title: KKAy_Liver_16w_rep2 [methylation]

type: genomic

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

description:
DM-2-4-2-5
DNA methylation data from liver of KK.Cg-Ay/J mouse at 16 weeks old.

hyb_protocol: The arrays were hybridised for 17 hours at 45°C and 60 rpm and then subsequently washed (Affymetrix Fluidics Station 450) and lastly stained with streptavidin-phycoerythrin(GeneChip® Hybridization, Wash, and Stain Kit, 900720). Hybridization was performed against the Affymetrix GeneChip Mouse Promoter 1.0R array.

scan_protocol: The samples were scanned on an Affymetrix GeneChip® Scanner 3000 following the protocols of the commercial manufacturer.

data_processing:
The raw output data was processed by the Tiling Analysis Software of Affymetrix with the annotated library of NCBI version 33 included Mm_PromPR_v02-1_NCBIv33.bpmap and Mm_PromPR_v02.grc for probe analysis. The results contain the two separated types which were recorded, log2(value of signal intensity) and its p-value.
The analysis of differential DNA methylation was performed by Partek Analysis. It was set up with the default parameters: P-value < 0.01, Average fragment length: 600, Minimum number of probe in a region: 10, Fraction of highest and lowest probes excluded from calculation of mean: 0.1, promoter region of up-stream: 5000bp and down-stream: 3000bp.

source_name: Liver tissue of KK.Cg-Ay/J mice at 16 weeks old

label_protocol: 7.5 ug of amplified DNA was fragmented and labeled according to Affymetrix Chromatin Immunoprecipitation Assay Protocol P/N 702238 Rev. 3.

growth_protocol: The pathogenesis-grouped mice were isolated by following the experimental design with the stages and classified groups and the cages of these mice were put in a sterile room with securely controlling in temperature (22-25°C), relative humidity (50-70%), and applying to natural photoperiod with nearly 12-h light/12-h dark.

extract_protocol: The mouse liver tissues were weighted proportionally 40 mg were scraped and collected supernatant by centrifugation. By following the instructing manual of manufacturer, the methylated DNA was isolated by the MethylMiner Methylated DNA Enrichment Kit (Cat#: ME10025, Invitrogen).

treatment_protocol: These mice were fed barely with LabDiet 5k52 (St. Louis, MO, USA), which contains 19.3% protein, 13.2% total fat and 4.3% fiber.

tag: strain/background

tag: genotype/variation

value: mutant-Ay (Ay/a)

tag: gender

value: Male

tag: age

value: 16 weeks

value: Liver

tag: Stage

value: Early developing


title: KKAy_Liver_42w_rep1 [methylation]

status: Public on Dec 13 2018

description:
42W-1
DNA methylation data from liver of KK.Cg-Ay/J mouse at 42 weeks old.

label: biotin

molecule: genomic DNA

organism: Mus musculus

source_name: Liver tissue of KK.Cg-Ay/J mice at 42 weeks old

tag: phenotype

value: 42 weeks

tag: tissue

value: Late developing


title: LCM2_TU

type: SRA

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

library_source: transcriptomic

data_processing:
Alignment: hisat2 (2.1.0), using hisat2-align-s hg19 -1 <R1.fq> -2 <R2.fq>
Read count: featureCounts (1.5.0) using featureCounts --countSplitAlignmentsOnly -s 0 -p -a hg19_refFlat.gtf -o <outdir> <bam1> […] <bamx>
FPKM quantification: DESeq2 (1.10.1)
Coverage track generation: bedtools genomecov (2.19), using bedtools genomecov -ibam <bam> -g hg19.chrom.sizes -bg -split -trackline -trackopts ‘name=<name> description=<description>’
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format representing read depth coverage, tsv format representing normalised FPKM values

molecule: total RNA

organism: Homo sapiens

source_name: Laser capture microdissected HL tissue

growth_protocol: Frozen tumor tissue was fixed for 10 minutes with 100% ethanol and air dried. Following fixation 200-400 HRS and bystander cells were excised using a Zeiss PALM LCM system and catapulted onto adhesive caps (415190-9191-000 - Zeiss).

extract_protocol:
Cell lysis, RNA extraction and purification were performed using the Absolutely RNA Nanoprep Kit (400753  Agilent).
RNA-Seq libraries were produced using the SMARTer Stranded Total RNA-Seq Kit v2  Pico input Mammalian (Takara Bio).

tag: tissue type

value: Tumour cells


title: KKAy_Liver_42w_rep2 [methylation]

description:
42W-2
DNA methylation data from liver of KK.Cg-Ay/J mouse at 42 weeks old.


title: LCM1_TU


title: CBMS1_ESC_single_MidS_19

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

library_source: genomic

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

source_name: CBMS1 ESC

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: TRUE

tag: cell cycle phase

value: MidS


title: LCM1_NTC

value: Non tumour cells


title: KKAy_Liver_16w_rep1 [methylation]

description:
DM-2-1-2-2
DNA methylation data from liver of KK.Cg-Ay/J mouse at 16 weeks old.


title: CBMS1_ESC_single_MidS_18


title: KKAy_Liver_6w_rep2 [methylation]

description:
6W-2
DNA methylation data from liver of KK.Cg-Ay/J mouse at 6 weeks old.

source_name: Liver tissue of KK.Cg-Ay/J mice at 6 weeks old

value: 6 weeks

value: Pre-developing


title: KKAy_Liver_6w_rep1 [methylation]

description:
6W-1
DNA methylation data from liver of KK.Cg-Ay/J mouse at 6 weeks old.

value: mutant-Ay (Ay/a)


title: CBMS1_ESC_single_MidS_15


title: KKa_Liver_42w_rep1 [methylation]

description:
42WKKA
DNA methylation data from liver of KK-a/a mouse at 42 weeks old.

source_name: Liver tissue of KK-a/a mice at 42 weeks old

value: KK-a/a

value: wild-type (a/a)

value: Male


title: CBMS1_ESC_single_MidS_22


title: CBMS1_ESC_single_MidS_16


title: KKa_Liver_42w_rep2 [methylation]

description:
42WKKB
DNA methylation data from liver of KK-a/a mouse at 42 weeks old.

value: Liver


title: CBMS1_ESC_single_MidS_25


title: Kelly, H3K27Ac.ResVeh

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

country: USA

institute: Broad Institute

data_processing:
Basecalls performed using Illumina NextSeq500.
ChIP-seq data sets were aligned using bwa-0.7.15, parameters: bwa mem -M -t 8,  to the build version NCBI37/hg19 of the human genome.
Quality control tests were performed based on the FastQC v.0.11.2 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and by using the ChIPQC library available from Bioconductor v3.2. Duplicates were filtered out.
The peaks for H3K27Ac and BRD4 were identified using MACS v1.4.3 with the cut-off 1e-09 for the P-value. The peaks were annotated by using the Annotate Peaks function available in the Homer v4.7 package.
Genome_build: NCBI37/hg19
Supplementary_files_format_and_content: Bigwig files were generated using the bamCompare module available from the DeepTools v2.2.3 software. Scores represent the normalized H3K27Ac signal with background input subtracted in  Reads Per Kilobase per Million reads per 20 bp bin.

source_name: Kelly neuroblastoma cell line

growth_protocol: Neuroblastoma cells were plated in 15 cm dishes and grown to 70-80% confluence.

extract_protocol:
Cells were harvested, washed twice in ice cold PBS with protease inhibitors and then lysed in 50 mM Tris-HCl pH 8.1, 10 mM EDTA, 1% SDS supplemented with protease inhibitors (Roche). Chromatin was sheared to ~250 bp fragments using the Covaris ultra-sonication. The sonicated lysate was then diluted with ChIP dilution buffer (16.7 mM Tris-HCl pH 8.1, 16.7 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X100, 0.01% SDS).  Subsequently, 2.5% of the lysate was removed as the input control.  The remaining lysate was incubated over night at 4°C with 3 µg of H3K27Ac antibody (ab4729, Abcam). The precipitated lysate was then incubated with protein A/G sepharose beads (Pierce, catalog #20423) for 2 hours and then washed sequentially in ice cold low salt buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton-X100, 0.1% SDS), high salt buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 1% Triton-X100, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.1, 0.25 M LiCl, 1 mM EDTA, 1% deoxycholic acid, 1% IGEPAL CA-630) and TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA).  Samples were incubated at 65°C overnight with elution buffer (0.1 M NaHCO3, 1% SDS) supplemented with 0.2M NaCl to reverse crosslinking.
ChIP libraries were prepared using the Rubicon Genomics Thruplex DNA-seq prep kit optimized for low input samples.

treatment_protocol: Cells were crosslinked with 1% formaldehyde in cell culture media for 6 minutes and then quenched with 0.125 M glycine for 5 minutes.

