title: TFEbeta.mock.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A6_ad006

status: Public on Sep 14 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A7_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A6_ad004


title: H8 input: SMAD1

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
Aligned using bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

organism: Homo sapiens

growth_protocol: Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol). K562 cells were grown and maintained in  RPMI base media with FBS, Pen/Strep. G418 was used to select positive clones.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin and target bound fragments were isolated with antibody
The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol:
hrBMP4 25ng/ml 13hrs
25ng/ml hrBMP4 for 2hrs prior to collection

tag: cell type

value: immortalized erythroleukemia cells (overexpressinng PU1)

tag: purification target


title: TFEalpha.mock.chip-seq.r2

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

country: United Kingdom

institute: University College London

data_processing:
paired-end reads were trimmed to 50 bp and aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v 2 -m 1 --fr
we sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custom R script(www.github.com/fblombach)
Coverage was calculated using bamCoverage from the deeptools package
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with score representing either raw coverage after sampling ("Coverage") or coverage normalised to input after sampling ("normRatio")

organism: Saccharolobus solfataricus

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% tryptone to mid-exponential growth phase and mock treated with water, as control for 30 µM hydrogen peroxide treatment (GSE141033)

extract_protocol:
Cells were lysed in lysis buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100) and DNA was sheared by sonication. Lysates were cleared by centrifugation. Chromatin-immunoprecipitation was carried out with protein-A-purified polyclonal antibodies. Immunoprecipitated DNA was recovered by QIAquick PCR purification
NEBnext Ultra II DNA library preparation

treatment_protocol: Cells were crosslinked with 0.4% formaldehyde for 1 min before quenching by addition of 100 mM TRIS/Cl pH 8.0, cells were washed in PBS buffer 3x

tag: growth

value: mock treated cells, 0.2% tryptone

tag: chip antibody

value: polyclonal antibodies against TFEalpha


title: V2 SMAD1

treatment_protocol:
hrBMP4 25ng/ml 10hrs
25ng/ml hrBMP4 for 2hrs prior to collection

value: immortalized erythroleukemia cells (empty control)

tag: antibody manufacturer

value: Santa Cruz

tag: antibody catalog id


title: V2 input: SMAD1

treatment_protocol:
hrBMP4 25ng/ml 11hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: TFEalpha.mock.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A6_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A5_ad006


title: H8 input: PU1

treatment_protocol:
hrBMP4 25ng/ml 9hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: H8 SMAD1

treatment_protocol:
hrBMP4 25ng/ml 12hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A6_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A5_ad004


title: input.expon.chip-seq.r2

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% glucose, 0.1% tryptone to mid-exponential growth phase

value: exponential phase, 0.1% tryptone, 0.2% glucose

value: none (input)


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A7_ad001


title: TFEbeta.expon.chip-seq.r2

value: polyclonal antibodies against TFEbeta


title: input.expon.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A5_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A5_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A4_ad004


title: V2 PU1

treatment_protocol:
hrBMP4 25ng/ml 6hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A7_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A3_ad006


title: TFEbeta.mock.chip-seq.r1


title: TFEbeta.expon.chip-seq.r1


title: D5 input: KLF11

source_name: Erythrocyte precursors

treatment_protocol:
hrBMP4 25ng/ml 5hrs
25ng/ml hrBMP4 for 2hrs prior to collection

value: mobilised peripheral blood CD34+ cells


title: H8 PU1

treatment_protocol:
hrBMP4 25ng/ml 8hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A3_ad002


title: TFEalpha.expon.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A2_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A2_ad001


title: TFEalpha.expon.chip-seq.r1


title: V2 input: PU1

treatment_protocol:
hrBMP4 25ng/ml 7hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A4_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad008


title: D0 input: PU1

treatment_protocol:
hrBMP4 25ng/ml 3hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A2_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A2_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad010


title: TFB.expon.chip-seq.r2

value: polyclonal antibodies against TFB


title: D0 PU1

treatment_protocol:
hrBMP4 25ng/ml 2hrs
25ng/ml hrBMP4 for 2hrs prior to collection


title: Day4 Input: SmaD1, Gata1

description: D4 Input: Smad1, Gata1

growth_protocol: Human CD34+ cells, isolated from the peripheral blood of granulocyte colony-stimulating factor mobilized healthy volunteers, were used.Briefly the cells were expanded in StemSpan medium (Stem Cell Technologies Inc.) supplemented with StemSpan CC100 cytokine mix (Stem Cell Technologies Inc.). For studying differentiated cells after day 6 of expansion, cells were reseeded in differentiation medium (StemSpan SFEM Medium with 2% P/S, 20 ng/ml SCF, 1 U/ml Epo, 5 ng/ml IL-3, 2 mM dexamethasone, and 1 mM b-estradiol).

treatment_protocol: 25ng/ml hrBMP4 for 2hrs prior to collection

value: mobilized peripheral blood CD34+ cells

tag: time

value: day 4 of differentiation

tag: treatment

value: 25ng/ml hrBMP4 for 2hrs before collection


title: Day4 Gata1

description: D4 Gata1


title: TFB.expon.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad002


title: Day4 SmaD1

description: D4 Smad1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A11_ad008


title: D5 KLF1

treatment_protocol:
hrBMP4 25ng/ml 4hrs
25ng/ml hrBMP4 for 2hrs prior to collection

value: Abcam


title: aCPSF1.expon.chip-seq.r1

value: polyclonal antibodies against aCPSF1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad006

value: CA


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A3_ad004

value: male


title: Elf1.expon.chip-seq.r2

value: polyclonal antibodies against Elf1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A11_ad006


title: Elf1.expon.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A12_ad007


title: Day3 Input: SmaD1, Gata1

description: D3 Input: Smad1, Gata1

value: day 3 of differentiation


title: Spt45.expon.chip-seq.r2

value: polyclonal antibodies against Spt4/5


title: aCPSF1.expon.chip-seq.r2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A11_ad002


title: Day3 Gata2

description: D3 Gata2


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A10_ad008


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A11_ad001


title: Day3 H3K27ac

description: D3 H3K27ac


title: Day3 Input: Gata2, H3K27ac

description: D3 Input: Gata2, H3K27ac


title: Spt45.expon.chip-seq.r1


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A10_ad002


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A10_ad006


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A10_ad004


title: input.H2O2.chip-seq.r2

description:
13834X61_161123_D00294_0273_ACAAATANXX_7
15237X21_180711_D00294_0402_BCCK56ANXX_8

growth_protocol: Saccharolobus solfataricus str. P2 cells were grown in modified Brock medium with 0.2% tryptone to mid-exponential growth phase and treated with 30 µM hydrogen peroxide for 105 min

value: 30 µM hydrogen peroxide for 105 min


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A1_ad006


title: input.H2O2.chip-seq.r1

description:
13834X49_161123_D00294_0273_ACAAATANXX_7
15237X16_180711_D00294_0402_BCCK56ANXX_8


title: Day3 Gata1

description: D3 Gata1

value: Santa Cruz


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A1_ad004


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A1_ad001


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A1_ad002


title: TFEbeta.H2O2.chip-seq.r1

description:
13834X39_161123_D00294_0273_ACAAATANXX_7
15237X13_180711_D00294_0402_BCCK56ANXX_8


title: OXY_F_72_S23

city: Columbia

first: Cheryl

middle: S

last: Rosenfeld

state: MO

address: 1201 Rollins Street

department: BIOMEDICAL SCIENCES

institute: University of Missouri.edu

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to grcm38 whole genome using HISAT2 (v2.0.5).
The number of reads that aligned to each protein-coding gene were counted with the featureCount tool from Subread software suite (v2.0.1, Liao Y, Smyth GK, Shi W. Bioinformatics. 2014)
Genome_build: grcm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

extract_protocol:
Placenta tissue samples were collected, snap frozen in liquid nitrogen, and total RNA was harvested using Qiagen AllPrep DNA/RNA/miRNA Universal Kit (cat#80224). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 850 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: wild type

value: embryo day 12.5

value: Oxycodone

tag: tissue

value: placenta


title: OXY_M_73_S33


title: Hour6 Input: SmaD1, Gata1, Gata2

description: H6 Input: Smad1, Gata1, Gata2

value: hour 6 of differentiation


title: TFEbeta.H2O2.chip-seq.r2

description:
13834X51_161123_D00294_0273_ACAAATANXX_7
15237X19_180711_D00294_0402_BCCK56ANXX_8

value: polyclonal antibodies against TFEbeta


title: Day3 SmaD1

description: D3 Smad1

value: mobilized peripheral blood CD34+ cells


title: CEMBA190625_10E_1_CEMBA190625_10E_2_A11_ad004


title: CTL_F_71_S24

value: Saline


title: OXY_F_69_S26


title: Hour6_Input_forK27

value: 25ng/ml hrBMP4 for 2hrs before collection


title: CTL_M_68_S27


title: Hour6 H3K27ac

description: H6 H3K27ac

value: Abcam


title: OXY_M_70_S25


title: Hour6 Gata2

description: H6 Gata2


title: TFB.H2O2.chip-seq.r2

description: 13834X54_161123_D00294_0273_ACAAATANXX_7

value: polyclonal antibodies against TFB


title: CTL_F_67_S28


title: Hour6 Gata1

description: H6 Gata1


title: Hour6 SmaD1

description: H6 Smad1


title: TFEalpha.H2O2.chip-seq.r2

description:
13834X52_161123_D00294_0273_ACAAATANXX_7
15237X20_180711_D00294_0402_BCCK56ANXX_8

value: polyclonal antibodies against TFEalpha


title: CTL_F_6_S19


title: CTL_F_63_S30


title: TFB.H2O2.chip-seq.r1

description:
13834X42_161123_D00294_0273_ACAAATANXX_7
15237X15_180711_D00294_0402_BCCK56ANXX_8


