title: Nipponbare STARR-seq input library 1

city: Guangzhou

last: He

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China

department: Department of Basic Research

institute: Guangzhou National Laboratory

description: PCR amplified Plasmid library, used for Nipponbare STARR-seq library 1

data_processing:
Library strategy: STARR-seq
For Illumina X-ten generated 150mer paired-end reads, we used bowtie21 to map paired-end Illumina sequencing data to the Nipponbare genome (IRGSP1.0), And the default parameters were used to map the sequencing data except parameter “--no-discordant –X 2000”. After mapping, we used the samtools2 to filter the mapped reads, only kept the uniquely mapped reads with parameter “view -bS -f 2 -q 5”.  Then we used samtools rmdup to exclude the potential redundancies from PCR amplification to get the unique fragments(contain chromosome, start, end, strand). Significantly enriched regions (peaks) were called by R package BasicSTARRseq. And added bonferroni correction method to correct p value.  Only when peaks enrichment larger than threshold 1.3 was kept. Then merge two replicates peaks, as final enhancer peaks.
Genome annotation verison: MSU 7.0
Genome_build: IRGSP1.0
Supplementary_files_format_and_content: peaks files were generated using BasicSTARRseq, each row present a enhancer information, include the location, the enrichment and p-value.

organism: Oryza sativa Japonica Group

source_name: Nipponbare

growth_protocol: The rice cultivar Nipponbare  (Oryza sativa japonica)  seeds were placed on filter papers moistened with water in Petri dishes at room temperature to promote germination(3days) and were then transferred to culture box at 37°C for about 24h. and then transplant into the box with soil. The rice plants were grown in a growth room at 28°C with a 12/12 h light/dark photoperiod and illuminated by a bank of 400 W metal halide lamps, a light intensity at plant height of 400 μmol m–2 s–1 and a relative humidity of approximately 60%.Two-week-old rice seedlings were collected for the experiments.

extract_protocol: We isolated the protoplasts following a published protocol with minor modifications. Green tissues from the stem of 80-120 rice seedlings were used.

value: seedling

value: 2 weeks


title: Nipponbare STARR-seq input library 2

status: Public on Nov 08 2018

type: SRA

state: Guangdong

country: China

description: PCR amplified Plasmid library, used for Nipponbare STARR-seq library 2

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: age


title: Nipponbare STARR-seq library 2

description: PCR amplified cDNA (STARR-seq transcript)

library_source: transcriptomic

molecule: total RNA


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R2T3

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
MOAM-HeLa-MFCl-R2T3
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw

data_processing:
Reads were mapped to hg19 using bowtie2. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
PCR duplicates, ChrM etc were removed to obtain bam files of valid reads. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files of valid reads were converted to bed files for use for V-plots. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Bam files were converted to BigWigs binned at 20bp. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Peaks were called using HOMER. For more details see https://github.com/dekkerlab/CTCF_in_mitosis_GR_2018
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing valid reads for V-plots, bigwig files containing ATAC-seq signal of read ends, bed files containing peaks called by HOMER on ATAC-seq data

organism: Homo sapiens

source_name: HeLa-S3 cells

growth_protocol: HeLa-S3 and HFF cells were cultured glutamax DMEM supplemented with 10% heat-inactivated FBS and penicillin-streptomycin. U2OS cells were cultured in low glucose medium with 10% heat-inactivated FBS and pen-strep

extract_protocol:
For each ATAC-seq library, 50,000 cells or the equivalent in mitotic chromatin clusters were used
ATAC-seq was performed according to published protocol (Buenrostro et al, Curr. Protoc. Mol. Bio, 2015)

treatment_protocol: Cells were harvested as non-synchrous without treatment or arrested in mitosis using Thymidine treatment and Nocodazole (mitotic cells). Mitotic chromatin was purified from mitotic cells using percoll gradients.  See supplemental methods for more information

tag: protocol

value: ATAC-seq

tag: enzyme

tag: cell type

value: Human adenocarcinoma cells

tag: cell line

value: HeLa-S3 (CCL-2.2)


title: HeLa Mitotic Cell ATAC-seq R2T4


title: DICER knockdown

status: Public on Nov 07 2018

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

description: small RNA sequencing

data_processing:
FASTQ reads were subjected to adapter removal (cutadapt) per manufacturer’s instructions (NEXTflex Small RNA Sequencing Kit v3). The degenerate sequences (N4) at the 5’ and 3’ end of the reads were removed.
Trimmed reads were mapped to the human genome (build hg38) using Bowtie2 v2.2.8.
The resulting bam file was sorted (samtools sort), converted to bed (bamToBed), and intersected with all small RNA loci annotated from TCGA-BRCA dataset (intersectBed).
The number of reads overlapping each small RNA were tallied to generate a count file.
Genome_build: hg38
Supplementary_files_format_and_content: count file for each feature. Bed file with chromosomal coordinates for gene IDs is available on the series record.

growth_protocol: All cells were cultured in a 37°C, 5% CO2 humidified incubator. Cell lines MDA-LM2 were propagated in DMEM base media supplemented with 4.5 g/L glucose, 10% FBS, 4mM L-glutamine, 1mM sodium pyruvate, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin (1μg/mL).

extract_protocol:
RNA was extracted using miRNA purification kit (Norgen) per manufacturer's instructions
The libraries were constructed using the NEXTflex small RNA sequencing kit v3 for Illumina platforms (Bioo Scientific NOVA-5132-06). 15 ng of extracellular vesicle RNA and 10 ng of conditioned media RNA were used as starting material, and gel extraction was performed for all libraries.