tag: chip antibody

tag: status

value: resistant

tag: treatement

value: vehicle

tag: cell line

value: Kelly


title: Kelly, H3K27Ac.NaiveJQ1

value: naïve


title: CBMS1_ESC_single_MidS_12

value: CBA/MsM

value: embryonic stem cell


title: CBMS1_ESC_single_MidS_10

value: Single cell

value: XX


title: CBMS1_ESC_single_MidS_14

value: TRUE

value: MidS


title: CBMS1_ESC_single_MidS_11


title: CBMS1_ESC_single_MidS_20


title: Kelly, H3K27Ac.NaiveVeh


title: CBMS1_ESC_single_MidS_07


title: CBMS1_ESC_single_MidS_08


title: CBMS1_ESC_single_MidS_09


title: Kelly, Input.H3K27Ac.ResJQ1

value: Input


title: Kelly, Input.H3K27Ac.NaiveJQ1


title: KKa_Liver_16w_rep1 [methylation]

description:
CTL-1-4
DNA methylation data from liver of KK-a/a mouse at 16 weeks old.

source_name: Liver tissue of KK-a/a mice at 16 weeks old

tag: strain/background

tag: genotype/variation

tag: gender

tag: age

value: 16 weeks

value: Early developing


title: Kelly, Input.H3K27Ac.ResVeh


title: Pharate-adults ftz-f1 knocked-down workers_B2 (dye-swap)

type: RNA

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

hyb_protocol: The RNA was dye-coupled and combined with hybridization buffer (49% Formamide, 49% SSC 20x and 0.2% SDS), pre-heated at 55° C for 3 min, applied to arrays, and hybridized for 17 h at 42 °C in single slide hybridization chambers placed in a water bath. A series of 30s shaking washes in 2× SSC plus 0.1% SDS; 2× SSC; 0.1× SSC and Milli-Q water at room temperature removed excess probe.

scan_protocol: The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (dsftz-f1’s sample intensity/dsGFP’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for dsftz-f1 sample intensity/ dsGFP sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments (10 and 20 microgram aRNA)=Pharate-adult A/B samples. See normalized_data.txt (linked as supplementary file on Series record).
BeeOligo120406.txt (linked as supplementary file on Series record) contains block, row and column information with the Gene IDs for the probes on the array.

organism: Apis mellifera

source_name: dsGFP (pool of 5 individuals)

label_protocol: RNA amplification was done with and according to Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion). The amplified RNA samples (10 or 20 µg) were used for dual channel microarray hibridization with Cy3 and Cy5 dyes (with dye swaps). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

growth_protocol: Pharate-adults workers were obtained from hives of Africanized hybrid Apis mellifera kept in the Experimental Apiary of the University of São Paulo in Ribeirão Preto, Brazil.

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

treatment_protocol: Two groups of pharate-adults workers were treated with dsRNA for ftz-f1 or with dsRNA for GFP and mantained in an incubator (34 °C, 80% relative humidity) for 7 days until the control group bees had reached the Pbd stage.

tag: developmental stage

value: Pharate-adult

value: control

tag: tissue

value: whole body

tag: hyb protocol

value: Slides hybridized with 20 microgram aRNA

source_name: dsftz-f1 (pool of 5 individuals)

value: ftz-f1 KD


title: KKa_Liver_6w_rep2 [methylation]

description:
K02
DNA methylation data from liver of KK-a/a mouse at 6 weeks old.

source_name: Liver tissue of KK-a/a mice at 6 weeks old

value: KK-a/a

value: wild-type (a/a)

tag: phenotype

value: Male

value: 6 weeks

value: Liver

tag: Stage

value: Pre-developing


title: Kelly, H3K27Ac.ResJQ1

value: resistant

value: Kelly


title: CBMS1_ESC_single_MidS_04

tag: strain

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

value: TRUE

value: MidS


title: CBMS1_ESC_single_G1_04

description: control

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: BEC2, BRD4_ResJQ1

source_name: SK-N-BE(2)-C neuroblastoma cell line

tag: chip antibody

tag: status

tag: treatement

tag: cell line


title: CBMS1_ESC_single_G1_05

description: control


title: CBMS1_ESC_single_G1_03

description: control


title: Kelly, Input.H3K27Ac.NaiveVeh

value: Input

value: naïve

value: vehicle


title: CBMS1_ESC_single_G1_02

description: control


title: BEC2, BRD4_ResVeh


title: CBMS1_ESC_single_G1_01

description: control


title: Pharate-adults ftz-f1 knocked-down workers_B1

tag: developmental stage

value: Pharate-adult

tag: genotype/variation

value: ftz-f1 KD

value: whole body

value: Slides hybridized with 20 microgram aRNA

value: control


title: Pharate-adults ftz-f1 knocked-down workers_A2  (dye-swap)

source_name: dsGFP (pool of 3 individuals)

tag: tissue

tag: hyb protocol

value: Slides hybridized with 10 microgram aRNA

source_name: dsftz-f1 (pool of 3 individuals)


title: CBMS1_ESC_100cells_MidS_rep3


title: KKa_Liver_16w_rep2 [methylation]

description:
CTL-1-5
DNA methylation data from liver of KK-a/a mouse at 16 weeks old.

tag: strain/background

value: KK-a/a

value: wild-type (a/a)

tag: phenotype

tag: gender

value: Male

tag: age

value: 16 weeks

value: Liver

tag: Stage

value: Early developing


title: CBMS1_ESC_single_MidS_06

tag: strain

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

value: TRUE


title: Pharate-adults ftz-f1 knocked-down workers_A1

value: Pharate-adult


title: BEC2, BRD4_NaiveVeh

tag: chip antibody

tag: status

value: naïve

value: vehicle


title: BEC2, BRD4_NaiveJQ1

tag: treatement

tag: cell line


title: CBMS1_ESC_single_MidS_05

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: MidS


title: CBMS1_ESC_100cells_MidS_rep2


title: KKa_Liver_6w_rep1 [methylation]

description:
K01
DNA methylation data from liver of KK-a/a mouse at 6 weeks old.

tag: strain/background

tag: genotype/variation

value: 6 weeks

tag: tissue

value: Pre-developing


title: CBMS1_ESC_100cells_G1_rep1

description: control


title: BEC2, InputBRD4_ResJQ1

value: Input

value: resistant


title: Control population 3, female, rep 1

status: Public on Dec 14 2018

city: Lund

first: Jessica

middle: K.

last: Abbott

address: Sölvegatan 37

department: Dept. of Biology

country: Sweden

institute: Lund University

description: Control population 3 females

hyb_protocol: Sample preparation and hybridisation was carried out at the Uppsala Array Platform (following the manufacturer's instructions for GeneChip Drosophila Genome 2.0 Affymetrix microarrays)

scan_protocol: Image acquisition was carried out at the Uppsala Array Platform

data_processing: Analysis was carried out in BioConductor, and data were pre-processed using Robust Multichip Average (RMA) in the “affy” package.

label: Biotin

organism: Drosophila melanogaster

source_name: Whole fly

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Standard fly culturing protocol for LHm population, described in Abbott et al. PLoS One 2013;8(7):e70493

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

tag: Sex

value: female

tag: population

value: control


title: CBMS1_ESC_Pupulation_G1_rep1

description:
Without whole genome amplifications
control

tag: strain

value: Population


title: HPV+ HNSCC cell line SCC-047 input

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Illumina's CASAVA 1.8.2 was used to convert BCL files to FASTQ files (default parameters)
bowtie2.2.1 (default parameters) was used to map paired end reads to hg19
MACS1.4.2 was used to call peaks (default parameters)
Genome_build: hg19 (GRCh37)