title: CTL_M_61_S42


title: CTL_M_64_S29


title: OXY_F_58_S32


title: aCPSF1.H2O2.chip-seq.r2

description: 15966X9_190412_D00550_0559_ACDL9LANXX_S3_L001

value: polyclonal antibodies against aCPSF1


title: Day0 H3K27ac

description: D0 H3K27ac

source_name: Hemoatopoietic stem and progenitor cells

value: day 0 of differentiation


title: aCPSF1.H2O2.chip-seq.r1

description: 15966X8_190412_D00550_0559_ACDL9LANXX_S5_L001


title: OXY_M_53_S35


title: OXY_M_52_S36


title: Day0 Gata1

description: D0 Gata1


title: OXY_M_57_S22


title: OXY_M_50_S38


title: CTL_F_51_S37


title: Elf1.H2O2.chip-seq.r2

description: 15966X4_190412_D00550_0559_ACDL9LANXX_S10_L001

value: polyclonal antibodies against Elf1


title: TFEalpha.H2O2.chip-seq.r1

description:
13834X40_161123_D00294_0273_ACAAATANXX_7
15237X14_180711_D00294_0402_BCCK56ANXX_8

value: 30 µM hydrogen peroxide for 105 min


title: Elf1.H2O2.chip-seq.r1

description: 15966X3_190412_D00550_0559_ACDL9LANXX_S12_L001


title: OXY_M_49_S39


title: Spt45.H2O2.chip-seq.r2

description:
13834X57_161123_D00294_0273_ACAAATANXX_7
15237X18_180711_D00294_0402_BCCK56ANXX_8

value: polyclonal antibodies against Spt4/5


title: OXY_F_48_S40

value: wild type


title: ATAC_Day4

data_processing:
Library strategy: ATAC-seq
All human ChIP-Seq datasets were aligned to build version NCBI37/HG19 of the human genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bed file of called peaks

extract_protocol:
5X104 CD34+ cells at specific differentiation stage tested were harvested by spinning at 500 x g for 5 min, 4° C. Cells were washed once with 50 uL of cold 1X PBS and spinned down at 500 x g for 5 min, 4° C. After discarding supernatant, cells were lysed using 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360) and spinned down immediately at 500 x g for 10 mins, 4 deg C. Then the cells were precipitated and kept on ice and subsequently resuspended in 25 uL 2X TD Buffer (Illumina Nextera kit), 2.5 uL Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5 uL Nuclease-free water in a total of 50 uL reaction. Transposase reaction was continued for 1 hr at 37° C. Immediately following the reaction, DNA was purified using Qiagen MinElute PCR purification kit (28004) in a final volume of 10 uL.
Libraries were purified according to Illumina protocol using the transposed DNA, NEB PCR master mix, Sybr green, universal and library-specific Nextera index primers. First round of PCR cycles was performed with the following cycles: 72° C, 5 min; 98° C, 30 sec; [98°C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 5 cycles; hold at 4°C. Reactions were kept on ice and using a 5 uL reaction aliquot, appropriate number of additional cycles required for further amplification were determined in a side qPCR reaction with the following procedure: 98 °C , 30 sec; [98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 20 cycles; hold at 4 °C. Upon determining the additional number of PCR cycles required further for each sample, library amplification was conducted using the following conditions: 98°C, 30 sec; [98°C,10 sec; 63°C, 30 sec; 72 °C, 1 min] X appropriate number of cycles; hold at 4°C. Libraries prepared went through quality control analysis using an Agilent Bioanalyzer. Samples with appropriate nucleosomal laddering profiles were selected for next generation sequencing using Illumina Hiseq 2500 platform

value: day 4 of differentiation


title: CTL_F_47_S41

value: embryo day 12.5


title: ATAC_Day3

value: day 3 of differentiation


title: Spt45.H2O2.chip-seq.r1

description:
13834X45_161123_D00294_0273_ACAAATANXX_7
15237X12_180711_D00294_0402_BCCK56ANXX_8

data_processing:
paired-end reads were trimmed to 50 bp and aligned with bowtie to the Saccharolobus solfataricus P2 genome using the following settings: -v 2 -m 1 --frP2 genome using the following settings: -v 2 -m 1 --fr
we sampled from the alignments to obtain a defined fragment size distribution (normal distribution, mean 120 bp, sd 18 bp) using a custum R script(www.github.com/fblombach)
Coverage was calculated using bamCoverage from the deeptools package
Coverage normalized to input ("normRatio") was calculated using deeptools bamCompare with SES scaling (10,000 bins, 200 bp bin width)
Genome_build: NC_002754.1
Supplementary_files_format_and_content: bigwig files with score representing either raw coverage after sampling ("Coverage") or coverage normalised to input after sampling ("normRatio")


title: ATAC_Day2

value: day 2 of differentiation


title: Rpo47.H2O2.chip-seq.r2

description:
13834X56_161123_D00294_0273_ACAAATANXX_7
15237X17_180711_D00294_0402_BCCK56ANXX_8

value: polyclonal antibodies against RNA polymerase subunits 4/7


title: CTL_M_45_S10

value: placenta


title: CTL_M_43_S3

value: Saline


title: OXY_F_54_S34

value: Oxycodone


title: CTL_F_44_S31


title: Rpo47.H2O2.chip-seq.r1

description:
13834X44_161123_D00294_0273_ACAAATANXX_7
15237X11_180711_D00294_0402_BCCK56ANXX_8


title: ATAC_Hour6

value: mobilized peripheral blood CD34+ cells

value: hour 6 of differentiation

value: 25ng/ml hrBMP4 for 2hrs before collection


title: OXY_M_35_S5


title: ATAC_Hour0

value: hour 0 of differentiation


title: CTL_M_24_S8


title: OXY_M_25_S7


title: Facs3

city: Irvine

first: Kai

last: Kessenbrock

address: 839 Health Sciences Road

department: Biological Chemistry

institute: UC Irvine

data_processing:
Alignment of scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger pipeline (version 2.1.0). Each library was aligned to an indexed mm10 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries from different libraries
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts expression matrices corresponding to each sample of this study

molecule: polyA RNA

source_name: mammary epithelial cells

extract_protocol:
Mammary glands number 4 were collected and pooled from a total of four 10-week old, female FVB/NJ mice. Glands were minced into pieces ~1mm in diameter and were incubated with a 2mg/ml collagenase type IV solution at 37C while shaking for 1 hour. Digested organoids were collected by differential centrifugation. Collected organoids were further dissociated with trypsin into single cells. Cells were stained for flow cytometry using fluorescently labeled antibodies for CD49f, EpCAM, CD31, CD45, Ter119, and SytoxBlue. Live epithelial cells were collected for sequencing
Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3’ Reagents Kits v2 User Guide: CG00052 Rev B. Libraries were sequenced on the Illumina HiSeq4000 platform targeting approximately 50,000 reads per cells.

tag: strain background

value: FVB/NJ

value: Mammary glands number 4

value: mammary epithelial cells


title: HT1080-ZFAT_2

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

description: HT1080 cells with transient HA-hZFAT-EGFP expression in the experiment 2.

data_processing:
Paired-end sequencing (76 bp x2) was performed on the NextSeq550 system (Illumina).
Basecalls were performed using the Real-Time Analysis (RTA) version 2.4.11 (Illumina). Fastq files were generated using bcl2fastq v2.20.0.422 (Illumina).
Paired-end reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a human reference genome sequence set using hisat2 (v2.1.0) with the following options: -p, --dta, --rna-stranness RF. The resultant .sam files were converted to .bam files and de-duplicated using samtools-1.6. The reference genome sequence set used consists of the sequences of the autosomal (1 to 22) and sex (X, Y) chromosomes, and the mitochondrial DNA from the GRCh38 assembly (GenBank assembly accession: GCA_000001405.15), the human gammaherpesvirus 4 (Epstein-Barr virus) genome sequence (GenBank accession: NC_007605), and the decoyJRGv1 sequence (available at https://jmorp.megabank.tohoku.ac.jp/dj1/datasets/tommo-jrgv1/files/decoyJRGv1.fasta.zip?download=true). The resultant bam files were subjected to stringtie (ver. 2.0.6) to determine read counts for each gene described in the gtf file for NCBI RefSeq genes (GRCh38/hg38) with the following options: -A -B -C -e -G --rf. The gtf file was obtained using the Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables).
Genome_build: hg38
Supplementary_files_format_and_content: *_gene_abund.tab: Tab-delimited text files generated by stringtie (ver. 2.0.6) containing "Gene ID", "Gene Name", and normalized mapped read count values (Coverage, FPKM and TPM).

source_name: HT1080 cells

growth_protocol: Culture conditions: Cells were cultured at 37C with 5% CO2 in Dulbecco’s Modified Eagle Medium supplemented with fetal calf serum and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIZOL reagents.
Libraries for RNA-sequencing (RNA-seq) were prepared using NEBNext rRNA Depletion Kit (NEB #E6310L) and NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7760S) using 750 ng of total RNA as a starting material by following the manufacturer's instructions with 6 cycles of PCR amplification.

treatment_protocol: HT1080 cells were transiently transfected with expression vectors for HA-hZFAT-EGFP or EGFP using Lipofectamine 3000. At 24 h after transfection, EGFP-positive cells were sorted by flow cytometry.

tag: cell line

value: Human fibrosarcoma cell line

tag: transient expression

value: HA-hZFAT-EGFP


title: HT1080-ZFAT_3

description: HT1080 cells with transient HA-hZFAT-EGFP expression in the experiment 3.


title: ATAC_Day5

value: day 5 of differentiation


title: CTL_M_5_S20

value: wild type

value: embryo day 12.5


title: CTL_F_23_S9


title: OXY_F_22_S21


title: HT1080-ZFAT_1

description: HT1080 cells with transient HA-hZFAT-EGFP expression in the experiment 1.


title: CTL_M_46_S12


title: HT1080-EGFP_3

description: HT1080 cells with transient EGFP expression in the experiment 3.

value: EGFP


title: Facs2


title: OXY_F_20_S1


title: Facs1


title: OXY_M_21_S11


title: CTL_M_16_S14


title: OXY_F_36_S4


title: OXY_F_26_S6


title: HT1080-EGFP_1

description: HT1080 cells with transient EGFP expression in the experiment 1.