tag: rep

tag: sirna

value: DICER


title: HeLa Mitotic Chromatin (frozen) ATAC-seq R2T4

description:
MOAM-HeLa-MFCl-R2T4
MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz
MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed
MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw


title: Nipponbare STARR-seq library 1


title: TARBP2 knockdown rep 1

description: small RNA sequencing


title: DROSHA knockdown rep 2

description: small RNA sequencing

value: DROSHA


title: DROSHA knockdown rep 1

description: small RNA sequencing


title: DCGR8 knockdown rep 2

description: small RNA sequencing


title: DCGR8 knockdown rep 1

description: small RNA sequencing


title: Control rep 1

description: small RNA sequencing

value: control


title: IL-10+ CD4+ T-cells spleen p2_P7

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

description: spleen.counts.txt

data_processing:
After demultiplexing based on Nextera-adapters and the 384-well plate layout, the single-end reads were aligned to the reference genome using STAR
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in tab delimited text file

molecule: polyA RNA

organism: Mus musculus

source_name: T-cells from spleen

extract_protocol: Libraries were constructed using the SMART-seq2 protocol

value: spleen

tag: treatment


title: IL-10+ CD4+ T-cells spleen p2_P3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_P11

description: spleen.counts.txt


title: TARBP2 knockdown rep 2

description: small RNA sequencing


title: IL-10+ CD4+ T-cells spleen p2_P10

description: spleen.counts.txt


title: ARPE H2O2 3H-2: ARPE19 H2O2_Rep2

type: RNA

first: Lili

last: Gong

address: Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Gene expression data from GFP-Satllite alpha transfected ARPE19 cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® PrimeView™ Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

source_name: ARPE-19 cells treated with 10 mU/ml glucose oxidase for 3h

label_protocol: Total RNAs were amplified, biotin labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit (Affymetrix, #902416).

growth_protocol: ARPE19 cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/ streptomycin.

extract_protocol: RNA was extracted using RNeasy mini kit, (QIAGEN, #P/N74104).

treatment_protocol: ARPE cells of 90% confluence were transfected with GFP. After 48 h, cells were treated with or without 10 mU/ml glucose oxidase for 3h, then lysed-stored in Trizol reagent before sending off for microarray analysis

value: Retinal pigment epithelia cell line


title: ARPE H2O2 3H-1: ARPE19 H2O2_Rep1


title: ARPE H2O2 0H-1: ARPE19_Rep1

description: Gene expression data from GFP transfected ARPE19 cells

source_name: ARPE-19 cells


title: ARPE H2O2 0H-2: ARPE19_Rep2


title: IL-10+ CD4+ T-cells spleen p2_P1

description: spleen.counts.txt


title: ARPE H2O2 3H-3: ARPE19 H2O2_Rep3


title: ARPE H2O2 0H-3: ARPE19_Rep3


title: IL-10+ CD4+ T-cells spleen p2_O8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O9

description: spleen.counts.txt


title: naïve only culture_OVA 24hr

city: Tokyo

first: Naoko

last: Negishi

address: 2-1-1 Hongo, Bunkyo-ku

department: Atopy (Allergy) Research Center

country: Japan

institute: Juntendo University Graduate School of Medicine

hyb_protocol: cDNA was hybridized to a SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Spleen CD4 T cell, naïve only culture_OVA 24hr

label_protocol: Total RNA were amplified with Ovation RNA Amplification System V2 (NuGEN Technologies). Amplified cDNA were labeled with Genomic DNA Enzymatic Labeling Kit (Agilent technologies).

extract_protocol: Total RNA was isolated from cells using RNeasy Plus mini kit (Qiagen）

treatment_protocol: Spleen cells of OVA-TCR-Tg mice were stimulated at 2.5×106 cells/mL with 0.1μg/mL TSST-1.Then, equally number of OVA-TCR-Tg mice spleen cells(1.25×106/mL)  were co-cultured with OVA(0.1mg/mL). For naïve cell only culture, spleen cells of OVA-TCR-Tg mice were stimulated at (2.5×106 cells/mL) with OVA. 24hours later, the cells were collected and CD4+ T cells by cell sorter.

tag: gender

value: female

tag: strain

value: OVA-TCR-Tg

tag: tssue


title: IL-10+ CD4+ T-cells spleen p2_O5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O7

description: spleen.counts.txt


title: coculture with anergic_OVA 24hr

source_name: Spleen CD4 T cell, coculture with anergic_OVA 24hr


title: IL-10+ CD4+ T-cells spleen p2_P9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O6

description: spleen.counts.txt


title: Control rep 2

description: small RNA sequencing


title: IL-10+ CD4+ T-cells spleen p2_P4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_O1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_N1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_M11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_L4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_K1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_J2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_H1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_I10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_G7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_F12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_E10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_D8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_C1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_A1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p2_B8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_P16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_N15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_M11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_K23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_J1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_I2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_O17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_H19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_L6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_G16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_F15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_D10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C20

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C2

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_E6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells from PBMCs (donor 2)

data_processing:
Pair-ended UMI-indexed Illumina reads were demultiplexed using cellranger mkfastq pipeline,trimmed using Trimmomatic (to 26 bp and 98 bp) followed by standard CellRanger pipeline in order to perform alignment Mm8 respective genome, read filtering and UMI counting for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Sparse matrix output files from Cellranger

source_name: T-cells from peripheral blood

extract_protocol: Libraries were generated using the 10x Genomics Chromium platform

value: blood


title: IL-10+ CD4+ T-cells from PBMCs (donor 1)


title: IL-10+ CD4+ T-cells spleen p1_C14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B8

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B7

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B5

description: spleen.counts.txt


title: MEF CRISPR KO D4 rep1

city: Oxford

first: Michal

middle: R.

last: Gdula

address: South Parks Road

country: United Kingdom

institute: Oxford University

description:
processed files in allele-sepcific alignments were generated from merged replicates
merged_data_file: HiC_D4_SmcHD1ko_Cast.homer.mergedReps.070718.txt
merged_data_file: HiC_D4_SmcHD1ko_FVB.homer.mergedReps.070718.txt

data_processing:
Hi-C reads were mapped with HiCUP pipeline 66 using bowtie2 indexes based on the FVB- Cast SNP N-masked mm10 genome. Valid sets of Hi-C ditags were obtained after removing uninformative reads (re-ligations, dangling ends, etc), as well as exact duplicates.#
Hi-C ditags were then sorted based on confident SNP content with SNPsplit into following groups: FVB-FVB, FVB-unassigned, Cast-Cast, Cast-unassigned, FVB-Cast, unassigned- unassigned. For allele-specific analysis subsets "FVB-FVB" and "FVB-unassigned" were merged into one "FVB" and similarly subsets "Cast-Cast" and "Cast-unassigned" were merged into subset "Cast".
Bam files resulting from HiCUP either sorted with SNPsplit or not sorted were conevrted with the HiCUP script “hicup2homer” into HiC ditag table (descri[tion below). Allele-sorted ditags with only one tag with informative SNP/SNPs were counted as if other ditag belonged to the same parental genome.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C ditag table
The hicup2homer script converts HiCUP BAM/SAM files to a format compatible with  Homer i.e. 7 columns, with read pairs on the same line:  Column1: index number (integer 1, 2, 3,..) Column2: forward read chromosome name Column3: forward read position Column4: forward read strand (0 = positive strand, 1 = negative strand) Column5: reverse read chromosome name  Column6: reverse read position Column7: reverse read strand (0 = positive strand, 1 = negative strand)

source_name: female clonal MEFs

growth_protocol: SmcHD1 WT, MommeD1 and CRISPR KO cell lines were grown on 5-8x145mm petri dishes in EC10 medium to semi-confluency.

