title: WT_1

city: Birmingham

first: Laurie

middle: E

last: Harrington

state: AL

address: 845 19th street south, BBRB 467

department: CDIB

institute: University of Alabama at Birmingham

data_processing:
Library strategy: Tn-Seq
Basecalls performed using Illumina bcl2fastq version 2.18.0.12
Sequence reads were trimmed with Trim Galore! version 0.6.0 with parameters --paired --trim1
Trimmed reads were aligned to UCSC mm9 using Bowtie2 version 2.3.3.1 with parameters -X 2000 -x -1 -2 -S
Alignments were sorted using Picard version 2.9.2 SortSam with default options
Duplicates were removed from the sorted alignments using Picard version 2.9.2 MarkDuplicates with default options
Peaks were called using MACS2 version 2.1.2 with parameters -t -f BAMPE -g mm -n -B -q 0.05 --call-summits --nomodel --nolambda --keep-dup all
Peaks were then annotated and motifis identified with Homer version 4.10.3 annotatePeaks and findMotifsGenome, respectively
Genome_build: mm9 from UCSC
Supplementary_files_format_and_content: Tab delimited Excel files containing peaks identified in each sample from MACS2 output

source_name: colonic lamina propria

extract_protocol:
Lymphocytes from the colonic and small intestine LP were isolated using the Lamina Propria Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol. ILCs were enriched using the Pan-ILC enrichement kit (Stem Cell Technologies), and 20,000-30,000 ILC1s were FACS sorted as Lineage(TCRβ, TCRγδ, CD8α, CD8β, CD19, CD11b, DX5, Gr-1, Ter119)-Thy1.2+CD127+NK1.1+NKp46+. ILC1s were lysed  and transposase reaction was performed with Tn5 transposase (Illumina) at for 30 min at 37C. DNA was purified using the MinElute kit (Qiagen).
Libraries were amplified using Nextara primers with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolegends), and reactions were purified with the PCR Purification Kit (QIAGEN).

value: colonic lamina propria

tag: genotype

value: wildtype


title: WT_3

status: Public on Jun 17 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue


title: Tabula Muris Senis (bulk RNA-seq) [E4_384Bulk_Plate3_S100]

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

library_source: transcriptomic

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316.
Reads were aligned to the mm10plus genome using STAR version 2.5.2b with parameters TK.
Gene counts were produced using HTSEQ version 0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Genome_build: GRCm38
Supplementary_files_format_and_content: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv: Comma-separated text file includes gene count table for all organs and ages.
Supplementary_files_format_and_content: MACA_Bulk_metadata.csv: Comma-separated text file includes experiment metadata.

molecule: total RNA

extract_protocol:
RNeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT.
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

tag: strain/background

value: Marrow

tag: age

value: 9 months postnatal

tag: Sex

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [E23_384Bulk_Plate1_S119]

value: MAT

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E3_384Bulk_Plate1_S99]

value: Lung

value: 15 months postnatal

value: Female


title: S4KO_1


title: Tabula Muris Senis (bulk RNA-seq) [E3_384Bulk_Plate2_S99]

value: GAT

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E22_384Bulk_Plate2_S118]

value: WBC

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E5_384Bulk_Plate2_S101]

value: Small Intestine


title: Tabula Muris Senis (bulk RNA-seq) [E21_384Bulk_Plate2_S117]

value: BAT


title: Tabula Muris Senis (bulk RNA-seq) [E21_384Bulk_Plate1_S117]


title: S4KO_2


title: Tabula Muris Senis (bulk RNA-seq) [E23_384Bulk_Plate2_S119]

value: 21 months postnatal


title: RNA-seq_LSK_G12D_Ezh2-KO_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads from all RNA-seq experiments were aligned to mouse (GENCODE version M9) reference genome by STAR 2.5.2b with the parameters: --outFilterMultimapNmax 1.
The number of reads aligned to GENCODE annotated genes' exons were counted using HTseq and further normalized to be of unit TPM (transcripts per million)using RSEM.
Differential gene expression analyses were performed using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: text file of gene read count, TPM values

growth_protocol: Bone marrow cells were obtained by flushing femurs and tibias with a 25G needle or by crushing femurs, tibias, vertebrae and pelvic bones with a mortar in Ca2+ and Mg2+-free Hank’s buffered salt solution (HBSS; Gibco) supplemented with 2% heat-inactivated bovine serum (HIBS, Gibco). For flow cytometric analysis and isolation, cells were incubated with combinations of antibodies listed in the key resource table. Lineage markers for HSCs and progenitors were CD3, CD5, CD8, B220, Gr1 and Ter119. Antibody staining was performed at 4 °C for 30 min, or, when CD34 was included in the cocktail, on ice for 90 min. Biotinylated antibodies were visualized by incubation with PE/Cy7-conjugated streptavidin at 4°C for 30 min. DAPI (4′,6-diamidino-2-phenylindole; 2 μg/ml in PBS) or PI (propidium iodide; 1 μg/ml) were used to exclude dead cells during flow cytometry.

extract_protocol: For RNA-seq analysis using the illumina NextSeq 500, 0.1-1 ug of total RNA was processed for library generation using the Ovation RNA-seq system (NuGEN) following the manufacturer’s protocol.

tag: strain background

tag: genotype/variation

tag: cell type

value: Bone marrow cells

tag: cell population

value: FACS-sorted LSK cells


title: RNA-seq_LSK_G12D_Ezh2-KO_rep1


title: RNA-seq_LSK_G12D_rep4


title: RNA-seq_LSK_Ezh2-KO_rep1


title: RNA-seq_LSK_G12D_rep3


title: Tabula Muris Senis (bulk RNA-seq) [E20_384Bulk_Plate1_S116]

value: Brain


title: RNA-seq_LSK_Ezh2-KO_rep2


title: Tabula Muris Senis (bulk RNA-seq) [F19_384Bulk_Plate2_S139]

value: Liver

value: 12 months postnatal


title: RNA-seq_LSK_G12D_Ezh2-KO_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E2_384Bulk_Plate3_S98]

value: Spleen

value: 24 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [E2_384Bulk_Plate2_S98]

value: Lung

value: 27 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E20_384Bulk_Plate2_S116]

value: MAT

value: 15 months postnatal

value: Female


title: RNA-seq_LSK_G12D_rep2


title: RNA-seq_LSK_G12D_rep1


title: RNA-seq_LSK_WT_rep3

value: WT


title: RNA-seq_LSK_WT_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E19_384Bulk_Plate1_S115]

value: Marrow

value: 3 months postnatal


title: RNA-seq_LSK_WT_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E22_384Bulk_Plate1_S118]

value: WBC


title: RNA-seq_LSK_Ezh2-KO_rep3

value: Bone marrow cells


title: Tabula Muris Senis (bulk RNA-seq) [E19_384Bulk_Plate2_S115]

value: 21 months postnatal


title: Input_LSK_G12D_Ezh2-KO_rep2

data_processing:
ChIP-seq raw reads were aligned to the (GENCODE version M9) genome assembly using Bowtie2 with the default parameters. Only tags that uniquely mapped to the genome were used for further analysis.
Bigwig files were generated by deepTools  bamCoveragewith with the parameters  of "--outFileFormat bigwig -- normalizeTo1x  --ignoreDuplicates --minMappingQuality 30 --extendReads 200"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 1-10 ng of ChIP DNA was processed for library generation using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference mouse genome (mm10) were retained for downstream data analysis.

value: FACS-sorted LSK cells


title: Tabula Muris Senis (bulk RNA-seq) [E18_384Bulk_Plate2_S114]

value: GAT


title: Tabula Muris Senis (bulk RNA-seq) [E18_384Bulk_Plate1_S114]

value: SCAT

value: 6 months postnatal


title: Input_LSK_G12D_Ezh2-KO_rep1


title: Input_LSK_Ezh2-KO_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E17_384Bulk_Plate2_S113]

value: Spleen


title: Input_LSK_Ezh2-KO_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E16_384Bulk_Plate1_S112]

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [E16_384Bulk_Plate2_S112]

value: Brain


title: Tabula Muris Senis (bulk RNA-seq) [E2_384Bulk_Plate1_S98]

value: Bone

value: 9 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E15_384Bulk_Plate2_S111]

value: MAT


title: Tabula Muris Senis (bulk RNA-seq) [E17_384Bulk_Plate1_S113]

value: Female


title: Input_LSK_WT_rep2

value: WT


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K27me3_rep2

tag: chip antibody


title: Input_LSK_G12D_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E15_384Bulk_Plate1_S111]

value: Kidney

value: 12 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E14_384Bulk_Plate2_S110]


title: Input_LSK_G12D_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E14_384Bulk_Plate3_S110]

value: missing


title: Tabula Muris Senis (bulk RNA-seq) [E13_384Bulk_Plate3_S109]

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E13_384Bulk_Plate2_S109]

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E13_384Bulk_Plate1_S109]

value: 15 months postnatal


title: ChIP-seq_LSK_G12D_H3K27me3_rep2

value: Bone marrow cells

value: FACS-sorted LSK cells


title: ChIP-seq_LSK_G12D_H3K27me3_rep1


title: ChIP-seq_LSK_Ezh2-KO_H3K27me3_rep1


title: ChIP-seq_LSK_WT_H3K27me3_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E12_384Bulk_Plate3_S108]

value: Small Intestine

value: 24 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E12_384Bulk_Plate2_S108]

value: Skin


title: Tabula Muris Senis (bulk RNA-seq) [E12_384Bulk_Plate1_S108]

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [E11_384Bulk_Plate3_S107]

value: SCAT

value: 6 months postnatal


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K27ac_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E11_384Bulk_Plate2_S107]

value: 27 months postnatal


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K27me3_rep1


title: ChIP-seq_LSK_WT_H3K27me3_rep1


title: Input_LSK_WT_rep1


title: ChIP-seq_LSK_Ezh2-KO_H3K27me3_rep2


title: ChIP-seq_LSK_G12D_H3K27ac_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E10_384Bulk_Plate3_S106]

value: MAT


title: ChIP-seq_LSK_WT_H3K27ac_rep2

value: WT


title: ChIP-seq_LSK_Ezh2-KO_H3K27ac_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E11_384Bulk_Plate1_S107]

value: Limb Muscle


title: Tabula Muris Senis (bulk RNA-seq) [E10_384Bulk_Plate2_S106]

value: 21 months postnatal


title: ChIP-seq_LSK_Ezh2-KO_H3K27ac_rep2


title: ChIP-seq_LSK_G12D_H3K27ac_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E1_384Bulk_Plate3_S97]

value: Kidney

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E14_384Bulk_Plate1_S110]

value: 12 months postnatal


title: ChIP-seq_LSK_WT_H3K27ac_rep1


title: Tabula Muris Senis (bulk RNA-seq) [E1_384Bulk_Plate2_S97]

value: GAT


title: ChIP-seq_LSK_Ezh2-KO_H3K4me3_rep2

value: Bone marrow cells


title: Tabula Muris Senis (bulk RNA-seq) [D9_384Bulk_Plate3_S81]

value: BAT


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K4me3_rep1

value: FACS-sorted LSK cells


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K27ac_rep2


title: ChIP-seq_LSK_G12D_Ezh2-KO_H3K4me3_rep2


title: Tabula Muris Senis (bulk RNA-seq) [E1_384Bulk_Plate1_S97]


title: Tabula Muris Senis (bulk RNA-seq) [D9_384Bulk_Plate2_S81]

value: Female


title: ChIP-seq_LSK_G12D_H3K4me3_rep2


title: ChIP-seq_LSK_Ezh2-KO_H3K4me3_rep1


title: Tabula Muris Senis (bulk RNA-seq) [D8_384Bulk_Plate3_S80]

value: Small Intestine


title: Tabula Muris Senis (bulk RNA-seq) [D9_384Bulk_Plate1_S81]

value: 9 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [D8_384Bulk_Plate2_S80]

value: Marrow

value: 18 months postnatal


title: ChIP-seq_LSK_WT_H3K4me3_rep2


title: ChIP-seq_LSK_G12D_H3K4me3_rep1


title: ChIP-seq_LSK_WT_H3K4me3_rep1


title: Tabula Muris Senis (bulk RNA-seq) [D8_384Bulk_Plate1_S80]

value: Heart

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [E10_384Bulk_Plate1_S106]


title: Tabula Muris Senis (bulk RNA-seq) [D7_384Bulk_Plate3_S79]


title: ATAC-seq_LSK_G12D_Ezh2-KO_rep2

data_processing:
ATAC-seq raw reads were aligned to the (GENCODE version M9) genome assembly using Bowtie2 with the default parameters. Only tags that uniquely mapped to the genome were used for further analysis.
Bigwig files were generated by deepTools  bamCoveragewith with the parameters  of "--outFileFormat bigwig -- normalizeTo1x  --ignoreDuplicates --minMappingQuality 30 --extendReads 200"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file

extract_protocol: For ATAC-seq analysis using the Illumina NextSeq500, ~20,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference mouse (mm10) genome were retained for downstream data analysis.