source_name: SCC-047-2 input

extract_protocol:
ChIP-DNA was prepared using recently developed SimpleChIP Enzymatic Chromatin IP Kit #9005 (Cell Signaling Technology) following manufacturer’s protocol with sample-specific adjustments in micrococcal nuclease and sonication steps. 10X phosphate buffered saline (PBS) pH 7.4 from Quality Biological Inc. was used wherever PBS is indicated. Samples were digested by both micrococcal nuclease and sonication. This process was additionally optimized and followed by gel electrophoresis to ensure uniform lysis of DNA across the genome. Samples were treated with 0.5 µl of micrococcal nuclease (Cell Signaling Technologies) per IP prep for 20 minutes (500 µL total reaction volume in 1.7 mL Eppendorf tube), followed by 30 seconds sonication on intensity #2 out of 10 (550 Sonic Dismembrator, Fisher Scientific) in iced-call water-bath.  Sonicated samples were left for one minute on ice. This was repeated 10 times over a 15-minute period. Freshly iced water was replaced 3 times during the cycle. Cleared chromatin preparation was analyzed for the level of digestion and DNA concentration, using recommended IV step from the kit protocol. Only chromatin preps with the distribution of chromatin DNA ranging from 150 bp to 900 bp in size were used for the immunoprecipitation step. DNA concentration was analyzed with a NanoDrop 1000 (Thermo Scientific) using the nucleic acid application module. Equal amounts of chromatin were used per IP step with exceptional performance (XP®) monoclonal antibodies validated for ChIP application (Cell Signaling Technology). Rabbit monoclonal antibodies were added in particular dilution based on an optimized concentration evaluated across a wide variety of commercial monoclonal antibodies. A 1:50 dilution for H3K4me3 (9751), H3K9ac (9649), H9K9me3 (13969) antibodies and a 1:100 dilution for H3K27ac (8173) antibody were used to isolate DNA segments bound by individual histone modification. We used 1:50 diluted total H3 (4620) antibody as a positive control and 1:250 diluted Normal Rabbit IgG (2729) as a negative control. A 3527-5 Incubator Shaker (Lab-Line) was used during elution. ChIP-DNA was purified and measured following the ChIP kit protocol. The 1/50 portion (2%) of the same chromatin for each sample  was used for DNA extraction skipping the antibody enrichment steps and was further used for sequencing as an input control.
ChIP-DNA for individual sample/antibody and their input controls were sonicated, end-repaired, and ligated to SOLiD P1 and P2 sequencing adaptors lacking 5' phosphate groups, using the NEBNext DNA Library Prep Set for SOLiD per the manufacturer's recommended protocol (NEB). Libraries were then nick-translated with Platinum Taq. ChIP-DNA was sequenced at the Experimental and Computational Genomics Core (ECGC) at Johns Hopkins University with a target sequencing coverage of approximately 45,000,000x and paired-end reads of 150 bp. Illumina CASAVA 1.8.2 was used to convert BCL files to FASTQ files using default parameters. Bowtie 2.2.1 was used to map paired-end reads to the hg19 human reference genome using default parameters and samtools 0.1.19 was used to convert, sort, and index SAM files. The count functionality IGVTools package was used to generate a tiled data file using default parameters. MACS (Model-based Analysis of ChIP-Seq algorithm, version 1.4.2) called ChIP-Seq peaks for each mark and each sample using the input DNA in that sample as a control. ChIP-Seq peaks were called significant if MACS modeled peak p-values are below a threshold of 0.000001, and these peaks were represented as genomic intervals. The cis-regulatory element annotation system (CEAS) was used to associate these genomic intervals with genes.

tag: cell type

value: HPV+ HNSCC cell line

tag: patient id

tag: hpv integration

value: Integrated

tag: hpv type

tag: age

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use

tag: antibody

value: input


title: CBMS1_ESC_Pupulation_EarlyS_rep1

description: Without whole genome amplifications

value: CBA/MsM

value: embryonic stem cell

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: EarlyS


title: CBMS1_ESC_BrdUIP_LateS_rep2

description:
P276_21_22_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph
P276_21_22_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph
P276_21_22_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph

tag: strain

tag: cell type

value: BrdUIP

value: LateS


title: HPV+ HNSCC cell line SCC-047 h3k9ac

tag: patient id

tag: hpv integration

tag: hpv type


title: CBMS1_ESC_BrdUIP_LateS_rep1

description:
P239_01_02_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph
P239_01_02_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph
P239_01_02_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph


title: CBMS1_ESC_BrdUIP_EarlyS_rep1


title: BEC2, InputBRD4_NaiveVeh

tag: chip antibody

tag: status

value: naïve

tag: treatement

value: vehicle

tag: cell line


title: BEC2, InputBRD4_ResVeh


title: CBMS1_ESC_BrdUIP_EarlyS_rep2


title: BEC2, InputBRD4_NaiveJQ1


title: HPV+ HNSCC cell line SCC-047 H3K27ac

tag: age

tag: gender

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use


title: BEC2, H3K27Ac_PI3K_engineered


title: CBMS1_ESC_100cells_MidS_rep1

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase

value: MidS


title: HPV+ HNSCC cell line SCC-047 H3K4me3

tag: cell type

tag: patient id

tag: hpv integration

tag: hpv type

tag: antibody


title: HPV+ HNSCC cell line SCC-090 input

source_name: SCC-090 input

tag: age

tag: gender


title: BEC2, H3K27Ac_GFP_control

tag: chip antibody

tag: status

tag: treatement

tag: cell line


title: HPV+ HNSCC cell line SCC-090 h3k9me3

source_name: SCC-090 h3k9me3

tag: race

tag: smoking

tag: type of tobacco

tag: pack years

tag: alcohol use


title: BEC2, Input_PI3K_engineered


title: HPV+ HNSCC cell line SCC-047 h3k9me3


title: BEC2, Input_GFP_control


title: HPV+ HNSCC cell line SCC-090 h3k9ac

source_name: SCC-090 h3k9ac


title: Kelly neuroblastoma cell line, Resistant_JQ1_treated_rep3

data_processing:
Illumina NextSeq 500 / Illumina Four-Channel SBS Sequencing  for base calling
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using Tophat2 v2 (Kim et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads(counts) were computed using the Feature Counts method implemented in the Bioconductor v3.2 RSubread package (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include reads(counts) values for each sample.

extract_protocol:
RNA was extracted from cells with the RNeasy Kit and on-column DNA digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
Strand-specific mRNA seq libraries were pooled and sequenced on a NextSeq500 instrument with single-end 75bp reads to a depth of 30-40M reads/sample.

value: Kelly


title: Kelly neuroblastoma cell line, Resistant_JQ1_treated_rep2


title: HPV+ HNSCC cell line SCC-090 h3k4me3

source_name: SCC-090 h3k4me3


title: HPV+ HNSCC cell line SCC-090 h3k27ac

source_name: SCC-090 h3k27ac


title: Kelly neuroblastoma cell line, Naïve_JQ1_treated_rep3


title: Patient derived xenograft for HPV+ HNSCC tumor sample 37 h3k9ac

description: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

source_name: XENO202 h3k9ac

value: Patient-derived HPV+ HNSCC xenograft

value: Male

value: Caucasian

value: Former smoker

value: Cigarette

value: Yes


title: Patient derived xenograft for HPV+ HNSCC tumor sample 37 h3k4me3

source_name: XENO202 h3k4me3

value: Integrated


title: Kelly neuroblastoma cell line, Naïve_JQ1_treated_rep2

source_name: Kelly neuroblastoma cell line


title: Kelly neuroblastoma cell line, Resistant_JQ1_treated_rep1_

value: resistant


title: ind117 2015

city: Haifa

first: Ayelet

last: Alpert

address: Techion

country: Israel

institute: Technion

description:
ind117
RNA expression value derived from Affymetrix Launcher software

hyb_protocol: Labeled complementary RNA (cRNA) was synthesized and amplified by in vitro transcription (IVT) of the second-stranded cDNA template using T7 RNA polymerase. Purified cRNA was fragmented by divalent cations and elevated temperature. 11ug of labelled and fragmented cRNA was hybridized onto the PrimeView GenChip, washed, scanned, and extracted by following the user guides: GeneChip Fluidics Station 450 User Guide AGCC (P/N 08-0295), the GeneChip Expression Wash, Stain, and Scan User Guide for Cartridge Arrays (PN 702731), and the GeneChip Command Console User Guide (P/N 702569).

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

label: biotinylated UTP

source_name: whole blood

label_protocol: For each sample, 100 ng of total RNA were used for first-strand cDNA synthesis by using T7 oligo(dT) primer  at 42°C for 2 hr, then for at least 2 min at 4°C. Single-stranded cDNA was converted to double-stranded cDNA for 1 hr at 16°C, then for 10 min at 65°C, then for at least 2 min at 4°C.

growth_protocol: No growth protocol was applied on the cells.

extract_protocol: RNA was extracted from the PAXgene RNA blood tubes (PreAanalytiX GmbH,VWR part # 77776-026, USA) using the QIAcube automation RNA extraction procedure according to the manufacturer’s protocol (Qiagene Inc.,Valencia, CA, USA).

treatment_protocol: No additional treatment was applied on the samples.

tag: ID

value: Female


title: ind52 2015

description:
ind52
RNA expression value derived from Affymetrix Launcher software


title: ind121 2015

description:
ind121
RNA expression value derived from Affymetrix Launcher software


title: ind36 2015

description:
ind36
RNA expression value derived from Affymetrix Launcher software


title: ind13 2015

description:
ind13
RNA expression value derived from Affymetrix Launcher software


title: ind116 2015

description:
ind116
RNA expression value derived from Affymetrix Launcher software


title: Patient derived xenograft for HPV+ HNSCC tumor sample 37 h3k27ac

source_name: XENO202 h3k27ac

tag: cell type


title: ind62 2015

description:
ind62
RNA expression value derived from Affymetrix Launcher software


title: ind110 2015

description:
ind110
RNA expression value derived from Affymetrix Launcher software


title: ind32 2015

description:
ind32
RNA expression value derived from Affymetrix Launcher software


title: ind89 2015

description:
ind89
RNA expression value derived from Affymetrix Launcher software


title: ind26 2015

description:
ind26
RNA expression value derived from Affymetrix Launcher software


title: ind133 2015

description:
ind133
RNA expression value derived from Affymetrix Launcher software


title: Kelly neuroblastoma cell line, Naïve_JQ1_treated_rep1


title: ind98 2015

description:
ind98
RNA expression value derived from Affymetrix Launcher software


title: Patient derived xenograft for HPV+ HNSCC tumor sample 20 h3k9me3

source_name: XENO201 h3k9me3

tag: patient id

value: Non-integrated

value: Current smoker


title: ind34 2015

description:
ind34
RNA expression value derived from Affymetrix Launcher software