extract_protocol:
Hi-C was performed as described in Belton et al. 2012 (PMID: 22652625) . For each Hi-C library 25 x 10^6 cells were cultured in EC10 media. The day of harvesting, cells were incubated in 22.5 mL of fresh media without serum, and cross-linked by adding 625 μL of 37% formaldehyde (1% final concentration). Plates were immediately mixed thoroughly after formaldehyde addition, and subsequently rocked every 2 minutes for exactly 10 minutes at RT. The cross-linking was quenched by addition of 1.25 mL of 2.5 M glycine. After 5 minutes at RT, plates were placed on ice for an additional 15 minutes. Cells were finally harvested by a cell lifter, transferred to a 15 mL falcon tubes, and centrifuged at 800 g for 10 min (4oC). The cell pellet was snap-frozen in liquid nitrogen, and stored at -80oC until use. Hi-C libraries were then sequenced on a HiSeq4000 (paired end reads of 100 bases each). Two biological replicates of WT and SmcHD1 null MEFs were sequenced in separate lanes, each yielding ~350 million reads per replicate.
Hi-C library was constructed as described in Belton et al. 2012 (PMID: 22652625)

tag: genetic background

value: Inter-specific:F2, M.m.domesticus FVB x M.m.Castaneus

tag: genotype

value: SmcHD1 CRISPR KO

tag: clone

value: D4 (derived from Wt2A1)


title: MEF CRISPR KO A3 rep2

description:
processed files in allele-sepcific alignments were generated from merged replicates
merged_data_file: HiC_A3_SmcHD1ko_Cast.homer.mergedReps.070718.txt
merged_data_file: HiC_A3_SmcHD1ko_FVB.homer.mergedReps.070718.txt

value: A3 (derived from Wt2A1)


title: MEF CRISPR KO D4 rep2


title: MEF CRISPR KO A3 rep1


title: IL-10+ CD4+ T-cells spleen p1_C22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B4

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells small intestine

data_processing:
Pair-ended UMI-indexed Illumina reads were demultiplexed using cellranger mkfastq pipeline,trimmed using Trimmomatic (to 26 bp and 98 bp) followed by standard CellRanger pipeline in order to perform alignment Mm8 respective genome, read filtering and UMI counting for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Sparse matrix output files from Cellranger

source_name: T-cells from small intestine

value: small intestine


title: IL-10+ CD4+ T-cells spleen p1_B23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B9

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen


title: MEF MUT new rep2

description:
processed files in allele-sepcific alignments were generated from merged replicates
merged_data_file: HiC_SmcHD1mutNew_Cast.homer.mergedReps.070718.txt
merged_data_file: HiC_SmcHD1mutNew_FVB.homer.mergedReps.070718.txt

value: SmcHD1 MomeD1 mutant


title: IL-10+ CD4+ T-cells spleen p1_C1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B20

description: spleen.counts.txt


title: MEF MUT rep2

description:
processed files were generated from merged replicates
mut.merged.all.260617.homer.gz
FVB.mut.mereged.all.260617.homer.gz
Cast.mut.mereged.all.260617.homer.gz

data_processing:
Library strategy: HiC-Seq
Hi-C reads were mapped with HiCUP pipeline 66 using bowtie2 indexes based on the FVB- Cast SNP N-masked mm10 genome. Valid sets of Hi-C ditags were obtained after removing uninformative reads (re-ligations, dangling ends, etc), as well as exact duplicates.#
Hi-C ditags were then sorted based on confident SNP content with SNPsplit into following groups: FVB-FVB, FVB-unassigned, Cast-Cast, Cast-unassigned, FVB-Cast, unassigned- unassigned. For allele-specific analysis subsets "FVB-FVB" and "FVB-unassigned" were merged into one "FVB" and similarly subsets "Cast-Cast" and "Cast-unassigned" were merged into subset "Cast".
Bam files resulting from HiCUP either sorted with SNPsplit or not sorted were conevrted with the HiCUP script “hicup2homer” into HiC ditag table (descri[tion below). Allele-sorted ditags with only one tag with informative SNP/SNPs were counted as if other ditag belonged to the same parental genome.
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C ditag table
Supplementary_files_format_and_content: The hicup2homer script converts HiCUP BAM/SAM files to a format compatible with  Homer i.e. 7 columns, with read pairs on the same line:  Column1: index number (integer 1, 2, 3,..) Column2: forward read chromosome name Column3: forward read position Column4: forward read strand (0 = positive strand, 1 = negative strand) Column5: reverse read chromosome name  Column6: reverse read position Column7: reverse read strand (0 = positive strand, 1 = negative strand)


title: MEF MUT rep1

description:
processed files were generated from merged replicates
wt.merged.all.260617.homer.gz
FVB.mereged.all.260617.homer.gz
Cast.mereged.all.260617.homer.gz


title: IL-10+ CD4+ T-cells spleen p1_B21

description: spleen.counts.txt


title: MEF WT new rep1

description:
processed files in allele-sepcific alignments were generated from merged replicates
merged_data_file: HiC_SmcHD1wtNew_Cast.homer.mergedReps.070718.txt
merged_data_file: HiC_SmcHD1wtNew_FVB.homer.mergedReps.070718.txt

value: wild-type


title: MEF MUT new rep1


title: MEF WT new rep2


title: IL-10+ CD4+ T-cells spleen p1_B6

description: spleen.counts.txt


title: MEF WT rep2


title: MEF WT rep1


title: IL-10+ CD4+ T-cells spleen p1_B18

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B3

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B17

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_C23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B15