title: Luminal3 [scATAC-seq]

data_processing:
Alignment of scATACseq analyses was completed utilizing 10x Genomics Cell Ranger ATAC pipeline (version 1.1.0). Each library was aligned to an indexed mm10 genome using Cell Ranger Count and Cell Ranger ATAC Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries
A quality control cutoff of a minimum of 2500 fragments per cell was applied to trim the data set of low-quality cells
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data files are tab-delimited .txt files of counts of transposase accessible regions of chromatin corresponding to each sample of this study

source_name: mammary luminal epithelial cells

extract_protocol:
Mammary glands number 4 were collected and pooled from a total of four 10-week old, female FVB/NJ mice. Glands were minced into pieces ~1mm in diameter and were incubated with a 2mg/ml collagenase type IV solution at 37C while shaking for 1 hour. Digested organoids were collected by differential centrifugation. Collected organoids were further dissociated with trypsin into single cells. Cells were stained for flow cytometry using fluorescently labeled antibodies for CD49f, EpCAM, CD31, CD45, Ter119, and SytoxBlue. Basal and Luminal cells were sorted separately.
Library generation for single cell ATACseq were performed following the Chromium Single Cell ATAC Reagent Kits User Guide: CG000168 Rev B. Libraries were sequenced on the Illumina HiSeq4000 platform targeting approximately 50,000 reads per cells.

value: mammary luminal epithelial cells


title: Balb/c_IL-8R2KO_Cocci_infected_2

first: Aaron

middle: F

last: Carlin

state: California

address: 9500 Gilman Drive GPL Rm 118

department: Pathology and Medicine

institute: University of California, San Diego

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
RNA-seq reads were mapped to the mouse genome (GRCm38/mm10) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
Gene expression was measured using HOMER with the following parameters analyzeRepeats rna mm10 -noadj -pc 3 -condenseGenes -count exons followed by DESeq normalized abundance measurements with settings of -log2fold 1 -fdr 0.01.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: RNA-seq tab-delimited text files include RPKM values for each sample

source_name: lung

growth_protocol: BALB/c CXCR2tm (IL-8R2 KO) breeding pairs were purchased from Jackson Laboratory and subsequently bred at our facility. Wild type (WT) BALB/c DBA/2 Nramp1 congenic (Potter M et al. (1983) PMID: 6343242) (BALB/c.D2SLC11A1) (CD2) mice were bred at our facility and were originally a gift from B.A. Mock at the NIH.  We found that IL-8R2 KO mice homozygous females could be bred if trimethoprim-sulfamethoxazole (TMP-SFX) was added to their drinking water. To control for any effects of TMP-SFX on the normal microbial flora both WT and IL-8R2 KO mice were bred with TMP-SFX added to their drinking water. TMP-SFX treatment was continued in both WT and IL-8R2 KO mice until 3 days prior to the start of this experiment (Cocci infection or uninfected control) when it was stopped.

extract_protocol:
At 14 days post-infection, lungs were rapidly removed and one lobe of the left lung was immediately frozen in liquid nitrogen and stored at −70°C. Lung tissue was thawed in the presence of Trizol (Life Technologies) and homogenized using the Tissuelyser II (Qiagen). RNA was isolated with Trizol according to the manufacturer’s instructions, DNase-treated using TURBO DNase (Ambion) according to the manufacturer’s instructions and ethanol-precipitated.
PolyA-RNA was selected from total RNA using the MicroPoly(A)Purist kit (Ambion), according to the manufacturer’s instructions. Isolated RNA was hydrolyzed in a total volume of 20 μl with 2 μl RNA fragmentation buffer (Ambion) for 10 min at 70 °C. The reaction was stopped with stop buffer, and buffer was exchanged to Tris, pH 8.5, using P30 size-exclusion columns (Bio-Rad). The fragmented RNA (30 ng) was 5′-decapped in a total volume of 21 μl containing 0.5 μl tobacco acid pyrophosphatase (TAP, Epicentre), 2 μl 10× TAP buffer and 1 μl SUPERase-IN, and incubated for 2 h at 37 °C. To dephosphorylate RNA 3′ ends, 0.5 μl 10× TAP buffer, 1.5 μl water, 0.5 μl of 0.25 M MgCl2 (4.17 mM final; 1 mM EDTA for maximum phosphatase activity), and 0.5 μl of 10 mM ATP (0.2 μM final to protect PNK) where added, and the reaction was incubated with 1 μl PNK (Enzymatics) for 50 min at 37 °C. RNA fragments were 5′-phosphorylated by adding 10 μl 10× T4 DNA ligase buffer, 63 μl water and 2 μl PNK, and incubated for 60 min at 37 °C. RNA fragments were isolated using Trizol LS, precipitated in the presence of 300 mM sodium acetate and 2 μl glycoblue (Ambion), washed twice with 80% ethanol and dissolved in 4.5 μl water. To prepare sequencing libraries, 0.5 μl of 9 μM 5′-adenylated 3′MPX adaptor/5Phos/AGATCGGAAGAGCACACGTCTGA/3AmMO/ (IDT, desalted; adenylated with Mth ligase (NEB) according to the manufacturer’s instructions, phenol–chloroform/chloroform-extracted, ethanol-precipitated with glycogen and dissolved in water at 9 µM) was heat-denatured together with the RNA for 2 min at 70 °C, and ligated with 100 U truncated T4 RNA ligase 2 K227Q (NEB) in 10 μl 1× T4 RNA ligase buffer without ATP, containing 10 U SUPERase-In and 15% PEG8000 for 2 h at 16 °C. To reduce adaptor dimer formation, 0.5 μl of 10 μM MPX_RT primer 5′-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′ (IDT, desalted) was added and annealed to the ligation product by incubating at 75 °C for 2 min, then 37 °C for 30 min, and 25 °C for 15 min. Finally, 0.5 μl of 5 μM hybrid DNA/RNA sRNA 5′h adaptor 5′-GTTCAGAGTTCTACArGrUrCrCrGrArCrGrArUrC-3′ (IDT) was ligated to previously capped RNA 5′ ends by adding 2 μl T4 RNA ligase buffer, 6 μl 50% PEG8000 (15% final), 1 μl of 10 mM ATP, 9.5 μl water and 0.5 μl (5 U) T4 RNA ligase 1 for 90 min at 20 °C. To 15 μl of ligation reaction, an additional 0.5 μl of 10 μM MPX_RT primer was added, reactions were denatured at 70 °C for 1 min and then placed on ice. RNA was reverse-transcribed by adding 3 μl 10× first-strand buffer (4.5 µl water, 1.5 μl of 10 mM dNTP, 3 μl of 0.1 M DTT, 1.5 μl RNaseOUT and 1 μl Superscript III reverse transcriptase (Invitrogen)), and incubating for 30 min at 50 °C. Complementary DNA was isolated by adding 35 μl AMPure XL beads (Beckman), binding and washing according to manufacturer’s instructions, and dissolving in 40 μl TET (0.1% Tween 20 in TE buffer). Libraries were PCR-amplified for 12-15 cycles, with 0.75 μM oNTI201 primer and TruSeq-compatible indexed primers using Phusion Hot Start II in Phusion HF buffer (Thermo Scientific) containing 0.5 M betaine (98 °C, 30 s; 12× (98 °C, 10 s; 57 °C, 25 s; 72 °C, 20 s); 72 °C, 1 min; stored at 4 °C, and 225–400-bp fragments were size-selected on 10% PAGE gels. Libraries were diluted with TET buffer and quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), pooled and sequenced on a Hi-Seq 2000 sequencer (Illumina) using single end 50bp reads.

treatment_protocol: Arthroconidia from C. immitis (RS strain) were harvested, suspended in buffered saline and kept at 4°C prior to infecting the mice. Mice were infected intra-nasally (i.n.) with 50-100 arthroconidia from C. immitis RS. Mice were sacrificed after 14 days.

value: Balb/c CXCR2tm

value: IL-8R2 KO

tag: infection status

value: Coccidioides immiitis infection 14 days post-infection


title: ATAC_Day1

value: mobilized peripheral blood CD34+ cells

value: day 1 of differentiation


title: Luminal2 [scATAC-seq]


title: Knockdown replicate 4

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description:
GA4
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data analysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-2.3.0. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (from Ensembl) and corresponding gene model is extracted from Ensembl version 90.
Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.
Genome_build: BDGP6
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell.

organism: Drosophila melanogaster

source_name: Third instar brain

extract_protocol:
Third instar brains from control and repo>AmaRNAi were dissociated into single cells using a combination of Trypsin and Collagenase. We then performed Drop-seq on the single cell suspension.
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol).

value: brain

tag: developmental stage

value: wandering third instar larvae

value: repo>AmaRNAi


title: Luminal1 [scATAC-seq]

value: FVB/NJ

value: Mammary glands number 4


title: OXY_F_12_S17

tag: age

value: Oxycodone

value: placenta


title: OXY_F_13_S16

tag: strain


title: Basal3 [scATAC-seq]

source_name: mammary basal epithelial cells

tag: cell type

value: mammary basal epithelial cells


title: Balb/c_IL-8R2KO_Cocci_infected_1


title: Balb/c_IL-8R2KO_uninfected_2

value: uninfected


title: Knockdown replicate 3

description:
GA3
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.


title: CTL_M_18_S13

value: wild type

value: embryo day 12.5

value: Saline


title: OXY_M_11_S18


title: Basal1 [scATAC-seq]


title: Balb/c_IL-8R2KO_uninfected_1

value: Balb/c CXCR2tm


title: PH120M2

city: Cambridge

first: Alex

middle: K

last: Shalek

address: 77 Massachusetts Avenue

department: Chemistry

institute: MIT

data_processing:
FASTQs were aligned to mm10 with STAR aligner
Barcode is the first 12 bases of read 1. UMI is the next 8 bases of read 1.
Barcodes with fewer than 400 genes detected were discarded as non-cells
TPM-like (base 10,000) then log normalize
Run PCA and shared nearest neighbor (SNN) cluster data over top 13 PCs. 14 clusters identified.
Remove clusters which contain non-hepatocytes and a low quality, high percent mitochonrial cluster so that only clusters of high quality hepatocytes remain.
Genome_build: mm10
Supplementary_files_format_and_content: ALI_allcell_400gene.txt: UMI dge genes x cells matrix for all cells expressing >400 genes from all samples. Sample of origin is appended to the cell barcode name. No additional quality or hepatocyte identity filtering
ALI_filterHQhep.txt: Filtered for high quality hepatocytes only.

source_name: Mouse Liver

extract_protocol:
Mouse hepatic cells were isolated with the two-step collagenase profusion method.
Libraries were prepared according to the Seq-Well protocol.

