title: saP1

description:
P1_S11_L003
processed data file: f1.glyphosate.csv.gz


title: DR3ZT06

status: Public on Apr 25 2019

type: SRA

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

country: USA

institute: Texas A&M University

description:
RAW_Table.txt
TPM_Table.txt

library_source: transcriptomic

data_processing:
Libraries were sequenced on an Illumina NextSeq. Base calling and demultiplexing were performed with the accompanying software
Sequenced reads were trimmed to remove the first 12nt, trailing and embedded polyA sequences, poor quality bases at the 3' end, and removed if under 36nt
Trimmed reads were aligned to mm10 transcriptome using STAR v2.4.2a with options "--outSAMstrandField intronMotif --quantMode GeneCounts --outFilterIntronMotifs RemoveNoncanonical"
Read counts were quantified to raw values with the R package GenomicRanges and normalized to 1 million transcripts per library (TPM)
Genes with under 1 TPM in 36 or more of the 72 libraries were removed from final consideration
Genome_build: mm10, GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text files with RAW (unnormalized or filtered) or TPM values for each gene and sample

molecule: polyA RNA

organism: Mus musculus

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT06

growth_protocol: Male C57BL/6J mice from Charles River Laboratories (starting age 43-49 days) were housed in a 12 hour light:12 hour dark facility with ad libitum access to water and variable access to food

extract_protocol:
Total RNA was extracted using TRIzol reagent and purified with an acid phenol-chloroform extraction
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used

tag: strain

tag: genotype

value: Wild-type

tag: Sex

value: male

tag: tissue

value: Liver


title: DR3ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT10


title: sP30

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
F3_P30_S72_L006
processed data file: f3.glyphosate.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 40 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window. The PBS and DMSO controls were added together into a single control goup.
Windows with an edgeR p-value less than 10-6 were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: F3_DMSO control_sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats treated were designated as the F0 generation. Subsequent generations were derived from the F0 generation. F1- F3 generation control and glyphosate lineages were housed in the same room and racks with lighting. There was a founder effect observed in the offspring of a specific male from the control population treated with PBS, manifesting as abnormally high rates of obesity in decedents. Therefore, a portion of original control colony was excluded from the study due to the obesity founder effects identified. These animals were replaced with offspring from DMSO-treated controls from a concurrent study.

extract_protocol:
The epididymis from each rat was dissected free of fat and connective tissue, a small cut made to the cauda and the tissue placed in 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature and then kept at 4ºC to immobilize the sperm.  The epididymal tissue was coarsely minced and the released sperm centrifuged at 4ºC 3,000 x g for 10 min and pellet resuspended in fresh NIM buffer and stored at -80ºC until processed further. Twenty–fifty to 50 μl of rat sperm suspension were used for DNA extraction. The suspension was sonicated for five seconds (Fisher Sonic Dismembrator, model 300, power 25), then centrifuged 5 min at 6000 x g, supernatant discarded and sperm washed again to remove somatic cells and debris. Then the pellet was resuspended in 820 μL DNA extraction buffer and 80 μl 0.1M DTT added. The sample was incubated at 65°C for 15 minutes. Following this incubation 80 μl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for at least 2 hours under constant rotation. Then 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was transferred to a 2 ml tube and 2 μl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by vortexing the tube then left in -20°C freezer for at least one hour. After precipitation, the sample was centrifuged at 13,500 x g for 30 min at 4°C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol, then tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 μl of nuclease free water. For all generations equal amounts of DNA from each individual’s sample was used to produce 6 different DNA pools per lineage and the pooled DNA used for methylated DNA immunoprecipitation (MeDIP). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA was performed as follows: The genomic DNA was sonicated using the Covaris M220 as follows: 6μg of pooled or individual animal sperm genomic DNA was diluted to 130 μl with TE buffer (10mM Tris HCl, pH7.5; 1mM EDTA) into the appropriate Covaris tube. Covaris was set to 300 bp program and the program was run for each tube in the experiment. 10 μl of each sonicated DNA was run on 1.5% agarose gel to verify fragment size. The sonicated DNA was then diluted with TE buffer to 400 μl, heat-denatured for 10min at 95˚C, then immediately cooled on ice for 10 min. Then 100μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added to the denatured (single-stranded) sonicated DNA. The DNA-antibody mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After the incubation, the bead-DNA-antibody samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples are then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml) and incubated for 2-3 hours on a rotator at 55˚. Samples were then extracted with Phenol-Chloroform-Isoamyalcohol and the final supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for >1 hour to overnight.  The DNA precipitate was centrifuged at 14,000rpm for 20min at 4˚C, the pellet was washed with 500μl cold 70% ethanol and then air-dried at RT (about 5 minutes). It was resuspended in 20μl H2O or TE. DNA concentration was measured in Qubit (Life Technologies) with ssDNA kit (Molecular Probes Q10212).
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer.