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B12

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B11

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B10

description: spleen.counts.txt


title: MEF MUT G1

description: BedGraphs for chrX : unsorted reads (both), Domesticus-FVB(Xa), Castaneus (Xa); value represent repli-seq score (ratio of the read count from the cells in S-phase to the read count in the cells in G1 phase ) within 500 kb bins

data_processing:
Repli-seq reads were mapped with bowtie2
With SNPsplit programme6 and confident Cast/FVB SNPs reads were sorted into paternal, maternal and unassigned subsets.
Reads from S and G1 cell fractions were analysed in 100 kb and 500 kb bins and for each bin read number normalized S/G1 ratio was plotted.  S/G1 ratios or Z-scores of S/G1 ratios were further used for detailed analysis and visualization of chromosome-wide replication timing profiles
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
Supplementary_files_format_and_content: bedGraph file: UCSC bedgraph heading followed by the table with following columns: chr,start, end, value. Value  represents repli-seq score: ratio of the read count from the cells in S-phase to the read count in the cells in G1 phase  within 500 kb bins

growth_protocol: SmcHD1 WT, MommeD1 MUT cell lines were grown on 5-8x145mm petri dishes in EC10 medium to semi-confluency.

extract_protocol:
Asynchronously proliferating cells were flow-sorted based on their DNA content (Hoechst 33342) into G1 and S phase fractions (Fig.S6) into ice-cold PBS. Genomic DNA was isolated immediately after flow-sorting with Quick-gDNA™ MiniPrep (Zymo Research).
Sequencing libraries were prepared with Illumina TruSeq DNA PCR-Free whole genome sequencing kit and sequenced on NextSeq 550 with 150 cycles High Output kit using paired end protocol.
Repli-seq


title: MEF WT G2


title: IL-10+ CD4+ T-cells spleen p1_B2

description: spleen.counts.txt


title: MEF WT S2

description:
BedGraphs for chrX : unsorted reads (both), Domesticus-FVB(Xa), Castaneus (Xa); value represent repli-seq score (ratio of the read count from the cells in S-phase to the read count in the cells in G1 phase ) within 500 kb bins
wild_type_both_X_repliSeq_score.txt
wild_type_active_X_repliSeq_score.txt
wild_type_inactive_X_repliSeq_score.txt


title: MEF WT G1


title: MEF MUT S1


title: IL-10+ CD4+ T-cells spleen p1_A9

description: spleen.counts.txt


title: MEF MUT G2


title: IL-10+ CD4+ T-cells spleen p1_A8

description: spleen.counts.txt


title: MEF WT S1


title: CTCF_mut_rep2_ChIP_Lib_C10B_rec

description:
CTCF_mut_IP_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_IP_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_IP_Cast_merged_MEF_reciprocal030718.bedGraph.bw

data_processing:
ChIP-seq reads were mapped with bowtie2 with SNP N-masked genome index and sorted with SNP-split to separate subsets of reads originating from parental genomes.
For SmcHD1, CTCF and Rad21 ChIP-seqs macs2 was used to detect significant enrichments – narrow peaks, q-value < 0.05.
For visualisation genome-wide coverage within 50 bp were calculated normalised for sequencing depth (rpm, for all samples apart from H3K27me3 where enrichment values were scaled down to equalize the total read number to the sample with smaller number of reads). BigWig files were generated to visualize the data in the UCSC browser.
for SmcHD1 and H3K27me3 ChIP-seq geneome-wide coverages were additionally binned into 500 bp bins and log2(IP/input) tracks were generatad.
Genome_build: mm10
Supplementary_files_format_and_content: bed: Table with three columns: chr, start, end; contains peak coordinates
Supplementary_files_format_and_content: bigWig: created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

extract_protocol:
Cells were trypsinised, washed in PBS and counted. For SmcHD1 and Rad21 5x107 cells were then crosslinked in 2M Ethylene glycol-bis(succinic acid N-hydroxysuccinimide ester) (EGS, Sigma) in PBS at RT for 1hr followed by 15 min crosslinking in 1% formaldehyde. For H3K27me3 and CTCF 1x107 cells were crosslinked in 1% formaldehyde alone for 15 min at RT. Formaldehyde was quenched by addition of glycine to a final concentration of 125mM and incubation at RT for 3min. Cells were spun down at 700rpm for 4 min at 4oC and lysed in 50mM HEPES pH 7.9, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.25% Triton X100 and 2% NP40. Cellular lysis was assisted by 20 strokes of large clearance pestle in Dounce grinder and subsequent incubation for 10 min at 4oC with constant rotation. Released nuclei were spun down and washed once in 10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA and 0.5mM EGTA. Nuclei were lysed by addition of 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine. All solutions contained cOmplete EDTA-free protease inhibitors (Sigma) added fresh. Chromatin was sonicated on BioRuptor sonicator (Diagenode) to produce fragments of approximately 500 bp. Triton X100 was added to a final concentration of 1%, and insoluble pellet was removed by centrifugation at maximum speed for 10 min at 40C. Chromatin was aliquoted and stored at -80C until use.  Immunoprecipitation was performed overnight at 40C with 3-5g of specific antibody and 100 l of chromatin corresponding to 1x105 (H3K27me3, CTCF) or 5x105 cells (Rad21, SmcHD1) in 20 mM Tris-HCl pH 8.0, 1mM EDTA, 150 mM NaCl and 1% triton-x-100, with proteinase inhibitors. Antibody-bound chromatin was isolated on rProtein A Sepharose Fast Flow beads (GE Healthcare) that had been blocked for 1 h at 4°C with 1 mg/ml bovine serum albumin (NEB) and 1 mg/ml yeast tRNA (Sigma). Agarose beads with immunoprecipitated material were washed thoroughly in low salt buffer (LSB, 20mM Tri-HCl pH8.0, 2mM EDTA, 150mM NaCl, 0.1% SDS, 1% Triton X100), high salt buffer (HSB, the same as LSB but with 500mM NaCl), LiCl buffer (10MM Tris-HCl pH8.0, 1mM EDTA, 0.25 M LiCl, 1% NP40, 1% deoxycholate) and twice in TE buffer, all with proteinase inhibitors. Immunoprecipitated material was eluted from beads in elution buffer (0.1M NaHCO3, 1% SDS) with shaking on Thermomixer at RT for 30min.  Beads were removed by centrifugation, eluted chromatin was reverse cross-linked and treated with RNAse and proteinase K in the presence of 200mM of NaCl at 370C for 2 hrs followed by 650C overnight with shaking at 800rpm for 1 min every 2 min. DNA was purified using ChIP DNA Clean and Concentrator kit (Zymo Research) according to the manufacturer’s instructions.  DNA size was assessed on Bioanalyser (Agilent) and DNA was post-sonicated on Bioruptor Pico sonicator for 18-20 cycles of 30s on/30s off if necessary. DNA Concentration was quantified using PicoGreen® dsDNA Quantitation Kit (Molecular Probes), Bioanalyser High sensitivity DNA assay and/or Qubit dsDNA HS assay kit.
NEBNext (H3K27me3) or NEBNext Ultra II (CTCF, Rad21, SmcHD1) DNA Library Prep Kits for Illumina were used to prepare libraries for sequencing, following the manufacturer’s instructions.

