title: NBM_ERCCH6

description: Normal donor 1991_with_ERCC


title: OX750_PL1G6

status: Public on May 15 2017

type: SRA

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

library_source: transcriptomic

data_processing:
RNA-Seq:Short reads (51-bp) were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat with a supplied set of known RefSeq transcripts as the input.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM) based on the RefSeq gene model using the rpkmforgenes
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: RPKM values from RNA sequencing

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
From single FACS sorted cells, cDNA was generated according to Smart-seq2 protocol
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.

treatment_protocol: Cell populations isolated by FACS sorting from human bone marrow of CML patients or normal donors

tag: bcr-abl status

value: negative

tag: tumor stage

tag: phenotype


title: OX750_PL1D11


title: OX750_PL1G2

value: positive


title: NBM_ERCCF5

description: Normal donor 1991_with_ERCC

data_processing:
RNA-Seq:Short reads (51-bp) were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat6 with a supplied set of known RefSeq transcripts as the input.
RNA-Seq: Filtering for uniquely mapping reads (removal of reads aligning with same number of mismatches to several coordinates).
RNA-Seq: Expression values were quantified as read per kilobase of transcript length per million mapped reads (RPKM) based on the RefSeq gene model using the rpkmforgenes
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: RPKM values from RNA sequencing

extract_protocol:
From single FACS sorted cells, cDNA was generated according to Smart-seq2 protocol
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.
RNA-Seq samples were sequenced on Illumina HiSeq 2000