treatment_protocol: APAP-treated mice were given a single dose of acetaminophen at 300mg/kg. PH mice recived a ~70% partial hepatectomy. Mice were then used for hepatocyte isolation after the indicated number of hours.

value: liver

tag: Sex

value: Male

value: PH (partial hepatectomy)

tag: time point

value: 120 hours


title: Knockdown replicate 2

description:
GA2
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.

value: brain


title: Control replicate 4

description:
BC4
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.

value: wandering third instar larvae

value: repo>+


title: CTL_F_1_S2


title: Knockdown replicate 1

description:
GA1
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.

value: repo>AmaRNAi


title: Basal2 [scATAC-seq]

value: FVB/NJ

value: Mammary glands number 4


title: Balb/c_WT_Cocci_infected_2

value: Balb/c.D2 (CD2)

value: Wild type (WT)

value: Coccidioides immiitis infection 14 days post-infection


title: HT1080-EGFP_2

description: HT1080 cells with transient EGFP expression in the experiment 2.

value: Human fibrosarcoma cell line

value: EGFP


title: PH120M1


title: Balb/c_WT_Cocci_infected_1


title: CTL_F_15_S15

value: wild type

value: embryo day 12.5

value: Saline

value: placenta


title: Balb/c_WT_uninfected_2

value: uninfected


title: Control replicate 3

description:
BC3
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.


title: xenograft of breast cancer cell line, C29+5-azadC_rep1

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

country: Canada

institute: Université de Montréal

description:
C29_aza_vs_DMSO_DMR_q_0_01_mm10_genes_promoters.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_genes_introns.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_genes_intergenic.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_genes_exons.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_cpg_shores.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_cpg_shelves.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_cpg_islands.csv
C29_aza_vs_DMSO_DMR_q_0_01_mm10_cpg_inter.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_genes_promoters.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_genes_introns.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_genes_intergenic.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_genes_exons.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_cpg_shores.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_cpg_shelves.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_cpg_islands.csv
C29_aza_vs_DMSO_DMC_q_0_01_mm10_cpg_inter.csv

data_processing:
Sequencing was performed in single-end mode, generating 50 bases reads (SE50) on an Illumina HiSeq 3000/4000. Quality control of sequencing reads was performed using FastQC version 0.11.8. Adapter removal was perfomed using Trim Galore! version 0.4.1. Reads were then aligned to the murine reference genome mm10/GRCm38 using bismark v0.20.0. The cytosine2coverage and bismark_methylation_extractor modules of Bismark were used to infer the methylation state of all cytosines (for every single uniquely mappable read) and their context, and to compute the percentage methylation. The reported cytosines were filtered to get only the CpGs covered in each sample.
Methylkit v1.7.0, a R/Bioconductor package, was used to perform the differential methylation analysis between the two groups of samples. The CpG data set was filtered for low coverage (CpGs with coverage less than 10X in all samples per comparative group were discarded) and for extremely high coverage to discard reads with possible PCR bias (CpGs with coverage higher than the 99.9th percentile were discarded). The data was then normalized for read coverage distribution between samples. A pairwise comparison was performed for first versus second group of samples to identify differentially methylated CpGs (DMCs) and differentially methylated regions (DMRs), the latter with a window and step size of 1000bp After the p-values have been computed, methylkit uses the sliding window model (SLIM) to correct P-values to q-values for multiple comparison tests. Statistically significant DMCs and DMRs were identified with a q-value cutoff < 0.01 and a methylation difference higher than 25%. All DMCs and DMRs were annotated with the R/Bioconductor package annotatr, with the refGene and CpG island annotations from UCSC. The annotation comprised two categories: (i) distance to a CpG island and (ii) regional annotation. The distance related annotation classified DMCs and DMRs whether they overlapped a known CpG island, 2000bp of the flanking regions of the CpG islands (shores), 2000bp of the flanking regions of the shores (shelves) or outside these regions (open sea). The regional analysis classified DMCs and DMRs in four groups, namely, exons, introns, promoters and intergenic regions.
Genome_build: mm10
Supplementary_files_format_and_content: .csv (Comma Separated Values). Contain choromosome coordinates of differentially methylated cytosines (DMC) or regions (DMR) along with gene identification)
.tsv (tabulation separated values). Contain methylation values for each CpG identified. Column headers: chromosome - start and end position (same as it is one nucleotide) - strand - methylation level (from 0 to 1) - coverage (number of reads covering the position)

source_name: xenograft NIC5231 mouse breast cancer cell line

growth_protocol: NIC-5231 were maintained in DMEM supplemented with 5% FBS, 5 ng ml−1 EGF, 1 μg ml−1 hydrocortisone, 5 μg ml−1 insulin and 35 μg ml−1 Bovine Pituitary Extract. Then, 1x10^6 cells were injected into the mammary fat pad of 5-7-week-old NSG mice

extract_protocol: when the largest tumor had reached the maximum tumor size limit (1.5 mm3), mice were sacrificed, tumors were collected and genomic DNA was purified using the Blood and Tissue purification kit (Qiagen, #69506) following the manufacturer’s protocol. Genomic DNA was then sent to Diagenode for RRBS analysis (2 replicates consisting of a pool of DNA from 2 mice per condition).

treatment_protocol: When tumors were palpable, mice were randomly assigned to either a control group (vehicle) or a treatment group (5 mice per group). C29 (10 mg/kg) and/or 5-azadC (1 mg/kg) were resuspended in saline/30%PEG/5%DMSO and administered by intraperitoneal injection every 2 days.


title: Control replicate 1

description:
BC1
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.


title: Nelfe_LPS1h

city: Beijing

first: Li

last: Yu

address: Medicial Science Building, Tsinghua University

department: The Institution of Immunology

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using Real Time Analysis.
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.1.2
Peaks were called using HOMER (version4.7.2) FDR< 10^-3)
bedGraph files were generated by HOMER (version 4.7.2)
Genome_build: mm10

source_name: Macrophages

growth_protocol: Bone marrows cells from C57BL/6 mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

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

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for 1 hour.

value: Bone marrow-derived macrophages

value: LPS 1 hour

tag: antibody

value: NELFE (Proteintech, #10705-1-AP)


title: Balb/c_WT_uninfected_1


title: PH48M3

value: liver

value: Male

value: PH (partial hepatectomy)

value: 48 hours


title: PH48M1


title: PH48M2


title: xenograft of breast cancer cell line, 5-azadC_rep1

description:
aza_vs_DMSO_DMR_q_0_01_mm10_genes_promoters.csv
aza_vs_DMSO_DMR_q_0_01_mm10_genes_introns.csv
aza_vs_DMSO_DMR_q_0_01_mm10_genes_intergenic.csv
aza_vs_DMSO_DMR_q_0_01_mm10_genes_exons.csv
aza_vs_DMSO_DMR_q_0_01_mm10_cpg_shores.csv
aza_vs_DMSO_DMR_q_0_01_mm10_cpg_shelves.csv
aza_vs_DMSO_DMR_q_0_01_mm10_cpg_islands.csv
aza_vs_DMSO_DMR_q_0_01_mm10_cpg_inter.csv
aza_vs_DMSO_DMC_q_0_01_mm10_genes_promoters.csv
aza_vs_DMSO_DMC_q_0_01_mm10_genes_introns.csv
aza_vs_DMSO_DMC_q_0_01_mm10_genes_intergenic.csv
aza_vs_DMSO_DMC_q_0_01_mm10_genes_exons.csv
aza_vs_DMSO_DMC_q_0_01_mm10_cpg_shores.csv
aza_vs_DMSO_DMC_q_0_01_mm10_cpg_shelves.csv
aza_vs_DMSO_DMC_q_0_01_mm10_cpg_islands.csv
aza_vs_DMSO_DMC_q_0_01_mm10_cpg_inter.csv

value: xenograft NIC5231 mouse breast cancer cell line


title: Control replicate 2

description:
BC2
Single cell RNA
Single cell RNA-seq was performed using Drop-seq.

value: brain

value: wandering third instar larvae

value: repo>+


title: xenograft of breast cancer cell line, C29+5-azadC_rep2


title: PH3M3

value: 3 hours


title: xenograft of breast cancer cell line, C29_rep2

description:
C29_vs_DMSO_DMR_q_0_01_mm10_genes_promoters.csv
C29_vs_DMSO_DMR_q_0_01_mm10_genes_introns.csv
C29_vs_DMSO_DMR_q_0_01_mm10_genes_intergenic.csv
C29_vs_DMSO_DMR_q_0_01_mm10_genes_exons.csv
C29_vs_DMSO_DMR_q_0_01_mm10_cpg_shores.csv
C29_vs_DMSO_DMR_q_0_01_mm10_cpg_shelves.csv
C29_vs_DMSO_DMR_q_0_01_mm10_cpg_islands.csv
C29_vs_DMSO_DMR_q_0_01_mm10_cpg_inter.csv
C29_vs_DMSO_DMC_q_0_01_mm10_genes_promoters.csv
C29_vs_DMSO_DMC_q_0_01_mm10_genes_introns.csv
C29_vs_DMSO_DMC_q_0_01_mm10_genes_intergenic.csv
C29_vs_DMSO_DMC_q_0_01_mm10_genes_exons.csv
C29_vs_DMSO_DMC_q_0_01_mm10_cpg_shores.csv
C29_vs_DMSO_DMC_q_0_01_mm10_cpg_shelves.csv
C29_vs_DMSO_DMC_q_0_01_mm10_cpg_islands.csv
C29_vs_DMSO_DMC_q_0_01_mm10_cpg_inter.csv


title: PH3M2


title: CD4Cre_Il7rf_rep3

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
Raw sequencing reads were aligned to the genome using Bowtie2 (Galaxy Version 2.3.2.2)
wigcoverage files were generated using MACs version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS v1.4.2; scores represent read coverage

source_name: CD4 T cells

extract_protocol:
Spleens from infected mice were recovered 14-18 days following the first treatment with tamoxifen, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi tdRFP+ IL-7Ra- 2W1S-specific CD4 T cells using a BD FACSAria Fusion cell sorter (BD) to greater than 95% purity
Cells were resuspended in 50 µl ATAC transposition reaction mix containing 25 ml 2x Tagment DNA Buffer (Illumina), 2.5 ml Tn5 transposase (Illumina), 16.5 ml PBS, 0.5 ml 10% Tween-20 and 0.5 µl 1% Digitonin (Promega #G9441) and incubated for 20 minutes at 37oC. DNA was purified using the MinElute Reaction Clean up kit (Qiagen #28204). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

treatment_protocol: Mice were infected with 10e7 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein. 19-21 days later 200 ul 20 mg/ml tamoxifen was administered by oral gavage for four consecutive days.

