title: MEF H3K36me3 ChIP-seq

status: Public on Nov 01 2012

data_processing:
Basecalls performed using Illumina software
Alignment: Alignment was performed with Novoalign 2.06 (www.novocraft.com) using default parameters with modifications: -i 300 100 -t 180 -R 10 -h 180 180 -v 180. Uniquely aligned pairs were selected, discarding duplicate fragments
Normalized coverage calculation: Positional coverage was normalized by input coverage with a pseudocount of 1 and balanced for potential inequality of total input and experiment coverages: n_norm = [(n+1)/(n_i+1)] * [N_i/N], where n, n_i, are positional coverages and N, N_i are total genome coverages in experiment and input, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using normalized coverage for two chromosomes analyzed in the publication (chr13 and chrX)

source_name: Transformed mouse embryonic fibroblast line

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, 1% L-glutamine, high-glucose DMEM) with either 15% FBS (MEFs) or 30% FBS (ES cells)

extract_protocol: ChIP was performed as described in Lee et al. Nat Protoc. 2006;1(2):729-48. Paired-end Solexa ChIP libraries were prepared as described in Illumina ChIP sequencing manual with minor modifications and using NEB Next DNA sample prep reagent Set 1 (E6000S) (NEB). Input DNA was used as a control and for normalization. Modifications to the Illumina protocol were: 1- 30 ng of ChIP products were used as template, 2- paired-end adapters were ligated to end-repaired and A-tailed DNA using T4 DNA ligase (NEB) for 2 hours at 16°C, and 2- Phusion polymerase in GC buffer (Finzyme) was used instead of Phusion polymerase in HF buffer. DNA products were purified with QIAquick spin columns (Qiagen). Concentration, size distribution (400-500bp), and purity of libraries were assessed on  DNA1000 Bioanalyzer chip (Agilent). Genome Analyzer II (Illumina) was used to perform 2x36 cycles of paired end sequencing.

treatment_protocol: d0 ES cells were cultured in the presence of LIF under adherent conditions. d7 ES cells were cultured without LIF under non-adherent conditions for 4 days and plated for an additional 3 days.

value: transformed embryonic fibroblast cell line

tag: cell line

value: MEF

tag: Sex

value: Female

tag: passage

value: passage 14

value: F1:129S1 x CastEiJ

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog #


title: MEF input DNA_1

type: SRA

city: Boston

first: Ruslan

last: Sadreyev

state: MA

address: 185 Cambridge St

country: USA

institute: Harvard Medical School/ Mass General Hospital

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain


title: MEF H3K4me3 ChIP-seq


title: MEF input DNA_2


title: MEF H3K27me3 ChIP-seq


title: MEF RNA-POLII-Ser5P Chip-seq


title: Myeloid cells from 2 mo old female Xist wild-type (2lox/+)

status: Public on Feb 20 2013

type: RNA

description:
Gene expression data from myeloid cells from 2 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

hyb_protocol: Following fragmentation, 5ug of cDNA were hybridized for 16 hrs at 45C on Affymetrix Mouse Gene 1.0ST microarrays. GeneChps were washed and stained in the Affymetric Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Genechip Scanner 3000 7G. The data was collected using the Command Console Version 3.2.

data_processing: The data were analyzed using R Bioconductor Affy package, with RMA applied as summarization and normalization method (Irizarry et al., 2003).

label: Biotin

molecule: total RNA

source_name: FACS sorted CD11b+ myeloid cells

label_protocol: RNA was labeled using NuGen Ovation Pico WTA v2 System paired with the Encore Biotin Module (NuGEN).

extract_protocol: Total RNA from cells was isolated using Trizol reagent (Invitrogen).