value: normal


title: OX750_PL1E1


title: OX750_PL1C6


title: OX750_PL1B6


title: NBM_ERCCG1

description: Normal donor 1991_with_ERCC


title: OX750_PL1D4


title: NBM_ERCCF2

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3A2


title: NBM_ERCCF1

description: Normal donor 1991_with_ERCC


title: NBM_ERCCF3

description: Normal donor 1991_with_ERCC


title: NBM_ERCCF4

description: Normal donor 1991_with_ERCC


title: NBM_ERCCH2

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3A11


title: CML1266_DIAG_PL3A9


title: NBM_ERCCG4

description: Normal donor 1991_with_ERCC


title: NBM_ERCCE5

description: Normal donor 1991_with_ERCC


title: NBM_ERCCE6

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3A1


title: NBM_ERCCE3

description: Normal donor 1991_with_ERCC


title: NBM_ERCCE4

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL1B3


title: NBM_ERCCE2

description: Normal donor 1991_with_ERCC


title: NBM_ERCCE1

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL1A1


title: NBM_ERCCD6

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3E5


title: NBM_ERCCD4

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3F11


title: NBM_ERCCD3

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3F3


title: CML1266_DIAG_PL3D11


title: NBM_ERCCD1

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3A10


title: CML1266_DIAG_PL3E12


title: CML1266_DIAG_PL1A7


title: CML1266_DIAG_PL3F12


title: NBM_ERCCC5

description: Normal donor 1991_with_ERCC


title: NBM_ERCCC4

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3G12


title: CML1266_DIAG_PL3E7


title: NBM_ERCCC6

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3E11


title: CML1266_DIAG_PL3F2


title: CML1266_DIAG_PL3D6


title: NBM_ERCCC3

description: Normal donor 1991_with_ERCC


title: NBM_ERCCC2

description: Normal donor 1991_with_ERCC


title: NBM_ERCCB6

description: Normal donor 1991_with_ERCC


title: NBM_ERCCC1

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL1E5


title: CML1266_DIAG_PL3A7


title: CML1266_DIAG_PL3D2


title: NBM_ERCCB4

description: Normal donor 1991_with_ERCC


title: NBM_ERCCB3

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3D3


title: CML1266_DIAG_PL1D2


title: NBM_ERCCB2

description: Normal donor 1991_with_ERCC


title: NBM_ERCCD2

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3D8


title: NBM_ERCCA6

description: Normal donor 1991_with_ERCC


title: NBM_ERCCB1

description: Normal donor 1991_with_ERCC


title: NBM_ERCCA5

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL1G4


title: NBM_ERCCA3

description: Normal donor 1991_with_ERCC


title: NBM_ERCCA4

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3D7


title: CML1266_DIAG_PL3G8


title: NBM_ERCCA2

description: Normal donor 1991_with_ERCC


title: NBM_ERCCB5

description: Normal donor 1991_with_ERCC


title: CML1266_DIAG_PL3E4


title: CML1266_DIAG_PL1F11


title: NBM_91H2

description: Normal donor 1991


title: CML1266_DIAG_PL1B4


title: NBM_91G3

description: Normal donor 1991


title: NBM_91F5

description: Normal donor 1991


title: CML1266_DIAG_PL3G5


title: CML1266_DIAG_PL1D4


title: NBM_91F4

description: Normal donor 1991


title: CML1266_DIAG_PL3F6


title: NBM_91G5

description: Normal donor 1991


title: CML1266_DIAG_PL3E6


title: CML1266_DIAG_PL1A4


title: NBM_91F3

description: Normal donor 1991


title: NBM_91F2

description: Normal donor 1991


title: CML1266_DIAG_PL3E9


title: NBM_91E6

description: Normal donor 1991


title: NBM_91F1

description: Normal donor 1991


title: CML1266_DIAG_PL3F8


title: NBM_91E5

description: Normal donor 1991


title: CML1266_DIAG_PL3F7


title: NBM_91E4

description: Normal donor 1991


title: CML1266_DIAG_PL3D5


title: NBM_91E3

description: Normal donor 1991


title: CML1266_DIAG_PL1D10


title: NBM_91E2

description: Normal donor 1991


title: NBM_91D5

description: Normal donor 1991


title: NBM_91D2

description: Normal donor 1991


title: NBM_91D3

description: Normal donor 1991


title: CML1266_DIAG_PL3D1


title: CML1266_DIAG_PL3E8


title: CML1266_DIAG_PL1G5


title: CML1266_DIAG_PL3G6


title: NBM_91D1

description: Normal donor 1991


title: NBM_91C6

description: Normal donor 1991


title: CML1266_DIAG_PL1F6


title: CML1266_DIAG_PL1D5


title: CML1266_DIAG_PL1H7


title: CML1266_DIAG_PL3A3


title: NBM_91C3

description: Normal donor 1991


title: NBM_91B5

description: Normal donor 1991


title: NBM_91B4

description: Normal donor 1991


title: CML1266_DIAG_PL1C3


title: CML1266_DIAG_PL1F3


title: NBM_91B2

description: Normal donor 1991


title: NBM_91A5

description: Normal donor 1991


title: NBM_91B3

description: Normal donor 1991


title: CML1266_DIAG_PL3G1


title: CML1266_DIAG_PL3D9


title: NBM_91C2

description: Normal donor 1991


title: NBM_91A4

description: Normal donor 1991


title: CML1266_DIAG_PL1G7


title: NBM_91C5

description: Normal donor 1991


title: NBM_91A2

description: Normal donor 1991


title: NBM_89H8

description: Normal donor 1989


title: CML1266_DIAG_PL3A8


title: NBM_89H9

description: Normal donor 1989


title: CML1266_DIAG_PL3A4


title: NBM_91A3

description: Normal donor 1991


title: CML1266_DIAG_PL3G7


title: CML1266_DIAG_PL3A5


title: CML1266_DIAG_PL3F9


title: CML1266_DIAG_PL1H10


title: CML1266_DIAG_PL3A6


title: CML1266_DIAG_PL3A12


title: NBM_89H10

description: Normal donor 1989


title: NBM_89H6

description: Normal donor 1989


title: NBM_89H5

description: Normal donor 1989


title: CML1266_DIAG_PL3F4


title: NBM_89H4

description: Normal donor 1989


title: NBM_89G9

description: Normal donor 1989


title: CML1266_DIAG_PL3G10


title: CML1266_DIAG_PL1B8


title: CML1266_DIAG_PL1A3


title: NBM_89G8

description: Normal donor 1989


title: NBM_89G7

description: Normal donor 1989


title: CML1266_DIAG_PL3G11


title: CML1266_DIAG_PL1D7


title: NBM_89G6

description: Normal donor 1989


title: NBM_89H7

description: Normal donor 1989


title: NBM_89G5

description: Normal donor 1989


title: NBM_89G11

description: Normal donor 1989


title: CML1266_DIAG_PL1E4


title: CML1266_DIAG_PL1A6


title: NBM_89F9

description: Normal donor 1989


title: CML1266_DIAG_PL3D10


title: NBM_89G10

description: Normal donor 1989


title: NBM_89F8

description: Normal donor 1989


title: CML1266_DIAG_PL3G2


title: CML1266_DIAG_PL1A10


title: CML1266_DIAG_PL3E10


title: NBM_89F6

description: Normal donor 1989


title: CML1266_DIAG_PL1B11


title: NBM_89F11

description: Normal donor 1989


title: NBM_89E9

description: Normal donor 1989


title: NBM_89F10

description: Normal donor 1989


title: CML1266_DIAG_PL3D4


title: NBM_89E8

description: Normal donor 1989


title: CML1266_DIAG_PL1E2


title: CML1266_DIAG_PL1C4


title: NBM_89D9

description: Normal donor 1989


title: NBM_89D8

description: Normal donor 1989


title: NBM_89E11

description: Normal donor 1989


title: CML1266_DIAG_PL1F1


title: CML1266_DIAG_PL3D12


title: OX1931C12_1


title: NBM_89D11

description: Normal donor 1989


title: NBM_89D10

description: Normal donor 1989


title: OX1931H6_1


title: NBM_89C9

description: Normal donor 1989


title: OX1931C8_1


title: OX1931B8_1


title: OX1931A3_1


title: NBM_89C10

description: Normal donor 1989


title: OX1931A1_1


title: OX1931D9_1


title: NBM_89C11

description: Normal donor 1989


title: NBM_89B8

description: Normal donor 1989


title: CML1266_DIAG_PL1C10


title: OX1931E9_1


title: NBM_89C8

description: Normal donor 1989


title: NBM_89B9

description: Normal donor 1989


title: OX1931E1_1


title: NBM_89B11

description: Normal donor 1989


title: NBM_89B7

description: Normal donor 1989


title: OX1931F7_1


title: NBM_89D7

description: Normal donor 1989


title: OX1931C5_1


title: OX1931G6_1


title: OX1931A6_1


title: NBM_89A8

description: Normal donor 1989


title: CML1266_DIAG_PL3E2


title: NBM_89A9

description: Normal donor 1989


title: OX1931D7_1


title: NBM_89A7

description: Normal donor 1989


title: OX1931D1_1


title: NBM_89A6

description: Normal donor 1989


title: OX1931F9_1


title: NBM_89A5

description: Normal donor 1989


title: OX1931E6_1


title: OX1931B7_1


title: NBM_89A10

description: Normal donor 1989


title: K562H8

source_name: Cell line

value: Cell line


title: OX1931A2_1


title: NBM_89A11

description: Normal donor 1989


title: OX1931D6_1


title: OX1931H9_1


title: K562H7


title: OX1931G12_1


title: K562H6


title: K562H5


title: K562H3

value: primers


title: OX1931F5_1


title: K562H2


title: NBM_89B10

description: Normal donor 1989


title: OX1931E5_1


title: OX1931H7_1


title: K562H1


title: OX1931B6_1


title: OX1931A4_1


title: OX1931C9_1


title: K562G8


title: K562G5


title: K562G4


title: K562G3


title: OX1931D12_1


title: OX1931H1_1


title: K562G2


title: OX1931B1_1


title: K562G1


title: K562F8


title: K562F7


title: K562F5


title: OX1931D10_1


title: OX1931G7_1


title: K562F4


title: OX1931F1_1


title: OX1931G10_1


title: OX1931H11_1


title: OX1931G3_1


title: K562F2


title: K562E7


title: OX1931G8_1


title: K562E6


title: K562E5


title: K562E4


title: OX1931H8_1


title: OX1931G2_1


title: OX1931F11_1


title: OX1931G5_1


title: K562E2


title: K562D8


title: K562E1


title: OX1931C4_1


title: K562D5


title: OX1931F4_1


title: K562D4


title: OX1931B9_1


title: OX1931E4_1


title: OX1931A9_1


title: K562C7


title: K562D2


title: K562C5


title: OX1931D4_1


title: OX1931A5_1


title: OX1931C3_1


title: OX1931A8_1


title: K562C1


title: OX1931D2_1


title: OX1931C10_1


title: K562E3


title: K562B5


title: K562B4


title: K562B8


title: K562B2


title: OX1931H2_1


title: OX1931B10_1


title: OX1931F3_1


title: K562C8


title: OX1931A11_1


title: K562A8


title: OX1931E2_1


title: NBM89NEWG4

description: Normal donor 1989


title: OX1931B12_1


title: NBM89NEWC4

description: Normal donor 1989


title: NBM89NEWF4

description: Normal donor 1989


title: K562C4


title: NBM89NEWE4

description: Normal donor 1989


title: K562A5


title: K562A3


title: K562A1


title: NBM89_NEWB3

description: Normal donor 1989


title: NBM89_NEWD3

description: Normal donor 1989


title: NBM89_NEWA3

description: Normal donor 1989


title: NBM89NEWH4

description: Normal donor 1989


title: NBM89_NEWE3

description: Normal donor 1989


title: NBM89_NEWC3

description: Normal donor 1989


title: K562B1


title: NBMrunxE1

description: Normal donor lonza_age_22


title: OX1931F8_1


title: p52 ChIP-seq rep.2

city: Boston

first: Benjamin

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

department: Medicine

country: USA

institute: Brigham and Women's Hospital

description:
p52.TagDens.bd150.st50.wig.tdf
Please note that this antibody (catalog number A300-BL7037) is not listed in the company's public catalog.  You need to call them to inquire about this specific antibody.

library_source: genomic

data_processing:
Read mapping. Adaptor-trimmed Illumina reads for each individual library were mapped back to the hg19/GRCh37 build of the human genome using Bowtie v0.12.8. Aligned reads that had more than 2 mismatches or that did not map to a unique position in the genome were discarded. The "--best" and "--strata" flags were used to enable the breaking of ties using read quality scores. Samtools v0.1.19 was used to generate compressed BAM files from the bowtie output. We eliminated all reads that were mapped to genomic regions that were blacklisted by the ENCODE consortium because of their potential to cause high-signal artifacts.The blacklisted regions include centromeric and telomeric repeats, satellites and high mappability islands. For more information about how the blacklisted regions were generated, see:  https://sites.google.com/site/anshulkundaje/projects/blacklists.   To generate signal tracks for visualization, BAM files for replicate samples are merged using samtools before generating bigWig, wiggle and TDF files.
Peak calling. We used SPP v1.10 (Kharchenko et al., 2008), available from http://compbio.med.harvard.edu/Supplements/ChIP-seq/  to identify regions with high enrichment of ChIP-seq tags ("peaks"). SPP was first used to call peaks at a relaxed threshold to obtain ~300,000 peaks for each ChIP-seq replicate. To determine a threshold at which peaks were deemed to be reproducible across replicates in a statistically significant manner, we used the Irreproducible Discovery Rate (IDR) framework [Not in PubMed:  http://projecteuclid.org/euclid.aoas/1318514284]. For each subunit, we directly compared the peaks obtained in replicate experiments and set the peak calling threshold to yield an IDR of 1%.
Generation of continuous ChIP signal tracks. To generate ChIP signal tracks for visualization, we first used the fragment length estimates from SPP to computationally extend mapped reads to their predicted fragment size. Afterwards, we used Wiggler (Hoffman et al., 2013) with a smoothing window (-w) parameter of 300 to generate bigWig files for all of the experiments.   Wiggle files were converted from BAM files using the script below: https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py  Wiggle files were subsequently converted to TDF using Integrative Genomics Viewer (IGV)  (Version 2.3)
Genome_build: hg19
Supplementary_files_format_and_content: genome coverage files are provided in tdf format

molecule: genomic DNA

source_name: Lymphoblastoid cell lines

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplemented with 10% Fetalplex (Gemini) in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
GM12878 cells were cross-linked with 1% formaldehyde. Chromatin was sonicated to an average size of 500 bp. Biological replicates were obtained using cells grown on separate days. Antibodies against RelA, RelB, cRel, p50 and p52 were used to immunoprecipitate protein-DNA complexes. Captured protein-DNA complexes were eluted from protein A beads and reverse-crosslinked. Eluted DNA was purified using PCR purification columns (Qiagen).
ChIP-seq libraries were prepared using NEBNext library preparation kits (New England Biolabs)