title: ind86 2015

description:
ind86
RNA expression value derived from Affymetrix Launcher software


title: Patient derived xenograft for HPV+ HNSCC tumor sample 20 h3k9ac

source_name: XENO201 h3k9ac

tag: hpv integration


title: ind71 2015

description:
ind71
RNA expression value derived from Affymetrix Launcher software


title: ind134 2015

description:
ind134
RNA expression value derived from Affymetrix Launcher software


title: Kelly neuroblastoma cell line, Resistant_vehicle_treated_rep3


title: Kelly neuroblastoma cell line, Resistant_vehicle_treated_rep2


title: ind21 2015

description:
ind21
RNA expression value derived from Affymetrix Launcher software


title: Kelly neuroblastoma cell line, Resistant_vehicle_treated_rep1


title: Kelly neuroblastoma cell line, Naive_vehicle_treated_rep3


title: ind35 2015

description:
ind35
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 111 h3k9me3

description: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

source_name: UPPP111 h3k9me3

value: Normal UPPP

tag: hpv type


title: Patient derived xenograft for HPV+ HNSCC tumor sample 20 h3k27ac

source_name: XENO201 h3k27ac

tag: antibody


title: ind83 2015

description:
ind83
RNA expression value derived from Affymetrix Launcher software

tag: age


title: ind124 2015

description:
ind124
RNA expression value derived from Affymetrix Launcher software

tag: gender


title: ind129 2015

description:
ind129
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 111 h3k9ac

source_name: UPPP111 h3k9ac


title: Kelly neuroblastoma cell line, Naïve_vehicle_treated_rep1


title: Patient derived xenograft for HPV+ HNSCC tumor sample 20 h3k4me3

source_name: XENO201 h3k4me3


title: ind99 2015

description:
ind99
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 111 H3K4me3

source_name: UPPP111 H3K4me3


title: ind47 2015

description:
ind47
RNA expression value derived from Affymetrix Launcher software


title: ind39 2015

description:
ind39
RNA expression value derived from Affymetrix Launcher software


title: Kelly neuroblastoma cell line, Naive_vehicle_treated_rep2


title: ind73 2015

description:
ind73
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 107 h3k9me3

source_name: UPPP107 h3k9me3

value: African american

value: Non-smoker

value: No


title: Normal UPPP control sample 111 H3K27AC

source_name: UPPP111 H3K27ac


title: ind132 2015

description:
ind132
RNA expression value derived from Affymetrix Launcher software


title: ind90 2015

description:
ind90
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 107 h3k9ac

source_name: UPPP107 h3k9ac


title: ind125 2015

description:
ind125
RNA expression value derived from Affymetrix Launcher software


title: ind14 2015

description:
ind14
RNA expression value derived from Affymetrix Launcher software


title: ind12 2015

description:
ind12
RNA expression value derived from Affymetrix Launcher software


title: ind130 2015

description:
ind130
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 107 H3K27AC

source_name: UPPP107 H3K27ac


title: ind105 2015

description:
ind105
RNA expression value derived from Affymetrix Launcher software


title: ind82 2015

description:
ind82
RNA expression value derived from Affymetrix Launcher software


title: ind33 2015

description:
ind33
RNA expression value derived from Affymetrix Launcher software


title: ind5 2015

description:
ind5
RNA expression value derived from Affymetrix Launcher software


title: ind59 2015

description:
ind59
RNA expression value derived from Affymetrix Launcher software


title: ind66 2015

description:
ind66
RNA expression value derived from Affymetrix Launcher software


title: ind29 2015

description:
ind29
RNA expression value derived from Affymetrix Launcher software


title: ind18 2015

description:
ind18
RNA expression value derived from Affymetrix Launcher software


title: ind56 2015

description:
ind56
RNA expression value derived from Affymetrix Launcher software


title: shTDG_SK28_R3

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Genetique et de biologie moleculaire et cellulaire

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel table (.xls format) containing raw read counts, counts normlalized by library size, counts normalized by both library size and gene length as well as log2(foldchange) and p-values computed by deseq2 for the shTDG vs shControl comparison for all genes. The excel table contains two additionnal sheets comprising only upregulated and downregulated genes.

molecule: polyA RNA

growth_protocol: SK28 were validated by CGH and cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% L-glutamine. A non-transformed epidermal melanocytic line HEMn-LP (from Raza Zaidi) was cultured in Medium 254 (Invitrogen) supplemented with Human Melanocyte Growth Supplement (Invitrogen).

extract_protocol:
RNA (biological triplicates) was prepared with the RNeasy Mini kit (Qiagen), and quality control was performed on a Bioanalyzer.
Complementary DNA were generated and linearly amplified from 6 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN technologies Inc., Leek, Netherlands), according to manufacturer's instructions. Amplified cDNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France) in a 1.8:1 ratio of beads to sample and fragmented by sonication using a Covaris E220 instrument (with duty factor: 10 percent, peak incident power: 175 watts and cycles/burst: 200 for 120 seconds). RNA-Seq libraries were generated from 100 ng of fragmented ds-cDNA using Ovation Ultralow Library System v2 (NuGEN technologies Inc., Leek, Netherlands) according to manufacturer's instructions with only 8 PCR cycles for library amplification. The final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Two different TDG shRNA lentiviral constructs, named C8 (Thermo Scientific Open Bio-Systems) and sh4575 (Sigma-Aldrich), and the empty pLKO.1 lentiviral vector were used in this study. Control pLKO.1 and TDG shRNA lentivirus-infected melanoma cell lines were selected in puromycin (0.5 μg/mL) for 3 to 5 days.

tag: treatment

value: shTDG


title: shCtrl_SK28_R3

value: shControl


title: shCtrl_SK28_R2


title: ind9 2015

description:
ind9
RNA expression value derived from Affymetrix Launcher software


title: ind79 2015

description:
ind79
RNA expression value derived from Affymetrix Launcher software


title: ind57 2015

description:
ind57
RNA expression value derived from Affymetrix Launcher software


title: shCtrl_SK28_R1


title: ind120 2015

description:
ind120
RNA expression value derived from Affymetrix Launcher software


title: Patient derived xenograft for HPV+ HNSCC tumor sample 37 h3k9me3

description: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

source_name: XENO202 h3k9me3

value: Patient-derived HPV+ HNSCC xenograft


title: ind11 2015

description:
ind11
RNA expression value derived from Affymetrix Launcher software

value: Male


title: ind115 2015

description:
ind115
RNA expression value derived from Affymetrix Launcher software


title: shTDG_SK28_R1


title: ind77 2015

description:
ind77
RNA expression value derived from Affymetrix Launcher software


title: ind1 2015

description:
ind1
RNA expression value derived from Affymetrix Launcher software


title: ind74 2015

description:
ind74
RNA expression value derived from Affymetrix Launcher software


title: ind80 2015

description:
ind80
RNA expression value derived from Affymetrix Launcher software


title: Q1267E/L1270S

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The base calling was done by RTA (Real Time Analysis. v1.18)
In the preprocessing step, low-quality base-calling reads were discarded using fastq_quality_filter (-q 20 –p 90). Next, reads containing a 3′ Illumina adapter sequence were filtered and the adapter sequence was removed using cutadapt (-a TGGAATTCTCGGGTGCCAAGG --trimmed-only). Then, PCR duplicate sequences were removed using fastx_collapser. Random tetramer sequences were trimmed at both the 5′ and 3′-ends to reduce the ligation bias and reads within the miRNA size range were obtained using cutadapt (-u 4 -u -4 -m 18 -M 26).
In the alignment and read counting steps, reads were mapped onto the hg38 human genome using bowtie2, allowing no mismatches, deletions, or insertions at all but the terminal modification with at most 2 (-f --local -p 4 --score-min L,-4,2 --ma 2 -k 5). Among all mapped reads, only unambiguously mapped reads were used for further steps using Samtools. The locus of the remaining mapped reads to the miRNA hairpin annotation in miRBase v21 was used to count miRNA reads using bedtools.
In a miRNA abundance analysis, the number of reads mapped within each pri-miRNA as well as spike-in was counted and 1 was added to each as a pseudocount. Among 30 spike-ins, 15 were randomly selected for normalization. The raw read counts were normalized by the geometric mean of 15 selected spike-ins and the quality of normalization was validated by checking the normalized results for the remaining 15 spike-ins. To make the normalized count to larger than 1, a scaling factor of 5,000 was multiplied with each normalized count.
Genome_build: hg38
Supplementary_files_format_and_content: Provided are tab-delimited text files containing raw and normalized read counts.

source_name: HCT116 DROSHA-null

growth_protocol: HCT116 DROSHA null cells were cultured in McCoy’s 5A medium (Welgene) supplemented with 9% fetal bovine serum (Welgene).