tag: genotype

value: Xist wild-type (2lox/+) mouse

tag: age

value: 2 months old

tag: gender

value: female

tag: genetic background

value: CD11b+ myeloid cells


title: MEF Ezh2 ChIP-seq


title: ES cell d7 RNA-POLII-Ser5P Chip-seq

source_name: Differentiating mouse embryonic stem cell line

value: differentiating embryonic stem cell line

value: passage 27

value: F2:129S1/CastEiJ x 129S1


title: B cells from 2 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from B cells from 2 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted B220+ B-lymphocytes

value: Xist heterozgous (2lox/-)  mutant mouse

value: 129Sv/Jae x B6.Cg-Tg (Vav1-cre)A2Kio/J

value: B220+ B-lymphocytes


title: B cells from 6 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from B cells from 6 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

value: 6 months old


title: Erythroid cells from 6 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from Erythroid cells from 6 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted Ter119+ erythroid cells

value: Xist  wild-type (2lox/+) mouse

value: Ter119+ erythroid cells


title: Myeloid cells from 6 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from myeloid cells from 6 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: ES cell d7 H3K36me3 ChIP-seq

value: Female


title: Erythroid cells from 6 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from erythroid cells from 6 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

value: Xist heterozgous (2lox/-) mutant mouse


title: B cells from 2 mo old female Xist wild-type (2lox/+)

description:
Gene expression data from B cells from 2 months old female Xist wild-type (2lox/+) mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: LSK+CD34- HSCs from 6 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from LSK+CD34- HSCs from 6 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

source_name: FACS sorted LKS+CD34- hematopoietic stem cells (HSC)


title: LSK+CD34- HSCs from 2 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from LSK+CD34- HSCs from 2 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.

value: LKS+CD34- hematopoietic stem cells (HSC)


title: B cells from 6 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from B cells from 6 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: Myeloid cells from 6 mo old female Xist heterozygous (2lox/-) mutant

description:
Gene expression data from myeloid cells from 6 months old female Xist heterozgous (2lox/-) mutant mouse.
Hematopoietic cells were isolated from bone or spleen of mouse, indicated cell lineages were FACS sorted and used to isolate RNA  as described under Methods in Yildirim et al. Cell 2013.


title: ES cell d7 H3K4me3 ChIP-seq

value: Abcam


title: ES cell d7 H3K27me3 ChIP-seq


title: ES cell d7 Ezh2 ChIP-seq


title: ES cell d0 H3K36me3 ChIP-seq

source_name: Undifferentiated mouse embryonic stem cell line

value: undifferentiated embryonic stem cell line


title: ES cell d0 RNA-POLII-Ser5P Chip-seq


title: ES cell d0 H3K4me3 ChIP-seq


title: ES cell d0 input DNA_1


title: ES cell d0 H3K27me3 ChIP-seq


title: ES cell d0 Ezh2 ChIP-seq


title: ES cell d0 input DNA_2


title: MEF input 2_DNA

status: Public on Jan 06 2012

description: To generate the EY.T4 clonal hybrid cell line, female mice of Mus musculus (129S1) and male mice of Mus castaneus (CAST/EiJ) origins were crossed, F1 embryos were collected at day 13.5 and mouse embryonic fibroblasts (MEFs) were prepared using female embryos. MEFs were later immortalized by SV-40 T-antigen and subcloned by limiting dilution.

data_processing:
Alignment: Alignment was performed with Novoalign 2.06 (www.novocraft.com) using default parameters with modifications: -i 300 100 -t 180 -R 10 -h 180 180 -v 180. Uniquely aligned pairs were selected, discarding duplicate fragments.

Normalized coverage calculation: Positional coverage was normalized by input coverage with a pseudocount of 1 and balanced for potential inequality of total input and experiment coverages: n_norm = [(n+1)/(n_i+1)] * [N_i/N], where n, n_i, are positional coverages and N, N_i are total genome coverages in experiment and input, respectively.