value: Spleen

value: CD4creERT2 x Il7rf/f x ROSA26tdRFP


title: Nelfe_UT

value: unstimulated


title: xenograft of breast cancer cell line, DMSO_rep2

value: DMSO


title: xenograft of breast cancer cell line, C29_rep1


title: CD4Cre_Il7rf_rep1


title: xenograft of breast cancer cell line, DMSO_rep1


title: PH3M1


title: Il7rf control rep3

extract_protocol:
Spleens from infected mice were recovered 14-18 days following the first treatment with tamoxifen, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi IL7Ra+ 2W1S-specific CD4 T cells using a BD FACSAria Fusion cell sorter (BD) to greater than 95% purity
Cells were resuspended in 50 µl ATAC transposition reaction mix containing 25 ml 2x Tagment DNA Buffer (Illumina), 2.5 ml Tn5 transposase (Illumina), 16.5 ml PBS, 0.5 ml 10% Tween-20 and 0.5 µl 1% Digitonin (Promega #G9441) and incubated for 20 minutes at 37oC. DNA was purified using the MinElute Reaction Clean up kit (Qiagen #28204). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

value: Il7rf control cells

value: Il7rf/f x ROSA26tdRFP


title: CD4Cre_Il7rf_rep2


title: Il7rf control rep2


title: xenograft of breast cancer cell line, 5-azadC_rep2


title: Il7rf control rep1


title: Sample 12_IL-14-12_12 [re-analysis]

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

description:
IL-14-12_12_GTGAAA_L000
This is duplicated sample record of GSM2730549 for the convenient retrieval of the complete raw data from SRA

data_processing:
Illumina NovaSeq6000 RTA3 software used for basecalling: version 3.4.4
For comparison between FG1924 and FG1817, all forward reads were trimmed to a final size of 50 nt using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) using TopHat (version 2.0.13) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 1.9) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9) (Anders et al., 2015)
Differentially expressed genes were identified using DESeq version 1.34.1 (run in R version 3.5.2) (Anders and Huber, 2010) and data were further processed using Microsoft Excel
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; BaseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj; sample x; Name; Best hit; Description; Alternate descriptions; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component

organism: Anguilla anguilla

source_name: unexercised eels (SC)

growth_protocol: European eels were caught by local fishermen and kept in freshwater for a few days.

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 0.5 µg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2.

treatment_protocol: Two weeks prior to the experiments, the salinity was increased to 35 PSU. Eels were transferred to the swim tunnel and acclimatized to the new environment at a pressure of 1 bar and a flow rate of 0.1 m s-1 for 2 h at a temperature of 14°C. Over a period of 16 h, eels were acclimatized to higher flow rates of up to 0.5 bl s-1, which corresponds to the estimated swimming speed of the spawning migration. Pressure was elevated at a rate of 1 bar min-1 which corresponds to the natural diving speed of 0.15 m s-1 to finally 8 bar. The 24 h experiment was terminated by 8 h of exercise at a velocity of 0.5 bl s-1 and a pressure of 8 bar (= 0.8 MPa). At the end of the experiment, pressure was reduced to atmospheric pressure at a rate of 1 bar min-1 and water velocity was reduced to 0.1 m s-1. Eels were removed from the tunnel, immediately anesthetized with 2-phenoxyethanol (1 ml l-1), and subsequently decerebrated and spinally pithed. The swimbladder was dissected and the epithelium, consisting of gas gland cells, was carefully freed from connective tissue. The epithelium was transferred into RNAlater™ solution and stored at -80oC until further use.

tag: swimming exercise

value: unexercised

value: gas gland tissue


title: Sample 9_IL-14-12_9 [re-analysis]

description:
IL-14-12_9_ATGTCA_L000
This is duplicated sample record of GSM2730546 for the convenient retrieval of the complete raw data from SRA


title: Th17 rep2

extract_protocol:
Colons were recovered 7 days dpi. Tissue was digested in complete RPMI with 0.85 mg/ml Collagenase V (Sigma), 1.25 mg/ml Collagenesae D (Roche), 1mg/ml Dispase (Gibco) and 30 μg/ml DNAse I (Roche) at 37oC . Cells were passed through 100 and 70 μm strainers and stained with LIVE/DEADTM Fixable Near-IR stain (Invitrogen) for 20 min on ice. Cells were purified as tdRFP+ CD4 T cells (fate mapping IL-17 expression) using a BD FACSAria Fusion cell sorter (BD) to greater than 95% purity.
Cells were resuspended in 50 µl ATAC transposition reaction mix containing 25 ml 2x Tagment DNA Buffer (Illumina), 2.5 ml Tn5 transposase (Illumina), 16.5 ml PBS, 0.5 ml 10% Tween-20 and 0.5 µl 1% Digitonin (Promega #G9441) and incubated for 20 minutes at 37oC. DNA was purified using the MinElute Reaction Clean up kit (Qiagen #28204). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

treatment_protocol: Mice were orally infected with ~2 x 10e9  Citrobacter rodentium strain ICC169 in 200 ml PBS by oral gavage

value: colon

value: Th17 cells

value: Il17aCre x ROSA26tdRFP+


title: Sample 6_IL-14-12_6 [re-analysis]

description:
IL-14-12_6_CTTGTA_L000
This is duplicated sample record of GSM2730543 for the convenient retrieval of the complete raw data from SRA


title: Sample 3_IL-14-12_3 [re-analysis]

description:
IL-14-12_3_ACAGTG_L000
This is duplicated sample record of GSM2730541 for the convenient retrieval of the complete raw data from SRA


title: Th17 rep1


title: Th1 rep2

extract_protocol:
Spleens from infected mice were recovered 56 dpi, crushed through a nylon mesh and treated with Gey’s solution red blood lysis buffer. The 2W1S-specific memory T cell pool was enriched by magnetic enrichment before purfying CD44hi 2W1S-specific CD4 T cells using a BD FACSAria Fusion cell sorter (BD) to greater than 95% purity
Cells were resuspended in 50 µl ATAC transposition reaction mix containing 25 ml 2x Tagment DNA Buffer (Illumina), 2.5 ml Tn5 transposase (Illumina), 16.5 ml PBS, 0.5 ml 10% Tween-20 and 0.5 µl 1% Digitonin (Promega #G9441) and incubated for 20 minutes at 37oC. DNA was purified using the MinElute Reaction Clean up kit (Qiagen #28204). Nextera adaptors were added during PCR amplification of transposed DNA. Amplified DNA was subsequently purified using Ampure Beads (Beckman Coulter) prior to validation.

treatment_protocol: Mice were infected with 10e7 actA-deficient L. monocytogenes expressing OVA-2W1S through intravenous injection in the tail vein.

value: Th1 cells


title: HEK293-mock_antiHA-Ab

data_processing:
Paired-end sequencing (101bp x2) was performed on the HiSeq1500 system (illumina). Only the Read1fastq data were subjected to the following analysis.
Basecalls were performed using the Real-Time Analysis (RTA) version 1.12.4.2 and CASAVA_v1.8.1.
Reads from each sample were first trimmed by removing adapters and low quality bases at ends using cutadapt-1.7.1
The same number of read pairs (approximately nine million pairs) were aligned to the human reference genome (hg38) using the Burrows-Wheeler Aligner 0.6.2.
Uniquely mapped reads were selected by a custom script, converted from sam to bam using SAMtools-1.2. Reads with mapping quality < 20 were removed using SAMtools-1.2
The uniquely mapped reads were analysed using the MACS2 algorithm to identify ChIPseq peaks.
Genome_build: hg38
Supplementary_files_format_and_content: MACS peak calling output

source_name: Human Embryonic Kidney cells HEK293

growth_protocol: Culture conditions; Cells were cultured at 37C with 5% CO2 in Dulbecco’s Modified Eagle Medium supplemented with fetal calf serum and penicillin/streptomycin.

extract_protocol:
HEK293 cells expressing ZFAT-HA were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking reaction was quenched with 125 mM glycine for 5 min. The cells were rinsed with PBS twice and incubated in 600 µl of MNase treated buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% NP-40, 5 mM CaCl2) containing 375 unit MNase (Roche) for 0.5 h at 37°C. The MNase reaction was stopped by adding 600 µl of lysis buffer  (100 mM Tris-HCl, pH 8.0, 20 mM EDTA, 2% SDS, protease inhibitor cocktail (Roche)), and the lysate was sonicated using a Bioruptor (Cosmo Bio, Tokyo, Japan) for two cycles of one minute with 30 seconds on/off. The sonicated lysate was subjected to immunoprecipitation with a monoclonal antibody against HA-tag or control IgG.
The immunoprecipitated DNA was purified using MinElute Reaction Cleanup kit (Qiagen) according to the manufacturer’s instructions. ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set and Multiplex Oligos for Illumina (New England Biolabs) according to manufacturer's instructions. ChIP or input DNA (0.1ng) was subjected to end repair, dA-tailing, and adaptor-ligation, and amplified by 13 cycles of PCR.

