title: MPAL2_H3K9me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K9m3_A5_0323)


title: ALL1_IgG_AutoCUTnRUN_(20200504_JS_HsEc_042820_JFS1376)

status: Public on Jun 10 2021

type: SRA

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

country: USA

institute: Van Andel Institute

description: Automated CUT&RUN for IgG control in sorted CD45+ cells from the ALL-1 patient sample

library_source: genomic

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file hg19_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

molecule: genomic DNA

organism: Homo sapiens

source_name: CUT&RUN

extract_protocol:
AutoCUTnRUN_Protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: cut&run antibody

value: IgG Abcam cat# ab46540

tag: cell type

value: sorted CD45+ cells from the ALL-1 KMT2A-AF4 B-ALL patient sample


title: MPAL2_H3K27me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K27m_A5_0323)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the MPAL-2 patient sample

source_name: CUT&Tag

extract_protocol:
AutoCUT&Tag_Protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: cut&tag antibody

value: H3K27me3 Cell Signaling Technologies cat# 9733S

value: sorted CD45+ cells from the MPAL-2 KMT2A-AF4 patient sample


title: MPAL2_H3K27me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K27m_A5_0520)


title: MPAL2_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_A5_0520)

description: Automated CUT&Tag for ELL in sorted CD45+ cells from the MPAL-2 patient sample

value: ELL Cell Signaling Technologies cat# 14468S


title: MPAL2_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_A5_0520)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the MPAL-2 patient sample

value: Dot1L Cell Signaling Technologies cat# 90878S


title: SEM_H3K36me3_AutoCUTnTag_(20200313_DJ_Hs_K36m3_SE_0310)

description: Automated CUT&Tag for H3K36me3 in the SEM KMT2Ar cell line

value: H3K36me3 Epicypher cat# 13-0031

value: SEM KMT2A-AF4 B-ALL cell line


title: MPAL1_IgG_AutoCUTnTag_Rep1_(20200324_DJ_Hs_IgG_TB11_0323)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the MPAL-1 patient sample

value: sorted CD45+ cells from the MPAL-1 KMT2A-AF9 patient sample


title: MPAL1_H3K9me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K9m3_TB11_0520)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the MPAL-1 patient sample

value: H3K9me3 Abcam cat# ab8898


title: MPAL1_H3K4me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m3_TB11_0520)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the MPAL-1 patient sample

value: H3K4me3 Active Motif cat# 39159


title: MPAL1_H3K4me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m3_TB11_0323)


title: MPAL1_H3K4me1_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m1_TB11_0520)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the MPAL-1 patient sample

value: H3K4me1 Thermo cat# 710795


title: MPAL2_H3K4me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m3_A5_0520)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL1_H3K4me1_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m1_TB11_0323)


title: MPAL1_H3K36me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K36m_TB11_0323)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL1_H3K27me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K27m_TB11_0323)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL2_H3K4me1_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m1_A5_0323)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL1_H3K27me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K27m_TB11_0520)


title: MPAL1_H3K36me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K36m3_TB11_0520)


title: MPAL1_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_TB11_0520)

description: Automated CUT&Tag for ELL in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL2_H3K36me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K36m3_A5_0520)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the MPAL-2 patient sample


title: MPAL1_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_TB11_0520)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the MPAL-1 patient sample

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: MPAL1_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_TB11_0520)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the MPAL-1 patient sample


title: MPAL2_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_A5_0520)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the MPAL-2 patient sample


title: ML2_H3K4me3_AutoCUTnTag_(20200313_DJ_Hs_K4m3_ML_0310)

description: Automated CUT&Tag for H3K4me3 in the ML-2 KMT2Ar cell line

value: ML-2 KMT2A-AF6 AML cell line


title: ML2_H3K9me3_AutoCUTnTag_(20200313_DJ_Hs_K9m3_ML_0310)

description: Automated CUT&Tag for H3K9me3 in the ML-2 KMT2Ar cell line


title: ML2_H3K36me3_AutoCUTnTag_(20200313_DJ_Hs_K36m3_ML_0310)

description: Automated CUT&Tag for H3K36me3 in the ML-2 KMT2Ar cell line


title: MPAL1_IgG_AutoCUTnTag_Rep2_(20200528_DJ_Hs_IgG_TB11_0520)


title: KOPN8_IgG_AutoCUTnTag_(20200313_DJ_Hs_IgG_KO_0310)

description: Automated CUT&Tag for IgG control in the KOPN-8 KMT2Ar cell line

value: KOPN-8 KMT2A-ENL B-ALL cell line


title: ML2_H3K27me3_AutoCUTnTag_(20200313_DJ_Hs_K27m_ML_0310)

description: Automated CUT&Tag for H3K27me3 in the ML-2 KMT2Ar cell line


title: KOPN8_H3K9me3_AutoCUTnTag_(20200313_DJ_Hs_K9m3_KO_0310)

description: Automated CUT&Tag for H3K9me3 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K4me3_AutoCUTnTag_(20200313_DJ_Hs_K4m3_KO_0310)

description: Automated CUT&Tag for H3K4me3 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K36me3_AutoCUTnTag_(20200313_DJ_Hs_K36m3_KO_0310)

description: Automated CUT&Tag for H3K36me3 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K4me1_AutoCUTnTag_(20200313_DJ_Hs_K4m1_KO_0310)

description: Automated CUT&Tag for H3K4me1 in the KOPN-8 KMT2Ar cell line


title: KOPN8_H3K27me3_AutoCUTnTag_(20200313_DJ_Hs_K27m_KO_0310)

description: Automated CUT&Tag for H3K27me3 in the KOPN-8 KMT2Ar cell line


title: MPAL1_H3K9me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K9m3_TB11_0323)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the MPAL-1 patient sample


title: K562_IgG_AutoCUTnTag_(20200313_DJ_Hs_IgG_K5_0310)

description: Automated CUT&Tag for IgG control in K562 cells

value: K562 human immortalized myelogenous leukemia cell line


title: K562_H3K9me3_AutoCUTnTag_(20200313_DJ_Hs_K9m3_K5_0310)

description: Automated CUT&Tag for H3K9me3 in K562 cells


title: K562_H3K4me3_AutoCUTnTag_(20200313_DJ_Hs_K4m3_K5_0310)

description: Automated CUT&Tag for H3K4me3 in K562 cells


title: K562_H3K36me3_AutoCUTnTag_(20200313_DJ_Hs_K36m3_K5_0310)

description: Automated CUT&Tag for H3K36me3 in K562 cells


title: K562_H3K27me3_AutoCUT&Tag_(20200313_DJ_Hs_K27m_K5_0310)

description: Automated CUT&Tag for H3K27me3 in K562 cells


title: K562_H3K4me1_AutoCUTnTag_(20200313_DJ_Hs_K4m1_K5_0310)

description: Automated CUT&Tag for H3K4me1 in K562 cells


title: ML2_IgG_AutoCUTnTag_(20200313_DJ_Hs_IgG_ML_0310)

description: Automated CUT&Tag for IgG control in the ML-2 KMT2Ar cell line


title: H1_KMT2A_C1_AutoCUTnRUN_(20190710_DJ_HsEc_MLSp_HA_0705)

description: Automated CUT&RUN for the KMT2A C-terminal region in H1 hESCs

value: KMT2A-C1 Santa Cruz cat# sc-374392

value: H1 human embryonic stem cells


title: ML2_H3K4me1_AutoCUTnTag_(20200313_DJ_Hs_K4m1_ML_0310)

