “-q 20”. Regions enriched in the ChIP DNA samples over input RNA samples were identified using MACS2 peak-caller using default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak files were generated using MACS2.

source_name: hela cells

growth_protocol: Hela cells were grown in DMEM , 10% fetal bovine serum and 1% penicillin-streptomycin in a 5% CO2 incubator under 37°C.

extract_protocol: For ChIP-seq, nine 10-cm dishes of pCDNA4-SFB-Tre-METTL4 stable transfected cells were treated by doxycycline (1 ng/μl) for 24 hr to trigger the expression of METTL3, then subject to 2-step fixation by 2 mM DSG (AppliChem) for 30 min and 1% formaldehyde for 10 min at room temperature. The following processes were all carried out at 4°C unless otherwise emphasized noted. After quenching with 125 mM glycine, the cells were harvested and lysed by 200 ul RIPA buffer supplemented with 2 mM RVC, 1 mM DTT, 100 μM PMSF and protease inhibitor cocktail (Roche) per dish. The lysate were sonicated using Bioraptor (Diagenode), and subject to streptavidin Sepharose (GE) binding for 2 hr. After washing with by RIPA buffer for 3 times, and the bound protein-DNA complex were eluted by competition with 2 mg/ml biotin (Sigma) for 2 hr. Then the eluate were incubated with S-protein agarose (Millipore) overnight, washed with RIPA for 3 times, and eluted by proteinase K digestion at 56°C for 30 min. The DNA of input and IPed samples were incubated at 65°C overnight to reverse crosslink, and extracted by Phenol/Chloroform followed by ethanol precipitation. The libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: cell line

value: HeLa


title: placenta-input-4

description: Stomach.bed


title: brain-input-1

description: Brain.bed


title: kidney-input-3

description: Kidney.bed


title: m3


title: stomach-IP-4

description: Placenta.bed


title: stomach-IP-5

description: Placenta.bed


title: stomach-input-4

description: Placenta.bed


title: muscle-IP-5

description: Muscle.bed

value: muscle


title: lung-input-4

description: Lung.bed


title: lung-IP-5

description: Lung.bed


title: muscle-IP-4

description: Muscle.bed


title: kidney-input-4

description: Kidney.bed


title: muscle-input-5

description: Muscle.bed


title: lung-IP-4

description: Lung.bed


title: liver-IP-3

description: Liver.bed


title: liver-IP-2

description: Liver.bed


title: liver-IP-1

description: Liver.bed


title: brain-IP-1

description: Brain.bed


title: kidney-IP-4

description: Kidney.bed


title: heart-IP-3

description: Heart.bed


title: heart-IP-1

description: Heart.bed


title: kidney-IP-3

description: Kidney.bed


title: PIK3CA_H1047R_homozygous_cloneJ [WTC11_J]

status: Public on Feb 15 2019

city: Cambridge

first: Ralitsa

middle: Radostinova

last: Madsen

address: Addenbrookes Treatment Centre, Keith Day Road

department: Metabolic Research Laboratories, Clinical Biochemistry

institute: University of Cambridge

data_processing:
The raw reads were mapped to the human genome build GRCh38
Gene level counts were performed using Spliced Transcripts Alignment to a Reference (STAR) v2.5. The output results of this step are provided as processed data files.
All subsequent data analyses steps were performed in R using RStudio. Briefly, the edgeR package was used to calculate counts per million (CPM) for each gene and sample. Genes were included for further analysis if expressed at CPM > 1 in at least 1/3 of all samples. Sample library size was normalised by the TMM (trimmed mean of M values) method (Robinson and Oshlack, 2010 Genome Biology), followed by differential gene expression analysis with voom(), lmFit() and eBayes() according to the limma analysis pipeline described by Ritchie et al. (2015 Nucleic Acid Research).
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene count; column 1: gene ID; column 2: counts for unstranded RNA-seq column; 3: counts for the 1st read strand aligned with RNA; column 4: counts for the 2nd read strand aligned with RNA. However, due to the nature of our library preparation, only the counts in column 4 are of relevance for downstream analyses. Counts in column 2 and 3 should be ignored.