title: ATAC-seq_LSK_G12D_Ezh2-KO_rep3


title: Tabula Muris Senis (bulk RNA-seq) [D6_384Bulk_Plate3_S78]

value: Liver

value: 15 months postnatal


title: ATAC-seq_LSK_Ezh2-KO_rep3


title: ATAC-seq_LSK_G12D_Ezh2-KO_rep1


title: Tabula Muris Senis (bulk RNA-seq) [D6_384Bulk_Plate2_S78]

value: Bone


title: ATAC-seq_LSK_Ezh2-KO_rep1


title: Tabula Muris Senis (bulk RNA-seq) [D6_384Bulk_Plate1_S78]

value: Lung

value: 21 months postnatal


title: ATAC-seq_LSK_G12D_rep4


title: ATAC-seq_LSK_Ezh2-KO_rep2


title: RNA-seq_LSK_G12D_Ezh2-KO_rep4


title: Tabula Muris Senis (bulk RNA-seq) [D5_384Bulk_Plate2_S77]

value: Brain


title: ATAC-seq_LSK_G12D_rep3

value: Bone marrow cells


title: ATAC-seq_LSK_G12D_rep2


title: Tabula Muris Senis (bulk RNA-seq) [D4_384Bulk_Plate3_S76]

value: Spleen

value: 3 months postnatal


title: ATAC-seq_LSK_G12D_rep1

value: FACS-sorted LSK cells


title: ATAC-seq_LSK_WT_rep4

value: WT


title: Tabula Muris Senis (bulk RNA-seq) [D5_384Bulk_Plate1_S77]

value: GAT


title: Tabula Muris Senis (bulk RNA-seq) [D7_384Bulk_Plate2_S79]

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [D7_384Bulk_Plate1_S79]

value: Marrow

value: Female


title: ATAC-seq_LSK_WT_rep3


title: ATAC-seq_LSK_WT_rep2


title: Tabula Muris Senis (bulk RNA-seq) [D3_384Bulk_Plate1_S75]

value: Limb Muscle

value: 12 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D3_384Bulk_Plate2_S75]

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D4_384Bulk_Plate1_S76]

value: Heart

value: 15 months postnatal


title: iXist-ChrX_WT_C7H8_Dox2

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description:
Raw_Ratio_C7H8_chrX.txt
C7H8_Dox_Rep2

data_processing:
Library strategy: ChrRNA-seq
The RNA-seq data mapping pipeline was similar to our previous study (Pintacuda et al., 2017). Briefly, the raw fastq files of read pairs were first mapped to an rRNA build by bowtie2 (v2.3.2) (Langmead and Salzberg, 2012) and rRNA-mapped reads discarded. The remaining unmapped reads were aligned to the ‘N-masked’ genome (from mm10 coordinates) with STAR (v2.4.2a) using parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 4 --alignEndsType EndToEnd” for all the sequencing libraries (Dobin et al., 2013). Unique alignments were retained for further analysis. We made use of 23,005,850 SNPs between Cast and 129S genomes and employed SNPsplit to split the alignment into distinct alleles (Cast and 129S) using the parameter “--paired”. The (allelic) read numbers were counted by the program featureCounts (-t transcript -g gene_id -s 2) (Liao et al., 2014) and the alignments were sorted by Samtools (Li et al., 2009). Bigwig files were generated by Bedtools (Quinlan and Hall, 2010) and visualized by IGV (Robinson et al., 2011) or UCSC Genome Browser. For biallelic analysis, counts were normalized to 1 million mapped read pairs (as CPM) by the edgeR R package. Genes with at least 10 SNP-covering reads across all the samples were further taken to calculate the allelic ratio of where Xi and Xa indicate inactive and active allele, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files report allelic ratio between Xi and (Xi+Xa)

growth_protocol: ES cells were grown in DMEM media supplemented with 10% fetal calf serum (Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 µM β-mercaptoethanol, 1X penicillin / streptomycin (all from Life Technologies) and 1000 U/mL LIF (made in-house). Mitomycin-inactivated mouse fibroblasts were used as feeders. All ES cells were grown in feeder-dependent conditions on gelatinised plates at 37°C with 5% CO2. Inducible Xist expression was driven by a TetOn promoter induced by addition of 1.0 to 1.5 µg/mL of doxycycline for 24 hours.

extract_protocol:
Chromatin RNA was extracted from one confluent 15 cm dish of mESCs. Briefly, cells were trypsinised and washed in PBS. Cells were lysed on ice in RLB (10 mM Tris pH 7.5, 10 mM KCl, 1.5 mM MgCl2, and 0.1% NP40), and nuclei were purified by centrifugation through a sucrose cushion (24% sucrose in RLB). The nuclei pellet was resuspended in NUN1 (20 mM Tris pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol), then lysed with NUN2 (20 mM Hepes pH 7.9, 300 mM, 7.5 mM MgCl2, 0.2 mM EDTA, 1 M Urea). Samples were incubated for 15 minutes on ice then centrifuged at 2800 g to isolate the insoluble chromatin fraction. The chromatin pellet was resuspended in TRIzol by passing multiple times through a 23 gauge needle. Finally chromatin-associated RNA was purified through standard TRIzol/chloroform extraction followed by isopropanol precipitation. Samples were then treated with Turbo DNAse, and 500ng – 1µg of RNA was used for library preparation using the Illumina TruSeq stranded total RNA kit. Libraries were quantified by qPCR with KAPA Library Quantification DNA standards (KAPA Biosystems). The libraries were pooled and 2X 81 paired end sequencing was performed using Illumina NextSeq 500.
TruSeq RNAseq

treatment_protocol: Dox treatment

value: 129S X Cast

tag: gender

tag: cell line

value: Endogenous Xist promoter was replaced with TetOn Promoter (Cast allele, reciprocal line to iXist_ChrX_WT_129S allele)

value: mESC

tag: agent

value: Dox

tag: time course

tag: medium

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [D3_384Bulk_Plate3_S75]

value: 27 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D4_384Bulk_Plate2_S76]

value: Bone

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D23_384Bulk_Plate2_S95]

value: SCAT


title: ATAC-seq_LSK_WT_rep1

value: WT

value: Bone marrow cells

value: FACS-sorted LSK cells


title: iXist-ChrX_WT_C7H8_Dox1

description:
Raw_Ratio_C7H8_chrX.txt
C7H8_Dox_Rep1

value: Female


title: iXist-ChrX_WT_C7H8_NoDox2

description:
Raw_Ratio_C7H8_chrX.txt
C7H8_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [D22_384Bulk_Plate2_S94]

value: Limb Muscle

value: 12 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [D23_384Bulk_Plate1_S95]


title: iXist-ChrX_WT_C7H8_NoDox1

description:
Raw_Ratio_C7H8_chrX.txt
C7H8_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [D22_384Bulk_Plate1_S94]

value: Skin

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D21_384Bulk_Plate2_S93]

value: 24 months postnatal


title: iXist-ChrX_XistDelPID_diff_6day_NoDox3

description:
Ratio_chrX_B2_day6.txt
DelB_NoDox_Diff_6d_Rep3

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: mESC

value: Diff medium


title: Tabula Muris Senis (bulk RNA-seq) [D5_384Bulk_Plate3_S77]


title: iXist-ChrX_XistDelPID_diff_6day_Dox3

description:
Ratio_chrX_B2_day6.txt
DelB_Dox_Diff_6d_Rep3

value: Dox


title: iXist-ChrX_XistDelPID_diff_6day_Dox1

description:
Ratio_chrX_B2_day6.txt
DelBDox_Diff_6d


title: Tabula Muris Senis (bulk RNA-seq) [D20_384Bulk_Plate2_S92]

value: Bone


title: iXist-ChrX_XistDelPID_diff_6day_NoDox2

description:
Ratio_chrX_B2_day6.txt
DelB_NoDox_Diff_6d_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [D20_384Bulk_Plate1_S92]

value: WBC


title: iXist-ChrX_XistDelPID_diff_6day_NoDox1

description:
Ratio_chrX_B2_day6.txt
DelB_Diff_6d


title: Tabula Muris Senis (bulk RNA-seq) [D2_384Bulk_Plate2_S74]


title: Tabula Muris Senis (bulk RNA-seq) [D2_384Bulk_Plate3_S74]

value: 3 months postnatal


title: iXist-ChrX_XistDelPID_diff_6day_Dox2

description:
Ratio_chrX_B2_day6.txt
DelB_Dox_Diff_6d_Rep2


title: iXist-ChrX_XistDelA_diff_6day_Dox3

description:
Ratio_chrX_B2_day6.txt
DelA_Dox_Diff_6d_Rep3


title: Tabula Muris Senis (bulk RNA-seq) [D19_384Bulk_Plate2_S91]

value: GAT


title: Tabula Muris Senis (bulk RNA-seq) [D2_384Bulk_Plate1_S74]

value: 21 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D19_384Bulk_Plate1_S91]

value: Kidney


title: Tabula Muris Senis (bulk RNA-seq) [D18_384Bulk_Plate2_S90]

value: MAT

value: 6 months postnatal

value: Female


title: iXist-ChrX_XistDelA_diff_6day_NoDox3

description:
Ratio_chrX_B2_day6.txt
DelA_NoDox_Diff_6d_Rep3


title: iXist-ChrX_XistDelA_diff_6day_NoDox2

description:
Ratio_chrX_B2_day6.txt
DelA_NoDox_Diff_6d_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [D18_384Bulk_Plate1_S90]

value: BAT

value: 18 months postnatal

value: Male


title: iXist-ChrX_XistDelA_diff_6day_NoDox1

description:
Ratio_chrX_B2_day6.txt
DelA_Diff_6d

value: 129S X Cast


title: iXist-ChrX_WT_diff_6day_Dox3

description:
Ratio_chrX_B2_day6.txt
WT_Dox_Diff_6d_Rep3

source_name: iXist-ChrX(mESC)

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: Tabula Muris Senis (bulk RNA-seq) [D17_384Bulk_Plate1_S89]


title: Tabula Muris Senis (bulk RNA-seq) [D16_384Bulk_Plate2_S88]

value: Lung

value: 9 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D16_384Bulk_Plate1_S88]


title: iXist-ChrX_WT_diff_6day_Dox2

description:
Ratio_chrX_B2_day6.txt
WT_Dox_Diff_6d_Rep2

value: mESC

value: Dox

value: Diff medium


title: iXist-ChrX_WT_diff_6day_NoDox3

description:
Ratio_chrX_B2_day6.txt
WT_NoDox_Diff_6d_Rep3


title: Tabula Muris Senis (bulk RNA-seq) [D17_384Bulk_Plate2_S89]

value: Heart


title: Tabula Muris Senis (bulk RNA-seq) [D15_384Bulk_Plate1_S87]

value: Pancreas

value: 15 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D14_384Bulk_Plate3_S86]

value: missing


title: iXist-ChrX_XistDelA_diff_6day_Dox2

description:
Ratio_chrX_B2_day6.txt
DelA_Dox_Diff_6d_Rep2


title: iXist-ChrX_WT_diff_6day_NoDox2

description:
Ratio_chrX_B2_day6.txt
WT_NoDox_Diff_6d_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [D15_384Bulk_Plate2_S87]

value: Marrow

value: 1 months postnatal


title: iXist-ChrX_WT_diff_6day_NoDox1

description:
Ratio_chrX_B2_day6.txt
WT_Diff_6d

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [D14_384Bulk_Plate2_S86]

value: MAT


title: iXist-ChrX_iXistDelPID_6day

description:
Ratio_chrX_B2_day6.txt
DelB_Undiff_6d

value: ES medium


title: iXist-ChrX_iXistDelPID_Dox_6day

description:
Ratio_chrX_B2_day6.txt
DelBDox_Undiff_6d


title: Tabula Muris Senis (bulk RNA-seq) [D13_384Bulk_Plate3_S85]

value: GAT

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [D14_384Bulk_Plate1_S86]


title: iXist-ChrX_XistDelA_diff_6day_Dox1

description:
Ratio_chrX_B2_day6.txt
DelADox_Diff_6d

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: iXist-ChrX_WT_diff_6day_Dox1

description:
Ratio_chrX_B2_day6.txt
WTDox_Diff_6d


title: iXist-ChrX_iXistDelA_6day

description:
Ratio_chrX_B2_day6.txt
DelA_Undiff_6d


title: Tabula Muris Senis (bulk RNA-seq) [D13_384Bulk_Plate2_S85]