description: Automated CUT&Tag for H3K4me1 in the ML-2 KMT2Ar cell line


title: H1_KMT2A_C2_AutoCUTnRUN_(20190710_DJ_HsEc_MLMp_HA_0705)

value: KMT2A-C2 Millipore cat# 05-765


title: H1_KMT2A_N2_AutoCUTnRUN_(20190710_DJ_HsEc_MLD2_HA_0705)

description: Automated CUT&RUN for the KMT2A N-terminal region in H1 hESCs

value: KMT2A-N2 Cell Signaling Technologies cat# 14689S


title: AML2_H3K9me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K9m3_A6_0323)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the AML-2 patient sample

value: sorted CD45+ cells from the AML-2 KMT2A-ENL patient sample


title: AML2_IgG_AutoCUTnTag_Rep2_(20200528_DJ_Hs_IgG_A6_0520)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the AML-2 patient sample

value: IgG Abcam cat# ab46540


title: H1_IgG_AutoCUTnRUN_(20190710_DJ_HsEc_IgG_HA_0705)

description: Automated CUT&RUN for IgG control in H1 (hESCs)


title: AML2_H3K4me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m3_A6_0323)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the AML-2 patient sample


title: AML2_IgG_AutoCUTnTag_Rep1_(20200324_DJ_Hs_IgG_A6_0323)


title: AML2_H3K4me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m3_A6_0520)


title: AML2_H3K9me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K9m3_A6_0520)


title: AML2_H3K4me1_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m1_A6_0323)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the AML-2 patient sample


title: AML2_H3K4me1_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m1_A6_0520)


title: AML2_H3K36me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K36m_A6_0323)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the AML-2 patient sample


title: AML2_H3K27me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K27m_A6_0520)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the AML-2 patient sample

value: H3K27me3 Cell Signaling Technologies cat# 9733S


title: AML2_H3K27me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K27m_A6_0323)


title: AML2_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_A6_0520)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-2 patient sample


title: AML2_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_A6_0520)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-2 patient sample

value: Dot1L Cell Signaling Technologies cat# 90878S


title: AML2_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_A6_0520)

description: Automated CUT&Tag for ELL in sorted CD45+ cells from the AML-2 patient sample

value: ELL Cell Signaling Technologies cat# 14468S


title: AML1_IgG_AutoCUTnTag_Rep2_(20200528_DJ_Hs_IgG_A4_0520)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the AML-1 patient sample

value: sorted CD45+ cells from the AML-1 KMT2A-Sept6 B-ALL patient sample


title: AML1_H3K9me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K9m3_A4_0323)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the AML-1 patient sample

value: H3K9me3 Abcam cat# ab8898


title: AML1_H3K9me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K9m3_A4_0520)


title: AML1_H3K4me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m3_A4_0323)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the AML-1 patient sample

value: H3K4me3 Active Motif cat# 39159


title: AML1_H3K4me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m3_A4_0520)


title: AML1_H3K4me1_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m1_A4_0520)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the AML-1 patient sample

value: H3K4me1 Thermo cat# 710795


title: AML1_H3K36me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K36m_A4_0323)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the AML-1 patient sample

value: H3K36me3 Epicypher cat# 13-0031


title: AML1_H3K36me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K36m3_A4_0520)


title: AML1_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_A4_0520)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the AML-1 patient sample

value: MLLT3/ENL Cell Signaling Technologies cat# 14893S


title: AML1_H3K4me1_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m1_A4_0323)


title: AML1_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_A4_0520)

description: Automated CUT&Tag for ELL in sorted CD45+ cells from the AML-1 patient sample


title: AML1_H3K27me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K27m_A4_0323)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the AML-1 patient sample


title: ALL1_H3K9me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K9m3_TB13_0520)

description: Automated CUT&Tag for H3K9me3 in sorted CD45+ cells from the ALL-1 patient sample

value: sorted CD45+ cells from the ALL-1 KMT2A-AF4 B-ALL patient sample


title: AML2_H3K36me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K36m3_A6_0520)


title: AML1_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_A4_0520)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the AML-1 patient sample


title: ALL1_H3K36me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K36m3_TB13_0520)

description: Automated CUT&Tag for H3K36me3 in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H3K9me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K9m3_TB13_0323)


title: ALL1_H3K4me1_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m1_TB13_0323)

description: Automated CUT&Tag for H3K4me1 in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H3K4me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K4m3_TB13_0323)

description: Automated CUT&Tag for H3K4me3 in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H3K36me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K36m_TB13_0323)


title: ALL1_H3K27me3_AutoCUTnTag_Rep1_(20200324_DJ_Hs_K27m_TB13_0323)

description: Automated CUT&Tag for H3K27me3 in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_H3K27me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K27m_TB13_0520)


title: AML1_IgG_AutoCUTnTag_Rep1_(20200324_DJ_Hs_IgG_A4_0323)


title: ALL1_H3K4me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m3_TB13_0520)


title: ALL1_IgG_AutoCUTnTag_Rep1_(20200324_DJ_Hs_IgG_TB13_0323)

description: Automated CUT&Tag for IgG control in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_ENL_AutoCUTnTag_(20200528_DJ_Hs_ENL_TB13_0520)

description: Automated CUT&Tag for ENL in sorted CD45+ cells from the ALL-1 patient sample


title: AML1_H3K27me3_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K27m_A4_0520)


title: ALL1_ELL_AutoCUTnTag_(20200528_DJ_Hs_ELL_TB13_0520)

description: Automated CUT&Tag for ELL in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_Dot1L_AutoCUTnTag_(20200528_DJ_Hs_Dot1_TB13_0520)

description: Automated CUT&Tag for Dot1L in sorted CD45+ cells from the ALL-1 patient sample


title: ALL1_IgG_AutoCUTnTag_Rep2_(20200528_DJ_Hs_IgG_TB13_0520)


title: NK-1892

status: Public on Mar 04 2021

city: Toronto

first: Gaia

last: Andreoletti

state: ON

address: 686 Bay St

country: Canada

institute: Sick Kids

description:
SLE patients
immune cell bulk RNAeq
cell sorted RNAseq from PBMC - for each sample CD4, CD14, CD19, and NK cells were sequenced

library_source: transcriptomic

data_processing:
Salmon v0.8.2 was used for our alignment-free pipeline. Adaptor-trimmed reads were used as input. We quantified gene expression using raw counts and kept the genes that showed an average FPKM value across the samples >0.5. FastQC (v0.11.8) was run to assess the quality of the sequence reads. To further assess for low quality samples we checked the expression of 10 housekeeping genes (e.g. SNRPD3, EMC7, and VPS29) called the Eisenberg housekeeping genes16. Finally, we conducted K-means clustering and removed all outlier samples that were > 1 standard deviation from the center of the cluster. The Davies-Bouldin’s index was also computed to confirm cluster stability. Batch correction was performed with limma (v 3.40.6).
Genome_build: hg19
Supplementary_files_format_and_content: csv, counts files of all samples for each cell line

molecule: total RNA

source_name: PBMC

extract_protocol: Participants were recruited from the California Lupus Epidemiology Study (CLUES). CLUES was approved by the Institutional Review Board of the University of California, San Francisco. Peripheral blood mononuclear cells were isolated from patient donors. Cells were isolated from peripheral blood utilizing magnetic beads (CD14+monocytes, B cells, CD4+T cells and NK cells) using EasySep protocol from STEM cell technologies on 120 patients. RNA and DNA were extracted using Qiagen column and quality was assessed on Agilent bioanalyzer. 1ng - 5ng of RNA was used with SmartSeqv2 protocol to get cDNA, followed by Illumina Nextera XT DNA library prep with input of 0.8ng cDNA and 15 cycles of PCR amplification. Both cDNA and DNA libraries qualities were controlled on Agilent bioanalyzer. Libraries were sequenced on HiSeq4000 PE150.