extract_protocol:
Total RNA was purified using TRIzol (Thermo Fisher).
10 μg of total RNA was mixed with 30 spike-in RNAs (Kim et al., bioRxiv, doi: 10.1101/339606); then, 18–30-nt fragments were purified through a 15% urea-polyacrylamide gel. Subsequently, a 3′ adapter containing 4 random nucleotides at the 5′-end was ligated, and gel purification was performed to purify 40–55-nt RNAs. The purified RNA was ligated with a 5′ adapter that also contained 4 random nucleotides at the 3′-end. Reverse transcription, PCR, and gel purification were performed following a general Illumina protocol.

treatment_protocol: AcGFP or DROSHA-TEV-HA (wild-type or mutant) plasmids were transfected into HCT116 DROSHA-null cells using FuGene HD (Promega, Madison, WI, USA) according to the manufacturer's protocol. Three days later, cells were harvested for RNA preparation.

tag: transfected gene

value: DROSHA, Q1267E/ L1270S

tag: experimental group

value: Group 2


title: L428_H3K4me3

data_processing:
Alignment: bowtie2 (2.1.0). Alignment was performed  using bowtie2 -x hg19 --very-sensitive-local
Peak detection and coverage track generation: MACS (1.4.1). macs14 -t <bam> -n <name> -g hs –keep-dup=auto -w -S
Genome_build: hg19
Supplementary_files_format_and_content: Variable step 10bp bin wig format representing depth coverage

source_name: Hodgkin's lymphoma cell line

growth_protocol: KM-H2, L1236 and L428 were cultured in IMDM, Namalwa and Reh cells in RPMI, both supplemented with 10% FCS, 2mM Glutamine, plus P/S. All cultures were incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For ChIP, 5x106 L428 cells were washed, resuspended at 3.3x106 cells/ml and initially crossklinked with 8.3 µl/ml DSG for 45 mins at room temperature. Cells were then washed 3 times with PBS using 500 g centrifugation, then subsequently crosslinked in 1% formaldehyde for 10 mins at room temperature. Quenching was carried out in by adding 1/10 volume of 2M glycine for a final concentration of 0.2M. Cells were Washed twice with ice-cold PBS, resuspended in1 ml 10 mM Hepes, 10 mM EDTA, 0.5 mM EGTA (all ph 8.0), 0.25 % Triton X100 and rotated 4 °C for 10 mins for lysis. Cells were then centrifuged at 500 g at 4 °C for 5 mins and nuclei resuspended in in 1ml 10 mM Hepes, 1mM EDTA, 0.5 mM EGTA (all pH 8.0), 200 mM NaCl, 0.01 % Triton X100 and rotated 4°C for 10 mins. Nuclei were then centrifuged at 500 g at 4°C for 5 mins and resuspended in 150 µl 25 mM Tris, 2 mM (both pH 8.0), 150 mM NaCl, 1 % Triton X100, 0.25 % SDS Sonication was performed using a Picoruptor sonicator (Diagenode, Belgium) using 30 30s on, 30s off cycles. Sonicated chromatin was centrifugated for 10 min at 16,000 g at 4 °C to pellet debris, then diluted in 300 µl 25 mM Tris, 2 mM (both pH 8.0), 150 mM NaCl, 1 % Triton X100, 0.25 %, 7.5 % Gylcerol ( final volume 450 µl ,0.083 % SDS, 5 % glycerol final concentration). All buffers contained 1:100 phosphatase inhibitor cocktail (Sigma-Aldrich, USA) and 0.1 mM PMSF. 5% of the sonicated chromatin was saved as input. 15 µl Protein G Dynabeads (Invitrogen, UK) were washed with 500 µl PBS + 0.0 2% Tween 20, resuspended in 15 µl PBS + 0.02 % Tween 20, 0.5 % BSA and 2 µg H3K4me3 millipore 04745 antibody, and rotated at 4 °C for 2 hours. Beads were washed with 500 µl PBS + 0.02 % Tween 20 and incubated with the sonicated chromatin (400 µl) on a rotating wheel overnight at 4 °C. Beads were then washed twice with 1ml 20 mM Tris, 2 mM EDTA 0.5 M (both pH 8.0), 150 mM NaCl, 1 % TritonX100, 0.1 % SDS, once with 1ml 20 mM Tris, 2 mM EDTA 0.5 M (both pH 8.0), 500 mM NaCl, 1 % TritonX100, 0.1 % SDS, once with 1 ml 10 mM Tris, 1 mM EDTA (both pH 8.0), 250 mM LiCl 0.5 % NP40, 0.5 % Na-deoxycholate and twice with 1ml 10 mM  Tris , 1 mM EDTA (both pH 8.0), 50 mM NaCl. Beads were subsequently incubated twice with 50 µl 100 mM NaHCO3, 1% SDS at 65 °C, and eluates reverse crosslinked overnight with 200 mM NaCl, 0.25 µg/µl proteinase K at 65 °C. Eluates were then incubated 1 hr with 0.1 µg/µl RNAse A at 37 °C. Phenol-chloroform extraction was performed by adding twice 100 µl equilibrated phenol-chloroform isoamyl alcohol (25:24:1), vortexing for 30s and spinning down at 16,000 g at 4°C for 5 mins, then adding 2.5 volumes 100% ethanol, 1/10 volume 5M NaCl and 1 µl glycogen, resuspending in 100 µl 0.1 H2O.
Libraries were generated using the Kapa Hyperkit protocol (Kapa Biosystems, USA) according to manufacturer’s instructions, using 16 cycles of amplification. 200-400 bp fragments were size-selected using a 2% agarose gel then subsequently purified using the QiaQuick Gel Extraction kit (QiaGen, Germany) according to manufacturer’s instructions. High-throughput sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina, USA).

tag: lymphoma type

value: Hodgkin's lymphoma cell line

value: millipore 04745


title: ind87 2015

description:
ind87
RNA expression value derived from Affymetrix Launcher software


title: ind135 2015

description:
ind135
RNA expression value derived from Affymetrix Launcher software


title: ind37 2015

description:
ind37
RNA expression value derived from Affymetrix Launcher software


title: ind58 2015

description:
ind58
RNA expression value derived from Affymetrix Launcher software


title: WT_DROSHA_2

value: Wild-type DROSHA


title: Q1266H

value: DROSHA, Q1266H


title: LongLinker3

value: DROSHA, DWN1257-1259DWGGSN

value: Group 1


title: LongLinker2

value: DROSHA, DWN1257-1259DWNNN


title: ind107 2015

description:
ind107
RNA expression value derived from Affymetrix Launcher software

value: Female


title: LongLinker1

value: DROSHA, DWN1257-1259DWNNNN


title: ind94 2015

description:
ind94
RNA expression value derived from Affymetrix Launcher software


title: ShortLinker2

value: DROSHA, DWN1257-1259G


title: ShortLinker1

value: DROSHA, DWN1257-1259DG


title: shTDG_SK28_R2

tag: cell line

value: shTDG


title: ind123 2015

description:
ind123
RNA expression value derived from Affymetrix Launcher software


title: Patient 54

city: Salt Lake City

first: Roberto

middle: Henrique

last: Nussenzveig

state: Utah

address: 2000 Circle of Hope

department: Oncology

institute: University of Utah/Huntsman Cancer Institute

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 54

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing:
The scanned data files were processed by GenomeStudio Genotyping using the cluster file HumanOmniExpress_24v1.0 (GPL21168), HumanOmniExpress_24v1.1 (GPL22678), and InfiniumOmniExpress_24v1.2  (Platform_InfiniumOmniExpress-24v1-2_A1.txt) all provided by Illumina.
Genotype: AA,AB,BB,or NC (no call)

label: C-Bio and A-DNP

source_name: Prostate Cancer

label_protocol: Standard Illumina labelling protocol

extract_protocol: Extraction of genomic DNA from separated leukocytes was performed using ice-cold alkaline phenol-chloroform extraction and precipitation with isopropanol followed by ethanol.