tag: antibody


title: CTCF_mut_rep3_input_Lib_C12E_rec

description:
CTCF_mut_input_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_input_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_input_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: IL-10+ CD4+ T-cells spleen p1_B19

description: spleen.counts.txt


title: CTCF_mut_rep2_input_Lib_C10E_rec


title: MEF MUT S2

description:
BedGraphs for chrX : unsorted reads (both), Domesticus-FVB(Xa), Castaneus (Xa); value represent repli-seq score (ratio of the read count from the cells in S-phase to the read count in the cells in G1 phase ) within 500 kb bins
MommeD1mut_both_X_repliSeq_score.txt
MommeD1mut_active_X_repliSeq_score.txt
MommeD1mut_inactive_X_repliSeq_score.txt


title: IL-10+ CD4+ T-cells spleen p1_A7

description: spleen.counts.txt


title: CTCF_mut_rep3_ChIP_Lib_C12B_rec


title: IL-10+ CD4+ T-cells spleen p1_A6

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A5

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_B16

description: spleen.counts.txt


title: CTCF_wt_rep3_input_Lib_C11E_rec

description:
CTCF_wt_input_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_input_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_input_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: CTCF_mut_rep1_ChIP_Lib_C8B_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : IP from unsorted reads, reads sorted into FVB and Cast genomes
CTCF_mut_IP_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_IP_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_IP_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: CTCF_wt_rep3_ChIP_Lib_C11B_rec

description:
CTCF_wt_IP_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_IP_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_IP_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: IL-10+ CD4+ T-cells spleen p1_A4

description: spleen.counts.txt


title: CTCF_wt_rep2_input_Lib_C9E_rec


title: IL-10+ CD4+ T-cells spleen p1_A3

description: spleen.counts.txt


title: CTCF_mut_rep1_input_Lib_C8E_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : input from unsorted reads, reads sorted into FVB and Cast genomes
CTCF_mut_input_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_input_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_mut_input_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: IL-10+ CD4+ T-cells spleen p1_A23

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A21

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A24

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A22

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A20

description: spleen.counts.txt


title: H3K27me3_mut_rep3_ChIP_Lib_K18B_rec

description:
mut_IPlog_merged_MEF_reciprocal110618.bedGraph.bw
mut_IPlog_merged_MEF_reciprocal110618_FVB.bedGraph.bw
mut_IPlog_merged_MEF_reciprocal110618_Cast.bedGraph.bw


title: H3K27me3_mut_rep2_ChIP_Lib_K12B_rec


title: IL-10+ CD4+ T-cells spleen p1_A19

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A2

description: spleen.counts.txt


title: H3K27me3_mut_rep1_input_Lib_K10E_rec


title: CTCF_wt_rep1_ChIP_Lib_C7B_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : IP from unsorted reads, reads sorted into FVB and Cast genomes
CTCF_wt_IP_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_IP_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_IP_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: H3K27me3_wt_rep3_input_Lib_K17E_rec

description:
wt_IPlog_merged_MEF_reciprocal110618.bedGraph.bw
wt_IPlog_merged_MEF_reciprocal110618_FVB.bedGraph.bw
wt_IPlog_merged_MEF_reciprocal110618_Cast.bedGraph.bw


title: H3K27me3_mut_rep3_input_Lib_K18E_rec


title: IL-10+ CD4+ T-cells spleen p1_A18

description: spleen.counts.txt


title: H3K27me3_mut_rep1_ChIP_Lib_K10B_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) :log2(IP/input), log2(IP_FVB/input_FVB), log2(IP_Cast/input_Cast)
mut_IPlog_merged_MEF_reciprocal110618.bedGraph.bw
mut_IPlog_merged_MEF_reciprocal110618_FVB.bedGraph.bw
mut_IPlog_merged_MEF_reciprocal110618_Cast.bedGraph.bw


title: IL-10+ CD4+ T-cells spleen p1_A17

description: spleen.counts.txt


title: H3K27me3_wt_rep3_ChIP_Lib_K17B_rec


title: H3K27me3_mut_rep2_input_Lib_K12E_rec


title: IL-10+ CD4+ T-cells spleen p1_A15

description: spleen.counts.txt


title: CTCF_wt_rep1_input_Lib_C7E_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : input from unsorted reads, reads sorted into FVB and Cast genomes
CTCF_wt_input_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_input_FVB_merged_MEF_reciprocal030718.bedGraph.bw
CTCF_wt_input_Cast_merged_MEF_reciprocal030718.bedGraph.bw


title: H3K27me3_wt_rep2_input_Lib_K11E_rec


title: H3K27me3_wt_rep2_ChIP_Lib_K11B_rec


title: IL-10+ CD4+ T-cells spleen p1_A13

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A12

description: spleen.counts.txt


title: H3K27me3_wt_rep1_ChIP_Lib_K9B_rec

description:
processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) :log2(IP/input), log2(IP_FVB/input_FVB), log2(IP_Cast/input_Cast)
wt_IPlog_merged_MEF_reciprocal110618.bedGraph.bw
wt_IPlog_merged_MEF_reciprocal110618_FVB.bedGraph.bw
wt_IPlog_merged_MEF_reciprocal110618_Cast.bedGraph.bw