tag: cell line

tag: antibody

value: Bethyl Laboratories #A300-BL7039


title: NBMrunxA7

description: Normal donor lonza_age_22


title: NBMrunxH1

description: Normal donor lonza_age_22


title: NBMrunxA1

description: Normal donor lonza_age_22


title: p52 ChIP-seq rep.1


title: p50 ChIP-seq rep.1

value: Santa Cruz Biotechnology #sc-1190


title: NBMrunxC5

description: Normal donor lonza_age_22


title: p50 ChIP-seq rep.2


title: K562A7


title: NBMrunxF9

description: Normal donor lonza_age_22


title: K562A6


title: K562A2


title: cRel ChIP-seq rep.2

value: Santa Cruz Biotechnology #sc-71


title: RelB ChIP-seq rep.2

value: Santa Cruz Biotechnology #sc-226


title: NBMrunxH8

description: Normal donor lonza_age_22


title: NBMrunxD2

description: Normal donor lonza_age_22


title: RelB ChIP-seq rep.1


title: NBMrunxA2

description: Normal donor lonza_age_22


title: NBMrunxA4

description: Normal donor lonza_age_22


title: cRel ChIP-seq rep.1


title: NBMrunxB8

description: Normal donor lonza_age_22


title: RelA ChIP-seq rep.1

value: Santa Cruz Biotechnology #sc-372


title: NBMrunxE4

description: Normal donor lonza_age_22


title: NBM_91_bulk100Cells

description: Normal donor 1991


title: OX967H9

value: diagnosis


title: OX1407_bulk100Cells

description: CML OX1407

value: negative/positive

value: remission


title: OX967H4


title: NBMrunxD5

description: Normal donor lonza_age_22


title: NBMrunxE9

description: Normal donor lonza_age_22


title: NBMrunxB1

description: Normal donor lonza_age_22


title: OX967H3


title: OX967H5


title: OX967H2


title: NBMrunxH3

description: Normal donor lonza_age_22


title: NBMrunxG1

description: Normal donor lonza_age_22


title: NBMrunxE7

description: Normal donor lonza_age_22


title: OX967H10_merged


title: NBMrunxE3

description: Normal donor lonza_age_22


title: NBMrunxF4

description: Normal donor lonza_age_22


title: NBMrunxD8

description: Normal donor lonza_age_22


title: OX967G2


title: NBMrunxD12

description: Normal donor lonza_age_22


title: NBMrunxB9

description: Normal donor lonza_age_22


title: NBMrunxC1

description: Normal donor lonza_age_22


title: OX967G3


title: OX967G4


title: OX967G5


title: NBMrunxD9

description: Normal donor lonza_age_22


title: OX967G9


title: OX967G11


title: NBMrunxG8

description: Normal donor lonza_age_22


title: NBMrunxF10

description: Normal donor lonza_age_22


title: OX967G10


title: OX967F9


title: NBMrunxA11

description: Normal donor lonza_age_22


title: OX967F12


title: OX967F11


title: NBMrunxA12

description: Normal donor lonza_age_22


title: OX967E6


title: NBMrunxC7

description: Normal donor lonza_age_22


title: NBMrunxC3

description: Normal donor lonza_age_22


title: NBMrunxA10

description: Normal donor lonza_age_22


title: NBMrunxG11

description: Normal donor lonza_age_22


title: OX967E5


title: OX967E3


title: NBM_NCG9

description: Normal donor NC


title: OX967G12


title: OX967E2


title: OX967E10_merged


title: NBM_NCA8

description: Normal donor NC


title: OX967E11


title: NBM_NCC10

description: Normal donor NC


title: OX967E12


title: NBM_NCF8

description: Normal donor NC


title: NBM_NCE10

description: Normal donor NC


title: NBM_NCD8

description: Normal donor NC


title: OX967D5


title: NBM_NCH9

description: Normal donor NC


title: NBM_NCG10

description: Normal donor NC


title: NBM_NCH8

description: Normal donor NC


title: OX967E1


title: OX967D6


title: NBM_NCB10

description: Normal donor NC


title: OX967D4


title: NBM_NCF9

description: Normal donor NC


title: OX967D1


title: OX967D12


title: NBM_NCG8

description: Normal donor NC


title: OX967C9


title: NBM_NCE9

description: Normal donor NC


title: NBM_NCB8

description: Normal donor NC


title: NBMpool19H6

description: Normal donor Petter


title: OX967C5


title: OX967C6


title: OX967C4


title: NBM_NCC8

description: Normal donor NC


title: OX967C3


title: OX967C12


title: OX967D9


title: NBMpool22H5

description: Normal donor Petter


title: NBMpool11H4

description: Normal donor Petter


title: NBMpool14H3

description: Normal donor Petter


title: OX967C11


title: OX967D11


title: NBMpool7H2

description: Normal donor Petter


title: NBMpool17G6

description: Normal donor Petter


title: OX967B9


title: OX967B8


title: NBMpool7G2

description: Normal donor Petter


title: OX967B5


title: OX967B6


title: NBMpool13G3

description: Normal donor Petter


title: NBMpool17G5

description: Normal donor Petter


title: NBMpool12G4

description: Normal donor Petter


title: OX967C1


title: OX967B4


title: OX967B3


title: OX967B2


title: OX967B11_merged


title: NBMpool22F5

description: Normal donor Petter


title: NBMpool19F6

description: Normal donor Petter


title: OX967B1


title: NBMpool15F4

description: Normal donor Petter


title: OX967A9


title: OX967A5


title: NBMpool7F1

description: Normal donor Petter


title: NBMpool21E6

description: Normal donor Petter


title: NBMpool8F2

description: Normal donor Petter


title: OX967A7


title: OX967A3


title: NBMpool4G11

description: Normal donor Petter


title: NBMpool1E2

description: Normal donor Petter


title: OX967A2


title: NBMpool17D5

description: Normal donor Petter


title: NBMpool13D4

description: Normal donor Petter


title: OX967A11_merged


title: OX824H9


title: NBMpool10D2

description: Normal donor Petter


title: NBMpool6G1

description: Normal donor Petter


title: NBMpool17D6

description: Normal donor Petter


title: NBMpool4D11

description: Normal donor Petter


title: NBMpool13D3

description: Normal donor Petter


title: OX967A1


title: OX824H7


title: NBMpool17C5

description: Normal donor Petter


title: NBMpool17C6

description: Normal donor Petter


title: NBMpool13F3

description: Normal donor Petter


title: OX824H5_merged


title: OX824H6


title: OX824H3


title: OX967A6


title: NBMpool6D1

description: Normal donor Petter


title: OX824H2


title: OX824H10


title: NBMpool11C4

description: Normal donor Petter


title: OX824H1_merged


title: NBMpool14C3

description: Normal donor Petter


title: OX967A12_merged


title: OX824G8


title: NBMpool14B3

description: Normal donor Petter


title: OX824G6


title: NBMpool17B6

description: Normal donor Petter


title: NBMpool6C1

description: Normal donor Petter


title: OX824H8


title: OX824G2_merged


title: NBMpool4C11

description: Normal donor Petter


title: NBMpool10B2

description: Normal donor Petter


title: NBMpool1B1

description: Normal donor Petter


title: OX824G12


title: OX824G11


title: OX824G9


title: NBMpool14B4

description: Normal donor Petter


title: OX824G3


title: NBMpool11A4

description: Normal donor Petter


title: NBMpool13A3

description: Normal donor Petter


title: OX824G10


title: OX824F9


title: NBMpool17A6

description: Normal donor Petter


title: NBMpool7A2

description: Normal donor Petter


title: OX824F8


title: NBMpool10C2

description: Normal donor Petter


title: OX824F3


title: OX824F6


title: NBMpool7A1

description: Normal donor Petter


title: CML15_diagD7


title: OX824F2


title: OX824F11


title: OX824F10


title: OX824F12


title: OX824F1_merged


title: CML15_diagD3


title: CML15_diagC10


title: OX824E9


title: CML15_diagA6


title: CML15_diagA9


title: CML15_diagA3


title: OX824E6_merged


title: OX824G1_merged


title: CML15_diagC6


title: CML15_diagD2


title: CML15_diagD6


title: OX824E1


title: CML15_diagD1


title: OX824E11


title: OX824E2_merged


title: CML15_diagA1


title: OX824E8


title: OX824D8


title: CML15_diagC8


title: OX824E10


title: OX824D9


title: CML15_diagB5


title: OX824D3_merged


title: CML15_diagB1


title: CML15_diagB2


title: OX824D2_merged


title: CML15_diagD10


title: CML15_diagA7


title: CML15_diagC11


title: OX824D11


title: CML15_diagA11


title: OX824C9


title: CML15_diagD9


title: OX824D10


title: OX824D1


title: OX824C8


title: CML15_diagB9


title: CML15_diagD4


title: OX824C3


title: CML15_diagD5


title: OX824C6


title: OX824C2_merged


title: CML15_diagC1


title: OX824C11


title: CML22_DIAGE2


title: CML22_DIAGE4


title: CML15_diagC9


title: OX824C1


title: OX824B9


title: OX824C10


title: CML22_DIAGB1


title: CML15_diagB11


title: CML22_DIAGC12


title: OX824B8


title: OX824B7


title: CML22_DIAGD8


title: OX824B6_merged


title: CML22_DIAGG1


title: CML22_DIAGA2


title: CML22_DIAGF6


title: OX824B4


title: OX824B12


title: OX824B2


title: CML22_DIAGD1


title: CML22_DIAGA9


title: OX824B11


title: OX824B1


title: CML22_DIAGA4


title: CML22_DIAGB12


title: OX824A9


title: OX824A8


title: CML22_DIAGA3


title: CML22_DIAGD9


title: OX824A7


title: CML22_DIAGE6


title: CML22_DIAGA8


title: OX824A4


title: OX824A2


title: CML22_DIAGH8


title: CML22_DIAGF8


title: OX824A12


title: OX824A11


title: CML22_DIAGH10


title: CML25_diagD3


title: OX824A10


title: CML25_diagB8


title: CML22_DIAGA6


title: CML25_diagB4


title: OX753H7


title: OX824B10


title: CML25_diagC2


title: CML25_diagA5


title: OX753H11


title: CML25_diagC12


title: CML25_diagH2


title: OX753G9


title: OX824A3


title: OX753G7


title: OX753G8


title: CML25_diagG8


title: CML25_diagF10


title: OX753G12


title: OX753G11


title: OX824A1


title: OX753H9


title: CML25_diagB1


title: CML25_diagD9


title: OX753G10


title: OX753F8


title: CML25_diagF12


title: OX753F11


title: CML25_diagF6


title: CML25_diagC1


title: CML25_diagC5


title: OX753F12


title: OX753F10


title: OX753H10


title: OX753E9


title: CML25_diagA4


title: OX753E8


title: OX753E12


title: CML655_diag_PL1B1


title: CML655_diag_PL1C1


title: CML25_diagG5


title: CML25_diagB9


title: OX753E11


title: CML655_diag_PL1H3


title: OX753D12


title: CML655_diag_PL1A2


title: OX753C12


title: CML655_diag_PL1B6


title: OX753D11


title: CML655_diag_PL1F9


title: OX753E10


title: CML25_diagE9


title: OX753B12


title: OX753B7


title: CML25_diagH8


title: CML655_diag_PL1G11


title: OX753C11


title: OX753E7


title: CML655_diag_PL1A1


title: CML655_diag_PL1F3


title: CML655_diag_PL1D7


title: OX753B11


title: OX753A8


title: OX753D9


title: OX753A12


title: CML655_diag_PL1F8


title: CML655_diag_PL1H4


title: CML655_diag_PL1C3


title: CML655_diag_PL1D5


title: OX753A10


title: OX753A11


title: OX714H9


title: CML655_diag_PL1H10


title: OX714H7


title: CML655_diag_PL1H5


title: OX753A9


title: OX714H5


title: CML655_diag_PL1G7


title: OX714H4


title: CML655_diag_PL1F12


title: CML655_diag_PL1E3


title: OX714H6


title: CML655_diag_PL1C5


title: OX714H1


title: CML655_diag_PL1B3


title: CML655_diag_PL1B5


title: CML655_diag_PL1A7


title: CML655_diag_PL1F11


title: OX714H3


title: OX714G6


title: CML655_diag_PL1D6


title: CML655_diag_PL1E11


title: OX714G7


title: OX714G5


title: OX714G4


title: CML655_diag_PL1H9


title: OX714G2


title: CML655_diag_PL1A10


title: CML655_diag_PL1F4


title: OX714G11_merged


title: CML655_diag_PL1D4


title: CML655_diag_PL1G12


title: OX714G1


title: CML655_diag_PL1C10


title: OX714F8


title: OX714H2


title: CML655_diag_PL1G4


title: CML655_diag_PL1G6


title: CML655_diag_PL1E12


title: unassigned reads from biological replicate - 3

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

institute: The Sainsbury Laboratory

description: Each biological replicate set of samples were sequenced in one lane. The raw file contains sequences unassigned to any barcode from biological replicate - 3 sequencing library.

data_processing:
Library strategy: Tag-seq
Illumina Casava1.7 software used for basecalling.
Illumina sequence library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded. Read qualities are converted from Illumina fastq to sanger fastq format
EXPRSS libraries are separated using perfect match to the barcode (at 5' end). Each sub-library is quality filtered (-q20 and -p50) and artefact filtered using FASTX-toolkit.
Quality-filtered libraries were aligned to Arabidopsis TAIR10 using Bowtie version 0.12.8, and reads with unique reportable alignments were selected. Unaligned reads from previous steps were used to align to transcript sequences of Arabidopsis Col-0 (ftp://ftp.Arabidopsis.org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/TAIR10_cdna_20101214_updated) using Bowtie version 0.12.8. Linking of each sequenced read (Tag) to gene was carried out using the following considerations: reads aligning to each gene limits were assigned to that gene; reads aligning to genes with overlapping gene limits were split equally between them; and reads aligning to more than one gene were discarded. Differential expression analysis was performed using the R statistical language version 2.11.1 with the Bioconductor package, edgeR version 1.6.15 with the exact negative binomial test using tagwise dispersions.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Arabidopsis plants were grown at 22°C and 60% humidity under a 10-h photoperiod and a 14-h dark period in environmentally controlled growth cabinets.

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
[EXPRSS] Typically 3 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Illumina flow-cell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library.

treatment_protocol: Five week old Arabidopsis plants were syringe-infiltrated with 5 x 10^5 cfu/ml of bacterial suspension at 12:00 (4h after lights on). Rosette leaf samples from non-treated, mock- and bacteria-infiltrated plants were harvested 24 hours later.

tag: ecotype

value: Columbia (Col-0)

tag: genotype

value: Wild type, 35S-StrepII-3HA-HaRxL106DSP, asil1-1, mos6-1, rcd1-1

tag: line

value: line 2B, line 5C

tag: tissue

value: leaves

tag: age

value: 5 weeks

tag: treatment

value: DC3000, Mock, untreated

tag: time point

value: 0 hpi, 24 hpi


title: unassigned reads from biological replicate - 1

description: Each biological replicate set of samples were sequenced in one lane. The raw file contains sequences unassigned to any barcode from biological replicate - 1 sequencing library.


title: CML655_diag_PL1D1

value: negative


title: CML655_diag_PL1C7


title: 106-5C no treatment rep 2

description:
Barcode sequence: TGTGCGAT
Barcode position: 5' end of the read

value: line 5C

value: untreated

value: 0 hpi


title: CML655_diag_PL1F2

value: positive


title: CML655_diag_PL1G5


title: CML655_diag_PL1D10


title: 106-5C no treatment rep 3


title: 106-5C no treatment rep 1


title: unassigned reads from biological replicate - 2

description: Each biological replicate set of samples were sequenced in one lane. The raw file contains sequences unassigned to any barcode from biological replicate - 2 sequencing library.