value: WBC

value: 21 months postnatal


title: iXist-ChrX_WT_Dox_6day

description:
Ratio_chrX_B2_day6.txt
WTDox_Undiff_6d

value: mESC

value: Dox


title: iXist-ChrX_iXistDelA_Dox_6day

description:
Ratio_chrX_B2_day6.txt
DelADox_Undiff_6d


title: Tabula Muris Senis (bulk RNA-seq) [D13_384Bulk_Plate1_S85]

value: Heart

value: 12 months postnatal


title: iXist-ChrX_WT_6day

description:
Ratio_chrX_B2_day6.txt
WT_Undiff_6d


title: iXist-ChrX_Rbm15KO#A8_Dox3

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_Dox3


title: Tabula Muris Senis (bulk RNA-seq) [D12_384Bulk_Plate2_S84]

value: SCAT

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D12_384Bulk_Plate1_S84]

value: Liver

value: 27 months postnatal


title: iXist-ChrX_Rbm15KO#A8_Dox2

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_Dox2

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [D11_384Bulk_Plate2_S83]

value: Small Intestine


title: Tabula Muris Senis (bulk RNA-seq) [D11_384Bulk_Plate1_S83]

value: Marrow

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [D10_384Bulk_Plate3_S82]

value: Skin

value: Male


title: iXist-ChrX_Rbm15KO#A8_Dox4

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_Dox4

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [D10_384Bulk_Plate2_S82]

value: Limb Muscle


title: Tabula Muris Senis (bulk RNA-seq) [D10_384Bulk_Plate1_S82]

value: 15 months postnatal


title: iXist-ChrX_Rbm15KO#A8_NoDox3

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_NoDox3

value: mESC

value: Dox


title: iXist-ChrX_Rbm15KO#A8_NoDox1

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_NoDox1


title: Tabula Muris Senis (bulk RNA-seq) [D1_384Bulk_Plate3_S73]

value: GAT


title: Tabula Muris Senis (bulk RNA-seq) [D1_384Bulk_Plate2_S73]

value: Lung

value: 21 months postnatal


title: iXist-ChrX_Rbm15KO#E10_Dox2

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_DoxB


title: iXist-ChrX_Rbm15KO#A8_NoDox2

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_NoDox2


title: iXist-ChrX_Rbm15KO#E10_NoDox3

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_NoDox3


title: iXist-ChrX_Rbm15KO#E10_NoDox1

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_NoDox1


title: Tabula Muris Senis (bulk RNA-seq) [D1_384Bulk_Plate1_S73]

value: 18 months postnatal


title: iXist-ChrX_WtapKO#C6_Dox2

description:
Raw_Ratio_chrX.xlsx
WtapKO_C6_Dox2

value: Female


title: iXist-ChrX_Rbm15KO#A8_Dox1

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_A8_Dox1


title: iXist-ChrX_Rbm15KO#E10_Dox1

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_DoxA


title: Tabula Muris Senis (bulk RNA-seq) [C9_384Bulk_Plate1_S57]

value: SCAT

value: 12 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C8_384Bulk_Plate3_S56]

value: Spleen


title: Tabula Muris Senis (bulk RNA-seq) [D11_384Bulk_Plate3_S83]

value: Small Intestine

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C9_384Bulk_Plate3_S57]

value: Liver


title: iXist-ChrX_Rbm15KO#E10_NoDox2

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_NoDox2

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: iXist-ChrX_WtapKO#C6_Dox1

description:
Raw_Ratio_chrX.xlsx
WtapKO_C6_Dox1

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [C8_384Bulk_Plate2_S56]

value: Bone

value: Male


title: iXist-ChrX_WtapKO#C6_NoDox

description:
Raw_Ratio_chrX.xlsx
WtapKO_C6_NoDox

value: mESC

value: Dox


title: iXist-ChrX_WtapKO#C4_Dox2

description:
Raw_Ratio_chrX.xlsx
WtapKO_C4_Dox2


title: Tabula Muris Senis (bulk RNA-seq) [D12_384Bulk_Plate3_S84]

value: Heart

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C9_384Bulk_Plate2_S57]


title: iXist-ChrX_WtapKO#C4_Dox1

description:
Raw_Ratio_chrX.xlsx
WtapKO_C4_Dox1


title: iXist-ChrX_Rbm15KO#E10_Dox3

description:
Raw_Ratio_chrX.xlsx
Rbm15KO_E10_Dox


title: Tabula Muris Senis (bulk RNA-seq) [C8_384Bulk_Plate1_S56]

value: Marrow

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C7_384Bulk_Plate3_S55]

value: Skin


title: iXist-ChrX_WtapKO#C4_NoDox

description:
Raw_Ratio_chrX.xlsx
WtapKO_C4_NoDox

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [C7_384Bulk_Plate2_S55]

value: Brain


title: Tabula Muris Senis (bulk RNA-seq) [C6_384Bulk_Plate3_S54]


title: Tabula Muris Senis (bulk RNA-seq) [C6_384Bulk_Plate2_S54]

value: Kidney

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C6_384Bulk_Plate1_S54]

value: GAT

value: 21 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C5_384Bulk_Plate2_S53]

value: Liver

value: 27 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C5_384Bulk_Plate1_S53]


title: iXist-ChrX_SpenKO#C4_Dox

description:
Raw_Ratio_chrX.xlsx
SpC4_Dox

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [C4_384Bulk_Plate3_S52]

value: Limb Muscle

value: 12 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [C5_384Bulk_Plate3_S53]

value: WBC


title: iXist-ChrX_SpenKO#C4_NoDox

description:
Raw_Ratio_chrX.xlsx
SpC4_NoDox

value: mESC

value: Dox


title: Tabula Muris Senis (bulk RNA-seq) [C3_384Bulk_Plate2_S51]

value: 18 months postnatal

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [C3_384Bulk_Plate3_S51]

value: BAT


title: Tabula Muris Senis (bulk RNA-seq) [C4_384Bulk_Plate1_S52]

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C7_384Bulk_Plate1_S55]

value: Spleen


title: Tabula Muris Senis (bulk RNA-seq) [C23_384Bulk_Plate2_S71]


title: Tabula Muris Senis (bulk RNA-seq) [C23_384Bulk_Plate1_S71]

value: 9 months postnatal


title: iXist-ChrX_XistDelLBS#1C7_NoDox

description:
Raw_Ratio_chrX.xlsx
DelLBS_1C7_NoDox


title: iXist-ChrX_SpenKO#C3_Dox

description:
Raw_Ratio_chrX.xlsx
SpC3_Dox


title: iXist-ChrX_XistDelLBS#1G1_NoDox

description:
Raw_Ratio_chrX.xlsx
DelLBS_1G1_NoDox


title: iXist-ChrX_XistDelLBS#1G1_Dox

description:
Raw_Ratio_chrX.xlsx
DelLBS_1G1_Dox


title: Tabula Muris Senis (bulk RNA-seq) [C22_384Bulk_Plate2_S70]


title: iXist-ChrX_SpenKO#D4_Dox

description:
Raw_Ratio_chrX.xlsx
SpD4_Dox


title: iXist-ChrX_SpenKO#C3_NoDox

description:
Raw_Ratio_chrX.xlsx
SpC3_NoDox


title: iXist-ChrX_LbrKO#LE11_Dox

description:
Raw_Ratio_chrX.xlsx
LE11_Dox


title: iXist-ChrX_XistDelLBS#1C7_Dox

description:
Raw_Ratio_chrX.xlsx
DelLBS_1C7_Dox


title: iXist-ChrX_LbrKO#LH4_NoDox

description:
Raw_Ratio_chrX.xlsx
LH4_NoDox


title: iXist-ChrX_XistDelm6A/11G_Dox2

description:
Raw_Ratio_chrX.xlsx
Deltam6A_11G_24hrDox_Rep2


title: iXist-ChrX_SpenKO#D4_NoDox

description:
Raw_Ratio_chrX.xlsx
SpD4_NoDox


title: iXist-ChrX_LbrKO#LE11_NoDox

description:
Raw_Ratio_chrX.xlsx
LE11_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [C3_384Bulk_Plate1_S51]

value: Lung


title: iXist-ChrX_XistDelm6A/11G_NoDox1

description:
Raw_Ratio_chrX.xlsx
Deltam6A_11G_NoDox_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [C21_384Bulk_Plate2_S69]

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

value: SCAT

value: 1 months postnatal


title: iXist-ChrX_XistDelm6A/11G_Dox1

description:
Raw_Ratio_chrX.xlsx
Deltam6A_11G_NoDox_Rep2

value: 129S X Cast

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: Tabula Muris Senis (bulk RNA-seq) [C4_384Bulk_Plate2_S52]


title: Tabula Muris Senis (bulk RNA-seq) [C21_384Bulk_Plate1_S69]

value: Small Intestine


title: Tabula Muris Senis (bulk RNA-seq) [C20_384Bulk_Plate2_S68]

value: Bone


title: iXist-ChrX_LbrKO#LH4_Dox

description:
Raw_Ratio_chrX.xlsx
LH4_Dox

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [C22_384Bulk_Plate1_S70]

value: WBC

value: Male


title: iXist-ChrX_XistDelm6A/3A_Dox1

description:
Raw_Ratio_chrX.xlsx
Delm6A3A_Dox_ChrRNA_Rep1

value: mESC

value: Dox


title: iXist-ChrX_XistDelm6A/3A_Dox2

description:
Raw_Ratio_chrX.xlsx
Delm6A3A_Dox_ChrRNA_Rep2

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [C20_384Bulk_Plate1_S68]

value: 24 months postnatal


title: iXist-ChrX_XistDelm6A/11G_NoDox2

description:
Raw_Ratio_chrX.xlsx
Deltam6A_11G_24hrDox_Rep1


title: iXist-ChrX_XistDelm6A/3A_NoDox1

description:
Raw_Ratio_chrX.xlsx
Delm6A3A_NoDox_ChrRNA_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [C2_384Bulk_Plate3_S50]

value: 12 months postnatal


title: iXist-ChrX_XistDelPID_Dox2

description:
Raw_Ratio_chrX.xlsx
DeltaBE8_DoxB


title: iXist-ChrX_XistDelPID_Dox1

description:
Raw_Ratio_chrX.xlsx
DeltaBE8_DoxA


title: Tabula Muris Senis (bulk RNA-seq) [C2_384Bulk_Plate1_S50]

value: 15 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C2_384Bulk_Plate2_S50]

value: Limb Muscle

value: 9 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C19_384Bulk_Plate2_S67]

value: Heart

value: 27 months postnatal


title: iXist-ChrX_WT_Dox5(Heather)

description:
Raw_Ratio_chrX.xlsx
WTB2_24hrDox_Rep1

value: 129S X Cast


title: Tabula Muris Senis (bulk RNA-seq) [C17_384Bulk_Plate1_S65]

value: 18 months postnatal


title: iXist-ChrX_XistDelPID_NoDox

description:
Raw_Ratio_chrX.xlsx
DeltaBE8_NoDox

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: iXist-ChrX_XistDelA_Dox2

description:
Raw_Ratio_chrX.xlsx
DeltaA1H12_DoxB


title: Tabula Muris Senis (bulk RNA-seq) [C18_384Bulk_Plate2_S66]

value: Spleen


title: Tabula Muris Senis (bulk RNA-seq) [C19_384Bulk_Plate1_S67]

value: MAT


title: iXist-ChrX_XistDelA_NoDox

description:
Raw_Ratio_chrX.xlsx
DeltaA1H12_NoDox

value: ES medium


title: iXist-ChrX_WT_NoDox_Rep2(Tatyana)

description:
Raw_Ratio_chrX.xlsx
B2_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [C16_384Bulk_Plate1_S64]

value: Kidney

value: Male


title: iXist-ChrX_WT_Dox3(Heather)

description:
Raw_Ratio_chrX.xlsx
WT_Dox_ChrRNA_Rep1

value: mESC

value: Dox


title: iXist-ChrX_WT_NoDox_Rep5(Heather)

description:
Raw_Ratio_chrX.xlsx
WTB2_NoDox_Rep1

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [C15_384Bulk_Plate2_S63]

value: Liver

value: 3 months postnatal


title: iXist-ChrX_WT_Dox4(Heather)

description:
Raw_Ratio_chrX.xlsx
WT_Dox_ChrRNA_Rep2


title: iXist-ChrX_XistDelm6A/3A_NoDox2

description:
Raw_Ratio_chrX.xlsx
Delm6A3A_NoDox_ChrRNA_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [C14_384Bulk_Plate2_S62]

value: GAT


title: Tabula Muris Senis (bulk RNA-seq) [C17_384Bulk_Plate2_S65]

value: Bone

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C16_384Bulk_Plate2_S64]


title: iXist-ChrX_WT_NoDox_Rep4(Heather)

description:
Raw_Ratio_chrX.xlsx
WT_NoDox_ChrRNA_Rep2


title: iXist-ChrX_WT_Dox2

description:
Raw_Ratio_chrX.xlsx
B2_Dox


title: Tabula Muris Senis (bulk RNA-seq) [C13_384Bulk_Plate3_S61]