title: IL-10+ CD4+ T-cells spleen p1_A11

description: spleen.counts.txt


title: CTCF_wt_rep2_ChIP_Lib_C9B_rec


title: IL-10+ CD4+ T-cells spleen p1_A16

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells spleen p1_A1

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P20

description: SI.counts.txt


title: SmcHD1_CRISPRko_rep3

description: processed files were generated from merged bam files coming from all replicates and contain density plots (rpm, bigWigs) for both unsorted and allele-specific reads (FVB and M.m.castaneus) seperately fro each strand

data_processing:
Reads were mapped with STAR 2.5b aligner with index generated from FVB-Cast SNP N-masked genome and allele-specificaly sorted with SNPsplit.
For visualisation genome-wide coverage within 50 bp were calculated normalised for sequencing depth (rpm). BigWig files were generated to visualize the data in the UCSC browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
created form bedGraph file (table: chr, start, end, value) with the bedGraphToBigWig utility available form UCSC; scores represent sequencing-depth normalized read density or log2(IP/input)

extract_protocol:
WT, SmcHD1 null and acute SmcHD1 null MEFs were grown on 2x145mm petri dishes in EC10 medium to semi-confluency. RNA-Seq enriching for chromatin-bound nuclear RNA was performed according to a modified chromatin RNA-Seq protocol 59 . The cells were trypsinised, collected in EC10 medium and cell number was counted on LUNAII cell counter (Logos Biosystems). 1x10^7 cells for each line were spun down, resuspended in 12ml of ice cold PBS and supplemented with 2.5x10^6 SG4 drosophila cells for calibration. Cells were spun down at 500g, 5 min at 4 0 C and cell pellets were resuspended in 800l of HLBN hypotonic buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2.5 mM MgCl 2 , 0.05% NP40). 480 μl of buffer HLBNS (HLBN, 25% sucrose) was carefully under-layered to create sucrose cushion, and nuclei were isolated by centrifugation for 5 min at 1000g at 4 0 C. Supernatant containing cytoplasmic debris was discarded and the nuclear pellet was re-suspended in 100 μl of ice-cold buffer NUN1 (20 mM Tris-HCl pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol; 1 mM DTT and cOmplete EDTA free protease inhibitors (Sigma) added fresh). Nuclei were lysed in 1200 μl of ice-cold lysis buffer NUN2 (20 mM HEPES pH7.6, 300 mM NaCl, 7.5 mM MgCl 2 , 0.2 mM EDTA, 1 M urea, 1% NP40; 1 mM DTT) during 15min incubation on ice and RNA-bound chromatin was pelleted at 16000 g for 10min at 40C. Chromatin-RNA pellet was re-suspended in 200 μl of high salt buffer HSB (10 mM Tris-HCl pH 7.5, 500 mM NaCl, 10 mM MgCl 2 ). DNA and proteins were digested with Turbo DNAse (Life Sciences) and proteinase K (10 mg/ml, ThermoFisher, nuclease free), incubating on ThermoMixer at 37 0 C for 10 min and 30min, respectively. RNA was extracted with 1 ml of TRIzol (Life Sciences) according to the manufacturer guidelines. RNA was dissolved in 1xTURBO DNAse buffer, digested with TURBO DNAse for 30 min at 37o C on a ThermoMixer and extracted with TRIzol. RNA was washed three times with 75% ethanol, dissolved in water and quantified using a NanoDrop (ND-1000). RNA quality was checked with RNA 6000 Pico Chip (Agilent Technologies) on Agilent 2100 Bioanalyser (Agilent Technologies). Samples were depleted of ribosomal RNA with Ribo-Zero Gold Kit (MRZG12324, Illumina) according to manufacturer’s guidelines. RNA was isolated from 3 biological replicates. RNA-Seq libraries were prepared with NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420S) using NEBNext® Multiplex Oligos for Illumina for multiplexing (E7335S and E7500S). Libraries were sequenced on HiSeq2000 and NextSeq500 using NextSeq 500 High-Output Kit: 1 lane, 150 cycles, 75 bp paired end sequencing (Illumina).
NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®


title: SmcHD1_CRISPRko_rep1


title: SmcHD1_wt_ctr_rep3


title: IL-10+ CD4+ T-cells small intestine p2_P16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P17

description: SI.counts.txt


title: SmcHD1_wt_ctr_rep2


title: mut_rep3_input_Lib_8D


title: wt_rep3_input_Lib_7D


title: SmcHD1_CRISPRko_rep2


title: SmcHD1_wt_ctr_rep1


title: CRISPRko_D4_rep2_input_Lib_10D

value: CRISPR KO


title: CRISPRko_A3_rep2_input_Lib_9D


title: CRISPRko_D4_rep1_input_Lib_6D


title: IL-10+ CD4+ T-cells spleen p1_A14

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P14

description: SI.counts.txt


title: CRISPRko_A3_rep1_input_Lib_5D

description: processed files were generated from merged bam files coming from all replicates and contain: density plots (rpm, bidWigs) : input, input_FVB, input_Cast


title: mut_rep2_input_Lib_4D


title: H3K27me3_wt_rep1_input_Lib_K9E_rec


title: IL-10+ CD4+ T-cells spleen p1_A10

description: spleen.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_P13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O24

description: SI.counts.txt


title: wt_rep2_input_Lib_3D


title: IL-10+ CD4+ T-cells small intestine p2_P19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O21

description: SI.counts.txt


title: wt_rep1_input_Lib_1D


title: mut_rep1_input_Lib_2D


title: IL-10+ CD4+ T-cells small intestine p2_O20

description: SI.counts.txt


title: CRISPRko_A3_DC_rep2_input_Lib_19D


title: CRISPRko_D4_DC_rep1_input_Lib_16D


title: IL-10+ CD4+ T-cells small intestine p2_P15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O19

description: SI.counts.txt


title: CRISPRko_A3_DC_rep1_input_Lib_15D


title: IL-10+ CD4+ T-cells small intestine p2_O15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O17

description: SI.counts.txt


title: wt_DC_rep3_input_Lib_17D


title: CRISPRko_D4_DC_rep2_input_Lib_20D


title: mut_DC_rep3_input_Lib_18D


title: mut_DC_rep2_input_Lib_14D


title: wt_DC_rep2_input_Lib_13D


title: IL-10+ CD4+ T-cells small intestine p2_O13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_O14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N23