treatment_protocol: Timed-pregnant females on days 8 through 14 of gestation were administered daily intraperitoneal injections of glyphosate (25 mg/kg BW/day dissolved in PBS)(Chem Service, Westchester PA) or dimethyl sulfoxide (DMSO) or Phosphate Buffered Saline (PBS). Only the F0 generation was treated with glyphosate, DMSO, or PBS.

tag: strain background

value: an outbred strain Hsd:Sprague Dawley SD (Harlan) strain

tag: generation

tag: treatment

value: DMSO control

value: sperm


title: sP28

description:
F3_P28_S70_L006
processed data file: f3.glyphosate.csv.gz


title: PCGF2fl_TAM_PCGF2_rep2

city: Oxford

first: Nadezda

middle: A

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native cChIP-seq and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 (or hg19) reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6 (or hg19)/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
RING1B and SUZ12 peak sets were generated with MACS2 (--broad) using corresponding Input samples for background normalisation. For each factor, a set of peaks identified in all biological replicates (intersection) was manually curated to remove sequencing artefacts. Classical Polycomb chromatin domains were identified by k-means clustering of ±10 kb windows centred on RING1B peaks based on their RING1B and SUZ12 chromatin occupancy using deeptools (v.3.0.1). This generated three clusters, two of which displayed high enrichment of both RING1B and SUZ12 and were combined into one set of genomic intervals.
Allele-specific analysis of H2AK119ub1 cChIP-seq was performed as described previously (Pintacuda et al. 2017). Briefly, paired-end reads were aligned using STAR (with “--outFilterMultimapNmax 1”, “--outFilterMismatchNmax 2”, “--alignEndsType EndToEnd” parameters) against the concatenated mm10+dm6 genome, in which polymorphic SNPs for 129S1 and CAST mouse strains were N-masked. Reads that were mapped more than once were discarded and PCR duplicates were removed with Sambamba. Reads mapping to mm10 genome were randomly subsampled using downsampling factors calculated based on spike-in calibration as described previously. To separate reads specifically mapping to the 129S1 and CAST alleles, we used SNPsplit (Krueger et al. 2016) with the paired-end mode.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq and Input profiles
Supplementary_files_format_and_content: bed files with enrichment peaks for RING1B and SUZ12 generated with MACS2 (--broad) from at least three biological replicates (intersection)

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), PCGF2 ChIP-seq

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), 1x non-essential amino acids (Life Technologies), 0.5 mM beta-mercaptoethanol (Life Technologies), and 10 ng/mL leukemia inhibitory factor. Pcgf6fl/fl ESCs and Mus domesticus (129S1) x Mus castaneus F1 hybrid ESCs were grown on a monolayer of mitomycin-inactivated SNLP feeders (STO mouse fibroblasts expressing Neomycin, Puromycin resistance and Lif genes) in otherwise the same conditions as other mouse ESCs. Prior to harvesting these ES cells, the feeders were depleted by pre-plating trypsinised cells for 30 mins at 37°C on plates not coated with gelatin and discarding attached cells. Human HEK293T cells used for calibrated ChIP-seq were grown at 37°C and 5% CO2, in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (Labtech), 2 mM L-glutamine (Life Technologies), 1x penicillin-streptomycin solution (Life Technologies), and 0.5 Mm beta-mercaptoethanol (Life Technologies). Drosophila S2 (SG4) cells were grown adhesively at 25°C in Schneider’s Drosophila Medium (Life Technologies), supplemented with 1x penicillin-streptomycin solution (Life Technologies) and 10% heat-inactivated fetal bovine serum (Labtech).