value: SCAT

value: 27 months postnatal


title: iXist-ChrX_WT_Dox1.1

description:
Raw_Ratio_chrX.xlsx
WT_DoxA

value: 129S X Cast


title: iXist-ChrX_WT_NoDox_Rep1(Greta)

description:
Raw_Ratio_chrX.xlsx
WT_NoDox

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)


title: Tabula Muris Senis (bulk RNA-seq) [C14_384Bulk_Plate1_S62]

value: 18 months postnatal


title: iXist-ChrX_WT_Dox1.2

description:
Raw_Ratio_chrX.xlsx
WT_DoxB


title: Tabula Muris Senis (bulk RNA-seq) [C18_384Bulk_Plate1_S66]

value: WBC

value: 9 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C15_384Bulk_Plate1_S63]

value: Limb Muscle

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C14_384Bulk_Plate3_S62]

value: 15 months postnatal

value: Male


title: iXist-ChrX_WT_NoDox_Rep3(Heather)

description:
Raw_Ratio_chrX.xlsx
WT_NoDox_ChrRNA_Rep1

value: Female

value: mESC

value: Dox

value: ES medium


title: iXist-Chr3_LbrKO#4F9F_3day_diff_Dox

description:
LBR_Ratio_chr3_72h.txt
X9F_Dox

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: Diff medium


title: Tabula Muris Senis (bulk RNA-seq) [C13_384Bulk_Plate2_S61]

value: Bone

value: 12 months postnatal


title: iXist-Chr3_LbrKO#4F9F_3day_diff_NoDox

description:
LBR_Ratio_chr3_72h.txt
X9F_NoDox

value: 129S X Cast


title: Tabula Muris Senis (bulk RNA-seq) [C13_384Bulk_Plate1_S61]


title: Tabula Muris Senis (bulk RNA-seq) [C12_384Bulk_Plate3_S60]


title: Tabula Muris Senis (bulk RNA-seq) [C12_384Bulk_Plate1_S60]

value: MAT


title: iXist-Chr3_LbrKO#4C7A_3day_diff_NoDox

description:
LBR_Ratio_chr3_72h.txt
X7A_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [C12_384Bulk_Plate2_S60]

value: 21 months postnatal


title: iXist-Chr3_LbrKO#4C7A_3day_diff_Dox

description:
LBR_Ratio_chr3_72h.txt
X7A_Dox


title: Tabula Muris Senis (bulk RNA-seq) [C11_384Bulk_Plate2_S59]

value: Liver

value: 18 months postnatal


title: iXist-Chr3_LbrKO#4C8E_3day_diff_NoDox

description:
LBR_Ratio_chr3_72h.txt
X8E_NoDox


title: iXist-Chr3_WT_3day_diff_mRNA_Dox

description:
LBR_Ratio_chr3_72h.txt
WT_BB_Dox


title: iXist-Chr3_Suz12KO_Dox_3day_diff_Rep3

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_Dox3


title: iXist-Chr3_LbrKO#4C8E_3day_diff_Dox

description:
LBR_Ratio_chr3_72h.txt
X8E_Dox


title: Tabula Muris Senis (bulk RNA-seq) [C11_384Bulk_Plate1_S59]

value: WBC

value: 9 months postnatal


title: iXist-Chr3_Suz12KO_NoDox_3day_diff_Rep3

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_NoDox3


title: Tabula Muris Senis (bulk RNA-seq) [C10_384Bulk_Plate1_S58]

value: SCAT


title: iXist-Chr3_Suz12KO_Dox_3day_diff_Rep1

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_Dox1

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [C1_384Bulk_Plate3_S49]

value: Heart


title: iXist-Chr3_WT_3day_diff_mRNA_NoDox

description:
LBR_Ratio_chr3_72h.txt
WT_BB_NoDox

value: mESC


title: Tabula Muris Senis (bulk RNA-seq) [C10_384Bulk_Plate2_S58]

value: Lung

value: 24 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C1_384Bulk_Plate2_S49]

value: 27 months postnatal


title: iXist-Chr3_Suz12KO_NoDox_3day_diff_Rep2

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_NoDox2

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: Dox

value: Diff medium


title: iXist-Chr3_Suz12KO_Dox_3day_diff_Rep2

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_Dox2

value: 129S X Cast


title: Tabula Muris Senis (bulk RNA-seq) [C1_384Bulk_Plate1_S49]

value: GAT

value: 12 months postnatal

value: Female


title: iXist-Chr3_Suz12KO_NoDox_3day_diff_Rep1

description:
Ratio_chr3_WT_Suz12KO_3day.txt
Suz12KO_MA_NoDox1


title: Tabula Muris Senis (bulk RNA-seq) [B9_384Bulk_Plate3_S33]

value: Kidney

value: 21 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [C11_384Bulk_Plate3_S59]

value: 1 months postnatal


title: iXist-Chr3_WT_Dox_3day_diff_Rep2

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_Dox2


title: Tabula Muris Senis (bulk RNA-seq) [B9_384Bulk_Plate1_S33]

value: Small Intestine


title: Tabula Muris Senis (bulk RNA-seq) [C10_384Bulk_Plate3_S58]

value: 6 months postnatal

value: Male


title: iXist-Chr3_WT_Dox_3day_diff_Rep1

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_Dox1

value: mESC


title: iXist-ChrX_XistDelA_Dox1

description:
Raw_Ratio_chrX.xlsx
DeltaA1H12_DoxA

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [B7_384Bulk_Plate3_S31]

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

value: Lung


title: Tabula Muris Senis (bulk RNA-seq) [B8_384Bulk_Plate2_S32]

value: Liver


title: iXist-Chr3_WT_NoDox_3day_diff_Rep1

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_NoDox1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: Dox


title: iXist-Chr3_WT_NoDox_3day_diff_Rep2

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_NoDox2

value: 129S X Cast

value: Diff medium


title: Tabula Muris Senis (bulk RNA-seq) [B8_384Bulk_Plate3_S32]

value: SCAT

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B6_384Bulk_Plate3_S30]

value: 12 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B7_384Bulk_Plate1_S31]

value: 9 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B7_384Bulk_Plate2_S31]

value: Spleen

value: 1 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B6_384Bulk_Plate1_S30]

value: Kidney

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [B5_384Bulk_Plate3_S29]

value: BAT


title: iXist-Chr3_LbrKO#4F9F_NoDox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4F9F_NoDox

value: Male

value: mESC


title: iXist-Chr3_LbrKO#4C8E_Dox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4C8E_Dox

value: ES medium


title: iXist-Chr3_LbrKO#4C7A_Dox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4C7A_Dox


title: iXist-Chr3_WT_NoDox_3day_diff_Rep3

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_NoDox3


title: Tabula Muris Senis (bulk RNA-seq) [B5_384Bulk_Plate2_S29]

value: Lung


title: iXist-Chr3_LbrKO#4C7A_NoDox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4C7A_NoDox

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: iXist-Chr3_Suz12KO_Dox2

description:
Raw_Ratio_chr3.xlsx
Suz12KO_DoxB

value: Dox


title: Tabula Muris Senis (bulk RNA-seq) [B5_384Bulk_Plate1_S29]

value: GAT


title: iXist-Chr3_LbrKO#4C8E_NoDox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4C8E_NoDox

value: 129S X Cast


title: iXist-Chr3_WT_Dox_3day_diff_Rep3

description:
Ratio_chr3_WT_Suz12KO_3day.txt
WT_MA_Dox3

value: Diff medium


title: Tabula Muris Senis (bulk RNA-seq) [B9_384Bulk_Plate2_S33]


title: iXist-Chr3_Suz12KO_Dox1

description:
Raw_Ratio_chr3.xlsx
Suz12KO_DoxA


title: Tabula Muris Senis (bulk RNA-seq) [B4_384Bulk_Plate3_S28]

value: MAT


title: Tabula Muris Senis (bulk RNA-seq) [B8_384Bulk_Plate1_S32]

value: Marrow

value: 27 months postnatal


title: iXist-Chr3_LbrKO#4F9F_Dox

description:
Raw_Ratio_chr3.xlsx
LBRKO_4F9F_Dox


title: iXist-Chr3_TIR_Pcgf3/5DKO#C10_Dox2

description:
Raw_Ratio_chr3.xlsx
C10mut_DoxB

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + Tir


title: Tabula Muris Senis (bulk RNA-seq) [B3_384Bulk_Plate3_S27]

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B3_384Bulk_Plate1_S27]

value: Heart

value: 21 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B3_384Bulk_Plate2_S27]

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B4_384Bulk_Plate1_S28]

value: Kidney

value: 15 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [B23_384Bulk_Plate2_S47]

value: 1 months postnatal

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [B22_384Bulk_Plate1_S46]

value: 6 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B23_384Bulk_Plate1_S47]

value: SCAT

value: 24 months postnatal


title: iXist-Chr3_TIR_Pcgf3/5DKO#C10_NoDox

description:
Raw_Ratio_chr3.xlsx
C10mut_NoDox

value: 129S X Cast

value: mESC

value: Dox

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [B22_384Bulk_Plate2_S46]


title: iXist-Chr3_TIR_Pcgf3/5DKO#B7_Dox2

description:
Raw_Ratio_chr3.xlsx
B7mut_DoxB

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + Tir


title: Tabula Muris Senis (bulk RNA-seq) [B21_384Bulk_Plate2_S45]

value: MAT


title: iXist-Chr3_TIR_Pcgf3/5DKO#B7_Dox1

description:
Raw_Ratio_chr3.xlsx
B7mut_DoxA


title: iXist-Chr3_TIR_Pcgf3/5DKO#B7_NoDox

description:
Raw_Ratio_chr3.xlsx
B7mut_NoDox


title: iXist-Chr3_TIR_Dox1

description:
Raw_Ratio_chr3.xlsx
WT_TIR_DoxA


title: iXist-Chr3_TIR_NoDox

description:
Raw_Ratio_chr3.xlsx
WT_TIR_NoDox


title: iXist-Chr3_SpenKO#3H6_NoDox

description:
Raw_Ratio_chr3.xlsx
SpenKO_3H6_NoDox

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: iXist-Chr3_TIR_Pcgf3/5DKO#C10_Dox1

description:
Raw_Ratio_chr3.xlsx
C10mut_DoxA


title: Tabula Muris Senis (bulk RNA-seq) [B20_384Bulk_Plate1_S44]

value: Marrow


title: iXist-Chr3_SpenKO#3E5_Dox

description:
Raw_Ratio_chr3.xlsx
SpenKO_3E5_Dox


title: Tabula Muris Senis (bulk RNA-seq) [B21_384Bulk_Plate1_S45]

value: Pancreas

value: 18 months postnatal


title: iXist-Chr3_SpenKO#3H6_Dox

description:
Raw_Ratio_chr3.xlsx
SpenKO_3H6_Dox


title: iXist-Chr3_SpenKO#3E5_NoDox

description:
Raw_Ratio_chr3.xlsx
SpenKO_3E5_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [B2_384Bulk_Plate3_S26]

value: WBC


title: Tabula Muris Senis (bulk RNA-seq) [B2_384Bulk_Plate2_S26]

value: Limb Muscle

value: 9 months postnatal

value: Male


title: iXist-Chr3_SpenKO#2G9_NoDox

description:
Raw_Ratio_chr3.xlsx
SpenKO_2G9_NoDox


title: iXist-Chr3_SpenKO#2G9_Dox

description:
Raw_Ratio_chr3.xlsx
SpenKO_2G9_Dox


title: iXist-Chr3_Suz12KO_NoDox

description:
Raw_Ratio_chr3.xlsx
Suz12KO_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [B2_384Bulk_Plate1_S26]

value: 1 months postnatal

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [B4_384Bulk_Plate2_S28]

value: Skin

value: 27 months postnatal


title: iXist-Chr3_SpenKO#2E5_Dox

description:
Raw_Ratio_chr3.xlsx
SpenKO_2E5_Dox

value: 129S X Cast

value: mESC


title: Tabula Muris Senis (bulk RNA-seq) [B19_384Bulk_Plate2_S43]


title: Tabula Muris Senis (bulk RNA-seq) [B19_384Bulk_Plate1_S43]

value: Brain


title: iXist-Chr3_Mettl3KO_Dox2

description:
Raw_Ratio_chr3.xlsx
Mettl3KO_DoxB

value: Dox

value: ES medium


title: HS1-11 N2 barcode assignment 5p assay

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

description: telencephalon

data_processing:
Library strategy: lentivirus-based massively parallel reporter assay (lentiMPRA)
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed. For assignment of barcodes, insert consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). A minimum of three barcode observation was required for the assignment, further 90% of the barcode observations had to be with the specific insert.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
ChIP-seq peaks were called using the ENCODE pipeline with default parameters (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts. *_design.tsv.gz contain all designed oligo sequences for HAR and HAR-permutation, respectively. HAR5p_assigment.tsv.gz is the barcode-to-insert assignment obtained from sequencing data.