tag: sample type


title: NK-1958

value: cell sorted RNAseq from PBMC - for each sample CD4, CD14, CD19, and NK cells were sequenced


title: NK-1961


title: NK-1947


title: NK-1829


title: NK-1848


title: ALL1_H3K4me1_AutoCUTnTag_Rep2_(20200528_DJ_Hs_K4m1_TB13_0520)


title: NK-1815


title: NK-1811


title: NK-1804


title: NK-1768


title: NK-1827


title: NK-1799


title: NK-1891


title: NK-1785


title: NK-1763


title: NK-1754


title: NK-1791


title: NK-1743


title: NK-1767


title: NK-1726


title: NK-1731


title: NK-1682


title: NK-1730


title: NK-1672


title: NK-1667


title: NK-1660


title: NK-1641


title: NK-1623


title: NK-1615


title: NK-1614


title: NK-1602


title: NK-1771


title: NK-1760


title: NK-1597


title: NK-1741


title: NK-1775


title: NK-1545


title: NK-1588


title: NK-1582


title: NK-1567


title: NK-1569


title: NK-1558


title: NK-1584


title: NK-1716


title: NK-1543


title: NK-1535


title: NK-1496


title: NK-1522


title: NK-1510


title: NK-1492


title: NK-1514


title: NK-1480


title: NK-1479


title: NK-1633


title: NK-1420


title: NK-1472


title: NK-1419


title: NK-1414


title: NK-1404


title: NK-1596


title: NK-1366


title: NK-1368


title: NK-1621


title: NK-1417


title: NK-1341


title: NK-1315


title: NK-1338


title: NK-1337


title: NK-1324


title: NK-1297


title: NK-1340


title: NK-1329


title: NK-1326


title: NK-1294


title: NK-1259


title: NK-1334


title: NK-1279


title: NK-1262


title: NK-1270


title: NK-1281


title: NK-1251


title: NK-1250


title: NK-1418


title: NK-1248


title: NK-1243


title: NK-1240


title: NK-1226


title: NK-1234


title: NK-1221


title: NK-1222


title: NK-1219


title: NK-1216


title: NK-1197


title: NK-1203


title: NK-1127


title: NK-1196


title: NK-1122


title: NK-1195


title: NK-1132


title: NK-1165


title: NK-1130


title: NK-1110


title: NK-1121


title: NK-1193


title: NK-1063


title: NK-1087


title: NK-1119


title: NK-1068


title: NK-1054


title: NK-1031


title: NK-1046


title: NK-1056


title: NK-1019


title: NK-1022


title: NK-1045


title: NK-1051


title: NK-1004


title: NK-1014


title: CD4-1958


title: CD4-1961


title: CD4-1947


title: CD4-1892


title: CD4-1891


title: NK-1101


title: CD4-1827


title: CD4-1848


title: CD4-1811


title: NK-1078


title: CD4-1799


title: CD4-1815


title: CD4-1785


title: CD4-1804


title: CD4-1775


title: CD4-1829


title: CD4-1791


title: CD4-1763


title: CD4-1754


title: CD4-1743


title: CD4-1767


title: CD4-1768


title: CD4-1741


title: CD4-1731


title: CD4-1730


title: CD4-1682


title: CD4-1716


title: CD4-1726


title: CD4-1672


title: CD4-1667


title: CD4-1641


title: CD4-1660


title: CD4-1615


title: CD4-1633


title: CD4-1623


title: CD4-1614


title: CD4-1621


title: CD4-1596


title: CD4-1602


title: CD4-1584


title: CD4-1582


title: CD4-1588


title: CD4-1569


title: CD4-1558


title: CD4-1543


title: CD4-1760


title: CD4-1567


title: CD4-1545


title: CD4-1522


title: CD4-1514


title: CD4-1510


title: CD4-1535


title: CD4-1492


title: CD4-1496


title: CD4-1479


title: CD4-1480


title: CD4-1472


title: CD4-1420


title: CD4-1419


title: CD4-1597


title: CD4-1414


title: CD4-1417


title: CD4-1404


title: CD4-1368


title: CD4-1341


title: CD4-1340


title: CD4-1338


title: CD4-1366


title: CD4-1329


title: CD4-1326


title: CD4-1337


title: CD4-1281


title: CD4-1270


title: CD4-1315


title: CD4-1259


title: CD4-1297


title: CD4-1279


title: CD4-1294


title: CD4-1250


title: CD4-1248


title: CD4-1418


title: CD4-1243


title: CD4-1240


title: CD4-1234


title: CD4-1222


title: CD4-1226


title: CD4-1221


title: CD4-1216


title: CD4-1334


title: CD4-1219


title: CD4-1197


title: CD4-1203


title: CD4-1196


title: CD4-1165


title: CD4-1262


title: CD4-1324


title: CD4-1195


title: CD4-1251


title: CD4-1130


title: CD4-1127


title: CD4-1121


title: CD4-1122


title: CD4-1110


title: CD4-1078


title: CD4-1101


title: CD4-1087


title: CD4-1068


title: CD4-1063


title: CD4-1056


title: CD4-1054


title: CD4-1045


title: CD4-1051


title: CD4-1046


title: CD4-1193


title: CD4-1132


title: CD4-1019


title: CD4-1014


title: CD19-1892


title: CD19-1891


title: CD4-1119


title: CD19-1848


title: CD19-1804


title: CD19-1791


title: CD19-1811


title: CD19-1799


title: CD19-1785


title: CD19-1775


title: CD19-1768


title: CD4-1031


title: CD19-1760


title: CD19-1754


title: CD4-1004


title: CD19-1958


title: CD4-1022


title: CD19-1947


title: CD4-1771


title: CD19-1743


title: CD19-1829


title: CD19-1726


title: CD19-1961


title: CD19-1731


title: CD19-1827


title: CD19-1767


title: CD19-1682


title: CD19-1716


title: CD19-1741


title: CD19-1660


title: CD19-1667


title: CD19-1641


title: CD19-1633


title: CD19-1730


title: CD19-1623


title: CD19-1672


title: CD19-1771


title: CD19-1815


title: CD19-1621


title: CD19-1763


title: CD19-1614


title: CD19-1615


title: CD19-1582


title: CD19-1569


title: CD19-1597


title: CD19-1596


title: CD19-1588


title: CD19-1584


title: CD19-1567


title: CD19-1558


title: CD19-1535


title: CD19-1510


title: CD19-1522


title: CD19-1496


title: CD19-1492


title: CD19-1543


title: CD19-1545


title: CD19-1472


title: CD19-1420


title: CD19-1417


title: CD19-1419


title: CD19-1418


title: CD19-1414


title: CD19-1480


title: CD19-1404


title: CD19-1366


title: CD19-1602


title: CD19-1368


title: CD19-1340


title: CD19-1341


title: CD19-1338


title: CD19-1337


title: CD19-1329


title: CD19-1324


title: CD19-1514


title: CD19-1315


title: CD19-1334


title: CD19-1326


title: CD19-1297


title: CD19-1281


title: CD19-1270


title: CD19-1251


title: CD19-1262


title: CD19-1279


title: CD19-1294


title: CD19-1479


title: CD19-1250


title: CD19-1243


title: CD19-1240


title: CD19-1226


title: CD19-1219


title: CD19-1234


title: CD19-1221


title: CD19-1203


title: CD19-1222


title: CD19-1196


title: CD19-1216


title: CD19-1193


title: CD19-1195


title: CD19-1127


title: CD19-1130


title: CD19-1132


title: CD19-1165


title: CD19-1121


title: CD19-1259


title: CD19-1122


title: CD19-1119


title: CD19-1110


title: CD19-1087


title: CD19-1248


title: CD19-1078


title: CD19-1063


title: CD19-1056


title: CD19-1054


title: CD19-1051


title: CD19-1046


title: CD19-1031


title: CD19-1014


title: CD19-1022


title: CD19-1045


title: CD14-1961


title: CD19-1019


title: CD19-1197


title: CD14-1958


title: CD14-1892


title: CD14-1891


title: CD14-1815


title: CD14-1829


title: CD19-1101


title: CD14-1827


title: CD14-1804


title: CD14-1811


title: CD19-1068


title: CD14-1771


title: CD14-1775


title: CD14-1791


title: CD14-1799


title: CD14-1768


title: CD14-1763


title: CD14-1767


title: CD19-1004


title: CD14-1760


title: CD14-1754


title: CD14-1848


title: CD14-1741