growth_protocol: The cells were cultured in 6-well plates coated with hESC-qualified Geltrex (Thermo Fisher Scien- tific # A1413302) diluted 1:100 in DMEM/F12 (Sigma # D6421). Cells were maintained in Essential 8 Flex medium (Thermo Fisher Scientific # A2858501) and passaged every four days when 80-90 % confluent, with split ratios ranging from 1:10 to 1:15. ReLeSR (Stem Cell Technologies # 5872) was used to dissociate the cells non- enzymatically, and 1X RevitaCell (Thermo Fisher Scientific # A2644501) was included during the first 24 hours to promote survival.

extract_protocol:
Cells were washed in DPBS and lysed with QIAzol. The RNA was extracted with the Direct-zol RNA Miniprep Kit (ZymoResearch # R2051) according to the manufacturer's instructions (eluted in 50 μl nuclease-free water). The quality of the RNA was confirmed on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent # 5067-1511) according to the manufacturer’s instructions, with all samples pre-diluted to 250-300 ng/μl in nuclease-free water. All samples had high RNA Integrity Number (RIN) scores of 9.9-10.
A total of 1 μg RNA per sample was used as input to prepare indexed, 50-bp-long single-end mRNA libraries with Illumina's TruSeq Stranded mRNA Library Prep Kit (# 20020594) and TruSeq RNA Single Indexes Set A (# 20020492) according to the manufacturer's instructions. The integrity and quantity of the libraries were determined on the Agilent Bioanalyzer using the DNA 12000 Kit (Agilent # 5067-1508).
mRNA sequencing of pooled libraries on an Illumina HiSeq 4000

treatment_protocol: The cells were replenished with fresh Essential 8 Flex medium 3 hours before collection for RNA extraction.

tag: cell type

value: Induced pluripotent stem cell (iPSCs)

tag: passage

tag: genotype/variation


title: brain-IP-3

description: Brain.bed


title: PIK3CA_H1047R_heterozygous_cloneHet1 [WTC11_Het1]


title: PIK3CA_wild_type_cloneC [WTC11_C]


title: PIK3CA_H1047R_heterozygous_cloneHet3 [WTC11_Het3]


title: PIK3CA_H1047R_heterozygous_cloneHet2 [WTC11_Het2]


title: PIK3CA_wild_type_cloneB [WTC11_B]


title: PIK3CA_wild_type_cloneA [WTC11_A]


title: CpGdensityLib1_BCtoPr

status: Public on Jan 20 2019

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Barcode to promoter assignment
processed data file: CpGDensitylib1_results.tab

data_processing:
Basecalls performed using MiSeq and HiSeq control software.
For reporter assay libraries, fastq files were trimmed to the promoter sequence and aligned to mm9 using bowtie for libraries where the design allowed efficient alignment (See table 2). For mutant promoter libraries, reads were matched to the reference sequences using the "stringdistmatrix" function in R (van der Loo, 2014). The frequency of each barcode sequence was calculated to get counts for each sample. Genomic DNA and RNA samples were scaled to each other by normalizing to the smaller total number of counts. Only barcodes that were sufficiently represented on genomic DNA (more than 20 reads after scaling) were used for further analysis. Enrichments of barcodes in the RNA sample were then calculated as nr/nd + alpha, where nr are the RNA counts and nd the DNA counts for a particular barcode and alpha represents a pseudo-count, set to 0.05.
ChIP-seq samples were mapped to the mm9 assembly of the mouse genome using the R package QuasR (Gaidatzis et al, 2015), which internally uses bowtie (Langmead et al, 2009). ChIP-seq peaks were called using Peakzilla with default parameters (Bardet et al, 2013)
For amplicon Bis-seq, sequences were aligned to the mutant promoter libraries using QuasR (Gaidatzis et al, 2015), using default settings for Bis-converted samples. DNA methylation was quantified using qMeth and the average methylation across each promoter was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Activities (Act_*), number of barcodes (nBCs_*), activities relative to the wt sequence (relAct_*), percentage of C+Gs (GC), percentage of dinucleotides that are CpGs (CpG), CpG observed/expected (OE), number of CpGs (nCGs), coordinates (chr, start, end, strand), percentage of CpGs mutated (CpGmut), qPCR values (qPCR), fraction methylated (methylation).