value: mock

value: Human Embryonic Kidney cells HEK293

tag: chip antibody

value: anti-HA antibody (3F10, Merck/#11867423001)


title: Sample 2_IL-14-12_2 [re-analysis]

description:
IL-14-12_2_TGACCA_L000
This is duplicated sample record of GSM2730540 for the convenient retrieval of the complete raw data from SRA


title: DNAse-seq_TB_CD3CD28

data_processing:
Library strategy: DNase-seq
Raw sequencing reads were aligned to the genome using Bowtie2 (Galaxy Version 2.3.2.2)
wigcoverage files were generated using MACs version 1.4.2
Bam files from all samples were merged using BamTools (Galaxy Version 0.0.2)
A master set of peaks were determined using MACS2 callpeak (Galaxy Version 2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS v1.4.2; scores represent read coverage

growth_protocol:
CD4 T cells were purified from the spleen of mice using CD4 microbeads (MACs). Cells were cultured at 1x10e6 cells/ml in IMDM with CD3 and CD28 antibodies for 40 hours before maintainance at 5x10e5 cells/ml in IMDM supplemented with 50 U/ml recombinant murine IL-2 for 48 hours.
CD4 T cells were purified from the spleen of mice using CD4 microbeads (MACs). Cells were cultured in IMDM with 2 ug/ml ConA for 40 hours and then maintained in 50 U/ml cytokine for 2 days

extract_protocol:
Cells were permeabilised and treated with DNase I for three minutes at 22C. DNA was purified by phenol chloroform extraction and small DNA fragments (50-250bp) were purified before library preperation
Libraries were constructed using the Kapa Hyper prep kit according to the manufacturer's instructions

treatment_protocol: IL-2 /IL-7 was removed from cultures for 16 hour or Ruxolitinib/DMSO control was added to cultures for 16 hours

value: CD4 T cells

tag: cultured with

value: CD3 and CD28 antibodies, IL-2


title: FG1817_08

description:
FG1817_08_34089_S12_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx

source_name: exercised eels_ED

value: exercised

tag: swimbladder functional/non-functional

value: damaged, non-functional swimbladders (ED)

value: swimbladder gas gland cells


title: FG1817_07

description:
FG1817_07_34088_S11_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx


title: TB IL-2 STAT5 rep1

data_processing:
Raw sequencing reads were aligned to the genome using Bowtie2 (Galaxy Version 2.3.2.2)
Duplicate reads were removed using Picard MarkDuplicates (Galaxy version 2.3.2.2)
wigcoverage files were generated using MACs version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS v1.4.2; scores represent read coverage

growth_protocol: CD4 T cells were purified from the spleen of mice using CD4 microbeads (MACs). Cells were cultured in IMDM with 2 ug/ml ConA for 40 hours and then maintained in 50 U/ml cytokine for 2 days

extract_protocol:
Cells were crosslinked with 0.83mg/ml DSG followed by 1% formaldehyde before shearing by sonication to fragments of 500bp. Chromatin was immuoprecipitated for 2 hours with anti-STAT5 (sc-835X) or anti-JUND (sc-74X) before washing and reversing crosslinks overnight at 65C. DNA was purifiied using Agencourt AMPure (Beckman Coulter) before library preperation
Libraries were constructed using the Kapa Hyper prep kit according to the manufacturer's instructions

treatment_protocol: IL-2 was removed from cultures for 16 hours before purification

value: Spleen

value: Santa-Cruz sc-835X


title: HEK293-pEB-ZFAT-HA_antiHA-Ab

tag: treatment

value: pEB-ZFAT-HA


title: SAMP8 + STEE 2

type: RNA

city: Tsukuba

first: Kengo

last: Iwata

address: 1-1-1 Tennodai

institute: University of Tsukuba

hyb_protocol: Biotinylated cRNA was hybridized onto Affymetrix Mouse Genome 430 PM array strips (Affymetrix) for 16 hrs at 45℃ in the hybridization station.

scan_protocol: The hybridized arrays were washed, stained, and scanned with GeneAtlas Fluidics and Imaging Station.

data_processing:
The gene-level information (CHP files) was obtained from the probe intensity files (CEL files) using robust multichip analysis (RMA) summarization algorithm in Expression Console software (Affymetrix; http://www.affymetrix.com). Subsequent analysis of the obtained data was carried out in Transcriptome Analysis Console (TAC) ver.4 software (ThermoFisher Scientific). Microarray was conducted for two mRNA biological samples of each group. Differentially expressed genes (DEGs) with p-value < 0.05 (one-way between-subjects ANOVA) were included for gene ontology (GO) analysis. The Molecular Signatures Database (MSigDB) of Gene Set Enrichment Analysis (GSEA) web tool was used to determine whether the gene sets show statistically significant and concordant differences between two biological states (https://www.gsea-msigdb.org/gsea/index.jsp).
Signal intensity of all the samples deraived from Expression Console (2nd sheet). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files). Data are given in the sheets named as SAMP8Control vs SAMR1 and SAMP8STEE vs SAMP8Control

label: biotin

source_name: cerebral cortex, STEE-administered, 30+8days

label_protocol: RNA samples were amplified and biotinylated with Affymetrix 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA), according to the manufacturer’s instructions.

growth_protocol: SAMP8 mice and SAMR1 mice were purchased from Japan SLC (Shizuoka, Japan). The mice were housed individually under controlled temperature (21-23℃) and photoperiod (12-hr light/dark) and provided food and water ad libitum.

extract_protocol: The cerebral cortex was isolated from the extracted brain and homogenized with Isogen (Nippon Gene, Toyama, Japan).

treatment_protocol:
After one week of acclimatization, SAMP8 mice were fed with STEE orally at 20 mg/kg for 30 days. SAMP8 controls and SAMR1 mice were administered the equal volume of Mill-Q water to that of the extract. After completion of the 30 days administration, the mice were subjected to the behavioral test for 8 days, and the administration was continued during this period also.
Administration method: p.o.; Amount; 20 mg/kg/day.

tag: gender

value: male

tag: genotype

tag: tissue

value: cerebral cortex

value: sixteen weeks-old

value: sugarcane top ethanolic extract (STEE)


title: TB IL-2 JunD rep1

value: Santa-Cruz sc-74X


title: FG1817_05

description:
FG1817_05_34086_S9_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx

value: gas gland tissue


title: dgt meristem rep3

city: Corvallis

first: Molly

last: Megraw

state: Oregon

address: 2082 Cordley Hall

institute: Oregon State University

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reference transcripts were extracted and preprocessed from the NCBI Heinz 1706 genome sequence and gene annotation (GCF_000188115.4) using RSEM’s (RNA-Seq by Expectation Maximization, version 1.3.1) rsem-prepare-reference function
Using RSEM, raw sequence reads wer aligned to the reference transcript sequences and relative abundances were calculated using default parameters. Resulting gene-level estimates from biological replicates were merged into a single input matrix and EBSeq (version 1.26.0) was then used to test for differential expression between dgt and WT for each root-tip zone.
Genome_build: GCF_000188115.4
Supplementary_files_format_and_content: genes.results.txt files contain tab-delimited expression estimates including TPM and FPKM from RSEM at a gene-level, and isoforms.results.txt files contain the same estimate types at an isoform-level. Txt files present differential expression analysis from EBSeq of dgt as compared to WT.

organism: Solanum lycopersicum

source_name: Root

growth_protocol: Three biological replicates for each tissue and genotype were performed. Seven-day old tomato (Solanum lycopersicum) wild-type and dgt1-1 plants in the ‘AilsaCraig’ background7were used. Seeds were sterilized in 20% commercial bleach for 30 min and rinsed four times for 10 min with sterile water. Sterilized seeds were incubated at 4C for 2d to ensure even germination and then planted on media containing 0.2× Murashige and Skoog basal medium with vitamins (PhytoTechnology; http://www.phytotechlab.com), 1 % sucrose, 10 mM MES buffer pH5.7,and 0.8% agar. Seeds were germinated in Magenta dishes (16 seeds per dish) in a growth chamber at 21C under long day (16h light, 8h dark) conditions and light intensity as in Ivanchenko et al. (2013). Root samples were dissected under DIC optics at 4× objective as in Ivanchenko et al. (2006). On average, 50–100 root portions were collected per biological replicate. The meristem was dissected between the root tip and the root portion where tissue becomes more transparent. The elongation zone was collected from the proximal meristem border and the first hair bulge, and approximately 1 cm portions were collected above the first hair bulge for the differentiation zone.

extract_protocol:
Tissue was ground in liquid N2 and RNA extracted with Plant RNA Reagent (Life Technologies; http://www.lifetechnologies.com). Total RNA was treated with 1X RNA Secure Reagent (Ambion; http://www.lifetechnologies.com) at 65C for 10 min, treated with DNase I (Ambion; http://www.lifetechnologies.com) at 37C for 10 min, and purified with RNeasy kit (Qiagen; http://www.qiagen.com) following the manufacturer's instructions.
RNA-Seq library preparation and sequencing was performed at the Oregon State University Center for Genome Research and Biocomputing. Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA) and sequenced as single-end 51 bpreads on two lanes of the Illumina HiSeq 2000.

tag: cultivar

value: Ailsa Craig

value: Meristem


title: dgt meristem rep2


title: dgt elongation rep2

value: Elongation zone


title: FG1817_06

description:
FG1817_06_34087_S10_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx


title: dgt elongation rep3


title: dgt meristem rep1


title: SAMP8 + STEE 1


title: Th1 rep1

value: Th1 cells


title: SAMR1 + Water 2

source_name: cerebral cortex, water-administered, 30+8days

treatment_protocol:
After one week of acclimatization, SAMP8 mice were fed with STEE orally at 20 mg/kg for 30 days. SAMP8 controls and SAMR1 mice were administered the equal volume of Mill-Q water to that of the extract. After completion of the 30 days administration, the mice were subjected to the behavioral test for 8 days, and the administration was continued during this period also.
Administration method: p.o. Administered-water was equal volume to that of the extract.

value: Water


title: dgt elongation rep1


title: SAMP8 + Water 1


title: SAMP8 + Water 2


title: RNA-seq_TB+ IL-2nil rep2

data_processing:
Raw paired-end reads were processed prior to alignment with Trimmomatic v0.32
The processed reads were then aligned to the mouse genome (version mm9) using Hisat2 v2.1.0 with default parameters
Gene expression was measured as Transcripts Per Million (TPM) calculated with Stringtie v1.3.3 using RefSeq gene models as the reference transcriptome.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited table of GeneIDs and gene expression values (Transcripts Per Million)

growth_protocol: CD4 T cells were purified from the spleen of mice using CD4 microbeads (MACs). Cells were cultured in IMDM with 2 ug/ml ConA for 40 hours and then maintained in 50 U/ml IL-2 for 2 days

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and further purified using Rneasy MinElute Cleanup Kit (Qiagen). rRNA was depleted using the NEBNext® rRNA Depletion Kit (NEB)
Libraries were constructed using the NEB Next® Ultra II Directional RNA library preperation Kit (NEB).