title: CD14-1743


title: CD14-1785


title: CD14-1730


title: CD14-1726


title: CD14-1672


title: CD14-1682


title: CD14-1947


title: CD14-1667


title: CD14-1633


title: CD14-1641


title: CD14-1623


title: CD14-1660


title: CD14-1621


title: CD14-1615


title: CD14-1614


title: CD14-1602


title: CD14-1596


title: CD14-1584


title: CD14-1588


title: CD14-1597


title: CD14-1569


title: CD14-1582


title: CD14-1543


title: CD14-1558


title: CD14-1535


title: CD14-1522


title: CD14-1731


title: CD14-1545


title: CD14-1716


title: CD14-1496


title: CD14-1510


title: CD14-1480


title: CD14-1514


title: CD14-1492


title: CD14-1472


title: CD14-1479


title: CD14-1420


title: CD14-1419


title: CD14-1404


title: CD14-1414


title: CD14-1417


title: CD14-1418


title: CD14-1366


title: CD14-1368


title: CD14-1341


title: CD14-1567


title: CD14-1337


title: CD14-1340


title: CD14-1338


title: CD14-1334


title: CD14-1329


title: CD14-1315


title: CD14-1294


title: CD14-1297


title: CD14-1281


title: CD14-1279


title: CD14-1270


title: CD14-1259


title: CD14-1262


title: CD14-1250


title: CD14-1248


title: CD14-1243


title: CD14-1234


title: CD14-1219


title: CD14-1226


title: CD14-1222


title: CD14-1251


title: CD14-1221


title: CD14-1216


title: CD14-1203


title: CD14-1197


title: CD14-1193


title: CD14-1165


title: CD14-1132


title: CD14-1195


title: CD14-1326


title: CD14-1196


title: CD14-1240


title: CD14-1324


title: CD14-1130


title: CD14-1122


title: CD14-1121


title: CD14-1068


title: CD14-1119


title: CD14-1110


title: CD14-1101


title: CD14-1087


title: CD14-1063


title: CD14-1056


title: CD14-1051


title: CD14-1078


title: CD14-1031


title: CD14-1045


title: CD14-1054


title: CD14-1022


title: CD14-1019


title: CD14-1014


title: CD14-1046


title: duodenum, vehicle #3

status: Public on Sep 01 2020

first: Gilles

last: Laverny

address: 1 rue Laurent fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10
Supplementary_files_format_and_content: Raw reads.xlsx

molecule: polyA RNA

organism: Mus musculus

source_name: Duodenal RNA isolated from mice treated with vitamin D analogs for 6 h.

extract_protocol: RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: treatment

value: vehicle

tag: tissue

value: duodenum


title: duodenum, calcitriol #2

value: calcitriol


title: duodenum, calcitriol and ZK #2

value: calcitriol and ZK


title: CD14-1127


title: CD14-1004


title: duodenum, calcitriol #3


title: duodenum, calcitriol #1


title: duodenum, vehicle #1


title: Input_ChIP-seq_MCF-7_Veh_rep2

status: Public on Sep 25 2019

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
FastQC
Alignment using BOWTIE (version 0.12.7) with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF-7 cells, kindly provided by Dr. Benita Katzenellenbogen (University of Illinois, Urbana-Champaign, IL), were maintained in Minimum Essential Medium (MEM) Eagle with Hank’s salts (Sigma, M1018) supplemented with 5% HyClone calf serum (GE Healthcare, SH30072) and 20mM HEPES (ThermoFisher Scientific, BP310).  Prior to gene expression and ChIP experiments, the cells were grown for three days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.

extract_protocol:
ChIP was performed as previously described with a few modifications.  MCF-7 cells were plated at a density of 2.5 x 106 cells in a 15 cm diameter dish, grown for three days in estrogen-free medium, and treated as described above (± 45 minutes with 100 nM E2; ± 3 hour pretreatment with 500 nM JQ1). The cells were cross-linked with 1% formaldehyde for 10 min at 37oC and quenched in 125 mM glycine for 5 min at 4oC.  The cells were then collected and lysed in Farnham lysis buffer [5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM DTT, and 1x complete protease inhibitor cocktail (Roche, 11697498001)].  For acetyl-histone H4 ChIP assays, 10 mM sodium butyrate was added to all buffers to prevent deacetylation of the histones.  The crude nuclear pellet was collected by centrifugation, resuspended in lysis buffer [Tris-HCl pH 7.9, 1% SDS, 10 mM EDTA, 50 mM, 1 mM DTT, and 1x complete protease inhibitor cocktail], and incubated on ice for 10 minutes.  The chromatin was sheared by sonication at 4¡C using a Bioruptor UC200 at the highest setting for five 5-minute cycles of 30 seconds on and 60 seconds off to generate chromatin fragments of ~200-400 bp in length.  The soluble chromatin was diluted 1:10 with dilution buffer [20 mM Tris-HCl pH 7.9, 0.5% Triton X-100, 2 mM EDTA, 150 mM NaCl, 1 mM DTT and 1x complete protease inhibitor cocktail] and pre-cleared with protein A agarose beads.  Five percent of the material was removed and saved as input, and the rest of the pre-cleared supernatant was incubated overnight at 4oC with the specified antibodies of interest or without antibody as a control (each 15 cm diameter dish yielded two immunoprecipitations) with continuous mixing. After the incubation, the immune complexes were collected by adding protein A agarose beads and incubating for 2 hours at 4°C.  The immunoprecipitated material was washed once with low salt wash buffer [20 mM Tris-HCl pH 7.9, 2 mM EDTA, 125 mM NaCl, 0.05% SDS, 1% Triton X-100, and 1x complete protease inhibitor cocktail], once with high-salt wash buffer [20 mM Tris-HCl pH 7.9, 2 mM EDTA, 500 mM NaCl, 0.05% SDS, 1% Triton X-100, and 1x complete protease inhibitor cocktail], once with LiCl wash buffer [10 mM Tris-HCl pH 7.9, 1 mM EDTA, 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, and 1x complete protease inhibitor cocktail], and twice with Tris-EDTA (TE) containing 1x complete protease inhibitor cocktail.  The immunoprecipitated material was eluted at room temperature in elution buffer [100 mM NaHCO3, 1% SDS], and reverse crosslinked by adding 100 mM NaCl and incubating at 65oC overnight.  The eluted material was then digested with proteinase K and RNase A to remove protein and RNA, respectively, and the enriched genomic DNA was extracted with phenol:chloroform:isoamyl alcohol, followed by isopropanol precipitation.  The ChIPed DNA was dissolved in water and purified again using AMPure Beads XP.
ChIP-seq libraries were generated using two biological replicates the ChIPed DNA described above for each condition.  The DNA was purified using a MiniElute PCR Purification Kit (Qiagen, 28004).  After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described {Quail, 2008 #8;Quail, 2008 #8;Franco, 2015 #9}, with some modifications.  Briefly, the DNA was end-repaired and a single ÒAÓ-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (300-500 bp) was size-selected by agarose gel electrophoresis and purified using a QIAquick Gel Extraction kit (Qiagen, 28704).  The size-selected fragments were PCR amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter, A63881).  After quality control analyses, the libraries were sequenced on an Illumina HiSeq 2000 (single-end sequencing, 50 nt).