molecule: other

source_name: plasmid

growth_protocol: Mouse ES cells were cultured on cell culture plates coated with 0.2% gelatine in DMEM medium with 15% fetal calf serum, 2mM L-glutamine, 1 x non-essential amino acids, LIF and 0.001% b-mercaptoethanol. Cells were incubated at 37 °C with 7% CO2.

extract_protocol:
RNA was isolated from cell lines containing the expression libraries with Quiagen RNeasy Mini Kit with on-column DNase digestion and reverse transcribed using Takara PrimeScript RT Reagent Kit (#RR047A). For DNA isolation cell pellet was resuspended in Bradleys-Buffer, 6 ul RNaseA (10mg/ml) was added and samples were incubated for 1h at 37 degree C. Subsequently 30 ul protease K was added and samples were incubated at 50 degree C over night. Then DNA was extracted using Phenol and Chloroform. Bio-ChIP was performed as previously described (Baubec et al, 2013). For amplicon Bis-seq, cells containing integrated mutant CGI promoter libraries were thawed, plated at low density and 96 clones picked and expanded to a minimum cell number of 20,000 cells. Cells were lysed with Baradley Buffer (10mM Tris-HCl (pH 7.5), 10mM EDTA (pH 8.0), 0.5% SDS, 10mM NaCl) and DNA extracted with beads (Homemade). DNA was Bisulfite converted using Zymo lightning conversion kit (D5046) and cleaned up using MagBeads (Zymno). Bis-converted DNA was amplified with primers RSG353 and RSG354 (Table 1). Amplified DNA was purified with Ampure beads and sequencing libraries were prepared using the Illumina NEBNext ChIP-seq library prep kit with 96 dual indexing.
DNA and cDNA barcodes were amplified with KAPA HIFI Hotstart using Primer DH.P6 and indexing primer (Table 1). PCR products were purified using AmPure XP beads (Beckman Coulter, #A63880) and sequenced using 50 cycle Kit on HiSeq 2500.

treatment_protocol: Mouse embryonic stem cells with a RMCE site in the beta-globin locus were used for integration of expression libraries for the transcriptional reporter assay (Lienert et al, 2011). Dnmt1, Dnmt3a and Dnmt3b was deleted in these cells using CRISPR-Cas9 gene editing as previously described (Domcke et al, 2015). Mouse HA36 ES cells (mixed 129-C57Bl/6 strain) were used for Bio-ChIP (Baubec et al, 2013).

value: plasmid

tag: genotype

tag: library type

value: reporter assay


title: PIK3CA_H1047R_homozygous_cloneI [WTC11_I]


title: CpGdensitylib1_rep3_gDNA_S225

description:
DNA Barcodes
processed data file: CpGDensitylib1_results.tab

source_name: embryonic stem cells

value: embryonic stem cells

value: Wild Type


title: sorted human adult podocytes from Pt. 1

status: Public on Jan 15 2019

city: Kumamoto

first: Yasuhiro

last: Yoshimura

state: Japan

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Pt1_Podocyte
Sorted as Nephrin+/Podocalyxin+ population from 80-year-old Japanese male.
Two raw data files per Sample. One file includes the raw read data of the molecular barcodes outputted from the sequencer; 8 bp of index for sample classification with 8 bp of molecular barcode.
processed data file: Processed data file_Podocyte RNA-seq.xlsx