value: CD4 T cells

value: no IL-2

tag: activation

value: with PMA and calcium ionophore


title: dgt differentiation rep3

value: Differentiation zone


title: FG1817_03

description:
FG1817_03_34084_S7_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx

value: exercised

value: damaged, non-functional swimbladders (ED)

value: swimbladder gas gland cells


title: RNA-seq_TB+ IL-2nil rep1

value: Spleen


title: SAMR1 + Water 1

value: male

value: cerebral cortex

value: sixteen weeks-old


title: C.elegans_seip-1_KO_adult_worm_rep1

city: Taipei

first: Leng-Jie

last: Huang

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: stage:52 hours after L1

hyb_protocol: 1.65 μg of Cy3-labled cRNA was incubated at 60°C for 30 minutes, followed by hybridization to the Agilent C. elegans V2 4*44K Microarray chip (Agilent Technologies, USA) at 65°C for 17 hrs. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The microarray chip was scanned with the microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3

data_processing:
The array image was read by Feature Extraction software version 10.7.1.1, and data was subjected to further analysis by GeneSpring software (Agilent) by following parameter:Threshold: 1.0; Logbase: 2; Technology: Agilent.SingleColor.20186; Normalization: Shift to 75 percentile
Average value of N2 sample was used as the control

organism: Caenorhabditis elegans

label_protocol: A 0.2 μg of total RNA was subjected to Cy3 labeling by in vitro transcription with use of Low Input Quick-Amp Labeling kit (Agilent Technologies, USA).

growth_protocol: Embryos were isolated from gravid adults by hypochlorite disruption (0.5N NaOH and 1% NaOCl) followed by M9 washes. After overnight incubations in M9 without food, synchronized L1 were then seeded on a 5.5cm NGM plate (~150 L1 /plate). The synchronized young adult (52 hrs post L1 feeding) were harvested and washed by M9 buffer and pelleted. Embryos were isolated by hypochlorite disruption from young gravid adult (52 hrs after L1), washed with M9, and pelleted

extract_protocol: Synchronized young adult or embryos derived from ~40,000 young adults were resuspended in 500 μl TRIzol reagent followed by flash freezing in liquid nitrogen. Samples were thawed at 42°C and frozen in liquid nitrogen and the cycle was repeated 6-7 times. 100 μl chloroform was mixed with sample and spun at 12,000g for 15 minutes at 4°C. The corresponding aqueous layer was harvested and mixed with equal volume of 70% ethanol. RNeasy Mini kits (Qiagen) were used to obtain pure RNA for microarray analysis.

tag: developmental stage


title: RNA-seq_TB+ IL-2nil rep3


title: C.elegans_seip-1_KO_embryo_rep2

description: harvested from 52 hours after L1

value: embryo


title: C.elegans_WT_adult_worm_rep2

description: stage:52 hours after L1

value: wild-type


title: C.elegans_WT_adult_worm_rep1

description: stage:52 hours after L1


title: FG1817_04

description:
FG1817_04_34085_S8_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx

value: gas gland tissue


title: FG1817_02

description:
FG1817_02_34083_S6_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx


title: RNA-seq_TB+ IL-2 rep3


title: FG1817_01

description:
FG1817_01_34082_S5_R1_001
processed data file: IL-14-12_vs_FG1817.xlsx


title: RNA-seq_TB+ IL-2 rep1


title: WT meristem rep3

value: Ailsa Craig

value: Meristem

value: WT


title: WT meristem rep2


title: RNA-seq_TB IL-2nil rep3

value: CD4 T cells


title: Clone 28e

first: Don

middle: W.

last: Cleveland

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to GRCh38 whole genome using tophat-2.0.8b.Linux_x86_64 with parameters --no-coverage-search -G genes.gtf --transcriptome-index=transcriptome_data/known --prefilter-multihits --max-multihits 1 --library-type fr-firststrand -o *_thout genome *.fastq.bz2
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks version v2.1.1 with parameters -N -F 0 -G genes.gtf -o *_clout *_thout/accepted_hits.bam
Significant gene expression change between groups has been detected using cuffdiff
Genome_build: GRCh38
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: HeLa cells

growth_protocol: Cells were grown in DMEM (Gibco) containing 10% fetal bovine serum (Omega), supplemented with 100U/ml penicillin, 100U/ml streptomycin, and 2mM l-glutamine, at 37°C in a 5% CO2 incubator

extract_protocol:
RNA was extracted using a kit (nucleospin), and RNA integrity was validated using agaros gel analysis (28S and 18S bands). These RNA samples were used to create libraries for RNA sequencing using the stranded mRNA illumina kit
Library prepared according to Illumina's stranded mRNA illumina kit manual

treatment_protocol: Methotrexate was used at indicated concentrations to generate resistant clones. To obtain mitotic samples, cells were arrested at mitosis with nocodazole for 6 hours and mitotic cells were collected by shake-off

tag: resistance

value: 60nM MTX

tag: amplification type

value: HSR


title: dgt differentiation rep1

value: Differentiation zone


title: RNA-seq_TB+ IL-2 rep2

tag: strain

tag: cell type

value: with PMA and calcium ionophore


title: Sample 28f

value: 500nM MTX

value: HSR-->DM


title: Clone 24b

value: No amplification


title: RNA-seq_TB IL-2nil rep2

value: Spleen

value: no IL-2


title: dgt differentiation rep2


title: WT elongation rep3

value: Elongation zone


title: WT meristem rep1


title: C.elegans_seip-1_KO_embryo_rep1

description: harvested from 52 hours after L1

value: embryo


title: C.elegans_seip-1_KO_adult_worm_rep2

description: stage:52 hours after L1


title: Clone 24h

value: DM


title: RNA-seq_TB IL-2nil rep1


title: Clone 28c

value: 80nM MTX


title: SG_24h_CTRL_2

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor package limma in R

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

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

value: spiral ganglion (SG)

tag: status

value: CTRL

tag: timepoint


title: WT elongation rep2

value: Ailsa Craig

value: WT


title: RNA-seq_TB IL-2 rep3

value: CD4 T cells


title: SG_5h_CTRL_1

description: replicate 1


title: C.elegans_WT_embryo_rep2

description: harvested from 52 hours after L1

value: wild-type


title: OC_5h_KA_1

description: replicate 1

value: organ of Corti (OC)

value: KA


title: SG_5h_KA_1

description: replicate 1


title: Clone 24a

value: 40nM MTX


title: Clone 28b


title: WT differentiation rep3

value: Differentiation zone


title: Clone 25j

value: 60nM MTX

value: No amplification


title: Clone 26d


title: WT differentiation rep2


title: WT elongation rep1


title: BoneMarrow_TRNT1mut_1

type: genomic

city: Perugia

first: Cristina

last: Mecucci

address: piazzale Menghini n.9

department: Medicine

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 3.1 (ChAS) software with filters set at 100 Kb dimension for Copy Number Alterations (CNAs) and 10 Mb dimensions for copy neutral loss of heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from bone marrow cells of patients using Salting-out Method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: cytogenetics

tag: mutations

tag: age


title: RNA-seq_TB IL-2 rep2

value: Spleen

tag: cultured with


title: DNAse-seq_TB DMSO

value: DMSO


title: WT differentiation rep1


title: Clone 26g

city: La Jolla

value: 250nM MTX

value: HSR-->DM


title: DNAse-seq_TB Ruxolitinib

value: Ruxolitinib


title: RNA-seq_TB IL-2 rep1


title: DNAse-seq_TB+ IL-7

value: with PMA and calcium ionophore


title: Wild type HeLa

description: not sequenced


title: DNAse-seq_TB+ IL-7nil

value: no IL-7


title: Clone 25g

value: 80nM MTX

value: DM


title: SG_72h_KA_1

description: replicate 1

value: spiral ganglion (SG)


title: OC_72h_CTRL_2

description: replicate 2

value: CTRL


title: Clone 24j


title: SG_72h_CTRL_2

description: replicate 2


title: SG_24h_KA_1

description: replicate 1


title: OC_24h_CTRL_2

description: replicate 2

value: organ of Corti (OC)


title: SG_24h_KA_3

description: replicate 3

value: KA


title: OC_24h_CTRL_1

description: replicate 1


title: C.elegans_WT_embryo_rep1

description: harvested from 52 hours after L1

value: embryo

value: wild-type


title: Clone 25l


title: Clone 24d

value: 60nM MTX


title: DNAse-seq_TB+ IL-2nil rep2

value: CD4 T cells

value: no IL-2


title: DNAse-seq_TB IL-7nil rep2

value: Spleen


title: Clone 27d

value: No amplification


title: DNAse-seq_TB IL-7 rep2


title: DNAse-seq_TB IL-7 rep1


title: DNAse-seq_TB IL-7nil rep1


title: Clone 26h

value: 250nM MTX

value: HSR-->DM


title: Clone 24n

value: DM+HSR


title: Clone 24g


title: DNAse-seq_TB+ IL-2 rep2

value: with PMA and calcium ionophore


title: OC_72h_CTRL_3

description: replicate 3


title: OC_5h_CTRL_2

description: replicate 2


title: OC_72h_KA_2

description: replicate 2


title: Clone 25d

value: 80nM MTX


title: Clone 26a

value: 40nM MTX

value: HSR


title: DNAse-seq_TB+ IL-2 rep1


title: DNAse-seq_TB IL-2nil rep1


title: OC_72h_KA_3

description: replicate 3


title: SG_72h_CTRL_3

description: replicate 3

value: spiral ganglion (SG)

value: CTRL


title: DNAse-seq_TB+ IL-2nil rep1


title: OC_24h_KA_3

description: replicate 3

value: organ of Corti (OC)

value: KA


title: OC_5h_CTRL_1

description: replicate 1


title: Clone 27h


title: OC_5h_KA_2

description: replicate 2


title: OC_72h_CTRL_4

description: replicate 4


title: OC_24h_CTRL_3

description: replicate 3


title: DNAse-seq_TB IL-2 rep2


title: DNAse-seq_TB IL-2 rep1


title: Clone 27p


title: Clone 25b


title: Clone 27b


title: TB IL-2nil JunD

tag: antibody

value: Santa-Cruz sc-74X


title: e.1 40/80/160

description: not sequenced

value: 160nM MTX

value: DM


title: DNAse-seq_TB IL-2nil rep2

value: CD4 T cells

value: no IL-2


title: TB IL-2 JunD rep2

value: Spleen


title: Clone 26b

value: No amplification


title: TB IL-2nil STAT5

value: Santa-Cruz sc-835X


title: TB IL-2 STAT5 rep2


title: SG_5h_KA_3

description: replicate 3


title: Clone 27k


title: SG_5h_KA_2

description: replicate 2


title: A96M2

extract_protocol:
Mouse hepatic cells were isolated with the two-step collagenase profusion method.
Libraries were prepared according to the Seq-Well protocol.