treatment_protocol: Cells were treated with vehicle (EtOH) or 100 nM E2 for 45 min.

tag: cell line

value: EtOH, 45 min


title: Input_ChIP-seq_MCF-7_Veh_rep1


title: Lung Biopsy, control, VUHD68

status: Public on Sep 05 2019

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 N. Fifth Street

department: Integrated Cancer genomics division

institute: Translational Genomics Research Institute

data_processing:
Indivual sample reads were input into Cellranger 3.0.2 using reference hg38
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger output format with all samples aggregated together, includes celltype metadata

source_name: Lung Biopsy

extract_protocol:
Custom tissue dissociation
10X 5' Gene Expression (GEX) Library Construction

tag: disease state

value: control

value: Lung Biopsy


title: RNA-seq_Lung_control_2

status: Public on Jan 01 2019

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
reads were aligned using STAR
filtering step to remove: (i) reads with mapping quality less than 20, (ii) read pairs with unexpected orientations and greater than 500Kb mapping distance between the read pair, and (iii) reads that are mapped to greater than 10 positions in the genome
Read counts for each gene were obtained using FeatureCounts
DESeq2 was used for differential expression analysis
Batch effect is adjusted using ComBat with batch as a known covariate
genome_build: mm10
Supplementary_files_format_and_content: text file including gene list with read counts

source_name: Lung

growth_protocol: Six or seven-month-old wild-type (C57BL/6J) female mice weighing around 25-28 g were purchased from Jackson Laboratory (Bar Harbor, ME).  Without further indications, mice are kept under a 12-h light/12-h dark regimen.

extract_protocol:
Total RNA was extracted from mouse kidney, liver, lung and spleen using TRIzol RNA extraction (Thermo Fisher Scientific).  After phase separation, RNA was purified using the PureLink RNA Mini Kit (Thermo Fisher Scientific).  Purified total RNA sample was treated with DNase I (TURBO DNA-freeTM kit, Ambion Inc.) to remove traces of DNA.  RNA library was prepared using NEBNext Ultra RNA library prep kit (Illumina) according to manufacturer’s instruction.
Total RNA starting with 1ug was poly-A selected, fragmented by random priming and then converted to cDNA using ProtoScript II reverse transcriptase.  The cDNA was then end-repaired, adenylated and ligated with Illumina sequencing adaptors.  Libraries from all samples were pooled and sequenced using an Illumina HiSeq 4000 with 50-bp pair-end read.

treatment_protocol: All mice were treated with drug at ZT1 (8 am) and sacrificed at ZT5 (12 pm).  Single dose of clinical cisplatin (1mg/ml or 3.3 mM/L, Fresenius Kabi Pharceutical company) was administered by intraperitoneal injection at 10 mg cis-DDP/Kg body weight.  Same volume of saline solution (154 mM) was administered by intraperitoneal injection to control group mouse.

tag: strain

tag: Sex

value: female

value: Lung

tag: cisplatin

value: No

tag: time after treatment


title: RNA-seq_Spleen_control_2

source_name: Spleen

value: Spleen


title: RNA-seq_Spleen_cisplatin_1

value: Yes


title: RNA-seq_Lung_control_1


title: RNA-seq_Spleen_control_1


title: RNA-seq_Spleen_cisplatin_2


title: RNA-seq_Lung_cisplatin_2


title: duodenum, calcitriol and ZK #3


title: RNA-seq_Lung_cisplatin_1


title: VUMC_Xeno_IgG_(20180321_DJ_HsSc_IgG_VX1_0314)

status: Public on Dec 22 2018

description: AutoCUT&RUN for IgG in VUMC-10 Xenograft Tissue

data_processing:
Library strategy:  CUT&RUN
Genome_build: UCSC hg19
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We extracted fragments from properly paired reads from the results and merged replicates. 3. We used the bedtools 2.17.0 genomecov command with a scaling factor of 100000000/(number of base pairs in the mapped fragments) to create a fraction-normalized track file (Supplementary file .bedgraph.gz).

source_name: AutoCUT&RUN

value: Human VUMC-10 xenografts

tag: antibody

value: Rabbit IgG abcam ab46540


title: H3K27ac_SU-DIPG-XIII_(20180511_JS_HsSc_276_0413).

description:
CUT&RUN for H3K27ac in 1M SU-DIPG-XIII cells
identical to GSM3325612

data_processing:
Library strategy:  CUT&RUN
Genome_build: UCSC hg19
Genome_build: Masked UCSC dm6
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used bowtie 2.2.5 with options "--local --very-sensitive-local --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to masked UCSC dm6. 3. We extracted properly paired reads from the marked alignments to both genomes. 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).

value: Human SU-DIPG-XIII cells

value: anti-H3K27ac Millipore MABE647


title: VUMC_Xeno_H3K27ac_(20180321_DJ_HsSc_K27aVX1_0314)

description: AutoCUT&RUN for H3K27ac in VUMC-10 Xenograft Tissue

value: anti-H3K27ac abcam ab45173


title: VUMC_Xeno_H3K4me2_(20180321_DJ_HsSc_K4m2VX1_0314)

description: AutoCUT&RUN for H3K4me2 in VUMC-10 Xenograft Tissue

value: anti-H3K4me2 Millipore 07-030


title: VUMC_Cells_H3K4me2_(20180321_DJ_HsSc_K4m2VC1_0314)

description: AutoCUT&RUN for H3K4me2 in 100K VUMC-10 cells

value: Human VUMC-10 cells


title: VUMC_Xeno_H3K27me3_(20180321_DJ_HsSc_K27mVX1_0314)

description: AutoCUT&RUN for H3K27me3 in VUMC-10 Xenograft Tissue

value: anti-H3K27me3 Cell Signaling 9733S


title: duodenum, vehicle #2

value: vehicle

value: duodenum


title: VUMC_Cells_IgG_(20180321_DJ_HsSc_IgG_VC1_0314)

description: AutoCUT&RUN for IgG in 100K VUMC-10 cells


title: VUMC_Cells_H3K27me3_(20180321_DJ_HsSc_K27mVC1_0314)

description: AutoCUT&RUN for H3K27me3 in 100K VUMC-10 cells


title: VUMC_Cells_H3K27ac_Ab2_(20180608_JS_HsDmSc_0525_JS395)

description: CUT&RUN for H3K27ac using Ab2 in 1M VUMC-10 cells


title: VUMC_Cells_H3K27ac_(20180321_DJ_HsSc_K27aVC1_0314)