data_processing:
Basecalls performed using bcl2fastq v2.17.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.32 tool.
The sequence reads were aligned to the human reference genome (hg19) using TopHat 2.1.1 (bowtie2-2.2.3) with the option '-g 1 --no-discordant'.
NuDup ver.2.3 (NuGEN Technologies, San Carlos, CA) analyzing the redundancy of 8 bp molecular barcodes was used to remove PCR duplicate reads.
The read counts allocated for each gene and transcript (RefSeq version 2015.10.5) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.1 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Processed data file_Podocyte RNA-seq.xlsx: An Excel format file (XLSX) includes TMM quantification values and gene annotations of all samples.

source_name: human adult podocytes

growth_protocol: Nephron progenitor cells were induced from human iPS cells by the established protocol (A, Taguchi. et al., Cell Stem Cell 2014, 2017). Human iPS cell-derived podocytes were induced from sorted nephron progenitor cells (Itga8+/Pdgfra-) by our newly established protocol (Y, Yoshimura et al., unpublished). The immortalized podocytes were cultured and differentiated as reported previously (M, Saleem. et al., J Am Soc Nephrol 2002).

extract_protocol:
Nephron progenitor cells, human adult podocytes, and human adult non-podocytes were sorted by a FACS SORP Aria (Becton Dickinson) after single cell dissociation. Human iPS cells and the immortalized podocytes were detached from the culture dishes by treatment with accuate and 0.05% Trypsin-EDTA, respectively. Induced human podocytes were detached from the transwell insert by gentle pipetting. Total RNA was extracted using "RNeasy Plus Micro Kit" purchased from QIAGEN following manufacturer's protocol.
Total RNA obtained from each sample was subjected to a sequencing library construction using Ovation Solo RNA-Seq System (NuGEN Technologies, San Carlos, CA) according to the manufacturer's protocol.

value: adult podocytes


title: sequence deletion validation (eGLUL) clone 3 Bulk-seq

status: Public on Jan 04 2019

city: SEATTLE

first: Molly

last: Gasperini

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
two technical replicates (denoted A and B)
sequence_deletions_normalized_tpms.tsv

data_processing:
Single-cell RNA-seq datasets for the pilot screens were processed using 10x Genomics Cell Ranger 2.0.2.
Single-cell RNA-seq data for the at-scale screens was processed using 10x Genomics Cell Ranger 2.1.1.
bulkRNA-seq normalized transcripts per million (tpms) were generated using sleuth, and normalized by the sleuth 'between samples' size factors.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.cds.rds, *.phenoData, *.genes.txt, *.cells.txt, and *.exprs.mtx.txt files were generated using Monocle2; *.tpms.tsv were generated using sleuth.
Supplementary_files_format_and_content: grna_groups.pilot.txt: gRNAgroup identifiers used to assign gRNA to the pilot screen and their corresponding spacer sequences.
Supplementary_files_format_and_content: grna_groups.at_scale.txt: gRNAgroup identifiers for the at-scale screen and their corresponding spacer sequences.
Supplementary_files_format_and_content: 50k_reference_cells.rds: File storing the names of the 50,000 cells used for differential expression testing for the at-scale screen (to save computational resources).
Supplementary_files_format_and_content: gene_gRNAgroup_pair_table.pilot.txt: Table of pilot screen's gene-target (gRNAgroup) pairs considered for differential expression testing (with corresponding information columns about each target and candidate target gene).
Supplementary_files_format_and_content: gene_gRNAgroup_pair_table.at_scale.txt: Table of at-scale screen's gene-target (gRNAgroup) pairs considered for differential expression testing (with corresponding information columns about each target and candidate target gene).
Supplementary_files_format_and_content: all_deg_results.pilot.txt: All differential expression results from the pilot screen (along with 'empirical p-values', which are only calculated for gRNA_groups associated with decreases in candidate target gene's expression).
Supplementary_files_format_and_content: all_deg_results.at_scale: All differential expression results from the at-scale screen (along with 'empirical p-values', which are only calculated for gRNA_groups associated with decreases in candidate target gene's expression).
Supplementary_files_format_and_content: zero_inflated_outlier_genes_to_exclude.atscale.txt: We observed that genes with a very high mean expression value relative to what you would expect given the number of cells in which they are expressed tended to show up frequently as false positives in permutation tests (these may be outliers with respect to their dispersion given that monocle uses shrinkage to estimate smoothed dispersion values when parameterizing the regression model used for differential gene expression). To avoid this source of false positives, we ignored this small set of outliers in downstream analysis.
Supplementary_files_format_and_content: zero_inflated_outlier_genes_to_exclude.pilot.txt: We observed that genes with a very high mean expression value relative to what you would expect given the number of cells in which they are expressed tended to show up frequently as false positives in permutation tests (these may be outliers with respect to their dispersion given that monocle uses shrinkage to estimate smoothed dispersion values when parameterizing the regression model used for differential gene expression). To avoid this source of false positives, we ignored this small set of outliers in downstream analysis.