extract_protocol:
For RING1B, SUZ12, PCGF1, PCGF2, CBX7 and PHC1 cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C firstly with 2 mM DSG (Thermo Scientific) for 45 mins, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched by the addition of 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 min at 4˚C. The released nuclei were then washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 min at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to an average size of approximately 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST D22F2, 3 ul), anti-SUZ12 (CST D39F6, 3 ul), anti-PCGF1 (in-house, 3 ul), anti-PCGF2 (sc-10744, 3 ul), anti-Cbx7 (ab21873, 4 ul), anti-Phc1 (CST 1F3F3, 6 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 2 hours at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65°C with 200 mM NaCl and 2 µl of RNase A (Sigma). A matched input sample (corresponding to 10% of original ChIP reaction) was identically treated. The following day ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For H2AK119ub1 and H3K27me3 native cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4°C with 5 ul of anti-H2AK119ub1 (CST D27C4) or anti-H3K27me3 (in-house). Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicate unless otherwise specified. For allele-specific analysis in 129S1 x CAST hybrid ESC line with inducible fill-length Xist transgene, native cChIP-seq libraries were sequenced as 80 bp paired-end reads on Illumina NextSeq 500 platform to increase the number of reads overlapping allele-specific SNPs.

treatment_protocol: To induce conditional removal of distinct PRC1 complexes or their combinations in Pcgf4-/-; Pcgf2fl/fl, Pcgf1fl/fl, Pcgf3fl/fl, Pcgf5fl/fl, Pcgf6fl/fl, Pcgf3/5fl/fl, Pcgf1/3/5fl/fl, Pcgf1/3/5/2fl/fl, Pcgf1/3/5/6fl/fl and Ring1a-/-; Ring1bfl/fl ESC lines, cells were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 hours. To induce expression of Xist transgene, 129S1 x CAST ESCs were treated with 1.5 μg/mL doxycycline for 72 hours.

tag: cell line

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

tag: clone

tag: spike-in reference organism

value: Homo sapiens

tag: spike-in cell line

tag: ChIP

tag: antibody

value: Santa Cruz (Mel18, sc-10744)


title: sP29

description:
F3_P29_S71_L006
processed data file: f3.glyphosate.csv.gz


title: PCGF2fl_UNT_PCGF2_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, PCGF2 ChIP-seq

value: 0 hr


title: saP6

description:
P6_S16_L004
processed data file: f2.glyphosate.csv.gz

source_name: F2_DMSO control_sperm


title: 1E

type: RNA

city: Baton Rouge

first: Thanh

last: Dang

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description:
SKG HF 5.AVG_Signal
sample name:
1E
global knockout of Siah2

hyb_protocol: 750ng labeled RNA was hybridized to Illumina Mouse WG-6 v2 BeadChip arrays (Illumina) for females and Illumina MouseRef-8 v2.0 Expression BeadChip arrays for males according to manufacturer's protocol.

scan_protocol: Chips were scanned using Illumina iScan system with default settings

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6  Raw data were background-subtracted and normalized using the quantile normalization method using the preprocessCore package in R.
The "Matrix normalized" tab contains quantile normalized and background subtracted gene expression signals.  "Matrix non-normalized" contains background subtracted non-normalized data exported from GenomeStudio.

label: biotin

molecule: total RNA

source_name: brown adipose tissue

label_protocol: 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system

extract_protocol: The brown adipose tissue was quickly removed, frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc. Cincinnati, Ohio) with modifications to remove DNA using Qiagen RNAeasy columns.

treatment_protocol: The mice were weaned at 4 weeks of age and randomized to either a low fat (10% fat) diet (Research Diets, New Brunswick, NJ, #D12450B) or high fat (45%) diet (Research Diets, D12451).  The mice remained on these diets until 20 weeks of age.

value: brown adipose tissue

tag: gender

value: Female

tag: diet

value: high fat diet

tag: age

value: 20 weeks

value: Siah2 knockout


title: PCGF2fl_UNT_CBX7_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, CBX7 ChIP-seq

value: Abcam ab21873


title: sP27

description:
F3_P27_S69_L006
processed data file: f3.glyphosate.csv.gz

source_name: F3_PBS control_sperm

value: PBS control


title: DR2ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT22

tag: strain

tag: genotype

value: Wild-type

tag: Sex

value: male


title: PCGF2fl_UNT_PCGF2_rep2


title: DR3ZT02

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT02

tag: tissue

value: Liver


title: RING1Bfl_TAM_XInput_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), gDNA-seq


title: RING1Bfl_TAM_XInput_rep3


title: sP24

description:
F2_P24_S57_L005
processed data file: f2.glyphosate.csv.gz

source_name: F2_PBS control_sperm

tag: strain background

value: an outbred strain Hsd:Sprague Dawley SD (Harlan) strain

tag: generation

tag: treatment


title: DR2ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT18


title: sP26

description:
F3_P26_S68_L006
processed data file: f3.glyphosate.csv.gz

value: sperm


title: saP4

description:
P4_S14_L003
processed data file: f2.glyphosate.csv.gz

value: DMSO control


title: sP25

description:
F3_P25_S67_L006
processed data file: f3.glyphosate.csv.gz


title: DR2ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT14


title: sP22

description:
F2_P22_S55_L005
processed data file: f2.glyphosate.csv.gz


title: NR2ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under night-restricted feeding paradigm; sacrificed at ZT14