tag: disease state

value: Prostate Cancer

tag: abir. start date

tag: abir. failure date

tag: failure (yes=1, no=0)

tag: pfs (months)

tag: logpsa (at abir start)

value: BB

value: AA

tag: tissue

value: whole blood


title: Patient 53

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 53


title: ind67 2015

description:
ind67
RNA expression value derived from Affymetrix Launcher software

source_name: whole blood

tag: ID


title: ind40 2015

description:
ind40
RNA expression value derived from Affymetrix Launcher software

value: Male


title: ind114 2015

description:
ind114
RNA expression value derived from Affymetrix Launcher software


title: M4


title: M5


title: ind43 2015

description:
ind43
RNA expression value derived from Affymetrix Launcher software


title: Normal UPPP control sample 107 H3K4me3

description: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

source_name: UPPP107 H3K4me3

tag: cell type

value: Normal UPPP

tag: patient id

tag: hpv integration

tag: hpv type

tag: race

value: African american

tag: smoking

value: Non-smoker

tag: type of tobacco

tag: pack years

tag: alcohol use

value: No


title: Patient 52

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 52

tag: disease state


title: ind64 2014

description:
ind64
RNA expression value derived from Affymetrix Launcher software

tag: age

tag: gender


title: M3

tag: transfected gene

tag: experimental group


title: ind78 2015

description:
ind78
RNA expression value derived from Affymetrix Launcher software


title: ind109 2015

description:
ind109
RNA expression value derived from Affymetrix Launcher software


title: ind66 2014

description:
ind66
RNA expression value derived from Affymetrix Launcher software


title: M2


title: ind10 2014

description:
ind10
RNA expression value derived from Affymetrix Launcher software


title: ind37 2014

description:
ind37
RNA expression value derived from Affymetrix Launcher software


title: ind88 2015

description:
ind88
RNA expression value derived from Affymetrix Launcher software


title: ind87 2014

description:
ind87
RNA expression value derived from Affymetrix Launcher software


title: ind4 2015

description:
ind4
RNA expression value derived from Affymetrix Launcher software


title: ind23 2015

description:
ind23
RNA expression value derived from Affymetrix Launcher software


title: Patient 50

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 50

tag: abir. start date

tag: abir. failure date

tag: failure (yes=1, no=0)

tag: pfs (months)

tag: logpsa (at abir start)

value: AB


title: ind13 2014

description:
ind13
RNA expression value derived from Affymetrix Launcher software

tag: ID


title: ind118 2014

description:
ind118
RNA expression value derived from Affymetrix Launcher software


title: Patient 49

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 49

tag: last f/u

tag: tissue


title: PhosMut

value: DROSHA, K1262A/ Q1318A

value: Group 1


title: M1


title: del_dsRBD

value: DROSHA, deletion of C-terminal 114 amino acids


title: pup exposure VNO IP rep3

first: Catherine

last: Dulac

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: HHMI/Harvard University

data_processing:
RNA Star
Custom script in R to count reads
Genome_build: ftp://ftp.ensembl.org/pub/release-73/gtf/mus_musculus/Mus_musculus.GRCm38.73.gtf.gz
Supplementary_files_format_and_content: read counts of each sequencing data in csv

source_name: Vomeronasal organ

extract_protocol:
Lysates of dissected vomeronasal organs was clearified with DHPC/NP40 and served for immunoprecipitation by anti-phospho S6 antibody.
Library was prepared by SMARTer cDNA synthesis and Low Input Library Kits, the DNA was sheared to 200-500 bp by Covaris

tag: strain

tag: Sex

value: male

value: Vomeronasal organ


title: Patient 51

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 51


title: Patient 48

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 48


title: pup exposure VNO IP rep2


title: Patient 47

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 47


title: pup exposure VNO IP rep1


title: WT_DROSHA

value: Wild-type DROSHA


title: ind117 2014

description:
ind117
RNA expression value derived from Affymetrix Launcher software

value: Female


title: ind121 2014

description:
ind121
RNA expression value derived from Affymetrix Launcher software


title: ind130 2014

description:
ind130
RNA expression value derived from Affymetrix Launcher software


title: Patient 46

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 46

value: Prostate Cancer


title: Patient 44

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 44

value: BB


title: Patient 45

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 45

value: AA


title: control exposure VNO IP rep2


title: control exposure VNO IP rep3


title: Patient 42

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 42

value: whole blood


title: ind63 2014

description:
ind63
RNA expression value derived from Affymetrix Launcher software


title: control exposure VNO IP rep1


title: Hippocampus [TG_STR_4]

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

data_processing:
Read quality of RNA-seq data in fastq files was assessed using FastQC (v0.11.4) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR (v2.4.2a) allowing gapped alignments to account for splicing against the Ensembl MusMusculus genome v82
Raw counts describing gene-level abundances were derived from DESeq2 (v1.8.2) (Love et al., 2014) with default parameters.
Genome_build: Ensembl MusMusculus genome v82
Supplementary_files_format_and_content: comma seperated text file containing raw read counts per gene identified by Ensembl gene ID

source_name: Hippocampus

extract_protocol:
Hippocampi were removed, flash-frozen in liquid nitrogen, and RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen). TruSeq RNA Sample Prep Kit (Illumina) was used with 500 ng of total RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Poly(A)-selected single-end sequencing libraries were generated according to the manufacturer’s instructions. All libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 11–18 million single-end reads.

value: hippocampus

tag: genotype

value: transgenic overexpressing human SNCA

tag: environment

value: CUMS

value: 6 months


title: Hippocampus [TG_STR_3]


title: ind34 2014

description:
ind34
RNA expression value derived from Affymetrix Launcher software

value: Male


title: Tcell_wt3

city: Durham

first: Ergang

last: Wang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

data_processing:
Raw reads were alinged using hisat2
sam files were converted to bam files and indexed
Htseq was used to generate the count table of gene expression
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated file with columns of gene symbol and its corresponding raw count

source_name: Spleen

extract_protocol:
colon epithelial cells were isolated according to the method described in Sato et. al, 2011, and CD4+ T cells were isolated from spleen accoding to the method described in Weigmann et. al, 2007. RNA was extracted by the QIAGEN Rneasy plus mini kit.
library was prepared for sequencing using standard Illumina library construction protocol


title: Tcell_mir34aKO3


title: Tcell_mir34aKO2


title: Patient 41

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 41

tag: disease state

value: AB


title: GFP

value: GFP


title: Patient 40

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 40


title: Tcell_wt2


title: Tcell_wt1


title: Patient 39

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 39


title: Hippocampus [TG_STR_2]

tag: age


title: Hippocampus [TG_STR_1]


title: ind108 2014

description:
ind108
RNA expression value derived from Affymetrix Launcher software

tag: gender


title: ind35 2014

description:
ind35
RNA expression value derived from Affymetrix Launcher software


title: ind90 2014

description:
ind90
RNA expression value derived from Affymetrix Launcher software


title: Tcell_mir34aKO1


title: colon_mir34aKO3

source_name: Colon

value: Wild Type


title: ind71 2014

description:
ind71
RNA expression value derived from Affymetrix Launcher software


title: Hippocampus [TG_SE_4]

value: Standard


title: Patient 43

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 43


title: colon_mir34aKO2


title: Patient 37

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 37


title: colon_mir34aKO1


title: ind15 2014

description:
ind15
RNA expression value derived from Affymetrix Launcher software


title: Hippocampus [TG_SE_3]


title: ind14 2014

description:
ind14
RNA expression value derived from Affymetrix Launcher software


title: Patient 36

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 36


title: ind62 2014

description:
ind62
RNA expression value derived from Affymetrix Launcher software


title: Hippocampus [TG_SE_1]


title: colon_wt3


title: Hippocampus [WT_STR_4]

value: WT


title: colon_wt1


title: Patient 35

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 35


title: Patient 38

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 38


title: colon_wt2


title: Patient 33

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 33


title: Patient 34

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 34


title: ind110 2014

description:
ind110
RNA expression value derived from Affymetrix Launcher software


title: Hippocampus [TG_SE_2]


title: ind40 2014

description:
ind40
RNA expression value derived from Affymetrix Launcher software


title: ind11 2014

description:
ind11
RNA expression value derived from Affymetrix Launcher software


title: ind89 2014

description:
ind89
RNA expression value derived from Affymetrix Launcher software


title: LIN28B_X4_Total_RNA_Mouse

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
TX4

data_processing:
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome and rnaseq samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format

growth_protocol: standard cell culture in 10% FBS in DMEM

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent; small RNA isolation was performed using miRvana kit
Various: Illumina polyA Total RNA kit, Illumina Small RNA kit

treatment_protocol: LIN28B transgenes were induced using 10ng/ml Doxycycline; mature let-7a miRNAs (10nM) were introduced using Lipofectamine RNAiMAX

tag: cell line


title: ind5 2014

description:
ind5
RNA expression value derived from Affymetrix Launcher software


title: Patient 31

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 31


title: Hippocampus [WT_STR_1]


title: LIN28B_X3_Total_RNA_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
TX3


title: LIN28B_X2_Total_RNA_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
TX2


title: ind61 2014

description:
ind61
RNA expression value derived from Affymetrix Launcher software


title: Patient 30

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 30


title: Hippocampus [WT_SE_3]


title: Hippocampus [WT_STR_3]


title: ind29 2014

description:
ind29
RNA expression value derived from Affymetrix Launcher software


title: Patient 29

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 29


title: ind84 2014

description:
ind84
RNA expression value derived from Affymetrix Launcher software


title: Hippocampus [WT_SE_2]


title: Hippocampus [WT_STR_2]


title: Hippocampus [WT_SE_1]


title: LIN28B_X1_Total_RNA_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
TX1


title: Patient 28

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 28


title: LIN28B_X0_Total_RNA_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
TX0


title: Patient 32

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 32


title: Patient 27

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 27


title: P13_GSUSP_MB_RNASeq_rep3

city: Toronto

first: Chi-chung

last: Hui

state: Ontario

address: 686 Bay Street. Room 16-9712

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
fastq reads were aligned to the mm9 transcriptome using kallisto 0.42.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.42.2

extract_protocol:
Tumours were dissected and kept at -80°C prior to RNA extractuibn with PureLink RNA Mini kit (Invitrogen). RNA was treated with Turbo DNAfree kit to remove potential residual gDNA. 1 to 2µg of RNA were used to prepare the PolyA RNA library.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.