source_name: K562 cell line

extract_protocol:
TruSeq Stranded mRNA Library Prep
RNEasy Mini Kit QIAGEN


title: sequence deletion validation (eGLUL) clone 1 Bulk-seq


title: sequence deletion validation (eGLUL) clone 2 Bulk-seq


title: sequence deletion validation (eCITED2) clone 3 Bulk-seq


title: sequence deletion validation (eCITED2) clone 2 Bulk-seq


title: sequence deletion validation (eCITED2) clone 1 Bulk-seq


title: sequence deletion validation (eNMU) clone 6 Bulk-seq


title: kidney-IP-2

description: Kidney.bed

tag: age

value: 24 weeks


title: heart-IP-2

description: Heart.bed

value: heart


title: PIK3CA_H1047R_homozygous_cloneE [WTC11_E]


title: brain-IP-2

description: Brain.bed


title: sequence deletion validation (eNMU) clone 5 Bulk-seq


title: sequence deletion validation (eNMU) clone 4 Bulk-seq


title: sequence deletion validation (eNMU) clone 2 Bulk-seq


title: sequence deletion validation (eNMU) clone 3 Bulk-seq


title: sequence deletion validation (eNMU) clone 1 Bulk-seq


title: CRISPRi singleton (Null6_chr20.111) Bulk-seq

description:
two technical replicates (denoted A and B)
singletons_set2_normalized_tpms.tsv


title: CRISPRi singleton (NTC) Bulk-seq


title: CRISPRi singleton (Null4_chr12.1623) Bulk-seq


title: CRISPRi singleton (Null3_chr3.1742) Bulk-seq


title: CRISPRi singleton (Null5_chr1.5079) Bulk-seq


title: CRISPRi singleton (LSM3 TSS control) Bulk-seq


title: CRISPRi singleton (Null2_chr1.9507) Bulk-seq


title: CRISPRi singleton (eHHEX) Bulk-seq


title: CRISPRi singleton (eDECR1


title: CRISPRi singleton (eLBR) Bulk-seq


title: CRISPRi singleton (TFRC TSS control) Bulk-seq


title: CRISPRi singleton (ATP1B3 TSS control) Bulk-seq


title: CRISPRi singleton (eLSM3) Bulk-seq


title: CRISPRi singleton (eTFRC) Bulk-seq


title: CRISPRi singleton (DECR1 TSS control) Bulk-seq


title: CRISPRi singleton (HHEX TSS control) Bulk-seq


title: CRISPRi singleton (ePICALM) Bulk-seq


title: CRISPRi singleton (PTGER3 TSS control) Bulk-seq

description:
two technical replicates (denoted A and B)
singletons_set1_normalized_tpms.tsv