title: CML655_diag_PL1F5


title: rcd1 no treatment rep 3

description:
Barcode sequence: CATACGT
Barcode position: 5' end of the read


title: rcd1 no treatment rep 2


title: OX714G3


title: CML655_diag_PL1D8


title: rcd1 mock rep 3

description:
Barcode sequence: TTGCGCT
Barcode position: 5' end of the read

value: Mock

value: 24 hpi


title: rcd1 no treatment rep 1


title: rcd1 mock rep 2


title: CML656_diagD5

value: diagnosis


title: rcd1 mock rep 1


title: CML656_diagE2


title: CML656_diagD4


title: CML656_diagA12


title: CML656_diagD1


title: OX714F9


title: CML656_diagB8


title: CML656_diagD6


title: rcd1 DC3000 rep 3

description:
Barcode sequence: AACAGAGT
Barcode position: 5' end of the read


title: mos6 no treatment rep 3

description:
Barcode sequence: ACTGT
Barcode position: 5' end of the read


title: rcd1 DC3000 rep 1


title: mos6 no treatment rep 1


title: CML656_diagD9


title: CML656_diagD2


title: mos6 mock rep 3

description:
Barcode sequence: ATCCT
Barcode position: 5' end of the read


title: mos6 no treatment rep 2


title: CML656_diagB6


title: mos6 mock rep 2


title: mos6 mock rep 1


title: CML656_diagC1


title: CML656_diagB4


title: mos6 DC3000 rep 3

description:
Barcode sequence: TTGGAT
Barcode position: 5' end of the read


title: CML656_diagC8


title: CML656_diagC6


title: mos6 DC3000 rep 2


title: CML656_diagE3


title: CML656_diagB9


title: asil1 no treatment rep 3

description:
Barcode sequence: CGAGAT
Barcode position: 5' end of the read


title: rcd1 DC3000 rep 2


title: CML656_diagC12


title: CML656_diagC3


title: asil1 no treatment rep 2


title: CML656_diagB5


title: CML656_diagC5


title: asil1 mock rep 1

description:
Barcode sequence: GACACT
Barcode position: 5' end of the read


title: CML656_diagA9


title: asil1 mock rep 3


title: asil1 mock rep 2


title: asil1 DC3000 rep 3

description:
Barcode sequence: CAGAGT
Barcode position: 5' end of the read


title: asil1 no treatment rep 1


title: CML656_diagB1


title: CML656_diagB10


title: asil1 DC3000 rep 1


title: CML656_diagB3


title: CML656_diagB11


title: CML656_diagC7


title: 106-2B no treatment rep 1

description:
Barcode sequence: GCAT
Barcode position: 5' end of the read

value: line 2B


title: 106-2B no treatment rep 2


title: CML656_diagA11


title: 106-2B mock rep 3

description:
Barcode sequence: GCTCT
Barcode position: 5' end of the read


title: mos6 DC3000 rep 1


title: 106-2B mock rep 2


title: CML656_diagH9


title: CML656_diagA2


title: 106-2B mock rep 1


title: 106-2B DC3000 rep 3

description:
Barcode sequence: GTACT
Barcode position: 5' end of the read


title: 106-2B DC3000 rep 2


title: CML656_diagE4


title: CML656_diagF1


title: 106-2B DC3000 rep 1


title: CML656_diagA10


title: Col-0 no treatment rep 3

description:
Barcode sequence: AGCT
Barcode position: 5' end of the read

value: Wild type


title: asil1 DC3000 rep 2

value: Columbia (Col-0)


title: Col-0 no treatment rep 2


title: CML656_diagD11


title: CML656_diagA8


title: CML656_diagD3


title: CML656_diagB7


title: 106-2B no treatment rep 3


title: CML656_diagD12


title: Col-0 mock rep 2

description:
Barcode sequence: TCGT
Barcode position: 5' end of the read


title: Col-0 mock rep 3


title: CML656_diagA4


title: Col-0 mock rep 1


title: CML656_diagC11


title: CML656_diagB12


title: CML656_diagA3


title: Col-0 DC3000 rep 3

description:
Barcode sequence: CGGT
Barcode position: 5' end of the read


title: Col-0 DC3000 rep 2


title: Col-0 DC3000 rep 1


title: CML656_diagE7


title: CML656_diagC4


title: CML656_diagE6


title: CML940_diagB9


title: CML656_diagA7


title: CML940_diagA3


title: CML940_diagA10


title: CML940_diagA9


title: Col-0 no treatment rep 1


title: CML940_diagA7


title: CML940_diagA4


title: CML940_diagA5


title: CML940_diagA6


title: CML940_diagB12


title: CML940_diagB7


title: CML940_diagB4


title: CML940_diagB6


title: CML940_diagA11


title: CML940_diagA12


title: CML940_diagB5


title: CML940_diagA1


title: CML940_diagB3


title: CML940_diagA8


title: CML940_diagA2


title: CML656_diagC2


title: CML940_diagB8


title: CML960_diagB6


title: CML960_diagD7


title: CML960_diagB7


title: CML960_diagB4


title: macrophage regression sample 244

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse mm10) using Array Studio allowing one mismatch.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Mus musculus

source_name: macrophage

extract_protocol:
Single islet cells were captured with C1 Integrated Fluidic Circuit. Cell lysing, reverse transcription and cDNA amplification were performed on the C1 Single-Cell Auto Prep IFC, as specified by the manufacturer (Protocol #100-7168 E1). The SMARTer Ultra Low RNA Kit (Clontech) was used for cDNA synthesis from the single cells.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