organism: Homo sapiens

source_name: Human neural progenitor cells

growth_protocol:
http://www.pnas.org/content/107/11/5254.short
Human iPSC-derived neural progenitor cells were maintained in N2B27 media supplemented with 20ng/mL bFGF and EGF on matrigel-coated dishes. HepG2 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen). Messenger RNA (mRNA) was purified from the total RNA using Oligotex mRNA mini kit (Qiagen) and treated with Turbo DNase to remove contaminating DNA.
mRNA was reverse transcribed with SuperScript II (Invitrogen) using a primer downstream from the barcode. Resulting cDNA was split into multiple reactions to reduce PCR jack-potting effects and cDNA amplification performed with Kapa Robust polymerase for three cycles, incorporating unique molecular identifiers (UMIs) of 10 bp length. PCR products were cleaned with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification in 8 reactions per replicate for 15 cycles, with a reverse primer containing only P7. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA, each replicate was amplified for 3 cycles with UMI-incorporating primers, just as the RNA. First round products were cleaned up with AMPure XP beads, and amplified in split reactions, each for 20 cycles. Again, reactions were pooled and gel-purified and sequenced.

treatment_protocol: For the lentiMPRA, 6 million human iPSC-derived neural progenitor cells were plated on a 15 cm dish and cultured for 24 hours. The cells were infected with integrating lentivirus libraries and incubated for 4 days, when they have an estimated 50-100 viral particles/cell. Three independent replicate cultures were infected.

value: neural progenitors

tag: developmental stage


title: Tabula Muris Senis (bulk RNA-seq) [B20_384Bulk_Plate2_S44]

value: Heart


title: Tabula Muris Senis (bulk RNA-seq) [B18_384Bulk_Plate2_S42]

value: BAT


title: iXist-Chr3_Mettl3KO_NoDox

description:
Raw_Ratio_chr3.xlsx
Mettl3KO_NoDox

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: iXist-Chr3_Rbm15KO_Dox2

description:
Raw_Ratio_chr3.xlsx
Rbm15KO_DoxB


title: iXist-Chr3_Mettl3KO_Dox1

description:
Raw_Ratio_chr3.xlsx
Mettl3KO_DoxA


title: iXist-Chr3_Rbm15KO_NoDox

description:
Raw_Ratio_chr3.xlsx
Rbm15KO_NoDox


title: iXist-Chr3_Rbm15KO_Dox1

description:
Raw_Ratio_chr3.xlsx
Rbm15KO_DoxA


title: iXist-Chr3_WtapKO_Dox2

description:
Raw_Ratio_chr3.xlsx
WtapKO_DoxB


title: Tabula Muris Senis (bulk RNA-seq) [B17_384Bulk_Plate2_S41]

value: Kidney


title: Tabula Muris Senis (bulk RNA-seq) [B17_384Bulk_Plate1_S41]

value: MAT

value: 6 months postnatal


title: iXist-Chr3_WT_Dox4

description:
Raw_Ratio_chr3.xlsx
WT_TN_Dox

value: Male


title: iXist-Chr3_WT_NoDox_Rep3(Tatyana)

description:
Raw_Ratio_chr3.xlsx
WT_TN_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [B16_384Bulk_Plate2_S40]

value: GAT

value: 12 months postnatal


title: iXist-Chr3_WT_Dox3

description:
Raw_Ratio_chr3.xlsx
WT_QP_Dox


title: iXist-Chr3_SpenKO#2E5_NoDox

description:
Raw_Ratio_chr3.xlsx
SpenKO_2E5_NoDox


title: iXist-Chr3_WtapKO_Dox1

description:
Raw_Ratio_chr3.xlsx
WtapKO_DoxA


title: Tabula Muris Senis (bulk RNA-seq) [B16_384Bulk_Plate1_S40]

value: Spleen


title: iXist-Chr3_WtapKO_NoDox

description:
Raw_Ratio_chr3.xlsx
WtapKO_NoDox


title: iXist-Chr3_WT_NoDox_Rep2(Qi)

description:
Raw_Ratio_chr3.xlsx
WT_QP_NoDox


title: Tabula Muris Senis (bulk RNA-seq) [B18_384Bulk_Plate1_S42]

value: SCAT

value: 3 months postnatal

value: Female


title: iXist-Chr3_WT_NoDox_Rep1(Heather)

description:
Raw_Ratio_chr3.xlsx
WT_HC_NoDox

value: 129S X Cast

value: mESC


title: Tabula Muris Senis (bulk RNA-seq) [B15_384Bulk_Plate1_S39]

value: Limb Muscle


title: XistDelPID_Dox_Input_Rep1

data_processing:
The raw fastq read pairs were mapped onto “N-masked” genome mm10 by STAR (v2.4.2a) (Dobin et al., 2013), as same parameters as RNA-seq data, except “--alignIntronMax 10”. For the calibrated ChIP-seq with Drosophila SG4 cells, the reads were mapped to the “N-masked” genome concatenated with dm6 sequence. Allelic split of mm10 mapped reads was conducted by SNPsplit as same as RNA-seq. We normalized the mouse mapped reads to spiked-in Drosophila library size, and then scaled down to 10 million mapped, (all the parameters and normalization intermediates can be found in Supplementary Table), resulting in bedGraph files for normalized signal by Bedtools (Quinlan and Hall, 2010). Meanwhile, we calculated the gain of H3K27me3 and H2AK119ub upon Xist induction, [Dox(Xi - Xa) – NoDox(Xi - Xa)], for visualization. The custom scripts were used for exacting the value from certain region and averaged for metagene profle by DANPOS (Chen et al., 2013) with default parameters but “--bin_size 50 --excludeP 0.005”. The data sorted in bedGraph files can be extracted by our custom scripts (ExtractInfoFrombedGraph_AtBed.py) for different size of region, then calculate the FPKM to represent the corresponding region for comparison.
Genome_build: mm10, dm6
Supplementary_files_format_and_content: bigwig

growth_protocol: ES cells were grown in ES cell medium, which consisted of Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 9% foetal calf serum (FCS, from Seralab), 2mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50g/mL penicillin/streptomycin (all from Invitrogen) and LIF- conditioned medium, made in house, at a concentration equivalent to 1000U/mL. Cells were grown at 37ºC in a humid atmosphere with 5% CO2. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO.

extract_protocol:
For calibrated native ChIP (H3K27me3 and H2AK119ub), 40 million ES cells and 10 million Drosophila SG4 Cells were pooled and lysed in RSB (10 mM Tris pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) for 5 min on ice with gentle inversion. Nuclei were resuspended in 1 ml of RSB + 0.25 M sucrose + 3mM CaCl2, treated with 200U of MNase (Fermentas) for 5 minutes at 37ºC, quenched with 4 µl of 1M EDTA, then centrifuged at 5000 rpm for 5 minutes. The supernatant was transferred to a fresh tube as fraction S1. The chromatin pellet was incubated for 1 h in 300 µl of nucleosome release buffer (10 mM Tris pH 7.5, 10 mM NaCl, 0.2 mM EDTA), carefully passed 5 times through a 27G needle then centrifuged at 5000 rpm for 5 minutes. The supernatant from this S2 fraction was combined with S1. For each ChIP reaction, 80 µl of chromatin was diluted in Native ChIP incubation buffer (10 mM Tris pH 7.5, 70 mM NaCl, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton) to 1 ml and incubated with antibody overnight at 4ºC. Samples were incubated with 50 µl protein A agarose beads preblocked in Native ChIP incubation buffer with 1 mg/ml BSA and 1 mg/ml yeast tRNA, then washed for a total of 4 times in Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton) and once in TE. The DNA was eluted with 1% SDS and 100 mM NaHCO3, and was purified using ChIP DNA Clean and Concentrator kit (Zymo).
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium for 24 hours.

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

tag: spiked-in

value: Drosophila

value: Dox

tag: time

tag: antibody


title: Tabula Muris Senis (bulk RNA-seq) [B14_384Bulk_Plate3_S38]

tag: strain/background

tag: tissue

value: missing


title: XistDelPID_NoDox_Input_Rep1


title: XistDelPID_NoDox_Input_Rep2


title: iXist-Chr3_WT_Dox1

description:
Raw_Ratio_chr3.xlsx
WT_HC_DoxA

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [B14_384Bulk_Plate2_S38]

tag: age

value: 6 months postnatal

tag: Sex


title: WT(iXist-ChrX)_Dox_Input_Rep1

tag: strain background


title: Tabula Muris Senis (bulk RNA-seq) [B14_384Bulk_Plate1_S38]

value: Kidney

value: 21 months postnatal

value: Male


title: WT(iXist-ChrX)_NoDox_Input_Rep1

tag: cell type


title: WT(iXist-ChrX)_Dox_Input_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [B15_384Bulk_Plate2_S39]

value: Marrow

value: 24 months postnatal


title: iXist-Chr3_WT_Dox2

description:
Raw_Ratio_chr3.xlsx
WT_HC_DoxB


title: WT(iXist-ChrX)_NoDox_Input_Rep2


title: ILC [L58]

type: RNA

city: Brisbane

first: Peter

middle: T

last: Simpson

email: p.simpson@uq.edu.au, amy.reed@uq.edu.au

address: 71/918 RBWH Herston

department: Molecular & Cellular Pathology

country: Australia

institute: UQCCR

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma and batch effects were removed with combat in R

label: biotin

source_name: ABCTB

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: invasive lobular carcinoma

tag: tumour grade

tag: patient survival status

value: Alive


title: ILC [L23]


title: ILC [L34]


title: ILC [L38]


title: XistDelPID_Dox_Input_Rep2

value: 129S X Cast

tag: gender

value: Female


title: ILC [L16]


title: ILC [L25]


title: ILC [L20]


title: ILC [L30]


title: XistDelPID_Dox_H2AK119ub_Rep1

description: DelB-E8_uH2A_Dox-NoDox_20180728.chrX1.Norm.bw

tag: cell line

value: mESC

value: H2AK119ub (CST #8240S, rabbit mAb D27C4)


title: XistDelPID_Dox_H2AK119ub_Rep2

description: DelB-E8_uH2A_Dox-NoDox_20180630.chrX1.Norm.bw

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: Drosophila

tag: agent


title: XistDelPID_NoDox_H2AK119ub_Rep1

value: Dox


title: ILC [L55]


title: XistDelPID_NoDox_H2AK119ub_Rep2


title: ILC [L46]


title: ILC [L48]


title: Tabula Muris Senis (bulk RNA-seq) [B13_384Bulk_Plate3_S37]

value: Pancreas


title: WT(iXist-ChrX)_Dox_H2AK119ub_Rep1

description: WT_uH2A_Dox-NoDox_20180728.chrX1.Norm.bw


title: Tabula Muris Senis (bulk RNA-seq) [B13_384Bulk_Plate2_S37]


title: Tabula Muris Senis (bulk RNA-seq) [B12_384Bulk_Plate3_S36]

value: Brain

value: 3 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B13_384Bulk_Plate1_S37]

value: Bone

value: 6 months postnatal


title: WT(iXist-ChrX)_NoDox_H2AK119ub_Rep2

description: WT_uH2A_Dox-NoDox_20180630.chrX1.Norm.bw


title: Tabula Muris Senis (bulk RNA-seq) [B12_384Bulk_Plate2_S36]

value: Male


title: XistDelPID_Dox_K27me3_Rep2

description: DelB-E8_K27me3_Dox-NoDox_20180630.chrX1.Norm.bw

value: H3K27me3 (Diagenode C15410069, rabbit polyclonal)


title: WT(iXist-ChrX)_NoDox_H2AK119ub_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [B12_384Bulk_Plate1_S36]


title: XistDelPID_NoDox_K27me3_Rep2


title: WT(iXist-ChrX)_Dox_H2AK119ub_Rep2


title: XistDelPID_Dox_K27me3_Rep1

description: DelB-E8_K27me3_Dox-NoDox_20180728.chrX1.Norm.bw


title: ILC [L54]

value: Dead


title: Tabula Muris Senis (bulk RNA-seq) [B11_384Bulk_Plate3_S35]

value: SCAT


title: WT(iXist-ChrX)_Dox_K27me3_Rep2

description: WT_K27me3_Dox-NoDox_20180630.chrX1.Norm.bw


title: XistDelPID_NoDox_K27me3_Rep1


title: ILC [L12]

value: invasive lobular carcinoma

value: Alive


title: WT(iXist-ChrX)_Dox_K27me3_Rep1

description: WT_K27me3_Dox-NoDox_20180728.chrX1.Norm.bw

value: 129S X Cast

value: Female


title: WT(iXist-ChrX)_NoDox_K27me3_Rep2

value: mESC


title: Tabula Muris Senis (bulk RNA-seq) [B11_384Bulk_Plate2_S35]

value: Skin

value: 1 months postnatal


title: WT(iXist-ChrX)_NoDox_K27me3_Rep1

value: Endogenous Xist promoter was replaced with TetOn Promoter (129S allele)

value: Drosophila

value: Dox


title: Tabula Muris Senis (bulk RNA-seq) [B11_384Bulk_Plate1_S35]

value: Brain

value: 9 months postnatal


title: Suz12KO(iXist-Chr3)_Dox_H2AK119ub_Rep1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: H2AK119ub (CST #8240S, rabbit mAb D27C4)


title: Suz12KO(iXist-Chr3)_NoDox_H2AK119ub_Rep1

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [B10_384Bulk_Plate3_S34]

value: Marrow

value: 12 months postnatal


title: ILC [L40]

value: invasive lobular carcinoma


title: ILC [L09]