extract_protocol:
TruSeq RNA Sample Prep Kit v2
RNEasy Mini Kit QIAGEN


title: CRISPRi singleton (ePTGER3) Bulk-seq


title: CRISPRi singleton (CITED2 TSS control) Bulk-seq


title: CRISPRi singleton (eCITED2) Bulk-seq


title: CRISPRi singleton (eGYPC) Bulk-seq


title: CRISPRi singleton (GYPC TSS control) Bulk-seq


title: CRISPRi singleton (eATP1B3) Bulk-seq


title: CRISPRi singleton (eSLC25A37) Bulk-seq


title: CRISPRi singleton (SLC25A37 TSS control) Bulk-seq


title: CRISPRi singleton (PRKCB TSS control) Bulk-seq


title: CRISPRi singleton (ePRKCB) Bulk-seq


title: CRISPRi singleton (BEX4 TSS control) Bulk-seq


title: CRISPRi singleton (NMU TSS control) Bulk-seq


title: CRISPRi singleton (eNMU) Bulk-seq


title: At Scale Screen gRNA enrichment scRNA-seq

description:
at_scale_screen.cds.rds
at_scale_screen.phenoData.txt
at_scale_screen.genes.txt
at_scale_screen.cells.txt
at_scale_screen.exprs.mtx.txt
grna_groups.at_scale.txt
50k_reference_cells.rds
gene_gRNAgroup_pair_table.at_scale.txt
zero_inflated_outlier_genes_to_exclude.atscale.txt

extract_protocol:
Chromium Single Cell 3 + gRNA enrichment PCRs
Chromium Single Cell 3’ Reagents


title: At Scale Screen transcriptomes scRNA-seq

extract_protocol:
Chromium Single Cell 3
Chromium Single Cell 3’ Reagents


title: Pilot Screen (low MOI) gRNA enrichment scRNA-seq

description:
pilot_lowmoi_screen.rds
pilot_lowmoi_screen.phenoData.txt
pilot_lowmoi_screen.genes.txt
pilot_lowmoi_screen.cells.txt
pilot_lowmoi_screen.exprs.mtx.txt


title: Pilot Screen (high MOI) transcriptomes scRNA-seq

description:
pilot_highmoi_screen.rds
pilot_highmoi_screen.phenoData.txt
pilot_highmoi_screen.genes.txt
pilot_highmoi_screen.cells.txt
pilot_highmoi_screen.exprs.mtx.txt
grna_groups.pilot.txt
gene_gRNAgroup_pair_table.pilot.txt
all_deg_results.pilot.txt
zero_inflated_outlier_genes_to_exclude.pilot.txt


title: Pilot Screen (high MOI) gRNA enrichment scRNA-seq


title: CRISPRi singleton (eBEX4) Bulk-seq


title: CAP40-C82

status: Public on Jan 02 2019

city: Lausanne

first: Federico

last: Santoni

address: rue du Bugnon, 7

institute: CHUV

description:
Single cell fibroblast
ASE_gene_cell_ind.csv

data_processing:
Genome sequencing: For each individual,we used the Burrows- Wheeler Aligner (BWA mem v.0.7.10) to align the sequencing reads (fastq) to the human reference genome (GRCh37/hg19). We used SAMtools v.1.4 to remove paired-end duplicates and pile up the remaining reads. BCFtools v.1.4 was used to call the SNVs and Annovar (2016Feb01) for the annotation. SNVs with quality score <100 where excluded from the analysis.
Single cell RNA-seq: RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis
Allele specific expression: For each gene on the X chromosome, the aggregate monoallelic ratio (AR) per cell was calculated by averaging the allelic ratio of the reads covering the respective heterozygous sites (AR = sum of number of reads from the active X allele / total SNV reads; 0≤AR≤1). Since we do not have the availability of parental genotype for all the individuals, we designed an algorithm to estimate the active X allele per site based on the assumption that the active X allele is, on average, more transcribed than the inactive X. We validated this assumption comparing the prediction of our algorithm with the phasing of twins’ X alleles based on parental information (more details in Methods S1). According to this metric, inactivated genes cluster around AR=1 while known escapees appear as been uniformly distributed between 0.5≤AR≤0.95 (linear phase of the cumulative distribution, Figure S12). As support of this observation, AR distribution of autosomal genes clearly indicates AR=0.95 as the threshold separating biallelically expressed genes from monoallelic expressed genes (Figure S13). Therefore, we consider a gene as escapee in the relaxed set when the aggregate AR is ≤ 0.95 in at least 1 individual and as escapee in the robust set when the aggregate AR is ≤ 0.95 in at least 2 individuals. To reduce the effect of allele dropout, we only consider for the analysis SNV sites covered by at least 5 reads in at least three cells. To reduce sampling bias effects a gene is included in the analysis if detectable in more than 5 different cells and/or SNVs per sample.
Genome_build: GRCh37/hg19