value: aortic arch

tag: condition

value: regression

tag: cell type

value: macrophage


title: macrophage regression sample 242


title: CML960_diagC11


title: macrophage regression sample 241


title: CML960_diagA2


title: CML960_diagA3


title: CML960_diagA1


title: macrophage regression sample 239


title: macrophage regression sample 238


title: macrophage regression sample 240


title: macrophage regression sample 237


title: CML960_diagC5


title: CML960_diagC7


title: macrophage regression sample 235


title: CML960_diagD11


title: CML960_diagC1


title: CML960_diagA8


title: CML960_diagA11


title: CML960_diagD12


title: macrophage regression sample 236


title: macrophage regression sample 231


title: CML960_diagB11


title: CML960_diagA7


title: CML960_diagD9


title: macrophage regression sample 233


title: macrophage regression sample 232


title: macrophage regression sample 234


title: macrophage regression sample 243


title: CML960_diagA5


title: macrophage regression sample 230


title: CML960_diagD10


title: macrophage regression sample 229


title: CML960_diagC10


title: macrophage regression sample 227


title: CML960_diagA4


title: macrophage regression sample 225


title: macrophage regression sample 226


title: CML960_diagB9


title: CML960_diagD6


title: macrophage regression sample 224


title: OX2286_PL1E5


title: OX2286_PL1F1


title: macrophage regression sample 223


title: OX2286_PL1B11


title: macrophage regression sample 222


title: OX2286_PL1B1


title: OX2286_PL1C7


title: macrophage regression sample 220


title: macrophage regression sample 221


title: OX2286_PL1E4


title: CML960_diagB10


title: macrophage regression sample 218


title: OX2286_PL1C2


title: OX2286_PL1F2


title: OX2286_PL1E6


title: macrophage regression sample 219


title: macrophage regression sample 216


title: macrophage regression sample 217


title: macrophage regression sample 215


title: macrophage regression sample 228


title: OX2286_PL1C11


title: macrophage regression sample 214


title: macrophage regression sample 213


title: OX2286_PL1C8


title: macrophage regression sample 212


title: OX2286_PL1A9


title: macrophage regression sample 211


title: macrophage regression sample 210


title: OX2286_PL1E7


title: OX2286_PL1B2


title: macrophage regression sample 209


title: macrophage regression sample 208


title: macrophage regression sample 206


title: macrophage regression sample 207


title: macrophage regression sample 205


title: OX2286_PL1B6


title: OX2286_PL1G1


title: OX2286_PL1F3


title: OX2286_PL1C6


title: OX2286_PL1D11


title: macrophage regression sample 201


title: OX2286_PL1E1


title: OX2286_PL1F7


title: macrophage regression sample 202


title: macrophage regression sample 199


title: macrophage regression sample 203


title: OX2286_PL1F12


title: macrophage regression sample 200


title: macrophage regression sample 198


title: OX2286_PL1D4


title: OX2286_PL1A11


title: OX2286_PL1D6


title: OX2286_PL1A10


title: macrophage regression sample 197


title: OX2286_PL1B7


title: macrophage regression sample 196


title: OX2286_PL1B3


title: OX2286_PL1A1


title: macrophage regression sample 195


title: macrophage regression sample 204


title: macrophage regression sample 194


title: OX2286_PL1C10


title: OX2286_PL1A7


title: macrophage regression sample 193


title: OX2286_PL1F6


title: macrophage regression sample 192


title: OX2286_PL1G5


title: macrophage regression sample 190


title: macrophage regression sample 189


title: macrophage regression sample 188


title: OX2286_PL1B4


title: OX2286_PL1G6


title: macrophage regression sample 187


title: macrophage regression sample 185


title: OX2286_PL1H2


title: OX2286_PL1F4


title: macrophage regression sample 186


title: OX2286_PL1E3


title: OX2286_PL1D8


title: macrophage regression sample 182


title: macrophage regression sample 181


title: OX691F12


title: OX691E10


title: macrophage regression sample 180


title: OX2286_PL1B9


title: OX691F8


title: macrophage regression sample 179


title: macrophage regression sample 191


title: OX691D8


title: OX691H7


title: macrophage regression sample 178


title: macrophage regression sample 176


title: OX691H2


title: macrophage regression sample 175


title: macrophage regression sample 174


title: OX2286_PL1G4


title: OX691A3


title: macrophage regression sample 183


title: OX691A7


title: macrophage regression sample 184


title: OX691A5


title: OX2286_PL1D1


title: macrophage regression sample 173


title: macrophage regression sample 171


title: macrophage regression sample 172


title: OX691G1


title: macrophage regression sample 170


title: OX691A6


title: OX691G3


title: macrophage regression sample 169


title: macrophage baseline sample 167

value: baseline


title: macrophage regression sample 168


title: OX691C9


title: OX691D10


title: macrophage regression sample 177


title: macrophage baseline sample 165


title: macrophage baseline sample 166


title: OX691A11


title: OX691B6


title: OX691C2


title: macrophage baseline sample 164


title: macrophage baseline sample 163


title: macrophage baseline sample 162


title: OX691E1


title: OX691E8


title: OX691D5


title: macrophage baseline sample 161


title: macrophage baseline sample 160


title: OX691A1


title: macrophage baseline sample 159


title: macrophage baseline sample 158


title: OX691D11


title: macrophage baseline sample 157


title: OX691B9


title: OX691C10


title: macrophage baseline sample 156


title: OX691D4


title: macrophage baseline sample 154


title: macrophage baseline sample 153


title: OX691B11


title: OX691E12


title: OX691A9


title: macrophage baseline sample 152


title: OX691B5


title: OX710E9


title: OX710G5


title: OX710C4


title: OX710D4


title: macrophage baseline sample 151


title: macrophage baseline sample 148


title: macrophage baseline sample 149


title: OX691F3


title: OX710H1


title: OX710F11


title: macrophage baseline sample 146


title: OX710A4


title: macrophage baseline sample 147


title: OX710B9


title: macrophage baseline sample 145


title: macrophage baseline sample 144


title: OX710H4


title: macrophage baseline sample 155


title: macrophage baseline sample 142


title: macrophage baseline sample 143


title: OX710H6


title: macrophage baseline sample 141


title: OX710F5


title: OX710G6


title: macrophage baseline sample 150


title: macrophage baseline sample 140


title: macrophage baseline sample 138


title: OX710D6


title: macrophage baseline sample 139


title: macrophage baseline sample 137


title: OX710B8


title: OX710C2


title: OX710B7


title: OX710A5


title: macrophage baseline sample 136


title: macrophage baseline sample 135


title: OX710B10


title: macrophage baseline sample 134


title: OX710G10


title: macrophage baseline sample 133


title: OX710C8


title: OX710C11


title: macrophage baseline sample 130


title: macrophage baseline sample 132


title: macrophage baseline sample 128


title: macrophage baseline sample 129


title: OX710B3


title: OX710D5


title: OX710C6


title: macrophage baseline sample 127


title: OX710A7


title: macrophage baseline sample 126


title: macrophage baseline sample 125


title: OX710E7


title: OX710H3


title: OX710A8


title: OX710C12


title: macrophage baseline sample 123


title: OX710E6


title: macrophage baseline sample 124


title: macrophage baseline sample 122


title: OX710B2


title: macrophage baseline sample 120


title: macrophage baseline sample 119


title: OX710A1


title: macrophage baseline sample 131


title: OX710E2


title: macrophage baseline sample 118


title: macrophage baseline sample 117


title: OX710B5


title: macrophage baseline sample 116


title: OX710C5


title: OX710A6


title: macrophage baseline sample 115


title: macrophage baseline sample 113


title: OX710D7


title: OX710D3


title: OX710H9


title: macrophage regression sample 111


title: OX710E4


title: X714_NEWA6


title: macrophage regression sample 110


title: X714_NEWA1


title: macrophage regression sample 109


title: macrophage regression sample 108


title: X714_NEWA9


title: macrophage regression sample 106


title: X714_NEWA10


title: macrophage regression sample 104


title: macrophage regression sample 107


title: X714_NEWA2


title: X714_NEWA12


title: macrophage regression sample 105


title: macrophage baseline sample 114


title: macrophage regression sample 103


title: X714_NEWA4


title: OX710E10


title: X714_NEWA3


title: macrophage baseline sample 112


title: X714_NEWB1


title: macrophage regression sample 101


title: X714_NEWA5


title: macrophage regression sample 99


title: X714_NEWA8


title: X714_NEWB2


title: macrophage baseline sample 121


title: macrophage regression sample 98


title: X714_NEWB4


title: X714_NEWC10


title: macrophage regression sample 96


title: X714_NEWC6


title: macrophage regression sample 95


title: K562_BCR_ABLA8

value: primers

value: Cell line


title: K562_BCR_ABLE8


title: macrophage regression sample 102


title: K562_BCR_ABLD2


title: macrophage baseline sample 92


title: K562_BCR_ABLC2


title: OX710C7

value: negative


title: macrophage baseline sample 91


title: macrophage regression sample 93


title: K562_BCR_ABLG2


title: K562_BCR_ABLB2


title: K562_BCR_ABLF2


title: macrophage baseline sample 88


title: K562_BCR_ABLF8


title: macrophage regression sample 100


title: macrophage baseline sample 89


title: macrophage baseline sample 90


title: macrophage baseline sample 87


title: macrophage baseline sample 86


title: K562_BCR_ABLE2


title: K562_BCR_ABLG8


title: macrophage baseline sample 85


title: K562_BCR_ABLD8


title: macrophage baseline sample 84


title: macrophage baseline sample 83


title: K562_BCR_ABLA2


title: macrophage baseline sample 81


title: macrophage baseline sample 80


title: macrophage regression sample 97


title: macrophage baseline sample 79


title: K562_BCR_ABLB8


title: macrophage regression sample 94


title: K562_BCR_ABLH8


title: K562_STANDARDC1


title: K562_STANDARDG1


title: macrophage baseline sample 77


title: macrophage baseline sample 76


title: K562_STANDARDD4


title: macrophage baseline sample 78


title: K562_BCR_ABLH2


title: K562_STANDARDF1


title: macrophage baseline sample 75


title: K562_STANDARDB1


title: macrophage baseline sample 73


title: K562_STANDARDH4


title: macrophage baseline sample 72


title: K562_STANDARDH1


title: K562_STANDARDC4


title: macrophage baseline sample 82


title: macrophage baseline sample 70


title: macrophage baseline sample 69


title: K562_STANDARDB4


title: macrophage baseline sample 68


title: macrophage baseline sample 67


title: K562_STANDARDE4


title: macrophage baseline sample 66


title: K562_STANDARDA4


title: K562_STANDARDD1


title: macrophage baseline sample 65


title: K562_STANDARDF4


title: macrophage baseline sample 62


title: macrophage baseline sample 74


title: K562_T315IF12


title: K562_STANDARDA1


title: macrophage baseline sample 64


title: macrophage baseline sample 63


title: K562_T315IF6


title: K562_T315ID12


title: K562_T315IE12


title: macrophage baseline sample 61


title: macrophage baseline sample 59


title: K562_T315ID6


title: macrophage baseline sample 60


title: macrophage baseline sample 71


title: K562_T315IG12


title: K562_T315IG6


title: macrophage baseline sample 58


title: macrophage baseline sample 57


title: K562_T315IC12


title: K562_STANDARDG4


title: K562_T315IB12


title: macrophage baseline sample 56


title: macrophage baseline sample 55


title: K562_T315IH12


title: K562_T315IE6


title: macrophage baseline sample 54


title: K562_T315IA12


title: K562_T315IH6


title: K562_T315IA6


title: macrophage baseline sample 53


title: K562_T315IC6


title: macrophage baseline sample 48


title: macrophage baseline sample 51


title: macrophage baseline sample 52


title: macrophage baseline sample 50


title: CML1203F4


title: CML1203E12


title: macrophage baseline sample 49


title: macrophage baseline sample 47


title: macrophage baseline sample 45


title: CML1203F3


title: macrophage baseline sample 46


title: CML1203B5


title: macrophage baseline sample 44


title: CML1203E4


title: CML1203A4


title: macrophage baseline sample 42


title: macrophage baseline sample 43


title: CML1203A10


title: macrophage baseline sample 41


title: CML1203D8


title: CML1203A7


title: macrophage baseline sample 40


title: macrophage baseline sample 38


title: CML1203A1


title: macrophage baseline sample 37


title: CML1203D5


title: macrophage baseline sample 39


title: CML1203E1


title: macrophage baseline sample 36


title: CML1203A12


title: macrophage baseline sample 33


title: macrophage baseline sample 34


title: CML1203E6


title: macrophage baseline sample 32


title: CML1203H10


title: CML1203F6


title: macrophage baseline sample 31


title: CML1203B1


title: CML1203B6


title: macrophage baseline sample 30


title: CML1203F2


title: CML1203B10


title: macrophage baseline sample 27


title: CML1203C10


title: macrophage baseline sample 23


title: CML1203B8


title: macrophage baseline sample 24


title: CML1203A6


title: macrophage baseline sample 26


title: CML1203B7


title: CML1203C2


title: CML1203C3


title: macrophage baseline sample 25


title: macrophage baseline sample 22


title: macrophage baseline sample 21


title: CML1203G3


title: CML1203A9


title: CML1203D2


title: CML1203D6


title: macrophage baseline sample 29


title: macrophage regression sample 18


title: macrophage regression sample 19


title: CML1203B3


title: macrophage baseline sample 28


title: CML1203E2


title: macrophage regression sample 17


title: macrophage regression sample 16


title: macrophage regression sample 20


title: CML1203G6


title: macrophage regression sample 15


title: CML1203A5


title: CML1203E8


title: CML1203D9


title: macrophage baseline sample 35


title: macrophage regression sample 12


title: CML1203B4


title: macrophage regression sample 13


title: macrophage regression sample 11


title: macrophage regression sample 10


title: CML1203F10


title: CML1203C8


title: CML1203F11


title: CML1203C6


title: macrophage regression sample 7


title: macrophage regression sample 8


title: CML1203D12


title: macrophage regression sample 6


title: CML1266_PROGR_PL2H4


title: macrophage regression sample 4


title: CML1266_PROGR_PL2E9


title: CML1266_PROGR_PL2F6


title: macrophage regression sample 5


title: macrophage regression sample 3


title: CML1266_PROGR_PL2B3


title: macrophage regression sample 2


title: macrophage regression sample 1


title: CML1266_PROGR_PL2E2


title: CML1266_PROGR_PL2H1


title: macrophage regression sample 14


title: CML1203F5


title: CML1266_PROGR_PL2E8


title: CML1266_PROGR_PL2C12


title: naïve mice mPFC_MeDIP-Seq

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
MeDIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 2
wig file was generated using MeDIPS with window size 50
Genome_build: mm10
Supplementary_files_format_and_content: wig

source_name: naïve mice mPFC

extract_protocol:
Genomic DNA was extracted using standard Phenol-chloroform protocol and Rnase treated before MeDIP and library preparation
NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB, E6240 kit)

value: medial Prefrontal cortex

value: 3 months

tag: strain

value: MethyCytosine antibody (Eurogentech, BI-MECY-0100 )


title: macrophage regression sample 9


title: CML1266_PROGR_PL2C9

value: positive


title: CML1266_PROGR_PL2D9


title: CML1266_PROGR_PL2A4


title: Mouse_1cell_embryo_br1

city: Zagreb

first: Vedran

last: Franke

address: Horvatovac 102a

department: Department of biology

country: Croatia

institute: University of Zagreb

data_processing:
Reads were Mapped to the mm10/mesAur1 genome versions. Using the STAR aligner.
Coverage tracks were constructed using UCSC tools
Genome_build: mm10, mesAur1
Supplementary_files_format_and_content: bw files were generated in a non stranded mode using UCSC tools. The tracks are not normalized for library size

growth_protocol: Oocytes and early embryos were obtained from superovulated CBA/CAJxC57Bl6/J F1 hybrid mice as described previously (Nagy, 2003). Hamster fully-grown GV oocytes were collected the same way from as mouse oocytes except of superovulation, which was not used. Resumption of meiosis during culture of GV oocytes was prevented with 0.2 mM 3-isobutyl-1-methyl-xanthine (IBMX, Sigma). Animal experiments were approved by the Institutional Animal Use and Care Committees and were carried out in accordance with the law.

extract_protocol:
RNA was released from small number of oocytes upon incubation in water with RNase inhibitor for 5 min at 85°C. RNA was reverse-transcribed using RevertAid First Strand cDNA Synthesis Kit (Fermentas). Real-time PCR was carried out on LightCycler 480 System (Roche). Each reaction (10 µl) consisted of 5 µl Maxima® SYBR Green qPCR Master Mix (Fermentas), 0.4 µl mixed gene-specific forward and reverse primers (30 µM each) and 2 µl diluted cDNA. Each sample was run in triplicate.
Total RNA was extracted from 25 oocyte using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific, Philadelphia, PA). Each sample was spiked in with 0.2pg synthesized Renilla Luciferase mRNA before extraction as normalization control. RNAseq libraries were constructed by using Ovation RNA-seq system V2(NuGEN, San Carlos, CA) followed by Ovation Ultralow Library system(DR Multiplex System, NuGEN, San Carlos, CA).

value: zygote


title: Mouse_MII_oocyte_br2

extract_protocol: Total RNA was extracted from 25 oocyte using PicoPure RNA Isolation Kit with on-column genomic DNA digestion according to the manufacturer’s instruction (Thermo Fisher Scientific, Philadelphia, PA). Each sample was spiked in with 0.2pg synthesized Renilla Luciferase mRNA before extraction as normalization control. RNAseq libraries were constructed by using Ovation RNA-seq system V2(NuGEN, San Carlos, CA) followed by Ovation Ultralow Library system(DR Multiplex System, NuGEN, San Carlos, CA).

value: oocyte


title: Mouse_1cell_embryo_br3


title: CML1266_PROGR_PL2F4


title: Mouse_1cell_embryo_br2


title: CML1266_PROGR_PL2D7


title: Mouse_GV_oocyte_br2


title: CML1266_PROGR_PL1A8


title: RNAseq_A5-ProE-shPHB2-rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using DEseq.
Genome_build: hg19
Supplementary_files_format_and_content: text file of gene read count values
Supplementary_files_format_and_content: text file of gene RPKM values

source_name: Human primary adult proerythroblasts (ProEs)

growth_protocol: Human primary adult HSPCs and erythroblasts were expanded and differentiated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, 0.1-2 ug of total RNA was processed for library generation using the TruSeq RNA Sample Preparation v2 Kit (illumina) following the manufacturer’s protocol.