description: AutoCUT&RUN for H3K27ac in 100K VUMC-10 cells


title: SUDIPGXIII_Xeno_H3K4me2_(20180321_DJ_HsSc_K4m2DX1_0314)

description: AutoCUT&RUN for H3K4me2 in SU-DIPG-XIII Xenograft Tissue

value: Human SU-DIPG-XIII xenografts


title: SUDIPGXIII_Xeno_H3K27me3_(20180321_DJ_HsSc_K27mDX1_0314)

description: AutoCUT&RUN for H3K27me3 in SU-DIPG-XIII Xenograft Tissue


title: Lung Biopsy, control, VUHD70

value: control

value: Lung Biopsy


title: SUDIPGXIII_Xeno_IgG_(20180321_DJ_HsSc_IgG_DX1_0314)

description: AutoCUT&RUN for IgG in SU-DIPG-XIII Xenograft Tissue


title: SUDIPGXIII_Xeno_H3K27ac_(20180321_DJ_HsSc_K27aDX1_0314)

description: AutoCUT&RUN for H3K27ac in SU-DIPG-XIII Xenograft Tissue


title: SUDIPGXIII_Cells_IgG_(20180321_DJ_HsSc_IgG_DC1_0314)

description: AutoCUT&RUN for IgG in 100K SU-DIPG-XIII cells


title: SUDIPGXIII_Cells_H3K4me2_(20180321_DJ_HsSc_K4m2DC1_0314)

description: AutoCUT&RUN for H3K4me2 in 100K SU-DIPG-XIII cells


title: SUDIPGXIII_Cells_H3K27ac_(20180321_DJ_HsSc_K27aDC1_0314)

description: AutoCUT&RUN for H3K27ac in 100K SU-DIPG-XIII cells


title: SUDIPGXIII_Cells_H3K27me3_(20180321_DJ_HsSc_K27mDC1_0314)

description: AutoCUT&RUN for H3K27me3 in 100K SU-DIPG-XIII cells


title: K562_NPAT_(20180423_DJ_HsSc_NPAT_K1_0326)

description: AutoCUT&RUN for NPAT in 1M K562 cells

value: Human K562 cells

value: anti-NPAT Thermofisher PA5-66839


title: K562_IgG_(20180423_DJ_HsSc_IgG_K1_0326)

description: AutoCUT&RUN for IgG in 1M K562 cells


title: K562_H3K27ac_(20180423_DJ_HsSc_K27a_K1_0326)

description: AutoCUT&RUN for H3K27ac in 1M K562 cells


title: K562_H3K27me3_(20180423_DJ_HsSc_K27m_K1_0326)

description: AutoCUT&RUN for H3K27me3 in 1M K562 cells


title: K562_H3K4me3_(20180423_DJ_HsSc_K4m3_K1_0326)

description: AutoCUT&RUN for H3K4me3 in 1M K562 cells

value: anti-H3K4me3 Active Motif 39159


title: K562_CTCF_(20180423_DJ_HsSc_CTCF_K1_0326)

description: AutoCUT&RUN for CTCF in 1M K562 cells

value: anti-CTCF Millipore 07-729


title: H1_H3K27me3_(20180423_DJ_HsSc_K27m_H1_0326)

description: AutoCUT&RUNfor H3K27me3 in 1M H1 cells

value: Human H1 cells


title: H1_H3K27ac_(20180423_DJ_HsSc_K27a_H1_0326)

description: AutoCUT&RUN for H3K27ac in 1M H1 cells


title: CHU073-TURP-1

status: Public on Oct 11 2018

city: Atlanta

first: Carlos

middle: Sanchez

last: Moreno

state: GA

address: 101 Woodruff Circle NE, Room 2309

department: Pathology and Laboratory Medicine

institute: Emory University

description: Movreadcounts.csv

data_processing:
 Sequence reads were aligned to the hg38 genome build and annotated against gencode.v21 using STAR.v2.5
Genome_build: hg38
Supplementary_files_format_and_content: Movreadcounts.csv - Raw counts of sequencing reads

source_name: Prostate Tumor Tissue

extract_protocol:
RNA was isolated from FFPE tissue using the Omega Bio-tek E.Z.N.A. FFPE RNA Kit
Libraries were prepared using the Illumina TruSeq RNA Access Library Prep Kit

value: TURP

value: pre-ADT

tag: age at diagnosis (years)

tag: race

value: white

tag: psa at time of diagnosis

tag: primary gleason grade

tag: secondary gleason grade

tag: neoadjuvant adt duration

value: months,  none=0, unknown=999, na=888:888

tag: recurrence

value: none=0, biochemical=1, local=2, distal = 3:1

tag: metastasis


title: CHU073-TURP-2

description: Movreadcounts.csv

tag: sample type

tag: treatment

value: post-ADT


title: CHU069-TURP-2

description: Movreadcounts.csv


title: H1_CTCF_(20180423_DJ_HsSc_CTCF_H1_0326)

description: AutoCUT&RUN for CTCF in 1M H1 cells

tag: cell line


title: H1_H3K4me1_(20180423_DJ_HsSc_K4m1_H1_0326)

description: AutoCUT&RUN for H3K4me1 in 1M H1 cells

value: anti-H3K4me1 abcam ab8895


title: CHU068-TURP-2

description: Movreadcounts.csv

value: ng/ml, unknown = 999:160

value: months,  none=0, unknown=999, na=888:1

value: none=0, biochemical=1, local=2, distal = 3:3


title: CHU067-Bx

description: Movreadcounts.csv

value: Biopsy

value: none=0, biochemical=1, local=2, distal = 3:2


title: CHU028-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:12

value: none=0, biochemical=1, local=2, distal = 3:0


title: CHU067-TURP

description: Movreadcounts.csv


title: CHU069-TURP-1

description: Movreadcounts.csv


title: CHU028-RP

description: Movreadcounts.csv

value: Radical Prostatectomy


title: duodenum, calcitriol and ZK #1

value: calcitriol and ZK

tag: tissue

value: duodenum


title: H1_H3K4me3_(20180423_DJ_HsSc_K4m3_H1_0326)

description: AutoCUT&RUN for H3K4me3 in 1M H1 cells

value: Human H1 cells

value: anti-H3K4me3 Active Motif 39159


title: CHU026-RP

description: Movreadcounts.csv

value: white

value: months,  none=0, unknown=999, na=888:6


title: CHU025-Bx

description: Movreadcounts.csv

value: pre-ADT

value: months,  none=0, unknown=999, na=888:7

value: none=0, biochemical=1, local=2, distal = 3:1


title: K562_H3K4me2_(20180423_DJ_HsSc_K4m2_K1_0326)

description: AutoCUT&RUN for H3K4me2 in 1M K562 cells

value: Human K562 cells

value: anti-H3K4me2 Millipore 07-030


title: K562_H3K4me1_(20180423_DJ_HsSc_K4m1_K1_0326)

description: AutoCUT&RUN for H3K4me1 in 1M K562 cells

value: anti-H3K4me1 abcam ab8895


title: CHU025-RP

description: Movreadcounts.csv

value: post-ADT


title: CHU022-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:6.1

value: months,  none=0, unknown=999, na=888:3


title: H1_NPAT_(20180423_DJ_HsSc_NPAT_H1_0326)

description: AutoCUT&RUN for NPAT in 1M H1 cells

value: anti-NPAT Thermofisher PA5-66839


title: CHU022-Bx

description: Movreadcounts.csv

value: Biopsy

value: none=0, biochemical=1, local=2, distal = 3:0


title: CHU024-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:12.9

value: months,  none=0, unknown=999, na=888:2


title: H1_IgG_(20180423_DJ_HsSc_IgG_H1_0326)