tag: strain background

value: mixed (CD-1)

tag: genotype/variation

value: Sufu;Spop double knockout

tag: developmental stage

value: medulloblastoma


title: Lin28B_X3_Polysome_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
PX3

data_processing:
Library strategy: ribosome profiling
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
RPKM values were calculated for all polysome and rnaseq samples. For eCLIP samples, read densities were calculated to identify eCLIP peaks. eCLIP peaks were identified using clipper
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: RPKM files for all polysome samples. eCLIP input normalized peaks in BED format


title: Lin28B_X4_Polysome_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
PX4


title: P13_GSUSP_MB_RNASeq_rep2


title: Lin28B_X2_Polysome_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
PX2


title: Patient 26

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 26

value: Prostate Cancer

tag: abir. start date

tag: abir. failure date

tag: failure (yes=1, no=0)


title: Patient 25

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 25

tag: pfs (months)

tag: logpsa (at abir start)

value: BB


title: P13_GSUSP_MB_RNASeq_rep1

tag: tissue


title: Lin28B_X1_Polysome_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
PX1


title: Patient 24

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 24

value: AA


title: Lin28B_X0_Polysome_Mouse

description:
processed data file:
mouse_polysome_samples_rpkms.txt
sample name in processed data file:
PX0


title: P13_GM2_MB_RNASeq_rep3

value: SmoM2 overexpression


title: Patient 23

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 23

value: whole blood


title: P13_GM2_MB_RNASeq_rep2


title: P13_GM2_MB_RNASeq_rep1


title: Patient 21

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 21


title: Patient 22

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 22

tag: last f/u


title: P13_WT_Cb_RNASeq_rep2

value: wild type

value: cerebellum


title: P13_WT_Cb_RNASeq_rep1


title: Patient 20

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 20


title: Patient 18

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 18


title: P13_WT_Cb_RNASeq_rep3


title: Patient 19

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 19


title: DKO_H3K36me3_Rep2

data_processing:
Adaptor sequences were trimmed using Trimmomatic 0.36 with adaptor sequence file TruSeq3-PE-2.fa
Reads were aligned to the mm9 reference genome using default parameters of BWA MEM
Aligned reads were filtered using bamtools to exclude unmappped reads, mapping quality < 5, and not proper pairs.
ENCODE blacklist regions in mm9 were filtered out using bedtools
Peaks were called using MACS2 with q = 0.05. --broad was enabled for histone ChIP, and disabled for Gli2 ChIP-Seq.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are peaks called by MACS2.

extract_protocol:
Tumours were dissected, cut into small pieces, and crosslinked in solution A (1% formaldehyde, 50mM Hepes-KOH, 100 mM NaCl, 1mM EDTA, 0.5 mM EGTA) for 20 minutes at room temperature. 1/20 volume of 2.5 M glycine was added to quench formaldehyde. Tissues were rinsed in ice-cold PBS and dounced in Wheaton tissue grinder. Cell suspensions were passed through a 100μm cell strainer to remove connective tissues, then centrifuged at 4 °C at 2500 × rcf for 3 min, followed by a wash in PBS. Olig2 antibody (EMD Millipore, ab15328) was incubated with pre-blocked magnetic beads in 250μL total volume for 8 hours at 4 °C, then washed and resuspended in 100μL 0.5% BSA (w/v) solution. Cell pellets were lysed by sequentially resuspending and centrifuging in LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100), and LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA). Pellet was resuspended in LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine) and sonicated into 200-400bp fragments. Sonicated lysates were diluted with LB3. After saving 50μL for input control, they were split into tubes containing 10% v/v Triton X-100 with Gli2 (homemade), H3K27ac (Millipore 05-1334 lot 2489078), or H3K36me3 (Abcam ab9050 lot GR204353-1) antibody, and incubated overnight. Beads were washed 6 times in RIPA buffer (50 mM Hepes-KOH, pH 7.5; 500 mM LiCl; 1mM EDTA; 1% NP-40 or Igepal CA-630; 0.7% Na-Deoxycholate), and once in TBS (20 mM Tris-HCl, pH 7.6; 150 mM NaCl). Protein-DNA complexes were eluted and crosslink reversed with 200 μL of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS). The 50μL input lysate was also included in this step. Eluted DNA was diluted with 200 μL of TE, and treated with RNaseA for 30 min at 37°C, and subsequently with proteinase K for 2 hours at 55°C. Phenol:chloroform:isoamyl alcohol was used to extract DNA.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® kit.

tag: chip antibody


title: ind94 2014

description:
ind94
RNA expression value derived from Affymetrix Launcher software

tag: ID

value: Female


title: ind97 2014

description:
ind97
RNA expression value derived from Affymetrix Launcher software

value: Male


title: ind125 2014

description:
ind125
RNA expression value derived from Affymetrix Launcher software


title: ind129 2014

description:
ind129
RNA expression value derived from Affymetrix Launcher software


title: ind1 2014

description:
ind1
RNA expression value derived from Affymetrix Launcher software


title: DKO_H3K36me3_Rep1

tag: genotype


title: Patient 17

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 17

tag: disease state


title: ind7 2014

description:
ind7
RNA expression value derived from Affymetrix Launcher software

tag: age


title: Patient 16

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 16

value: AB


title: ind56 2014

description:
ind56
RNA expression value derived from Affymetrix Launcher software

tag: gender


title: ind12 2014

description:
ind12
RNA expression value derived from Affymetrix Launcher software


title: ind33 2014

description:
ind33
RNA expression value derived from Affymetrix Launcher software


title: ind133 2014

description:
ind133
RNA expression value derived from Affymetrix Launcher software


title: 301-Serum-nanoDLD_TAATGCGC-CCTATCCT_BHGHG5BCX2_L001

city: Yorktown Heights

first: Gustavo

last: Stolovitzky

state: NY

address: P.O.Box 218

institute: Icahn School of Medicine

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt), with a 3' adapter sequence of AAAAAAAAAA. Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contains RPM read counts for miRNAs / piRNAs / tRNAs / GENCODE annotations / circular RNAs.

source_name: Serum

extract_protocol:
Total RNA was extracted from EV-enriched nanoDLD and UC processed serum using the Total Exosome RNA and Protein Isolation Kit (Invitrogen 4478545). RNA quality was assessed by bioanalyzer  (Agilent 2100 Bioanalyzer, RNA 6000 Pico Kit, Agilent Technologies) and stored at -20 degrees C.
cDNA Libraries were prepared for small RNAs using the SMARTer smRNA-seq Kit for Illumina (Takara Bio 635030).  Final library quality was verified with Qbit and bioanalyzer.

treatment_protocol: NanoDLD chips were fabricated in 200 mm silicon wafers, diced into individual chips, wetted in DI water (Millipore) and primed with 5% bovine serum albumin (BSA) to reduce non-specific adsorption and fouling as described in [Smith, J.T. et al., Integrated Nanoscale Deterministic Lateral Displacement Arrays for Rapid, Reliable Separation of Extracellular Vesicles from Biological Samples, Lab on a Chip, in press].  Individual chips were placed in custom-built acrylic flow cells prior to running serum samples. Post filtered (Whatman 0.2 um filters) serum samples (500 ul) were processed using nanoDLD chips with a gap of G= 150 nm at a flow rate of 4 µl/min for 60 min.  Sample fluid enriched in EV’s of size between 60 nm and 150 nm (as determined by EM and NTA) was removed from the nanoDLD bump outlet. Samples were stored at 4 degrees C for RNA-seq processing. Serum samples were centrifuged in 5 ml tubes for 30 min at 2,000 g, 4 degrees C. Supernatant was transferred into 50 ml tubes and tubes were filled with PBS up to ¾ levels of total volume, for 45 min of centrifugation at 12,000 g, 4 degrees C. The supernatant was carefully transferred to UC tubes (Beckman coulter, thick wall polypropylene tube, Cat # 355642), and centrifuged for 2 hr at 110,000 g, 4 degrees C. Pellets were resuspended in 1 ml PBS and UC tubes were filled up to ¾ of total capacity. After another round of centrifugation for 2 hr at 110,000 , 4 degrees C, pellets were resuspended in 1 ml PBS and stored at -80 degrees C.

tag: serum processing

value: nanoDLD

value: Serum

value: Prostate cancer

tag: anatomical location

value: Entire cardiovascular system


title: ind114 2014

description:
ind114
RNA expression value derived from Affymetrix Launcher software


title: DKO_H3K27ac_Rep2


title: 215-Serum-nanoDLD-run1_GAATTCGT-CCTATCCT_AHGHHMBCX2_L002


title: ind59 2014

description:
ind59
RNA expression value derived from Affymetrix Launcher software


title: Patient 15

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 15


title: 213-Serum-nanoDLD_ATTCAGAA-CCTATCCT_AHGHHMBCX2_L002


title: DKO_H3K27ac_Rep1


title: Patient 14

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 14


title: ind98 2014

description:
ind98
RNA expression value derived from Affymetrix Launcher software


title: 212-Serum-nanoDLD_GAGATTCC-CCTATCCT_AHGHHMBCX2_L002


title: SR9009_rep3

city: Oxford

first: Xiaodong

last: Zhuang

state: Oxfordshire

address: Old Road Campus, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description: SR9009 treated Huh-7 cells

hyb_protocol: The labelled RNA was fragmented (as Agilent gene expression protocol recommendation)  and hybridized in 2xHiRPM Buffer (Agilent) at 65 degrees

scan_protocol: Images were quantified using Agilent CytoGenomics Software (version 4.0.1.21).