value: liver

tag: Sex

value: Male

tag: treatment

value: APAP(acetaminophen)

tag: time point

value: 96 hours


title: Clone 26c

value: 80nM MTX

value: HSR


title: SG_72h_KA_3

description: replicate 3

tag: tissue

value: spiral ganglion (SG)


title: A96M1


title: cut14SO biorep 2

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

institute: Waseda Institute for Advanced Study

data_processing:
basecalling with bcl2fastq v2.20.0
alignment using BWA 0.7.17
processing using Juicer 1.5.6
Genome_build: Schizosaccharomyces pombe ASM294v2
Supplementary_files_format_and_content: Juicer inter_30.hic file

organism: Schizosaccharomyces pombe

source_name: G2-arrested cells_condensin shut off

growth_protocol: Cells were grown in EMM supplemented with glutamate. Cells were arrested in G2 phase by the addition of 1 mM of 1NM-PP1. Condensin was depleted by 0.5 mM of IAA and 5 µg/mL of thiamine. For control, the equivalent amount of methanol was added instead of IAA.

extract_protocol:
Crosslinked chromatin was digested by DpnII. The sticky ends were filled in by Biotin-14-dATP and the other dNTPs. Proximal ligation was performed, followed by DNA recovery by Biotin-Streptavidin interaction.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.

treatment_protocol: G2 arrested cells were crosslinked with 0.5 % formaldehyde for 30 minutes at 25 ºC.

tag: cell cycle

value: G2 arrested cells

tag: restriction enzyme

value: DpnII

tag: condensin state

value: shut off

tag: biological replicate


title: SG_24h_CTRL_3

description: replicate 3

tag: strain

value: CTRL


title: SG_5h_CTRL_4

description: replicate 4


title: OC_5h_KA_3

description: replicate 3

value: organ of Corti (OC)

value: KA


title: OC_5h_CTRL_3

description: replicate 3


title: SG_5h_CTRL_2

description: replicate 2


title: A48M1

value: 48 hours


title: cut14+ biorep 2

source_name: G2-arrested cells_control

value: control


title: cut14+ biorep 1


title: A24M2

value: 24 hours


title: A24M1


title: SG_5h_CTRL_3

description: replicate 3


title: A6M1

value: 6 hours


title: OC_24h_KA_4

description: replicate 4


title: UTM6

value: liver


title: cut14SO biorep 1


title: Control 90

city: Jeonju

first: Jeong-Gu

last: Kim

address: 370 Nongsaengmoung-ro

country: South Korea

institute: Rural development administration

data_processing:
Quality-filtered reads were mapped to the reference genome sequence (http://www.ncbi.nlm.nih.gov/nuccore/58579623?report=fasta) using CLC Genomics Workbench 4.0 (CLC bio, Aarhus, Denmark).
Genome_build: NC_006834.1
Supplementary_files_format_and_content: tab-delimited text files include total read count values for each Sample

organism: Xanthomonas oryzae pv. oryzae

source_name: Untreated Xoo 90 min

extract_protocol:
Total RNA was extracted from each sample of the harvested Xoo cells separately using an RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.Total RNA from approximately 10 μg of each sample was used as the starting material for generating sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Untreatment


title: Control 0

source_name: Untreated Xoo 0 min


title: A48M2

data_processing:
FASTQs were aligned to mm10 with STAR aligner
Barcode is the first 12 bases of read 1. UMI is the next 8 bases of read 1.
Barcodes with fewer than 400 genes detected were discarded as non-cells
TPM-like (base 10,000) then log normalize
Run PCA and shared nearest neighbor (SNN) cluster data over top 13 PCs. 14 clusters identified.
Remove clusters which contain non-hepatocytes and a low quality, high percent mitochonrial cluster so that only clusters of high quality hepatocytes remain.
Genome_build: mm10
Supplementary_files_format_and_content: ALI_allcell_400gene.txt: UMI dge genes x cells matrix for all cells expressing >400 genes from all samples. Sample of origin is appended to the cell barcode name. No additional quality or hepatocyte identity filtering
ALI_filterHQhep.txt: Filtered for high quality hepatocytes only.

value: Male

value: APAP(acetaminophen)


title: UTM5


title: Control 120

source_name: Untreated Xoo 120 min


title: SG_72h_KA_4

description: replicate 4


title: SG_24h_KA_4

description: replicate 4


title: P-activated Xoo 120

source_name: RLX treated Xoo 120 min

value: Rice leaf homogente (RLX)


title: P-activated Xoo 90

source_name: RLX treated Xoo 90 min


title: OC_24h_CTRL_4

description: replicate 4


title: UTM1

source_name: Mouse Liver


title: OC_5h_KA_4

description: replicate 4


title: A6M2


title: SG_72h_CTRL_4

description: replicate 4


title: SG_5h_KA_4

description: replicate 4


title: WT1, NPCs, day2, rep3

status: Public on Sep 13 2020

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

description: Day2 WT1 3

data_processing:
Quantification using RSEM
Alignment to the mm9 mouse genome using STAR2
Preparation of bigWig files using wigToBigWIg
Genome_build: mm9
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage

source_name: NPCs

growth_protocol: R1 mouse ES cells were grown on a feeder layer of irradiated mouse embryonic fibroblasts (MEFs) on 0.1% gelatin-coated cell culture dishes. Culture medium consisted of DMEM (Gibco), 15% ES-grade fetal calf serum (FCS, Biological Industries), 1X Glutamax (Gibco), 1 mM sodium pyruvate (Gibco), 0.1 mM nonessential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 100 U/ml penicillin and 0.1 mg/ml streptomycin (Biological Industries), and 1000 U/ml LIF. Neuronal differentiation was performed as previously described (Ying et al., 2003). Pluripotent stem cells were first grown in the absence of MEFs for two passages and then seeded on gelatin-coated plates at a density of 2.1*104/cm2 in N2B27 medium: 1:1 mixture of DMEM/F12 (Sigma) supplemented with N2 (Gibco), and Neurobasal medium (Gibco) supplemented with B27 (Gibco), 1X Glutamax (Gibco) ), 0.1 mM β-mercaptoethanol (Sigma), 100 U/ml penicillin, and 0.1 mg/ml streptomycin (Biological industries). After four days under these conditions, the cells were dissociated and re-plated on plates coated with Poly-D-Lysine (Sigma) and Laminin (Sigma), at a density of 3.7*104/cm2 in N2B27 medium supplemented with 20ng/ml FGF2 (Peprotech). After 24 hr, FGF2 was removed from medium and cells were grown for three additional days.

extract_protocol:
Total RNA was extracted from cells, using the Trizol reagent (TRI, Sigma-Aldrich) according to the manufacturer’s protocol.
Lexogen  SENSE-mRNA-Seq

treatment_protocol: Short sequences (21nt) complementary to target genes were synthetized as 58nt single-stranded oligos as forward oligo: 5’-CCGG—21nt sense—CTCGAG—21nt antisense—TTTTTG-3’, and reverse oligo: 5’-AATTCAAAAA—21nt sense—CTCGAG—21nt antisense-3’. Forward and reverse oligos were phosphorylated and annealed to each other by the addition of T4 ligation buffer (NEB) and T4 PNK (NEB) and incubation at 37°C for 30 minutes followed by incubation at 95°C for five minutes and gradual cooling to room temperature at a rate of 5ºC/min. The annealed oligo pairs were ligated to pLKO.1 vector (Sigma # SHC001) which was digested by AgeI and EcoRI. Ligated plasmids were transformed into NEB stable competent bacteria. A plasmid containing an shRNA not targeting a mammalian sequence (Sigma #SHC002) was used as negative control.  To generate Reno m/m ES cells we deleted the promoter and first exon of Reno (a total of 631bp) by transfection of pCas9_GFP plasmid (Addgene #44719) and two gRNA plasmids. To generate Bahcc1 m/m cells we created short deletions containing the start codon of Bahcc1, thereby inhibiting its translation, by transfection of pCas9_GFP plasmid (Addgene #44719) and one gRNA plasmid targeting Bahcc1 start codon.

value: NPCs

tag: time

value: day 2


title: Renom/m2, NPCs, day2, rep2

description: Day2 Renom/m2 2


title: Renom/m1, NPCs, day2, rep2

description: Day2 Renom/m1 2


title: Renom/m2, NPCs, day2, rep3

description: Day2 Renom/m2 3


title: Renom/m2, NPCs, day2, rep1

description: Day2 Renom/m2 1


title: Renom/m1, NPCs, day2, rep3

description: Day2 Renom/m1 3


title: WT1, NPCs, day2, rep1

description: Day2 WT1 1


title: WT2, NPCs, day2, rep1

description: Day2 WT2 1


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad010

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

value: male


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad007


title: OC_72h_KA_4

description: replicate 4

tag: status

tag: timepoint


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad010


title: WT2, NPCs, day2, rep3

description: Day2 WT2 3


title: P-activated Xoo 0

source_name: RLX treated Xoo 0 min


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad012


title: WT2, NPCs, day2, rep2

description: Day2 WT2 2


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad007


title: Renom/m1, NPCs, day2, rep1

description: Day2 Renom/m1 1


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H9_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H7_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H8_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H6_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H5_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H5_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H5_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H3_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H5_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H12_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H2_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H1_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H5_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H1_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G9_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G9_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G9_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G9_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G8_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G8_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G8_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H4_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H11_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_H10_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G7_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G9_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad004


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G4_ad001


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G4_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G4_ad010


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G4_ad006


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G8_ad002


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G5_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G4_ad008


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G3_ad012


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G6_ad007


title: CEMBA181002_5C_7_CEMBA181002_5C_8_G3_ad006