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_Dox_H2AK119ub_Rep1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + TIR


title: ILC [L08]

value: Alive


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_NoDox_H2AK119ub_Rep1

value: 129S X Cast


title: Tabula Muris Senis (bulk RNA-seq) [B10_384Bulk_Plate2_S34]

value: Pancreas

value: 3 months postnatal

value: Female


title: WT(iXist-Chr3)_Dox_H2AK119ub_Rep1

value: mESC


title: Suz12KO(iXist-Chr3)_Dox_Input_K27me3_Rep2

value: Drosophila


title: Tabula Muris Senis (bulk RNA-seq) [B1_384Bulk_Plate3_S25]

value: Spleen


title: Suz12KO(iXist-Chr3)_NoDox_Input_K27me3_Rep2

value: Dox


title: Suz12KO(iXist-Chr3)_Dox_Input_K27me3_Rep1


title: Suz12KO(iXist-Chr3)_NoDox_Input_K27me3_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [B1_384Bulk_Plate1_S25]

value: 21 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [B1_384Bulk_Plate2_S25]

value: WBC


title: ILC [L53]


title: B7(iXist-Chr3_Pcgf3/5DKO)_NoDox_Input_K27me3_Rep1


title: ILC [L44]


title: Tabula Muris Senis (bulk RNA-seq) [A9_384Bulk_Plate3_S9]

value: MAT

value: 18 months postnatal


title: ILC [L51]


title: B7(iXist-Chr3_Pcgf3/5DKO)_NoDox_Input_K27me3_Rep2

value: Male


title: WT(iXist-Chr3)_Dox_Input_K27me3_Rep1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: B7(iXist-Chr3_Pcgf3/5DKO)_Dox_Input_K27me3_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [A9_384Bulk_Plate2_S9]

value: Brain

value: 9 months postnatal


title: WT(iXist-Chr3)_NoDox_H2AK119ub_Rep1

value: H2AK119ub (CST #8240S, rabbit mAb D27C4)


title: WT(iXist-Chr3)_Dox_Input_K27me3_Rep2

value: 129S X Cast


title: ILC [L29]

value: invasive lobular carcinoma

value: Alive


title: ILC [L27]


title: ILC [L52]


title: WT(iXist-Chr3)_NoDox_Input_K27me3_Rep2


title: ILC [L50]


title: ILC [L31]

value: Dead


title: Tabula Muris Senis (bulk RNA-seq) [A9_384Bulk_Plate1_S9]

value: 3 months postnatal


title: ILC [L28]


title: ILC [L32]


title: Suz12KO(iXist-Chr3)_Dox_K27me3_Rep2

value: mESC

value: Drosophila

value: H3K27me3 (Diagenode C15410069, rabbit polyclonal)


title: Suz12KO(iXist-Chr3)_Dox_K27me3_Rep1

value: Dox


title: Suz12KO(iXist-Chr3)_NoDox_K27me3_Rep2


title: Tabula Muris Senis (bulk RNA-seq) [A8_384Bulk_Plate3_S8]

value: Pancreas

value: 12 months postnatal

value: Female


title: ILC [L22]


title: Suz12KO(iXist-Chr3)_NoDox_K27me3_Rep1

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [A8_384Bulk_Plate2_S8]

value: Liver

value: 15 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [A8_384Bulk_Plate1_S8]

value: Bone


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_Dox_K27me3_Rep1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + TIR


title: ILC [L17]


title: Tabula Muris Senis (bulk RNA-seq) [B10_384Bulk_Plate1_S34]

value: BAT


title: HS1-11 N3 ChIP-seq H3K27ac rep2

description: telencephalon

data_processing:
Libraries were sequenced on MiSeq or NextSeq 500 instruments (Illumina) and base called using the instruments' Real Time Analysis softwarre. Multiplexed paired end (PE) Illumina sequencing data was split based on sample barcodes allowing up to one substitution in the barcode sequence.
Paired-end reads shorter or equal to read length were consensus called and adapter trimmed. For assignment of barcodes, insert consensus sequences were aligned to all designed oligo sequences using BWA MEM (Li and Durbin 2009) with parameters penalizing soft-clipping of alignment ends (-L 80). A minimum of three barcode observation was required for the assignment, further 90% of the barcode observations had to be with the specific insert.
To normalize RNA and DNA for different sequencing depths in each sample, we divided reads by the sum of observed counts and reported them as counts per million. Only barcodes observed in RNA and DNA of the same sample were considered.
Barcodes (consensus called paired-end reads) and UMI sequences containing unresolved bases (N) or not matching the designed length of 15bp were excluded. Each barcode x UMI pair was counted only once and only barcodes matching perfectly to those included the oligo design considered. To determine RNA/DNA ratios per insert, we summed up the counts of all barcodes belonging to the same insert and determined the ratio of the average of normalized counts.
ChIP-seq peaks were called using the ENCODE pipeline with default parameters (https://github.com/ENCODE-DCC/chip-seq-pipeline2).
Genome_build: GRCh37
Supplementary_files_format_and_content: All processed data files are in gzip-compressed tab-separated text file format. DNA.tsv.gz and RNA.tsv.gz files contain assigned RNA and DNA barcode counts. *_design.tsv.gz contain all designed oligo sequences for HAR and HAR-permutation, respectively. HAR5p_assigment.tsv.gz is the barcode-to-insert assignment obtained from sequencing data.

source_name: Human glial progenitor cells

value: neural progenitors


title: WT(iXist-Chr3)_Dox_K27me3_Rep1

value: 129S X Cast

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: HS1-11 N3 ChIP-seq input rep2

description: telencephalon


title: Tabula Muris Senis (bulk RNA-seq) [A7_384Bulk_Plate1_S7]

value: Lung

value: 18 months postnatal


title: Tabula Muris Senis (bulk RNA-seq) [A6_384Bulk_Plate3_S6]

value: Small Intestine

value: 9 months postnatal


title: HS1-11 N3 ChIP-seq H3K27ac rep1

description: telencephalon


title: HS1-11 N3 ChIP-seq input rep1

description: telencephalon


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_Dox_K27me3_Rep2

value: mESC

value: Drosophila

value: Dox

value: H3K27me3 (Diagenode C15410069, rabbit polyclonal)


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_NoDox_K27me3_Rep2

value: Male


title: WT(iXist-Chr3)_NoDox_K27me3_Rep1


title: Tabula Muris Senis (bulk RNA-seq) [A6_384Bulk_Plate2_S6]

value: Pancreas

value: 27 months postnatal


title: HS1-11 N2 ChIP-seq H3K27ac rep2

description: telencephalon


title: iXist-Chr3_Mettl3KO_m6A-seq

data_processing:
For conventional m6A-seq data, first we removed the rRNA reads computationally by mapping the single-end reads to the mouse rRNA build with Bowtie2 (Langmead and Salzberg, 2012). The remaining unmapped reads were then aligned to mm10 genome by STAR (v2.4.2a) (Dobin et al., 2013) with “--single-end” mode. BigWig files were generated by Bedtools (Quinlan and Hall, 2010) and normalized to 10 million mapped reads (Generate_BigWig_from_RNA_seq_Bam_mm10.sh), then visualized in IGV or UCSC.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol: Total RNAs were isolated by Trizol, and were used for m6A-seq.

value: male

tag: treatment

tag: rip antibody

value: anti-m6A antibody (Synaptic Systems, 202 003)


title: Tabula Muris Senis (bulk RNA-seq) [A6_384Bulk_Plate1_S6]

value: Liver

value: 3 months postnatal

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [A7_384Bulk_Plate3_S7]


title: WT(iXist-Chr3)_NoDox_K27me3_Rep2

value: 129S X Cast

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)


title: ILC [L14]

value: invasive lobular carcinoma

value: Alive


title: ILC [L13]


title: ILC [L07]


title: HS1-11 N2 ChIP-seq H3K27ac rep1

description: telencephalon

value: neural progenitors

tag: developmental stage


title: ILC [L41]


title: ILC [L42]


title: ILC [L03]


title: ILC [L24]


title: HS1-11 N2 ChIP-seq input rep2

description: telencephalon


title: ILC [L02]


title: Tabula Muris Senis (bulk RNA-seq) [A5_384Bulk_Plate3_S5]

value: Brain


title: B7(iXist-Chr3_TIR_Pcgf3/5DKO)_NoDox_K27me3_Rep1

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + TIR

value: mESC

tag: spiked-in

value: Drosophila


title: WT(iXist-Chr3)_NoDox_Input_K27me3_Rep1

value: Male

value: Dox

tag: time


title: iXist-Chr3_WtapKO_m6A-seq


title: HS1-11 N2 ChIP-seq input rep1

description: telencephalon


title: Tabula Muris Senis (bulk RNA-seq) [A5_384Bulk_Plate1_S5]

value: GAT

value: 1 months postnatal


title: iXist-Chr3_WT_m6A-seq

value: male

value: anti-m6A antibody (Synaptic Systems, 202 003)


title: iXist-Chr3_WtapKO_input


title: Tabula Muris Senis (bulk RNA-seq) [A4_384Bulk_Plate2_S4]

value: 12 months postnatal


title: iXist-Chr3_WT_input


title: Tabula Muris Senis (bulk RNA-seq) [A4_384Bulk_Plate3_S4]

value: BAT

value: 21 months postnatal


title: ILC [Q619]

source_name: UQCCR


title: ILC [L01]


title: MRC5_Lung Day5

city: Buffalo

last: Feng

state: NY

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

data_processing:
Fastq files were generated by Torrent Suite Software 3.6.2
Mapping to genome with TopHat (v2.1.1) with default parameters
Expression level was quantified as RPKM using Cufflink(v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: csv files include FPKM value for each sample

molecule: polyA RNA

growth_protocol: Primary human fibroblasts C002 and MRC5 were cultured in DMEM containing 10% FBS and 2mM L-glutamine. For the generation of induced dopaminergic neurons, fibroblasts were plated at 5x103/cm2 and infected 1 day later for 16h with lentiviruses of FUW-tetO-LoxP-cDNA (ASCL1, NURR1, LMX1A, miR124) and pLKO/p53shRNA(MOI 10 for pLKO/p53shRNA, MOI 20 for all others) in the presence of 8 μg/ml polybrene. Cells were then washed three time with DMEM/F12 to remove remaining serum and cultured in DMEM/F12 for 24h to arrest cell cycle. Then medium was changed to neural induction medium (DMEM/F12, 1x N2, 1x B27, 1xNEAA, 5 μM dorsomorphin,  2 μM purmorphamine and 10 μM SB431542, 3 μM CHIR99021, 0.2mM vitamin C, 10 μM Y27632, 0.5mM dcAMP, 20 ng/ml GDNF, 20 ng/ml BDNF, 1 ng/ml TGFb3 and 1 μg/ml doxycycline). The medium was changed every other day for the duration of the culture period.