Genome build: mm9

source_name: Transformed mouse embryonic fibroblast line, input

growth_protocol: Cells were cultured in regular fibroblast cell line culture medium (15%FBS, 1%Pen/Strep, 1% L-glutamine, high-glucose DMEM).

extract_protocol: ChIP was performed as described in Lee et al. Nat Protoc. 2006 (PMID 17406303) (MEF input 1, MEF POL-II_S2P, and MEF POL-II-S5P) and Takahashi et al. Science's STKE 2000 (PMID 11752617) (MEF input 2, MEF H3K4me3, and MEF H3K36me3). Paired-end Solexa ChIP libraries were prepared as described in the Illumina ChIP sequencing manual with minor modifications and using NEB Next DNA sample prep reagent Set 1 (E6000S) (NEB). Input DNA was used as a control and for normalization. Modifications to the Illumina protocol were: (1) 30 ng of ChIP products were used as template, (2) paired-end adapters were ligated to end-repaired and A-tailed DNA using T4 DNA ligase (NEB) for 2 hours at 16°C, and (3) Phusion polymerase in GC buffer (Finzyme) was used instead of Phusion polymerase in HF buffer. DNA products were purified with QIAquick spin columns (Qiagen). Concentration, size distribution (400-500bp), and purity of libraries were assessed on the DNA 1000 Bioanalyzer chip (Agilent). Genome Analyzer II (Illumina) was used to perform 2x36 cycles of paired-end sequencing.

value: transformed mouse embryonic fibroblasts

value: IgG rabbit serum

value: Sigma


title: MEF input 1_DNA

value: female


title: ES cell d7 input DNA

value: differentiating embryonic stem cell line

value: passage 27


title: MEF H3K4me3_ChIP-Seq

description:
To generate the EY.T4 clonal hybrid cell line, female mice of Mus musculus (129S1) and male mice of Mus castaneus (CAST/EiJ) origins were crossed, F1 embryos were collected at day 13.5 and mouse embryonic fibroblasts (MEFs) were prepared using female embryos. MEFs were later immortalized by SV-40 T-antigen and subcloned by limiting dilution.

Normalized using MEF input 2.

source_name: Transformed mouse embryonic fibroblast line, H3K4me3 ChIP


title: MEF H3K36me3_ChIP-Seq

source_name: Transformed mouse embryonic fibroblast line, H3K36me3 ChIP


title: MEF POL-II-S5P_ChIP-Seq

description:
To generate the EY.T4 clonal hybrid cell line, female mice of Mus musculus (129S1) and male mice of Mus castaneus (CAST/EiJ) origins were crossed, F1 embryos were collected at day 13.5 and mouse embryonic fibroblasts (MEFs) were prepared using female embryos. MEFs were later immortalized by SV-40 T-antigen and subcloned by limiting dilution.

Normalized using MEF input 1.

source_name: Transformed mouse embryonic fibroblast line, POL-II-S5P ChIP


title: MEF POL-II-S2P_ChIP-Seq

source_name: Transformed mouse embryonic fibroblast line, POL-II-S2P ChIP


title: hIPS 6C-1 c.III p.30 XIST-

status: Public on Dec 03 2013

description: Gene expression data from hiPS-6C-1

hyb_protocol: Biotinylated & fragmented cDNA is added to a hybridization solution containing several control oligos, then hybridized to a human U133 Plus 2.0 microarray chip overnight at 45C.

scan_protocol: Human U133 Plus 2.0 microarray chips were scanned using Affymetrix GCS3000

data_processing: The data were analyzed using R Bioconductor Affy package, with RMA applied as summarization and normalization method.

label: biotin

organism: Homo sapiens

source_name: hIPS 6C-1 c.III p.30 (HO); XIST-

label_protocol: The purified cDNA (starting with 300ng total RNA) is first fragmented using a chemical & enzymatic process, then the fragmented product is biotin-labeled to the 3'-hydroxyl end of the cDNA (NuGen Ovation V2 protocol).

growth_protocol: All hiPSCs were cultured with MEFs using hESC cell medium (Anguera et al Cell Stem Cell 2012)

extract_protocol: Total RNA was isolated with TriZOL according to their protocol.

treatment_protocol: All hiPSCs were treated & cultured using the same cell medium.

tag: line

value: hiPS- 6C-1

tag: source

value: Type I Diabetes Mellitus patient

value: XIST-