data_processing: BioConductor LIMMA package was used for data processing

source_name: Huh-7 cells (Reference)

label_protocol: RNA was labelled using the Agilent gene expression protocol. 200 ng of total RNA was reverse transcribed using oligodT-T7 promoter primer and second strand cDNA produced. The cDNA was then amplified and labelled using a T7 RNA polymerase, dNTPs and Cy-CTP. Following purification the resulting labelled mRNA was prepared for hybridization to Agilent 8x60k human gene expression arrays.

growth_protocol: Huh-7 cells were cultured in DMEM media containing 10% FBS

extract_protocol: Huh-7 cells were treated with SR9009 at 20 µM in DMEM media containing 10% FBS

tag: cell line

value: Hepatoma line

source_name: Huh-7 cells

tag: cell lines


title: Patient 13

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 13

tag: abir. start date


title: ind58 2014

description:
ind58
RNA expression value derived from Affymetrix Launcher software


title: SR9009_rep1

description: SR9009 treated Huh-7 cells


title: Patient 12

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 12

tag: abir. failure date


title: Ctrl._rep1

description: DMSO treated Huh-7 cells


title: 211-Serum-UC-run1_GAGATTCC-ATAGAGGC_BH3WFNBCX2_L002

value: ultracentrifugation


title: 211-Serum-nanoDLD-run1_ATTACTCG-CCTATCCT_AHGHHMBCX2_L001


title: DKO_input_DNA_Rep2

source_name: input DNA

tag: developmental stage

value: medulloblastoma

value: Sufu;Spop double knockout


title: DKO_Gli2_Rep2


title: Ctrl._rep2

description: DMSO treated Huh-7 cells


title: DKO_input_DNA_Rep1


title: 208-Serum-UC_TCCGGAGA-ATAGAGGC_BH3WFNBCX2_L002


title: DKO_Gli2_Rep1


title: GM2_H3K36me3_Rep2


title: ind91 2015

description:
ind91
RNA expression value derived from Affymetrix Launcher software


title: Patient 10

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 10

value: Prostate Cancer

tag: failure (yes=1, no=0)

tag: pfs (months)


title: ind47 2014

description:
ind47
RNA expression value derived from Affymetrix Launcher software


title: Ctrl._rep3

description: DMSO treated Huh-7 cells


title: SR9009_rep2

description: SR9009 treated Huh-7 cells


title: 208-Serum-nanoDLD_AGCGATAG-ATAGAGGC_AHGHHMBCX2_L001

tag: tissue


title: GM2_H3K36me3_Rep1


title: ind81 2014

description:
ind81
RNA expression value derived from Affymetrix Launcher software


title: ind83 2014

description:
ind83
RNA expression value derived from Affymetrix Launcher software


title: 317-Serum-UC_TCCGCGAA-ATAGAGGC_BHGHG5BCX2_L001


title: Patient 8

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 8

tag: logpsa (at abir start)

value: BB


title: Patient 11

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 11

value: AA


title: GM2_H3K27ac_Rep2

value: SmoM2 overexpression

tag: chip antibody


title: Patient 7

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 7

tag: last f/u

value: whole blood


title: 317-Serum-nanoDLD-run1_TCTCGCGC-CCTATCCT_BHGHG5BCX2_L001


title: GM2_H3K27ac_Rep1

tag: genotype


title: ind18 2014

description:
ind18
RNA expression value derived from Affymetrix Launcher software

tag: ID


title: ind9 2014

description:
ind9
RNA expression value derived from Affymetrix Launcher software

tag: age


title: 303-Serum-UC_TAATGCGC-ATAGAGGC_BH3WFNBCX2_L002

tag: disease state


title: GM2_Gli2_Rep2


title: ind77 2014

description:
ind77
RNA expression value derived from Affymetrix Launcher software

tag: gender


title: Patient 6

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 6


title: 303-Serum-nanoDLD-run1_CGGCTATG-CCTATCCT_AHGHHMBCX2_L002

tag: serum processing

tag: anatomical location


title: GM2_Gli2_Rep1


title: ind135 2014

description:
ind135
RNA expression value derived from Affymetrix Launcher software


title: ind36 2014

description:
ind36
RNA expression value derived from Affymetrix Launcher software


title: Patient 5

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 5


title: 204-Serum-UC_AGCGATAG-TATAGCCT_BH3WFNBCX2_L002


title: Patient 9

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 9


title: Patient 4

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 4


title: ind123 2014

description:
ind123
RNA expression value derived from Affymetrix Launcher software


title: GM2_input_DNA_Rep1


title: Patient 3

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 3


title: ind21 2014

description:
ind21
RNA expression value derived from Affymetrix Launcher software


title: ind57 2014

description:
ind57
RNA expression value derived from Affymetrix Launcher software


title: 204-Serum-nanoDLD_TCTCGCGC-ATAGAGGC_AHGHHMBCX2_L001


title: ind86 2014

description:
ind86
RNA expression value derived from Affymetrix Launcher software


title: ATAC_control

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were performed quality controll and trimmed for adaptor sequence by FASTX-Toolki
Clean reads were then mapped to the mouse mm9 genome assembly by Bowtie2 (Langmead and Salzberg, 2012) using default settings. After this, reads with multiple genomic loci were discarded. Then, non-redundant reads were analyzed using MACS2 software (Zhang et al., 2008) to identify peaks (transcription factor binding sites) with a threshold of a p-value less than 1 × 10-5. Distributions of ATAC-seq read density around the transcription start sites (TSSs) regions (the upstream and downstream 1 kb regions, respectively) were plotted using Sitepro from the CEAS package (Shin et al., 2009) with a bin size of 20 bp. Finally, the ICM and TE specific genes were reanalyzed from the published single cell RNA-Seq data in the GEO database GSE70605 (Liu et al., 2016).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files produced by MACS2

source_name: EGFP-overexpressing  blastomeres at the 8-cell stage

growth_protocol: All experiments were performed in accordance with ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines and regulations. Two-cell stage embryos were collected from 6-week-old super-ovulated female ICR mice crossed with ICR males, 46 hours after the injection of human chorionic gonadotropin (hCG). 8-cell stage embryos was flushed from the reproductive tract at 68–70 h after hCG administration. The zona pellucida was removed using Tyrode’s solution. Zona-free embryos were incubated for 5 min in Ca2+ and Mg2+ free M2 before disaggregation by careful pipetting. Single cells were separeted into two tubes according to GFP positive or negtive.

extract_protocol:
Cells from ATAC-seq libraries created from approximately fifty 8-cell embryos were prepared as described previously (Wu et al., 2016). Briefly, samples were lysed in 5 μL of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.15% NP-40) for 10 min on ice. Immediately after lysis, samples were then incubated with the Tn5 transposase and tagmentation buffer at 37°C for 30 min (Vazyme Biotech, TD502). Then, the stop buffer was added directly into the reaction to end the tagmentation. PCR was then performed to amplify the library for 15 cycles using the following PCR conditions: 72°C for 3 min; 98°C for 30 s. This was by thermocycling at 98°C for 15 s, 60°C for 30 s and 72°C for 3 min, followed by 5 min at 72°C. After the PCR reaction, libraries were purified with 1.2X AMPure (Backman, A63880) beads before proceeding to mitochondrial DNA depletion. A total of 400 sgRNAs targeting the mouse mitochondrial genome were provided as a gift by Wei Xie’s laboratory of School of Life Sciences, Tsinghua University. Next, in vitro transcription was performed to produce sgRNAs using the MEGAshortscript? Kit (Ambion, AM1354)). Each ATAC-seq library was incubated with 5 μg of sgRNA and 10 μg of Cas9 protein (PNA Bio, CP02-50) for 2 h at 37°C. After incubation, the reaction was treated by RNase A before being terminated by adding stop buffer (30% glycerol, 1.2% SDS, 250mM EDTA, pH 8.0).
The samples were then processed by an Illumina HiSeq 2500 sequencer with 50 bp paired-end sequencing reactions.

tag: strain

value: ICR

value: 8-cell embryos

tag: operation

value: Overexpressing EGFP


title: Patient 2

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 2

tag: abir. start date

tag: abir. failure date


title: Patient 1

description:
Genomic DNA extracted from whole blood was genotyped using HumanOmniExpress-24 v1 BeadChip (Illumina).
SAMPLE 1

tag: failure (yes=1, no=0)

value: AB


title: ATAC_CARM1_OE

source_name: CARM1-overexpressing blastomeres at the 8-cell stage

value: Overexpressing CARM1