extract_protocol:
Total RNA Extraction with TRIZOL Reagent and Purification with QIAGEN. RNeasy Mini Kit(cat # 74104).
cDNA libraries were prepared using Ion Total RNA-Seq Kit v2

value: Lung fibroblasts

tag: time point

value: Day 5

value: transdifferentiation to dopaminergic neuron induced by ANLmp


title: MRC5_Lung Day3

value: Day 3


title: Tabula Muris Senis (bulk RNA-seq) [A3_384Bulk_Plate3_S3]

tag: strain/background

value: Skin

value: 9 months postnatal


title: ILC [Q309]

tag: tissue

value: invasive lobular carcinoma

value: Alive


title: Ad_LipidChallenge_Control_pCHiC

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

data_processing:
Insert size for ATAC-seq will have multiple peaks representing nucleosome-free and (mono/di/tri)-nucleosome regions
Insert size for pCHi-C is theoretical length of Hi-C ditag based on alignment of paired-end read to HindIII fragments and calculation of read distance to ditag ligation sites. Ditags were size-selected for lengths between 250-550 bp prior to ligation of Illumina adapters (see "library construction protocol")
For ATAC-seq, we processed the sequencing reads and performed quality control using the ENCODE ATAC-seq Data Standards and Prototype Processing Pipeline. Briefly, we aligned reads to the human reference genome (GRCh37/hg19) using Bowtie252 v2.2.9 (with parameters -k 4 -X 2000 --local), filtered out unpaired mapped reads and reads with MAPQ < 30 (Samtools53) and duplicates (marked with Picard Tools). Only reads from the autosomes and the X chromosome were retained for downstream analyses.
For the untreated ATAC-seq read alignments, libraries were merged prior to peak calling. Peaks were called using MACS2 v2.1.1 (using the BEDPE function) and peaks with an FDR < 0.05 were retained. We filtered out peaks in blacklisted regions and peaks that did not replicate in two out of the three biological replicates in at least one condition. For differential accessibility analyses, we retained peaks with counts per million (cpm) >= 1 in at least 3 libraries. We then input aligned read counts per peak into cqn v1.20.0 and normalized the counts for GC content, peak length, and library size before inputting the counts into edgeR v3.16.5 to detect differentially accessible peaks between the preadipocytes and adipocytes using an FDR < 0.05.
For the lipid challenge ATAC-seq read alignments, libraries were processed identically up until the differential accessibility analysis. To detect open chromatin regions that exhibit differential accessibility in the lipid-challenged adipocytes, we performed a one-way analysis of variance (ANOVA) using the glm functionality in edgeR and an FDR threshold of 0.05. For the post hoc test to determine which comparison was significant after the one-way ANOVA (OA vs. BSA, PA vs. BSA, or OA vs. PA), we determined the least significant difference.
For the promoter Capture Hi-C, we processed the sequencing reads as described in [Pan et al. 2018 Nat Commun], using the Hi-C User Pipeline (HiCUP) v0.5.9. We called significant interactions on each library separately with the Capture Hi-C Analysis of Genome Organization (CHiCAGO) software v1.1.1. We used the default threshold of 5 for calling significant interactions. To create the consensus set of interactions for differential interaction analysis, we merged all pCHi-C final alignments and called interactions using CHiCAGO, again using a threshold of 5. To create a stringent set of interactions, we then filtered these interactions to include only those that were called in both biological replicates in at least one condition (BSA, OA, PA).
Genome_build: hg19
Supplementary_files_format_and_content: Narrowpeak files list the ATAC-seq peaks called using the MACS2 software. Promoter Capture Hi-C text file lists the baited (promoter-containing) HindIII fragment and the interacting (other end) HindIII fragment as well as the interaction score from the CHiCAGO software.

source_name: Human white adipocytes (Ad)

growth_protocol: Primary human white preadipocyte (PAd) cells were obtained and cultured as recommended by PromoCell (PromoCell C-12731, lot 395Z024) for preadipocyte growth and differentiation into adipocytes (Ad). Cell media (PromoCell) was supplemented with 1% penicillin-streptomycin. We maintained the cells at 37ºC in a humidified atmosphere at 5% CO2.

extract_protocol:
For the promoter Capture Hi-C in lipid-challenge adipocytes (Ad), 7-10M adherent Ad were rinsed with serum-free media prior to fixation. We fixed the adipocytes directly in culture plates with 2% formaldehyde (EMD Millipore 344198) in serum-free adipocyte nutrition media (PromoCell). We incubated cells in fixation medium with rocking at room temperature for 10 minutes, and then quenched with 1 M ice-cold glycine for a final concentration of 125 mM. After 5 minutes of rocking incubation at room temperature, we rinsed fixed cells twice with ice-cold PBS. Then we incubated the cells with rocking on ice with ice-cold permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % Igepal CA-630, Complete EDTA-free protease inhibitor cocktail [Roche])36 for 30 minutes. We scraped cells from the culture plate and centrifuged at 2500 x g for 5 minutes at 4ᵒC to pellet nuclei. The supernatant was discarded and nuclei were flash frozen in liquid nitrogen and put at -80ºC.
The Hi-C library was prepared as described in (Rao et al., Cell, 2014) with modifications. We processed 10M adipocyte nuclei in 5M cell aliquots, closely following Rao et al. protocol I.a.1 except we digested chromatin with 400U of HindIII (New England Biolabs R3104) at 37ºC overnight with shaking (950 rpm). After digestion, we pelleted nuclei with centrifugation at 2500 x g for 5 minutes at 4ºC. We performed end-filling and marked with biotin using biotin-14-dCTP (Invitrogen 19518-018), performed in-nucleus ligation, degraded protein using Proteinase K, and performed ethanol precipitation and purification. We sheared 5 μg of DNA to 250-550 bp using the Covaris M220 instrument. We performed double size-selection to retain fragments from 250-550 bp using Agencourt AMPure XP beads (Beckman Coulter A63881). We immobilized the fragments containing biotin using DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 (Invitrogen 65601) beads. After end-repair and attachment of dATP, we ligated Illumina paired-end adaptors to the bead-bound library following the SureSelectXT user manual for Illumina Paired-End Multiplexed Sequencing (Agilent Technologies). After washing, we resuspended the Hi-C library in 20 μl of 1x Tris buffer and subsequently removed the Streptavidin beads from the DNA by heating at 98ºC for 10 minutes. We then amplified the adaptor-ligated library using 8 PCR cycles and purified using Agencourt AMPure XP beads, following the SureSelectXT user manual. The RNA baits for promoter capture were designed in (Mifsud et al., Nature Genetics, 2015) for capturing HindIII fragments containing gene promoters (Dr. Cameron Osborne kindly shared the exact design). A total of 550 ng of the Hi-C library was hybridized to the biotinylated RNA baits, captured with DYNAL™ MyOne™ Dynabeads™ Streptavidin T1 beads, and amplified in a post-capture PCR to add indexes, using 6 PCR cycles. The library was sequenced on the Illumina HiSeq 4000 platform.

treatment_protocol: In vitro differentiated human adipocytes (Ad) were serum-starved for 16 hours using 0.5% fetal calf serum (FCS) in supplemented adipocyte (Ad) basal medium (PromoCell), prior to treatment with 0.23% fatty acid free bovine serum albumin as a control (BSA, Sigma Aldrich A8806), 200 uM palmitic acid, or 200 uM oleic acid (Sigma Aldrich O3008), all in media containing 0.5% FCS for 24 hours prior to nuclei collection for fixation

value: In vitro differentiated adipocytes (Ad)

tag: passage

value: Bovine serum albumin (control)


title: Tabula Muris Senis (bulk RNA-seq) [A3_384Bulk_Plate2_S3]

value: Lung

tag: age

value: 18 months postnatal

tag: Sex

value: Male


title: Ad_LipidChallenge_Palmitic_pCHiC

tag: cell type

value: Palmitic acid


title: ILC [Q376 A]

tag: tumour grade


title: Ad_LipidChallenge_Palmitic_ATACseq

description: AdLipChall.narrowpeak

extract_protocol:
For the ATAC-seq in primary human adipocytes that underwent lipid challenge, we performed omni-ATAC [Corces et al. 2017 Nat Methods] in 300,000 nuclei in three biological replicates.
Tagmented DNA samples were prepared for high-throughput sequencing as described in [Buenrostro et al. 2013 Nat Methods]

treatment_protocol: In vitro differentiated human adipocytes (Ad) were serum-starved for 16 hours using 0.5% fetal calf serum (FCS) in supplemented adipocyte (Ad) basal medium (PromoCell), prior to treatment with 0.23% fatty acid free bovine serum albumin as a control (BSA, Sigma Aldrich A8806), 200 uM palmitic acid, or 200 uM oleic acid (Sigma Aldrich O3008), all in media containing 0.5% FCS for 24 hours prior to nuclei collection for tagementation


title: iXist-Chr3_Mettl3KO_input

value: male

value: mESC

value: Dox


title: Ad_LipidChallenge_Oleic_pCHiC

value: Oleic acid


title: iXist-Chr3_TIR_Dox2

description:
Raw_Ratio_chr3.xlsx
WT_TIR_DoxB

tag: strain background

value: 129S X Cast

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + Tir

tag: time course

tag: medium

value: ES medium


title: Tabula Muris Senis (bulk RNA-seq) [A4_384Bulk_Plate1_S4]

value: Marrow

value: 12 months postnatal

value: Female


title: Ad_LipidChallenge_Oleic_ATACseq

description: AdLipChall.narrowpeak


title: MRC5_Lung Day1

tag: cell line

value: Lung fibroblasts

value: Day 1

value: transdifferentiation to dopaminergic neuron induced by ANLmp


title: Tabula Muris Senis (bulk RNA-seq) [A7_384Bulk_Plate2_S7]

value: Lung

value: 21 months postnatal


title: Ad_LipidChallenge_Control_ATACseq

description: AdLipChall.narrowpeak

value: In vitro differentiated adipocytes (Ad)

tag: treatment

value: Bovine serum albumin (control)


title: ILC [Q260]

value: invasive lobular carcinoma

tag: patient survival status

value: Dead


title: ILC [Q064]


title: ILC [L43]

value: Alive


title: Tabula Muris Senis (bulk RNA-seq) [A3_384Bulk_Plate1_S3]

value: Spleen

value: 3 months postnatal

value: Male


title: MRC5_Lung Day0

value: Day 0


title: ILC [Q058]


title: Human in vitro differentiated primary adipocyte ATAC-seq

extract_protocol:
We performed the ATAC-seq protocol in the untreated primary human adipocytes (Ad) in 300,000 nuclei in three biological replicates similarly as in [Buenrostro et al. 2013 Nat Methods] except we used 0.03-0.1% Tween-20 in place of NP40 for the lysis buffer. After washing adherent cells with ice-cold PBS, we lysed the cells directly in the culture plate and performed transposition and DNA purification.
Tagmented DNA samples were prepared for high-throughput sequencing as described in [Buenrostro et al. 2013 Nat Methods]

treatment_protocol: Untreated


title: C002_Skin Day5

value: Skin fibroblasts

value: Day 5


title: Tabula Muris Senis (bulk RNA-seq) [A22_384Bulk_Plate2_S22]

value: Liver

value: 1 months postnatal


title: CLC33

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
The reads were mapped to the human reference genome (HG38) using TopHat2
Cufflinks algorithm was used to calculate gene expressions. Then the expression profiles of all samples were normalized by the fragments per kilobase of exon per million fragments mapped (FPKM) method.
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: library barcodes

value: CATGCG


title: CLC34

value: CGGCCA


title: C002_Skin Day1

value: Day 1

value: transdifferentiation to dopaminergic neuron induced by ANLmp


title: ILC [L37]


title: N2_ints-4 RNAi_cadmium_rep3

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

description:
ints-4_cadmium
S4c_4

data_processing:
HISAT2 2.1.0-beta used for mapping to the C. elegans reference genome
HTSeq V0.6.1 used for Quantification
rMATS 3.0.8 used for Alternative Splicing analysis
cufflinks 2.1.1 used for novel gene prediction.
DEGSeq 1.12.0 used for differential expression analysis
Genome_build: WS220
Supplementary_files_format_and_content: Processed data files (in Excel format) include readcounts, differential gene expression and alternative splicing for each file.
The data are exported with the standard rMATS format:
IC refers to number of reads mapped to the exon inclusion isoform.
SC refers to number of reads mapped to the exon skipping isoform.
Sample_1 always refers to the experimental group on the name of the processed data file (e.g. cadmium, ints-4 RNAi, ints-4 RNAi + cadmium, etc.)
Sample_2 always refers to the control value (empty vector + control) that is used for all processed files.