description: SI.counts.txt


title: wt_DC_rep1_input_Lib_11D


title: CTCF_CRISPRko_D4_rep2_ChIP_Lib_10C


title: mut_DC_rep1_input_Lib_12D


title: IL-10+ CD4+ T-cells small intestine p2_N22

description: SI.counts.txt


title: CTCF_CRISPRko_A3_rep2_ChIP_Lib_9C


title: CTCF_wt_rep3_ChIP_Lib_7C


title: IL-10+ CD4+ T-cells small intestine p2_N20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N19

description: SI.counts.txt


title: CTCF_mut_rep3_ChIP_Lib_8C


title: CTCF_CRISPRko_D4_rep1_ChIP_Lib_6C


title: IL-10+ CD4+ T-cells small intestine p2_N16

description: SI.counts.txt


title: CTCF_mut_rep2_ChIP_Lib_4C


title: CTCF_wt_rep2_ChIP_Lib_3C


title: IL-10+ CD4+ T-cells small intestine p2_N17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N14

description: SI.counts.txt


title: Rad21_CRISPRko_D4_DC_rep2_ChIP_Lib_20B


title: IL-10+ CD4+ T-cells small intestine p2_N13

description: SI.counts.txt


title: CTCF_mut_rep1_ChIP_Lib_2C

description: processed files were generated from merged bam files coming from all replicates and contain: peaks, density plots (rpm, bidWigs) : IP,  log2(IP/input), IP_FVB, log2(IP_FVB/input_FVB), IP_Cast, log2(IP_Cast/input_Cast)


title: IL-10+ CD4+ T-cells small intestine p2_M24

description: SI.counts.txt


title: Rad21_CRISPRko_A3_DC_rep2_ChIP_Lib_19B


title: IL-10+ CD4+ T-cells small intestine p2_N18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_N15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M21

description: SI.counts.txt


title: Rad21_mut_DC_rep2_ChIP_Lib_18B


title: Rad21_CRISPRko_A3_DC_rep1_ChIP_Lib_15B


title: Rad21_CRISPRko_D4_DC_rep1_ChIP_Lib_16B


title: CTCF_wt_rep1_ChIP_Lib_1C


title: Rad21_wt_DC_rep2_ChIP_Lib_17B


title: IL-10+ CD4+ T-cells small intestine p2_M20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M19

description: SI.counts.txt


title: Rad21_mut_DC_rep1_ChIP_Lib_14B


title: IL-10+ CD4+ T-cells small intestine p2_M17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M16

description: SI.counts.txt


title: Rad21_wt_DC_rep1_ChIP_Lib_13B


title: CTCF_CRISPRko_A3_rep1_ChIP_Lib_5C


title: SmcHD1_mut_DC_rep3_ChIP_Lib_18A

value: SmcHD1 (in house)


title: SmcHD1_wt_DC_rep3_ChIP_Lib_17A


title: IL-10+ CD4+ T-cells small intestine p2_M14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M13

description: SI.counts.txt


title: SmcHD1_wt_DC_rep2_ChIP_Lib_13A


title: SmcHD1_mut_DC_rep2_ChIP_Lib_14A


title: IL-10+ CD4+ T-cells small intestine p2_M15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L24

description: SI.counts.txt


title: SmcHD1_mut_DC_rep1_ChIP_Lib_12A


title: IL-10+ CD4+ T-cells small intestine p2_L19

description: SI.counts.txt


title: SmcHD1_wt_DC_rep1_ChIP_Lib_11A


title: IL-10+ CD4+ T-cells small intestine p2_L20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_M18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_K15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_L23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_J13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_I20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_H16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F16

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_G21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E23

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E21

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_F13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E20

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E22

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E18

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E13

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E15

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E14

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_E16

description: SI.counts.txt


title: Thorax_D10_rescue_batch_2_rep_5

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Labeled cRNA were hybridized to the DroGene 1.0 ST GeneChip (Affymetrix, Santa Clara, CA) according to the manufacturer’s guidelines.

scan_protocol: The Affymetrix scanner 3000 was used in conjunction with Affymetrix GeneChip Operation Software to generate one .CEL file per hybridized cRNA.

data_processing: The Expression Console (Affymetrix) was used to summarize the data contained across all .CEL files and generate 16,322 RMA normalized probe expression values.

label: Biotin

organism: Drosophila melanogaster

source_name: D10 rescue

label_protocol: Extracted RNA were processed and labeled according to the manufacturer’s guidelines for use with the DroGene 1.0 ST GeneChip (Affymetrix, GeneChip Whole Transcript Sense Target Labeling).

growth_protocol: In this study, flies were aged to 3-, 10-, 30-, or 45-days old.  14 male and 10 female newly-eclosed flies were aliquoted into a vial containing standard KD food and a strip of tegocept paper; five sets of 10 vials were collected for each genotype and time point (each replicate consisted of 90-140 male flies).  Flies were maintained at 25°C with a 12 hr∶12 hr light∶dark cycle, and were transferred to fresh vials every three days.  Once at the appropriate age, flies were anesthetized under CO2, then flash frozen in liquid nitrogen; samples were stored at -80°C until all time points were collected. Eppendorf tubes containing frozen flies were transferred into liquid nitrogen to further chill them, then vortexed to separate the heads, wings, and legs from the rest of the bodies.  Keeping the samples cold on dry ice, the heads were manually transferred to a fresh tube.  Thoraces were separated from the abdomen using a surgical blade, and then transferred to their own tube.  Separated tissues were flash frozen and stored at -80°C until all samples were collected.

extract_protocol: Isolated tissue samples were stored at -80°C prior to phenol-chloroform extraction using the TRIzol reagent.  Samples were homogenized in TRIzol, chloroform was added, and the resultant mixture centrifuged; RNA was precipitated from the upper aqueous layer using isopropanol.  Following ethanol washes, the purified RNA was resuspended in RNAse-free water and stored at -80°C.

value: Thorax

value: rescue

value: 10 Days

tag: Sex

value: male

tag: batch

tag: cross batch technical replicate

value: No


title: Nelfb-cKO 24h-2b

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: NELF-B UtcKO uterine stroma cells cultured for 24 hours with estradiol and progesterone to induce decidualization

hyb_protocol: Five micrograms (5.0 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

source_name: cultured uterine stromal cells

label_protocol: Thirty five nanograms (35 ng) of total RNA were amplified as directed in the WT-Ovation Pico RNA Amplification System (Nugen, San Carlos, CA) protocol, sense-strand cDNA target was made using the Nugen Encore Exon Module, and after fragmentation the product was labelled with the Nugen Encore Biotin biotin module.