value: CD34+ HSPC-derived proerythroblasts

tag: developmental stage

value: bone marrow

tag: shRNA


title: CML1266_PROGR_PL2H3

tag: bcr-abl status


title: Mouse_GV_oocyte_br1


title: RNAseq_A5-ProE-shPHB2-rep1


title: Mouse_GV_oocyte_br3


title: CML1266_PROGR_PL2D1

tag: tumor stage


title: CML1266_PROGR_PL2G11

tag: phenotype


title: CML1266_PROGR_PL2C3


title: RNAseq_A5-ProE-shTFAM-rep2

value: shTFAM


title: CML1266_PROGR_PL2B5


title: Mouse_MII_oocyte_br3


title: CML1266_PROGR_PL2E3


title: CML1266_PROGR_PL2A5


title: naïve mice mPFC_input DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
MeDIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 2
wig file was generated using MeDIPS with window size 50
Genome_build: mm10


title: RNAseq_A5-ProE-shNT-rep2

value: shNT


title: RNAseq_A5-ProE-shTFAM-rep1


title: Mouse_MII_oocyte_br1


title: RNAseq_A5-ProE-shNT-rep1


title: CML1266_PROGR_PL1A9


title: Input_K562

description: Input DNA

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using Bowtie v0.12.7 with the following parameters: -v 2 -m 3 --strata --best. Duplicate reads were removed after the aligment with the Picard command-line tools.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by NextSeq500.
Genome_build: hg19
Supplementary_files_format_and_content: wig file and peak bed file

source_name: Human K562 cells

growth_protocol: Human K562 cells were cultured in IMDM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 10-20 ng of ChIP DNA was processed for library generation using the NEBNext ChIP-seq Library Prep Master Mix following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

tag: cell line

tag: chip antibody


title: H3K27ac_K562_TFAM-sh2

description: ChIP DNA

value: Abcam ab4729


title: CML1266_PROGR_PL2C8


title: CML1266_PROGR_PL2D5


title: CML1266_PROGR_PL2F1


title: H3K27ac_K562_TFAM-sh1

description: ChIP DNA


title: CML1266_PROGR_PL2B1


title: CML1203A11


title: CML1266_PROGR_PL2E7


title: AB1955

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Paired-end fastq files.  Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [A*.txt] tab-delimited text files include mRNA molecule count values for each Sample; single cell expression matrixes
[metadata.txt] Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: monocytes

growth_protocol: 7 to 16 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

tag: genotype/variation

value: wt

value: 7 W

tag: Sex

value: female

value: blood

tag: cell type (monocyte subset)

value: total monocytes

tag: selection marker

value: CD115-biotin MACS pre-enrichment followed by FACS sorting. Monocyte were sorted as lineage negative (B220, CD19, CD3, NK1.1, Ly6G, TCRγδ), CD11b+ and CD115+.


title: AB1954

tag: age

tag: tissue


title: CML1266_PROGR_PL2E11


title: AB1956

value: Ly6Cint monocytes

value: CD115-biotin MACS pre-enrichment followed by FACS sorting. Monocyte were sorted as lineage negative (B220, CD19, CD3, NK1.1, Ly6G, TCRγδ), CD11b+, CD115+ and Ly6Cint.


title: CML1266_PROGR_PL2A7


title: CML1266_PROGR_PL2C5


title: CML1266_PROGR_PL2E10


title: AB1953


title: CML1266_PROGR_PL1D11


title: AB1346


title: AB1345


title: CML1266_PROGR_PL2F11


title: CML1266_PROGR_PL2C6


title: Spleen-Trans-48h-B

description:
used for Suppl. Fig. 3
RNA_exp_spleen.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
FastQ files were indexed and mapped for Mm9 genome assembly using HISAT 0.1.5
SAM files were converted to BAM using SAMtools
Gene count and normalization was done using Homer
Genome_build: mm9
Supplementary_files_format_and_content: [RNA_Expression.txt, RNA_Exp_triplicates.txt, RNA_exp_spleen.txt] tab-delimited text files include mRNA molecule count values for each Sample

source_name: spleen

treatment_protocol: FACS sorted cells after ACK

value: spleen

tag: transfer

value: 48h after transfer


title: Spleen-Trans-48h-C


title: Spleen-Trans-36h-C

value: 36h after transfer


title: Spleen-Trans-24h-C

value: 24h after transfer


title: Spleen-Gr1-P-B

value: Ly6C+ host cells (24h)


title: Spleen-Trans-36h-B


title: H3K27ac_K562_shNT

description: ChIP DNA


title: CML1266_PROGR_PL2C1

value: positive


title: Spleen-Trans-24h-B


title: CML1266_PROGR_PL2G10


title: CML1266_PROGR_PL2H5


title: Spleen-Gr1-M-B

value: Ly6C- host cells (24h)


title: Spleen-Gr1-M-A


title: CML1266_PROGR_PL1A11


title: Spleen-Gr1-Int-B

value: Ly6Cint host cells (24h)


title: Spleen-Gr1-P-A


title: CML1266_PROGR_PL1D6


title: CML1266_PROGR_PL2D12


title: CML1266_PROGR_PL1E5


title: Spleen-Gr1-Int-A


title: CML1266_PROGR_PL2C7


title: CML1266_PROGR_PL2H2


title: CML1266_PROGR_PL1F2


title: Ly6C-P-Before-transf-A

description:
used for Fig. 2 and Suppl. Fig. 3
RNA_exp_spleen.txt

source_name: bone marrow

treatment_protocol: FACS sorted cells; BM was crushed and positive enriched without ACK with CD115-biotin MACS

value: bone marrow

value: Before transfer


title: CML1266_PROGR_PL1A7


title: CML1266_PROGR_PL2D8


title: Ly6C-P-Before-transf-B

value: Before Transfer


title: Gr1-P-Blood-B

description:
used for Fig. 2
RNA_exp_spleen.txt

source_name: blood

treatment_protocol: FACS sorted cells after ficoll


title: Gr1-M-Blood-B

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Gr1-P-Blood-A

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Gr1-M-Blood-A

description:
used for Fig. 2
RNA_exp_spleen.txt


title: CML1266_PROGR_PL1E3


title: CML1266_PROGR_PL1D5


title: CML1266_PROGR_PL1D9


title: CML1266_PROGR_PL1E4


title: CML1266_PROGR_PL2A11


title: CML1266_PROGR_PL1E7


title: Blood-Trans-36h-B

description:
used for Fig. 2
RNA_exp_spleen.txt


title: CML1266_PROGR_PL1A10


title: Gr1-INT-Blood-B

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Blood-Trans-36h-AC

description:
used for Fig. 2
RNA_exp_spleen.txt


title: CML1266_PROGR_PL1D12


title: CML1266_PROGR_PL2A12


title: Blood-Trans-48h-AC

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Blood-Trans-24h-B

description:
used for Fig. 2
RNA_exp_spleen.txt


title: CML1266_PROGR_PL1A3


title: CML1266_PROGR_PL1A6


title: CML1266_PROGR_PL1A5


title: CML1266_PROGR_PL1F3


title: CML1266_PROGR_PL1D10


title: Blood-Ly6Cneg-II-2

description:
used for Fig. 1 and Suppl. Fig. 1
RNA_Exp_triplicates.txt

treatment_protocol: FACS sorted cells; blood monocytes were positive enriched without ACK with CD115-biotin MACS


title: Blood-Ly6Cneg-I-1


title: CML1266_PROGR_PL1E12


title: CML1266_PROGR_PL1E11


title: Blood-Ly6Cint-I-1


title: Blood-Trans-48h-B

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Blood-Ly6Cint-II-2


title: CML1266_PROGR_PL1B4

value: negative


title: Gr1-INT-Blood-A

description:
used for Fig. 2
RNA_exp_spleen.txt

value: blood


title: Blood-Ly6Cint-III-3


title: CML1266_PROGR_PL2F10


title: Blood-Ly6Cpos-I-1


title: CML1266_PROGR_PL1B7


title: CML1266_PROGR_PL1F10


title: CML1266_PROGR_PL2D2


title: CML1266_PROGR_PL1A12


title: BM-Ly6Cneg-I-1


title: Blood-Ly6Cpos-III-3


title: CML1266_PROGR_PL1D7


title: CML1266_PROGR_PL1E10


title: BM-Ly6Cneg-IV-4


title: Blood-Trans-24h-AC

description:
used for Fig. 2
RNA_exp_spleen.txt


title: Blood-Ly6Cpos-IV-4


title: CML1266_PROGR_PL1H9


title: Blood-Ly6Cneg-III-3


title: CML1266_PROGR_PL1E2


title: BM-Ly6Cneg-II-2


title: BM-Ly6Cneg-III-3


title: BM-Ly6Cpos-IV-4


title: BM-Ly6Cpos-I-1


title: BM-Ly6Cpos-III-3


title: BM-cMoP-I-1


title: BM-cMoP-IV-4


title: BM-cMoP-II-2


title: BM-cMoP-III-3


title: WT_RNAseq_lot1

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Basecalls performed using bcl2fastq version 2.17.1.14
Sequence reads were aligned to the mm9 genome assembly using Tophat2 version 2.1.0
The quantification of transcripts, Fragments Per Kilobase of exon per Megabase of library size (FPKM) was calculated by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM_matrix.txt incuding FPKM for each sample

source_name: Embryonic stem cells

growth_protocol: Cells were cultured in Glasgow minimum essential medium (Sigma-Aldrich) containing 10% fetal bovine serum, 1000 U/ml recombinant LIF (Nacalai Tesque Inc.), 1 mM sodium pyruvate (Nacalai Tesque Inc.), 0.1 mM non-essential amino acids (Nacalai Tesque Inc.), 0.1 mM β-mercaptoethanol (Nacalai Tesque Inc.), and penicillin/streptomycin (Nacalai Tesque Inc.). They were cultured on gelatin-coated plates at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was harvested and Libraries were generated by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells

tag: passages

tag: genotype

value: wild type


title: Chd2KO_RNAseq_lot2

tag: cell type

tag: strain

value: Chd2 mut/mut


title: ZHBTc4_Dox_plus_input2_lot2

data_processing:
Basecalls performed using bcl2fastq version 2.17.1.14
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.2.6
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using the following specifications. We counted the number of ChIP-seq unique tags in each 1 kbp width and 100 bp sliding window on the genome and normalized as reads per kbp per million (RPKM)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's instructions.

tag: antibody


title: WT_RNAseq_lot2


title: Blood-Ly6Cpos-II-2


title: Chd2KO_RNAseq_lot1


title: BM-MDP-I-1


title: ZHBTc4_Dox_plus_input1_lot2


title: ZHBTc4_Dox_plus_H3v3_lot2

value: H3.3 (rat monoclonal antibody using in Harada,A et al, The EMBO Journal, 2012.)


title: ZHBTc4_Dox_plus_H3K27me3_lot2

value: H3K27me3 (mouse monoclonal antibody provided by Dr. H. Kimura using in Kimura H et al., Cell Struct. Funct., 2008.)