description: AutoCUT&RUN for IgG in 1M H1 cells

value: Human H1 cells

value: Rabbit IgG abcam ab46540


title: H1_H3K4me2_(20180423_DJ_HsSc_K4m2_H1_0326)

description: AutoCUT&RUN for H3K4me2 in 1M H1 cells


title: CHU021-Bx

description: Movreadcounts.csv

value: white

value: ng/ml, unknown = 999:8.1

value: months,  none=0, unknown=999, na=888:8


title: CHU068-TURP-1

description: Movreadcounts.csv

value: TURP

value: pre-ADT

value: ng/ml, unknown = 999:160

value: months,  none=0, unknown=999, na=888:1

value: none=0, biochemical=1, local=2, distal = 3:3


title: CHU020-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:9.97

value: none=0, biochemical=1, local=2, distal = 3:1


title: CHU021-RP

description: Movreadcounts.csv

value: Radical Prostatectomy

value: post-ADT


title: CHU018-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:20

value: months,  none=0, unknown=999, na=888:3

value: none=0, biochemical=1, local=2, distal = 3:0


title: CHU018-Bx

description: Movreadcounts.csv

value: Biopsy


title: CHU020-RP

description: Movreadcounts.csv


title: CHU016-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:8.26


title: CHU014-Bx

description: Movreadcounts.csv

value: white

value: ng/ml, unknown = 999:21


title: CHU015-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:5.2

value: months,  none=0, unknown=999, na=888:8


title: CHU016-RP

description: Movreadcounts.csv


title: CHU015-Bx

description: Movreadcounts.csv

value: pre-ADT


title: CHU014-RP

description: Movreadcounts.csv


title: CHU026-Bx

description: Movreadcounts.csv

value: months,  none=0, unknown=999, na=888:6


title: CHU013-Bx

description: Movreadcounts.csv


title: CHU011-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:5


title: CHU009-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:5.4


title: CHU024-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:12.9

value: months,  none=0, unknown=999, na=888:2


title: CHU009-RP

description: Movreadcounts.csv

value: Radical Prostatectomy


title: CHU008-RP

description: Movreadcounts.csv

value: post-ADT

value: ng/ml, unknown = 999:5.51

value: none=0, biochemical=1, local=2, distal = 3:1


title: CHU007-RP

description: Movreadcounts.csv

value: months,  none=0, unknown=999, na=888:3


title: CHU007-Bx

description: Movreadcounts.csv

value: Biopsy


title: CHU006-RP

description: Movreadcounts.csv

value: none=0, biochemical=1, local=2, distal = 3:0


title: CHU003-Bx

description: Movreadcounts.csv

value: white


title: CHU019-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:7.61


title: CHU006-Bx

description: Movreadcounts.csv


title: CHU003-RP

description: Movreadcounts.csv

value: ng/ml, unknown = 999:21


title: CHU001-Bx

description: Movreadcounts.csv

value: ng/ml, unknown = 999:23

value: months,  none=0, unknown=999, na=888:5


title: CHU019-Bx

description: Movreadcounts.csv

value: pre-ADT

value: months,  none=0, unknown=999, na=888:8


title: CHU001-RP

description: Movreadcounts.csv


title: CHU013-RP

description: Movreadcounts.csv


title: 22Rv1_MOCK_INPUT

status: Public on Aug 16 2018

city: Durham

first: Greg

last: Wang

state: NC

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

description: Barcode: GTGCTA

data_processing:
All reads were mapped to the human genome (hg19) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept, which were then subject to removal of reads generated by PCR- caused duplicates using the Picard and Samtools.
Profiles of ChIP-Seq read densities were displayed in the Integrative Genomics Viewer (IGV, Broad Institute) and  the Integrative Genomics Browser (IGB, Affymetrix).
The MACS2 software was used for peak identification with data from input as controls and default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cells were grown in RPMI plus 10% FBS and 1% antibiotics.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies against AR-FL, AR-V7, BRD4 or ZFX.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for up to 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: For ChIP-seq experiments, 22Rv1 cells were grown in regular medium to about 50% confluent and then switched to phenol red free RPMI medium containing 10% charcoal-stripped FBS for 3 days and then treated with either vehicle, or 10nM of DHT, or DHT plus 10uM of MDV3100, or DHT plus 500nM of JQ1, for 6hrs before the cells were collected.

value: prostate carcinoma epithelial cell line 22Rv1

tag: chip antibody

value: vehicle


title: 22Rv1_DTM_INPUT

description: Barcode: TTCAGC


title: 22Rv1_DHT_INPUT

description: Barcode: GGTTGG

value: DHT


title: 22Rv1_DHT_BRD4

description: Barcode: ATCACG

value: Anti-BRD4 (Bethyl)


title: 22Rv1_DTM_BRD4

description: Barcode: TTAGGC


title: 22Rv1_DTJ_BRD4

description: Barcode: CGATGT


title: 22Rv1_DTM_V7

description: Barcode: CAGATC

value: anti-AR-V7 specific (Precision#AG10008)


title: 22Rv1_ZFX_SE

description: Barcode: TACTAG

value: anti-ZFX serum (from Dr Huck-Hui Ng)

value: charcoal stripped


title: 22Rv1_DTJ_V7

description: Barcode: GCCAAT


title: 22Rv1_ZFX_FI

description: Barcode: TCAGAT

value: anti-ZFX (ThermoFisher)


title: CHU011-Bx

description: Movreadcounts.csv

value: Biopsy

value: ng/ml, unknown = 999:5

value: months,  none=0, unknown=999, na=888:3


title: 22Rv1_DTJ_INPUT

description: Barcode: TGAACT


title: 22Rv1_MOCK_BRD4

description: Barcode: CTTGTA

value: vehicle (charcoal stripped)


title: 22Rv1_DHT_V7

description: Barcode: ACAGTG


title: 22Rv1_MOCK_V7

description: Barcode: TGACCA


title: 22Rv1_DTM_C19

description: Barcode: TTAGGC

value: anti-AR-FL specific (Santa cruz bio#C-19)


title: 22Rv1_DTJ_C19

description: Barcode: CGATGT


title: CHU008-Bx

description: Movreadcounts.csv

value: white

value: ng/ml, unknown = 999:5.51

value: none=0, biochemical=1, local=2, distal = 3:1


title: 22Rv1_DHT_C19

description: Barcode: ATCACG


title: ChIP-seq_Input_Vehicle_rep2

status: Public on Mar 05 2015

description: ChIP 5% Input from MCF7 cells  after 40min of Vehicle treatment

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg19). Bowtie software package (Langmead et al., 2009) was used to align reads and the output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

growth_protocol: MCF-7 breast cancer cells were obtained from the ATCC and maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
ChIP-seq libraries were generated from two biological replicates for each condition.  The immunoprecipitated DNA was purified using a MiniElute PCR Purification Kit from Qiagen.  After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described (Quail et al., 2008), with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250-300 bp) was size-selected by agarose gel electrophoresis and purified using a Qiagen Gel Extraction Kit.
The size-selected fragments were amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter).  Quality control was performed to determine the size, purity, and concentration of the final libraries, which were sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: Prior to all treatments, the cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.  All treatments were performed for 40 min with 100 nM 17β-estradiol, 25 ng/mL TNFα, or both.