source_name: Coriell

growth_protocol: Cells were cultured in DMEM GlutaMAX™ (Life Technologies) supplemented with 10% fetal bovine serum (Life Technologies) and 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C in a 5% CO2 atmosphere as described

extract_protocol:
Single-cell capture was performed using the C1 single-cell auto prep system (Fluidigm) following the manufacturer’s procedure. The integrated fluidic circuit used for the study is the C1™ Single-Cell mRNA Seq IFC, 17–25 μm with a capacity of 96 chambers. During the capture, all 96 chambers were inspected under an inverted phase contrast microscope; only chambers containing a non-damaged single cell were considered for downstream analysis. SMARTer Ultra Low RNA kit for Illumina sequencing (version 2, Clontech) was used for the cell lysis and cDNA synthesis.
Libraries were prepared with 0.3 ng of pre-amplified cDNA using Nextera XT DNA kit (Illumina)
Libraries were sequenced on an Illumina HiSeq2000 sequencer as 100 bp single ended reads. RNA sequences were mapped with GEM. Uniquely mapping reads were extracted by filtering for mapping quality (MQ>=150). An in-house algorithm was used to quantify RPKM expression using GENCODE v26. Cells with less than 1 million uniquely mapped reads were excluded from further analysis.

tag: cell culture

value: primary skin fibroblast

tag: individual id

value: Individual 2


title: CAP40-C76


title: Pilot Screen (low MOI) transcriptomes scRNA-seq


title: CAP40-C72


title: CAP40-C65


title: CAP40-C49


title: CAP40-C51


title: CAP40-C60


title: CAP40-C47


title: CAP40-C70


title: CAP40-C48


title: CAP40-C27


title: CAP40-C37


title: CAP40-C32


title: CRISPRi singleton (eRHAG) Bulk-seq


title: CAP40-C20


title: CAP40-C26


title: CAP40-C11


title: CAP40-C17


title: CAP40-C09


title: CAP40-C12


title: CAP40-C40


title: CAP38-C88


title: CAP38-C94


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title: CAP38-C83


title: CAP38-C82


title: CAP38-C81


title: CAP38-C79


title: CAP38-C78


title: CAP38-C75


title: CAP38-C77


title: CRISPRi singleton (Null1_chr14.679) Bulk-seq


title: CAP38-C71


title: CAP38-C72


title: CAP38-C74


title: CAP38-C70


title: CAP38-C68


title: CAP38-C65


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title: CAP38-C09


title: CAP22-C77


title: CAP22-C76


title: CAP22-C74


title: CAP22-C71


title: CAP22-C72


title: CRISPRi singleton (LBR TSS control) Bulk-seq


title: CAP22-C81


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title: CAP22-C63


title: CAP22-C61


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title: CAP22-C14


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title: CAP49-C88

value: Individual 1


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title: CAP49-C09


title: CAP49-C07


title: CAP49-C06


title: CAP49-C04


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title: CAP49-C01


title: CAP49-C05


title: CAP41-C91


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