title: BM-MDP-IV-4


title: ZHBTc4_Dox_plus_H3K27me3_lot1


title: ZHBTc4_Dox_plus_H3v3_lot1


title: ko-I-Ly6Cint

description:
used for Fig. 5
RNA_Expression.txt

value: mixed background


title: BM-MDP-II-2


title: ko-I-Ly6C-P

description:
used for Fig. 5
RNA_Expression.txt


title: ko-II-Ly6Cint

description:
used for Fig. 5
RNA_Expression.txt


title: ZHBTc4_Dox_minus_input2_lot2


title: ko-II-Ly6C-P

description:
used for Fig. 5
RNA_Expression.txt


title: ZHBTc4_Dox_minus_input1_lot2


title: wt-II-Ly6C-M

description:
used for Suppl. Fig. 2 and Fig. 5
RNA_Expression.txt


title: ZHBTc4_Dox_minus_H3K27me3_lot2


title: ZHBTc4_Dox_minus_H3v3_lot2


title: wt-I-Ly6C-M


title: ZHBTc4_Dox_minus_input_lot1


title: wt-I-Ly6Cint


title: wt-II-Ly6Cint


title: wt-I-Ly6C-P


title: wt-II-Ly6C-P


title: ZHBTc4_Dox_minus_H3v3_lot1


title: Chd2KO_input2_lot2


title: ZHBTc4_Dox_minus_H3K27me3_lot1


title: BM-MDP-III-3


title: CMOPS-II

description:
used for Suppl. Fig. 2
RNA_Expression.txt


title: BM-Ly6C-P-II


title: Chd2KO_H3v3_lot2


title: ZHBTc4_Dox_plus_input1_lot1


title: CMOPS-I


title: Chd2KO_H3K4me3_lot2

value: H3K4me3 (mouse monoclonal antibody provided by Dr. H. Kimura using in Hayashi-Takanaka,Y et al., Nucleic Acids Research, 2011. )


title: BM-Ly6C-P-I


title: Chd2KO_H3K27me3_lot2


title: MDP-II


title: Chd2KO_H3K27ac_lot2

value: H3K27ac (mouse monoclonal antibody provided by Dr. H. Kimura using in Hayashi-Takanaka,Y et al., Nucleic Acids Research, 2011. )


title: MDP-I


title: Blood_Ly6C_P_K4me3

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired  end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

value: Ly6C+ monocytes

value: female

tag: chip antibody cat#


title: Blood_Ly6C_P_K4me2


title: Blood_Ly6C_P_K27ac


title: Chd2KO_H3K4me3_lot1


title: Chd2KO_H3K4me3_input_lot1


title: Chd2KO_H3_lot1

value: H3 (Abcam, ab1791)


title: B_Ly6C_int_I_K4me3

value: Ly6Cint monocytes


title: Chd2KO_H3_lot2


title: B_Ly6C_int_I_K4me2


title: Chd2KO_input1_lot2


title: Chd2KO_input_lot1


title: Chd2KO_H3K27ac_lot1


title: B_Ly6C_int_I_K27ac


title: B_Ly6C_M_K4me3

value: Ly6C- monocytes


title: Chd2KO_H3K27me3_lot1


title: WT_H3_lot2


title: B_Ly6C_M_K27ac


title: B_Ly6C_M_K4me2


title: WT_I_Ly6C_int_input


title: Rice ARF4 rep3

city: Shanghai

first: Zejun

last: Hu

address: Yangpu District Songhu Road No. 2005

country: China

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryza sativa Japonica Group

source_name: Grain

extract_protocol:
Rice grains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nipponbare

value: Caryopsis

value: post flowering day 9


title: Chd2KO_H3_input_lot1


title: Rice ARF4 rep1


title: Rice ARF4 rep2


title: WT_input2_lot2


title: WT_I_Ly6C_M_input_B


title: WT_input1_lot2


title: WT_H3K4me3_lot2


title: WT_H3K27ac_lot2


title: WT_I_Ly6C_M_input_A


title: WT_II_Ly6C_P_input


title: WT_H3K27me3_lot2


title: Rice GSK5 rep3


title: WT_H3v3_lot2


title: WT_I_Ly6C_P_input


title: Rice GSK5 rep1


title: Chd2KO_H3v3_lot1


title: WT_I_Ly6C_int


title: Rice WT rep3


title: WT_H3_input_lot1


title: WT_Ly6C_M


title: WT_Ly6C_P


title: Rice WT rep2


title: Rice WT rep1


title: WT_H3K4me3_input_lot1


title: WT_H3_lot1


title: WT_H3K4me3_lot1


title: Ez_PolII-GA0200_ChIPSeq

city: baltimore

first: Xin

last: Chen

state: MD

address: 3400 N Charles St

department: Biology

institute: The Joihns Hopkins University

data_processing:
All reads were aligned to the Drosophila genome (dm3) using the ELAND (Efficient Local Alignment of Nucleotide Data) software, allowing up to two mismatches with the reference sequence.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dm3 whole genome using ELAND software. Only uniquely mapped reads were retained. For multiple identical reads, at most three copies were retained to reduce the possibility of biases from PCR amplification.
The output of the Genome Analyzer pipeline was converted to browser extensible data (BED) files. The wig files used for visualization on the UCSC browser were generated from the uniquely mapped reads using a 4-bp window and 160 bp as the DNA fragment size, as previously described (Barski A, et al. Cell 2007).
To determine the regions used for modified histone and Pol II occupancy of annotated transcripts, we first plotted each histone modification and Pol II using the entire annotated transcripts that are applicable for ChIP-seq analysis. Based on the overall enrichment plot, we used the region of -250 to +250 bp (TSS was defined as 0) to calculate the Pol II enrichment of individual transcript. The 0 to +500 bp window was used for H3K4me3 enrichment calculations.
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: bed and graph files.

organism: Drosophila melanogaster

source_name: testis, E(z)61 bam double mutant, PolII ChIP

growth_protocol: Flies were raised using standard medium at 25oC unless stated otherwise.

extract_protocol:
For each modified histone and Pol II ChIP experiment, we dissected 200 pairs of bam testes and 200 pairs of E(z)61 bam testes in cold PBS and grouped them in 200ml PBS which contained protease inhibitor (Roche complete mini, # 11836153001) and 0.5mM PMSF (MP Biomedicals, #195381). We then added 5.5ml 37% fresh formaldehyde (Supelco, # 47083-U) and incubated at 37oC for 15 mins. The testes were washed twice with 450ml cold 1x PBS (with inhibitors and PMSF). Then 200ml lysis buffer (50mM Tris-HCl, pH7.6, 1mM CaCl2, 0.2% Triton X-100, 5mM butyrate, 1x proteinase inhibitor cocktail, and 0.5mM fresh PMSF) was added and the tissues were homogenized thoroughly followed by incubation at room temperature (RT) for 10 mins. Chromatin was sheared into approximately 200 bp fragments by sonication using Microtip (Misonix, Inc, Microson XL-2000). Chromatin was prepared and ChIP-seq experiments were performed similarly as described previously (Barski A, et al. Cell 2007) with the following antibodies: Pol II (Abcam ab5408), H3K4me3 (Abcam ab8580).
ChIP-seq library construction experiments were performed similarly as described previously (Barski A, et al. Cell 2007). Briefly, PNK and Klenow enzymes were used for ChIP DNA end repair, and Taq polymerase used for generating a protruding 3′ A base. After Solexa adaptor ligation, the ChIP DNA was amplified using the adaptor primers for 17 cycles, around 220 bp fragments were isolated from agarose gel. The purified DNAs were used directly for cluster generation and sequencing analysis using the Solexa 1G Genome Analyzer following manufacturer protocols.

treatment_protocol: The E(z)61 bam1/E(z)61 bam114-97 flies were raised at 29°C for three days before eclosion.

value: E(z)61 bam double mutant

value: Testis

value: RNA Pol II (Abcam, ab5408)


title: Blood_Ly6C_M_II

data_processing:
fastq using bcl2fastq
alignment using bowtie2  (--local,  mm9)
filter out reads that align to same place and sequence on R2 from nucleotides #1 to #15 are identical
makeTagDirectory -tbp
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9

value: monocytes

tag: isolation method

value: FACS sorted cells; blood monocytes were positive enriched without ACK with CD115-biotin MACS


title: Rice GSK5 rep2


title: Ez_H3K4me3_GA0199_ChIPSeq

source_name: testis, E(z)61 bam double mutant, H3K4me3 ChIP

value: H3K4me3 (Abcam, ab8580)


title: Blood_Ly6C_int_II


title: WT_input_lot1

value: Embryonic stem cells


title: WT_H3v3_lot1

value: H3.3 (rat monoclonal antibody using in Harada,A et al, The EMBO Journal, 2012.)


title: Blood_Ly6C_P_I


title: Blood_Ly6C_P_II


title: WT_H3K27ac_lot1

value: H3K27ac (mouse monoclonal antibody provided by Dr. H. Kimura using in Hayashi-Takanaka,Y et al., Nucleic Acids Research, 2011. )


title: Blood_Ly6C_int_I


title: Fetal HSC RISP KO rep3

data_processing:
Sequencing reads were aligned to mouse genome assembly mm9 by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: text file of gene RPKM values and read count values

source_name: Mouse fetal liver HSC

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, 1~10 ng of total RNA was processed for library generation using the SMARTer® Stranded Total RNA-seq Kit – Pico Input Mammalian (Takara-Clontech) following the manufacturer’s protocol.

value: RISP knockout

value: Hematopoietic cells


title: WT_H3K27me3_lot1

value: H3K27me3 (mouse monoclonal antibody provided by Dr. H. Kimura using in Kimura H et al., Cell Struct. Funct., 2008.)


title: Fetal HSC RISP KO rep2


title: PBAT_60_65

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
RRBS reads were trimmed to remove poor quality calls and adapters using Trim Galore v0.3.5 (parameters --rrbs) and mapped to the mouse genome GRCm38 assembly by Bismark (Krueger and Andrews, 2011) v0.14.0 (options --phred64-quals).  For PBAT data, trimmed reads (Trim Galore v0.3.5 using default parameters) were first aligned to GRCm38 in paired-end mode to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode.  Alignments were carried out with Bismark v0.10.0 with the following set of parameters: --pbat for paired-end mode, --pbat for single-end mode for read 1 and default parameters for single-end mode read 2.  Reads were then deduplicated with Bismark selecting a random alignment for positions that were covered more than once.  CpG, CHH and CHG methylation calls were extracted using the Bismark methylation extractor (v0.10.0) with the following parameters: --no_overlap --report --ignore 4 --ignore_r2 4 for paired-end mode and --report --ignore 4 for the single-end mode.  Published bisulphite-sequencing data were processed as described previously (Veselovska).  Raw RNA-seq reads were trimmed to remove both poor quality calls and adapters using TrimGalore v.0.2.8 and mapped to GRCm38 using TopHat v.2.0.9 (option –g 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Read counts (RPKM-like) RNA-Seq data file is comma delimited and contain the following columns: (1) Gene ID,(2) Chrromosome,(3) Start,(4) End,(5) Strand,(6-14) Sample Read Counts. The values were corrected for the length
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>. It combined both the single-end and paired-end alignments.