tag: cell type

value: ER Positive Breast Cancer Cells

value: Vehicle

value: input


title: MCF7.Input.rep1

status: Public on Dec 15 2017

city: Houston

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2.
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.3.6; Scores represent the ChIP-seq tag numbers.

source_name: MCF7 cells, input

growth_protocol: Cells were plated and expanded on 150mm plates until a minimum of 3.5 x 10^5 cells per plate were reached. The media conditions and split ratio for each cell line is depicted in the Excel sheet entitled “Cell line conditions”. Media is replaced every other day, until the desired confluency is reached.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells are harvested from the 150mm plates under sterile conditions into a 50ml conical tube. Aliquots of 100-200ul of this stock are then counted using the Biorad Cell Counter. Counts are repeated three times and the number of cells per ml are then determined. For growth curves, the schema in the Powerpoint entitled “Growthcurveprotocol” is followed. Briefly, 500-5000 cells (for each cell line) were plated onto each well of a 96-well plate on day 0. For each cell line, a total of 7 replicate plates were seeded. The media was changed every other day (days 1, 3, 5, 7, 9, 11, and 13). One plate from each cell line was subjected to MTT proliferation assay every other day (days 1, 3, 5, 7, 9, 11, and 13).

value: Breast cancer cell line

value: Control


title: ChIP-seq_Input_Vehicle_rep1


title: MCF7.Input.rep2


title: 22Rv1_MOCK_C19

description: Barcode: CTTGTA

value: prostate carcinoma epithelial cell line 22Rv1


title: Blastocyst_replicate3

status: Public on Feb 09 2014

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

description: pools of 10 embryos

data_processing:
CASAVA 1.6 software was used for basecalling.
Adaptor sequences and the first 5 bases were removed. Additionally, reads were trimmed from the 3'- and 5'-end with a quality cutoff of 20. Reads below a length of 30 were discarded.
Filtered reads were mapped with Tophat2 (v.2.0.3) to the bovine UMD3.1 reference genome with default parameters.
The number of reads falling into exons of genes were counted using HTSeq-count. Read counts were normalized by library size and by a variance stabilizing transformation with DESeq and differential abundances were calculated with an adj. p-value < 0.05.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file include normalized values for each gene and sample.

organism: Bos taurus

source_name: embryos

growth_protocol: IVP of bovine embryos was done as described previously . Briefly, cumulus-oocyte complexes (COCs) were aspirated from German Simmental ovaries obtained in a local abattoir and washed twice in preincubated (39°C, 5% CO2 in air) Tissue Culture Medium 199 (TCM 199; Invitrogen) supplemented with l-glutamine (100 mg/L), NaHCO3 (3 g/L), Hepes (1400 mg/L), sodium pyruvate (250 mg/L), l-lactic-Ca-salt (600 mg/L), gentamicin (55 mg/L), and 10% (v/v) estrous cow serum (ECS). For in vitro maturation (IVM) COCs were washed in TCM 199 supplemented with 0.01 U/ml of bovine FSH and bovine LH (both Sioux Biochem), transferred to four-well plates (Nunc), and matured in 400 μl of this medium for 20–24 h at 39°C in an atmosphere of 5% CO2 in humidified air. For in vitro fertilization (IVF) the matured COCs were transferred to 400 μl of Tyrode albumin lactate pyruvate (TALP) medium containing 2.2 mg/ml of sodium pyruvate, 10 μg/ml of heparin sodium salt, and 6 mg/ml of BSA, after three washes in the same medium. Then, the COCs and spermatozoa (artificial insemination straws from a commercially available Zebu bull, subjected to a 90 min swim-up after thawing) were co-incubated for 18 h at 39°C in an atmosphere of 5% CO2 in humidified air. Presumptive zygotes were mechanically denuded by vortexing and gentle pipetting; washed three times in synthetic oviduct fluid (SOF) culture medium enriched with 5% ECS, 20 μl/ml of 100× basal medium (Invitrogen), and 10 μl/ml of 100× minimum essential medium (Invitrogen). Batches of app. 20 embryos were transferred to 400-μl droplets of medium covered with mineral oil and cultured until reaching the respective stages. The culture atmosphere was 5% CO2, 5% O2, and 90% N2 at 39°C and maximum humidity. Pools of ten embryos were picked after visual inspection and snap frozen in liquid nitrogen after washing in PBS. Stages collected for sequencing were: denuded oocytes before and after maturation and embryos at the 4-cell, 8-cell, 16-cell, and blastocyst stages.

extract_protocol:
Frozen pools of ten oocytes or embryos were thawed and lysed in 10 µl of Lysis Buffer (Prelude kit from NuGEN, San Carlos USA). cDNA was generated and amplified with the ovation RNAseq v2 kit (NuGEN, San Carlos, USA).
In brief 1 µl of the lysate was used for mixed random-/polyA-primed first-strand cDNA synthesis. After second strand synthesis the double-stranded cDNA was amplified by single primer isothermal amplification and the amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter, Brea, USA) and fragmented by sonication (Bioruptor, Diagenode, Liege Belgium; 25 cycles 30 sec on/30 sec off). 500 ng of fragmented cDNA were used for preparation of Illumina-compatible sequencing libraries using the NuGEN Rapid library kit according to the manufacturer’s protocol. Adapter ligation was done with sample-specific barcodes. The resulting library was amplified (KAPA hifi polymerase, 8 cycles, 95°C 80 sec, 55°C 30 sec, 72°C 60 sec) and quantified on a Bioanalyzer 2100 (Agilent, Santa Clara, USA). Barcoded libraries were pooled at 10 nM concentration for multiplexed sequencing. Three replicates of each stage were sequenced on an Illumina GAIIx to a mean coverage of 20 Mio reads each. Sequencing runs were done in single-read mode with an 80 base read-length.

tag: Stage

value: Blastocyst

tag: breed

value: German Simmental x Brahman


title: bESC_B_P10

status: Public on Feb 11 2018

city: Davis

first: Pablo

last: Ross

state: CA

address: 1 Shields Ave

institute: University of California, Davis

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 platform
Sequence reads were mapped to the bovine UMD3.1 genome assembly and Ensembl 78 genebuild annotation using CLC Genomics Workbench 7.0 (CLCbio, Aarhus, Denmark).
Reads per million mapped reads per kilobase of exon model (RPKM) values were calculated for each gene and the levels of expression compared among groups using EdgeR with FDR correction for multiple testing.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each gene and sample.

source_name: bESC

growth_protocol: bESC were grown in CTFR medium [a custom basal medium similar to mTeSR medium (STEMCELL Technologies)] that is completely devoid of growth factors FGF2 and TGFb and contains low fatty acid BSA (MP Biomedicals NZ), similar to basal medium in the published recipe (Ludwig TE, et al. (2006) Feeder-independent culture of human embryonic stem cells. Nat Methods 3:637–646), and supplemented with 20 ng/mL human FGF2 and 2.5 μM IWR1, and were incubated at 37 °C and 5% CO2 (Wu J, et al. (2015) An alternative pluripotent state confers interspecies chimaeric competency. Nature 521:316–321) in wells containing MEFs and were passaged every 4–5 d at a 1:10 split ratio.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit and then was reverse-transcribed using iScript RT Supermix (Bio-Rad).
Libraries were constructed using the TruSeq RNA Sample Prep Kit (Illumina)

value: BL-derived ESC

tag: passage number


title: bESC_A_P10


title: Blastocyst_replicate2

description: pools of 10 embryos


title: Blastocyst_replicate1

description: pools of 10 embryos