growth_protocol: Females were mated overnight with B6D2F1/J males, and uterine  tissue was collected in the afternoon from 4 dpc females  (morning of plug detection = 0.5 dpc), slit longitudinally,minced  into 3- to 5-mm pieces, and washed several times with HBSS  (MilliporeSigma). Uteri (2 to 3 each) were then placed in a 50-ml  tubewith 5ml of 6 mg/ml dispase (Thermo Fisher Scientific) and  25 mg/ml pancreatin (MilliporeSigma) made in HBSS. Tissue  was incubated for 60 min on ice, followed by 60 min at room  temperature and then 10 min at 37°C.HBSS (30ml)with 10%FBS  was added to each tube. Tissue was washed 2 times with 10 ml  HBSS and moved to a 50-ml tube containing 0.5 mg/ml collagenase  (MilliporeSigma) and incubated for 45min at 37°C.Tubes  were vortexed until turbid. HBSS (30ml) + 10% FBS was added,  and the suspension passed through a 70-mMfilter (MACS Smart  Strainer;Miltenyi Biotec,Auburn, CA,USA). Cellswere collected  by centrifuging at 450 g for 10 min and washed twice in 10 ml  HBSS, then resuspended in DMEM-F12 (Thermo Fisher Scientific)  containing 10% heat-inactivated fetal calf serum. Cells  (400,000) in 3ml of media were seeded per well of a 6-well plate  and allowedto attach for 1 to 2 h.Wellswere thenwashed several  timeswithHBSS to remove nonadherent cells, and freshDMEMF12  containing 2%stripped fetal calf serumsupplementedwith P  (1 mM) and E (10 nM) (PE, decidual stimulus)

extract_protocol: cells were collected with Trizol for  RNA isolation

treatment_protocol: P4 (1 mM) and E (10 nM) for 24 hours

tag: nelf-b genotype

value: Cre+;flox/flox

tag: tissue

value: uterine stromal cells


title: WT24h -1b

description: WT uterine stroma cells cultured for 24 hours with estradiol and progesterone to induce decidualization

value: flox/flox


title: Nelfb-cKO 24h-2c


title: Nelfb-cKO  24h-2a


title: WT 24h-1a


title: WT 24h-1c


title: IL-10+ CD4+ T-cells small intestine p2_D24

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_D22

description: SI.counts.txt


title: Thorax_D10_rescue_batch_2_rep_1

tag: age


title: MS1227_Nicolaides-Baraitser syndrome

type: genomic

city: London

first: Bekim

last: Sadikovic

state: Ontario

address: 800 Commissioners Rd E

department: Pathology and Laboratory Medicine

country: Canada

institute: University of Western Ontario

description: SAMPLE 12

hyb_protocol: According to the manufacturer's protocol

scan_protocol: iScan

data_processing: Illumina Normalization method with background correction, using minfi package in R 3.4.2

label: Cy5 and Cy3

extract_protocol: Standard DNA extraction from blood

tag: disease state

value: Nicolaides-Baraitser syndrome

value: Whole Blood


title: Thorax_D10_rescue_batch_2_rep_2


title: MS1216_Coffin-Siris Syndrome 1

description: SAMPLE 21

label_protocol: According to the manufacturer's protocol

value: Coffin-Siris syndrome


title: IL-10+ CD4+ T-cells small intestine p2_D23

description: SI.counts.txt


title: Thorax_D10_rescue_batch_2_rep_3


title: Thorax_D10_control_batch_2_rep_6

source_name: D10 control

value: control


title: MS1237_Nicolaides-Baraitser syndrome

description: SAMPLE 13


title: MS1213_Coffin-Siris Syndrome 1

description: SAMPLE 19


title: Thorax_D10_rescue_batch_2_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_D20

description: SI.counts.txt

value: small intestine


title: Thorax_D10_control_batch_2_rep_3


title: Thorax_D10_control_batch_2_rep_5


title: MS1169_Coffin-Siris Syndrome 1

description: SAMPLE 5


title: MS1209_Coffin-Siris Syndrome 4

description: SAMPLE 17


title: IL-10+ CD4+ T-cells small intestine p2_D19

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_D18

description: SI.counts.txt


title: Thorax_D10_control_batch_2_rep_1

value: Yes


title: MS1215_Coffin-Siris Syndrome 1

description: SAMPLE 20


title: Thorax_D10_control_batch_2_rep_4


title: MS1201_Coffin-Siris Syndrome 1

description: SAMPLE 16


title: MS1243_Nicolaides-Baraitser syndrome

description: SAMPLE 15


title: IL-10+ CD4+ T-cells small intestine p2_D21

description: SI.counts.txt


title: MS1162_Coffin-Siris Syndrome 3

description: SAMPLE 2


title: Thorax_D45_control_batch_1_rep_5

source_name: D45 control

value: 45 Days


title: IL-10+ CD4+ T-cells small intestine p2_D16

description: SI.counts.txt


title: MS1170_Coffin-Siris Syndrome 1

description: SAMPLE 6


title: MS1212_Coffin-Siris Syndrome 1

description: SAMPLE 18


title: MS1223_Nicolaides-Baraitser syndrome

description: SAMPLE 11


title: IL-10+ CD4+ T-cells small intestine p2_D15

description: SI.counts.txt


title: MS1217_Coffin-Siris Syndrome 1

description: SAMPLE 22


title: MS1177_Coffin-Siris Syndrome 1

description: SAMPLE 8


title: MS1238_Nicolaides-Baraitser syndrome

description: SAMPLE 14


title: Thorax_D45_control_batch_1_rep_2


title: Thorax_D45_control_batch_1_rep_1


title: IL-10+ CD4+ T-cells small intestine p2_D14

description: SI.counts.txt


title: MS1176_Coffin-Siris Syndrome 1

description: SAMPLE 7


title: Thorax_D30_control_batch_1_rep_5

source_name: D30 control

value: 30 Days


title: Thorax_D30_control_batch_1_rep_4


title: IL-10+ CD4+ T-cells small intestine p2_D17

description: SI.counts.txt


title: IL-10+ CD4+ T-cells small intestine p2_C24

description: SI.counts.txt