source_name: 60-65um oocytes

extract_protocol:
As in Stewart et al. (2015): Cells were lysed in EB buffer (Qiagen) with 0.5% SDS (Sigma, 161-0418) and bisulfite-treated using theone-stepmodification procedure in the Imprint DNA modification kit(Sigma,MOD50-1KT).The resulting DNA was purified using the EZ DNA methylation direct kit (Zymo, D5020). First strand synthesis was performed using Klenow Exo− (New England Biolabs, M0212S) and a custom streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs (bp) of random sequence (9N). This was followed by exonuclease I treatment (New England Biolabs, M0293S), purification using SPRI beads (1.8× ratio; Fisher Scientific, 09-981123), and binding to biotin beads (Life Technologies, 11205D). Samples were then subjected to second strand synthesis, again using custom primer, followed by 10 cycles of library amplification using Phusion polymerase (Thermo Scientific, F-530S) before final purification using SPRI beads.
RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNasefree DNase I, Life Technologies).
For RNA-seq libraries:  Reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTP excision step by USER Enzyme (NEB) before PCR. RRBS: Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas).  Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 18 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene).  DNA was purified using SPRI beads (Agencourt).  For PBAT: As in Stewart et al. (2015): Cells were lysed in EB buffer (Qiagen) with 0.5% SDS (Sigma, 161-0418) and bisulfite-treated using theone-stepmodification procedure in the Imprint DNA modification kit(Sigma,MOD50-1KT).The resulting DNA was purified using the EZ DNA methylation direct kit (Zymo, D5020). First strand synthesis was performed using Klenow Exo− (New England Biolabs, M0212S) and a custom streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs (bp) of random sequence (9N). This was followed by exonuclease I treatment (New England Biolabs, M0293S), purification using SPRI beads (1.8× ratio; Fisher Scientific, 09-981123), and binding to biotin beads (Life Technologies, 11205D). Samples were then subjected to second strand synthesis, again using custom primer, followed by 10 cycles of library amplification using Phusion polymerase (Thermo Scientific, F-530S) before final purification using SPRI beads.

tag: background strain

tag: developmental stage

value: Oocytes

value: Wild-type


title: Root - Rep1

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
The reads were mapped onto Cucumis.melo3.5.1
To identify regions that were significantly enriched, we used MACS2.
MACS2 parameters for peaks detection were set as follows: Number of duplicate reads at a location:1; Bandwidth:300; mfold of 5:50; q-value cutoff:0.05.
For peak detection in H3K27me3 modified regions, we used SICER with the following criteria: Window size:200, Gap size:600
Genome_build: Cucumis.melo3.5.1
Supplementary_files_format_and_content: WIG file format
Supplementary_files_format_and_content: cufflinks file format

organism: Cucumis melo var. cantalupo

source_name: Root - Rep1

growth_protocol: Monoecious melon (Cucumis melo) cultivar charentais (Cucumis melo L. subsp. melo var cantalupensis ) were used for H3K9ac and H3K27me3 genome-wide descriptive analyses. For each replicate, 7-day old seedlings were transferred to individual pots and incubated in a growth chamber for 30 days (long day conditions, temperature: 27°C (day) and 21°C (night), relative humidity: 60%). Young male and female flowers (3 mm length; Developmental stage 8) were collected, organized according to their location in the plant (i.e. main stem or branches) and conserved at -80°c for epigenomic and transcriptomic analyses.

extract_protocol:
Total RNA were extracted from leaves, root, fruit, male and female flowers using the Nucleospin RNA kit (Macherey-Nagel). ChIP assays were performed using anti-H3K9ac (Millipore) or anti-H3K27me3 (Millipore) antibodies. Chromatin was reverse-crosslinked by adding 20μL of NaCl 5M and incubated over-night at 65°C. Reverse-cross-linked DNA was submitted to RNase and proteinase K digestion, and extracted with phenol-chloroform. DNA was ethanol precipitated in the presence of 20μg of glycogen and resuspended in 50μL of nuclease-free water (Ambion) in a DNA low-bind tube.
10 ng of IP or input DNA was used 501 for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s recommendations. For all libraries, twelve cycles of PCR were  used. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent), and  the libraries were subjected to high-throughput sequencing by Illumina Sequencing technology.

treatment_protocol: For the determination of a- and g-related epigenetic changes, we used two families of EMS451 treated C. melo lines carrying missense mutations in CmWIP1 and in CmACS11, both previously reported to lead to gynoecy and androecy, respectively. Germination, growth and flower collecting conditions were the same to the previously described for the monoecious WT plants.

tag: cultivar

value: charentais

value: Root

value: 30 days in growth chamber


title: RRBS_60_65A

extract_protocol:
Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas).  Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 18 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene).  DNA was purified using SPRI beads (Agencourt).
RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNasefree DNase I, Life Technologies).
For RNA-seq libraries:  Reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTP excision step by USER Enzyme (NEB) before PCR. RRBS: Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas).  Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 18 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene).  DNA was purified using SPRI beads (Agencourt).  For PBAT: As in Stewart et al. (2015): Cells were lysed in EB buffer (Qiagen) with 0.5% SDS (Sigma, 161-0418) and bisulfite-treated using theone-stepmodification procedure in the Imprint DNA modification kit(Sigma,MOD50-1KT).The resulting DNA was purified using the EZ DNA methylation direct kit (Zymo, D5020). First strand synthesis was performed using Klenow Exo− (New England Biolabs, M0212S) and a custom streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs (bp) of random sequence (9N). This was followed by exonuclease I treatment (New England Biolabs, M0293S), purification using SPRI beads (1.8× ratio; Fisher Scientific, 09-981123), and binding to biotin beads (Life Technologies, 11205D). Samples were then subjected to second strand synthesis, again using custom primer, followed by 10 cycles of library amplification using Phusion polymerase (Thermo Scientific, F-530S) before final purification using SPRI beads.


title: Leaves - Rep2

source_name: Leaves - Rep2

value: Leaves


title: RRBS_50_55B

source_name: 50-55um oocytes


title: Leaves - Rep1

source_name: Leaves - Rep1


title: Fetal HSC RISP KO rep1

tag: genotype/variation


title: Fruit - Rep2

source_name: Fruit - Rep2

value: Fruit


title: Fetal HSC RISP WT rep2

value: RISP wild type


title: Blood_Ly6C_M_I

value: monocytes

tag: Sex

value: female


title: RRBS_50_55A


title: RRBS_40_45B

source_name: 40-45um oocytes


title: Fetal HSC RISP WT rep1


title: RNAseq_Tfam-KO3

data_processing:
Sequencing reads were aligned to mouse genome assembly mm9 by TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads).
Differential gene expression analyses were performed using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: text file of gene RPKM values

source_name: Mouse E13.5 fetal liver erythroid cells

value: CD71+Ter119+ fetal liver erythroid cells

value: fetal liver


title: Fruit - Rep1

source_name: Fruit - Rep1


title: RNAseq_Tfam-KO2


title: RNA_GV

source_name: GV oocytes

extract_protocol:
RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNasefree DNase I, Life Technologies).  Reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTP excision step by USER Enzyme (NEB) before PCR.
RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNasefree DNase I, Life Technologies).
For RNA-seq libraries:  Reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTP excision step by USER Enzyme (NEB) before PCR. RRBS: Extracted DNA was spiked with a small amount of lambda DNA (0.05pg per 6ng of genomic DNA) for bisulphite conversion control, digested with MspI endonuclease (Fermentas), end-repaired (Klenow fragment exo-, Fermentas, with 10nM dATP, 1nM dCTP and 1nM dGTP) and ligated with 5mC-adaptors (Illumina) with T4 ligase (Fermentas).  Bisulphite conversion was done using the EZ DNA Methylation-Direct Kit (Zymo Research) and DNA was amplified by 18 cycles of PCR using Pfu Turbo Cx polymerase (Stratagene).  DNA was purified using SPRI beads (Agencourt).  For PBAT: As in Stewart et al. (2015): Cells were lysed in EB buffer (Qiagen) with 0.5% SDS (Sigma, 161-0418) and bisulfite-treated using theone-stepmodification procedure in the Imprint DNA modification kit(Sigma,MOD50-1KT).The resulting DNA was purified using the EZ DNA methylation direct kit (Zymo, D5020). First strand synthesis was performed using Klenow Exo− (New England Biolabs, M0212S) and a custom streptavidin-conjugated adaptor containing standard Illumina adaptor sequences and 9 base pairs (bp) of random sequence (9N). This was followed by exonuclease I treatment (New England Biolabs, M0293S), purification using SPRI beads (1.8× ratio; Fisher Scientific, 09-981123), and binding to biotin beads (Life Technologies, 11205D). Samples were then subjected to second strand synthesis, again using custom primer, followed by 10 cycles of library amplification using Phusion polymerase (Thermo Scientific, F-530S) before final purification using SPRI beads.


title: Female Flowers - Rep1

source_name: Female Flowers - Rep1

value: Flowers


title: Female Flowers - Rep2

source_name: Female Flowers - Rep2


title: RNA_60_65B


title: RNAseq_Tfam-WT3


title: RNAseq_Tfam-KO1


title: RRBS_60_65B


title: RNAseq_Tfam-WT2


title: RNA_50_55B


title: cmwip1 Female flowers (female position) H3K27me3


title: RNA_60_65A


title: Male Flowers - Rep1

source_name: Male Flowers - Rep1


title: Fetal HSC RISP WT rep3


title: RNA_50_55A


title: RNAseq_Tfam-WT1


title: cmwip1 Female flowers (male position) H3K27me3


title: RNA_40_45A


title: RNA_40_45B


title: acs11Female flowers (female position) H3K27me3


title: Root - Rep2

source_name: Root - Rep2


title: RRBS_40_45A


title: acs11Female flowers (male position) H3K27me3


title: ZZ@ExE4

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

data_processing:
Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.13 and cutadapt 1.7.1.
Using FastX and ShortRead 1.16.3, we filtered subsequently small reads (length < 35 bp), polyA-reads (>90% of the bases equal A), ambiguous reads (containing N) and low quality reads (>50% of the bases < Q25).
The reads are aligned to the reference genome with Tophat v2.0.12. As parameter options we use: --library-type unstranded --min-intron-length 70 --max-intron-length 500000.
Counting per gene was performed using the function summarizeOverlap() from the R package GenomicAlignment 1.2.2, using union method and TxDb.Mmusculus.UCSC.mm10.knownGene library for gene annotation.
Genome_build: GRCm38.73 (mm10)
Supplementary_files_format_and_content: raw counts in txt format

source_name: Lysates of E6.25 epiblast (E) or extra-embryonic (ExE) tissues

growth_protocol: Lysates of E6.25 epiblast (E) and extra-embryonic (ExE) tissues were pooled, based on retrospective genotyping, from at least 6 embryos (collected from 2-3 litters). Four pooled biological replicates were collected for each tissue compartment and each genotype (wt, Zwt and ZZ); in 3 of 4 pooled replicates, the E and ExE samples were obtained from the same litters and given the same numbering. One ExE sample of ZZ was lost.

extract_protocol:
RNA was purified using the RNeasy micro Kit (Qiagen) to obtain 1-10 ng of RNA per pool. RNA quality was assessed using a Bioanalyzer 6000 Pico chip and only samples with RNA integrity number (RIN) > 8.0 were processed further.
First-strand cDNA synthesis and amplification was performed by using the SMARTer Ultra Low Input RNA amplification kit v3 (Clontech). Libraries were prepared using NEBNext Ultra DNA library prep for Illumina and sequenced on NextSeq 500 in high-output to generate 75-bp single-end reads.

value: Extra-embryonic


title: ZZ@ExE3


title: RNA_10_30B

source_name: 10-30um oocytes


title: ZZ@ExE1


title: Male Flowers - Rep2

source_name: Male Flowers - Rep2


title: ZZ@E4

value: Epiblast


title: Female flowers H3K27me3 replicate 2

source_name: Female flowers H3K27me3 replicate 2


title: RNA_10_30A


title: Male flowers H3K27me3 replicate 2

source_name: Male flowers H3K27me3 replicate 2


title: ZZ@E3


title: ZZ@E2