organism: Caenorhabditis elegans

source_name: N2_ints-4 RNAi_cadmium, whole animal

extract_protocol:
Total RNA extracted using the RNAqueous Total RNA Isolation Kit
Standard Illumina protocols with oligo-dT beads

tag: strain

value: 300um Cadmium (12h)

tag: genotype

value: ints-4 knockdown

value: whole animal


title: Tabula Muris Senis (bulk RNA-seq) [A23_384Bulk_Plate2_S23]

value: MAT

value: Female


title: N2_ints-4 RNAi_cadmium_rep2

description:
ints-4_cadmium
S4c_3


title: CLC32

value: CGGTAT


title: N2_ints-4 RNAi_cadmium_rep1

description:
ints-4_cadmium
S4c_2


title: Human primary preadipocyte ATAC-seq

source_name: Human white preadipocytes (PAd)

extract_protocol:
We performed the ATAC-seq protocol in the untreated primary human preadipocytes (PAd) in 300,000 nuclei in three biological replicates similarly as in [Buenrostro et al. 2013 Nat Methods] except we used 0.03-0.1% Tween-20 in place of NP40 for the lysis buffer. After washing adherent cells with ice-cold PBS, we lysed the cells directly in the culture plate and performed transposition and DNA purification.
Tagmented DNA samples were prepared for high-throughput sequencing as described in [Buenrostro et al. 2013 Nat Methods]

value: Primary human white preadipocytes (PAd)


title: HepG2 DNA rep3

source_name: Human liver cells

growth_protocol:
https://genome.ucsc.edu/ENCODE/cellTypes.html
Human iPSC-derived neural progenitor cells were maintained in N2B27 media supplemented with 20ng/mL bFGF and EGF on matrigel-coated dishes. HepG2 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

tag: developmental stage


title: Tabula Muris Senis (bulk RNA-seq) [A21_384Bulk_Plate2_S21]

tag: strain/background

value: 6 months postnatal

value: Male


title: Tabula Muris Senis (bulk RNA-seq) [A23_384Bulk_Plate1_S23]

tag: tissue

value: WBC

value: 12 months postnatal


title: N2_ints-4 RNAi_control_rep3

description:
ints-4_control
S4_3

source_name: N2_ints-4 RNAi_control, whole animal

value: control


title: N2_ints-4 RNAi_control_rep2

description:
ints-4_control
S4_2


title: C002_Skin Day3

value: Skin fibroblasts

tag: time point

value: Day 3


title: ILC [L35]

value: invasive lobular carcinoma

value: Alive


title: Alternaria brassicicola treated, AGO1-immunoprecipiated, Col-0 rep 3

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

description:
index primer: GATCAG
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_alterAGO1.csv, DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv

data_processing:
Quality filtering: FASTQC(version v0.10.1), default parameters
Adapter removal and filtering low quality and/or too long or short reads, parameters:cutadapt -e 0.2 -a TGGAAT -m 16 -M 28
Quality filtering: FASTQC(version v0.10.1), default parameters
rRNA/tRNA filtering: UEA sRNA Workbench (version 3.2) Filtering tool, parameters: min.length 16, max. length 28, min. abundance 0, max. abundance not defined, don't filter low complexity reads, don't filter invalid sequences, output redundant files
Identify known miRNA profiles, collecting raw expression data: UEA sRNA Workbench (version 3.2) miRProf tool, parameters: genome: TAIR10, miRNA database:miRBase (version 21),mismatches=0, overhangs=true, group_mismatches=true, group_organisms=true, group_variant=true, group_mature_and_star=false, only_keep_best=true, min_length=18, max_length=25, min_abundance=15, mirbase_version=21, group_options_string=ignore mismatches, combine organisms, combine variants
Differential expression analysis: DESeq (version 1.2), default parameters
Genome_build: TAIR 10, MirBase version 21
Supplementary_files_format_and_content: [DESeq*.csv] DESeq2 differential expression analysis – differential expression data, total or significant data sets.  First column contains the number of hits, second column contains  MirBase version 21 reference microRNA IDs, third column "baseMean" contains the mean of normalized read counts averaged over all samples from both conditions, fourth column "baseMeanA" contains mean normalized counts from condition A, fifth column "baseMeanB" contains mean normalized counts from condition B, sixth column "foldChange" contains fold change from condition A to B, seventh column "log2FoldChange" contains the logarithm (to basis 2) of the fold change, eighth column  "pval" contains p-values for the statistical  significance of this change, ninth column "padj" contains p-values adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR).  In case of baseMeanA and baseMeanB, comparisons always following the sequence of samples in the file name (For example, for DESeq_srna_alter_alterAGO1.csv, baseMeanA = total alternaria samples, baseMeanB = AGO1-IP alternaria samples).
Supplementary_files_format_and_content: [mirprof_abundance_miRNA.csv] abundance measurement file

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under short day conditions (8 h light, 22°C) with a high humidity on soil for around 5 - 6 weeks.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA MiniPrep Kit (ZymoResearch) and concentrated with RNA Clean and ConcentratorTM-5 (ZymoResearch). For AGO1 immunoprecipitation, around 2.5 mg of plant material was ground in liquid nitrogen, resuspended in extraction buffer (50 mM Tris-HCl pH 7.5; 150 mM NaCl; 10 % glycerol; 0.05 % Nonidet P-40; Proteinase-Inhibitor Roche cOmplete (EDTA-free); 1 mM PMSF), incubated at 4 °C for 20-30 min. on a rotator and centrifuged at 4 °C at 3200 g for 30 min. The protein extract was filtered (2x Miracloth and 1x syringe driven filter unit) and pre‑cleared with 100 ml protein A agarose beads for 30 min. on a rotator. After removal of the beads, supernatant was split in two fractions and incubated with/without 5 µl of AGO1 antibody (Agrisera; AS09 527) at 4°C for 2h on a rotator and an additional hour with 50 µl protein A agarose beads. Beads were collected by centrifugation and washed several times with extraction buffer. AGO1 complex was eluted with AGO1 peptide (Agrisera; AS09 527P) as described in Qi and Mi (2010) with minor modifications. AGO1 complex was eluted in 100 µl peptide elution solution (50 µg/ml). RNA and protein from the complex was extracted by adding TRIzol® reagent and incubation at 50 °C for 5 min. With chloroform, aqueous and organic phase were separated. The RNA containing, aqueous phase was further cleaned with chloroform and precipitated over night with one vol. isopropanol at ‑20 °C followed by centrifugation and washed with 80% ethanol. The organic phase was precipitated with 3 vol. acetone at -20 °C followed by centrifugation and washed with 80 % acetone. The extracted RNA was concentrated with RNA Clean and ConcentratorTM-5 (ZymoResearch).
For total RNA libraries, small RNAs were isolated from 8 µg total RNA as described in Gilbert et al. (2014) and sRNA libraries were done with NEXTflexTM Small RNA Sequencing Kit (Bioo Scientific). sRNA libraries from the AGO1‑immunoprecipitated sRNAs were done according to the TruSeq® Small RNA Library Prep Kit (Illumina). All three biological replicates of each treatment of the total RNA sRNA libraries and the AGO1-immunoprecipitated sRNA libraries, respectively, were pooled and sequenced each on two different lanes.

treatment_protocol: Plants were sprayed with Alternaria brassicicola (strain MUCL 20297) spore solution (1 x 10^6 spores/ml) with 0.01 % Silwet L 77. Rosette leaves were harvested 3 days after inoculation.

tag: ecotype

value: Alternaria brassicicola treated

value: rosette leaves

tag: antibody for ip

value: AGO1 antibody (Agrisera; AS09 527)


title: Alternaria brassicicola treated, AGO1-immunoprecipiated, Col-0 rep 2

description:
index primer: ACTTGA
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_alterAGO1.csv, DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv


title: ILC [L36]


title: HepG2 DNA rep2

tag: cell type


title: ILC [L05]

tag: tumour grade

value: Dead


title: C002_Skin Day0

value: Day 0

value: transdifferentiation to dopaminergic neuron induced by ANLmp


title: Tabula Muris Senis (bulk RNA-seq) [A22_384Bulk_Plate1_S22]

extract_protocol:
RNeasy (mini and micro) Qiagen RNA isolation from homogenized tissue.
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT.
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2.

value: Spleen

tag: age

tag: Sex


title: N2_ints-4 RNAi_control_rep1

description:
ints-4_control
S4_1

value: ints-4 knockdown

value: whole animal


title: Alternaria brassicicola treated, AGO1-immunoprecipiated, Col-0 rep 1

description:
index primer: CAGATC
processed data files: DESeq_srna_alter_alterAGO1.csv, DESeq_srna_alter_alterAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_alterAGO1.csv, DESeq_srna_mock_alterAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_un_alterAGO1.csv, DESeq_srna_un_alterAGO1_sig.csv


title: N2_numr-1 RNAi_cadmium_rep3

description:
numr-1_cadmium
NC_4

source_name: N2_numr-1 RNAi_cadmium, whole animal

value: 300um Cadmium (12h)

value: numr-1 knockdown


title: Tabula Muris Senis (bulk RNA-seq) [A20_384Bulk_Plate2_S20]

value: Brain

value: 12 months postnatal

value: Male


title: HS1-11 N2 DNA rep3 (5' assay)

description: telencephalon

value: neural progenitors


title: HS1-11 N2 DNA rep2 (5' assay)

description: telencephalon


title: N2_numr-1 RNAi_cadmium_rep2

description:
numr-1_cadmium
NC_2


title: mock treated, AGO1-immunoprecipitated, Col-0 rep 2

description:
index primer: ACAGTG
processed data files: DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv

value: mock treated


title: Tabula Muris Senis (bulk RNA-seq) [A2_384Bulk_Plate3_S2]

description: processed data file: 190214_A00111_0269_AHH3J3DSXX__190214_A00111_0270_BHHMFWDSXX.csv

value: BAT

value: 27 months postnatal


title: HS1-11 N2 DNA rep1 (5' assay)

description: telencephalon


title: Tabula Muris Senis (bulk RNA-seq) [A2_384Bulk_Plate2_S2]

value: MAT

value: 9 months postnatal

value: Female


title: Tabula Muris Senis (bulk RNA-seq) [A21_384Bulk_Plate1_S21]

value: 1 months postnatal


title: mock treated, AGO1-immunoprecipitated, Col-0 rep 1

description:
index primer: TGACCA
processed data files: DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv

value: rosette leaves

value: AGO1 antibody (Agrisera; AS09 527)


title: N2_numr-1 RNAi_cadmium_rep1

description:
numr-1_cadmium
NC_1


title: HepG2 DNA rep1


title: WT(iXist-Chr3)_Dox_K27me3_Rep2

tag: strain background

value: 129S X Cast

tag: gender

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4)

value: mESC

tag: spiked-in

value: Drosophila

tag: agent

value: Dox

tag: time

tag: antibody

value: H3K27me3 (Diagenode C15410069, rabbit polyclonal)


title: B7(iXist-Chr3_Pcgf3/5DKO)_Dox_Input_K27me3_Rep1

value: Male

tag: cell line

value: Cell line integrating with FLXist randomly on Chr3 (P4D7F4) + TIR


title: HepG2 RNA rep3

tag: developmental stage


title: N2_numr-1 RNAi_control_rep3

description:
numr-1_control
N_4

source_name: N2_numr-1 RNAi_control, whole animal

tag: strain

tag: treatment

value: control

tag: genotype

value: numr-1 knockdown

value: whole animal


title: Tabula Muris Senis (bulk RNA-seq) [A19_384Bulk_Plate2_S19]

tag: strain/background

tag: tissue

value: Heart


title: Tabula Muris Senis (bulk RNA-seq) [A2_384Bulk_Plate1_S2]

value: MAT

value: 15 months postnatal


title: HepG2 RNA rep2

tag: cell type


title: untreated, AGO-immunoprecipitated, Col-0 rep 2

description:
index primer: CGATGT
processed data files: DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv

tag: ecotype

value: untreated

tag: antibody for ip


title: untreated, AGO-immunoprecipitated, Col-0 rep 3

description:
index primer: TTAGGC
processed data files: DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv

value: rosette leaves


title: N2_numr-1 RNAi_control_rep2

description:
numr-1_control
N_2


title: Tabula Muris Senis (bulk RNA-seq) [A19_384Bulk_Plate1_S19]

value: WBC

tag: age

value: 12 months postnatal

tag: Sex


title: Tabula Muris Senis (bulk RNA-seq) [A20_384Bulk_Plate1_S20]

value: Lung

value: 3 months postnatal


title: mock treated, AGO1-immunoprecipitated, Col-0 rep 3

description:
index primer: GCCAAT
processed data files: DESeq_srna_alter_mockAGO1.csv, DESeq_srna_alter_mockAGO1_sig.csv, DESeq_srna_mockAGO1_alterAGO1.csv, DESeq_srna_mock_mockAGO1.csv, DESeq_srna_mock_mockAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_mockAGO1.csv, DESeq_srna_un_mockAGO1_sig.csv

value: mock treated

value: AGO1 antibody (Agrisera; AS09 527)


title: HepG2 RNA rep1


title: N2_numr-1 RNAi_control_rep1

description:
numr-1_control
N_1


title: untreated, AGO-immunoprecipitated, Col-0 rep 1

description:
index primer: ATCACG
processed data files: DESeq_srna_alter_unAGO1.csv, DESeq_srna_alter_unAGO1_sig.csv, DESeq_srna_mock_unAGO1.csv, DESeq_srna_mock_unAGO1_sig.csv, DESeq_srna_unAGO1_alterAGO1.csv, DESeq_srna_unAGO1_alterAGO1_sig.csv, DESeq_srna_unAGO1_mockAGO1.csv, DESeq_srna_unAGO1_mockAGO1_sig.csv, DESeq_srna_un_unAGO1.csv, DESeq_srna_un_unAGO1_sig.csv


title: Tabula Muris Senis (bulk RNA-seq) [A18_384Bulk_Plate2_S18]

value: Limb Muscle

value: 6 months postnatal