title: sP21

description:
F1_P21_S45_L004
processed data file: f1.glyphosate.csv.gz

source_name: F1_PBS control_sperm


title: RING1Bfl_TAM_XInput_rep1

tag: cell line

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

value: 72 hr


title: RING1Bfl_UNT_XInput_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq

tag: treatment time point

tag: clone

tag: spike-in reference organism

value: Homo sapiens


title: sP19

description:
F1_P19_S43_L004
processed data file: f1.glyphosate.csv.gz


title: sP18

description:
F3_P18_S66_L006
processed data file: f3.glyphosate.csv.gz

value: Glyphosate


title: DR2ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT10


title: RING1Bfl_UNT_XInput_rep2

value: 0 hr

tag: spike-in cell line

tag: ChIP

tag: antibody


title: sP17

description:
F3_P17_S65_L006
processed data file: f3.glyphosate.csv.gz


title: DR2ZT06

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm (did not adapt fully); sacrificed at ZT06


title: RING1Bfl_UNT_XInput_rep1


title: sP14

description:
F3_P14_S62_L006
processed data file: f3.glyphosate.csv.gz


title: sP15

description:
F3_P15_S63_L006
processed data file: f3.glyphosate.csv.gz


title: DR1ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: RING1Bfl_TAM_RING1B_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), RING1B ChIP-seq

value: Cell Signaling Technology(#D22F2 )


title: sP16

description:
F3_P16_S64_L006
processed data file: f3.glyphosate.csv.gz


title: sP13

description:
F3_P13_S61_L006
processed data file: f3.glyphosate.csv.gz


title: RING1Bfl_TAM_RING1B_rep2


title: sP12

description:
F2_P12_S54_L005
processed data file: f2.glyphosate.csv.gz


title: DR2ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: DR1ZT18

description:
RAW_Table.txt
TPM_Table.txt


title: DR1ZT14

description:
RAW_Table.txt
TPM_Table.txt


title: sP11

description:
F2_P11_S53_L005
processed data file: f2.glyphosate.csv.gz


title: sP10

description:
F2_P10_S52_L005
processed data file: f2.glyphosate.csv.gz


title: sP20

description:
F1_P20_S44_L004
processed data file: f1.glyphosate.csv.gz


title: RING1Bfl_TAM_RING1B_rep1


title: sP9

description:
F2_P9_S51_L005
processed data file: f2.glyphosate.csv.gz


title: sP7

description:
F2_P7_S49_L005
processed data file: f2.glyphosate.csv.gz


title: sP8

description:
F2_P8_S50_L005
processed data file: f2.glyphosate.csv.gz


title: RING1Bfl_UNT_RING1B_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq


title: DR1ZT10

description:
RAW_Table.txt
TPM_Table.txt


title: RING1Bfl_UNT_RING1B_rep3


title: sP6

description:
F1_P6_S42_L004
processed data file: f1.glyphosate.csv.gz


title: RING1Bfl_UNT_RING1B_rep1


title: DR1ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: sP5

description:
F1_P5_S41_L004
processed data file: f1.glyphosate.csv.gz


title: DR1ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: sP2

description:
F1_P2Repeat_S38_L004
processed data file: f1.glyphosate.csv.gz


title: sP3

description:
F1_P3_S39_L004
processed data file: f1.glyphosate.csv.gz


title: sP4

description:
F1_P4_S40_L004
processed data file: f1.glyphosate.csv.gz


title: PCGF1356fl_TAM_XInput_rep3


title: sP1

description:
F1_P1Repeat_S37_L004
processed data file: f1.glyphosate.csv.gz


title: AR3ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT22


title: P10_Low

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

description:
sample name in processed data file:
16-01800

data_processing:
read trimming was done with Trimmomatic and the following parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:30 ILLUMINACLIP:Illumina_adaptors.fa:2:30:10
reads were mapped to the hg19 build of the human genome using STAR-2.4.1d
uniquely mapping reads were assigned to gene exons and splice-junctions using featureCounts (Rsubread package version 1.4.6)
Keep genes with least 1 count-per-million reads (cpm) in at least 3 samples
Apply TMM library-size normalization (edgeR)
Call differentially expressed genes using Limma-Voom
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of the gene-count matrix

organism: Homo sapiens

source_name: Adipocyte Progenitor Cell

extract_protocol:
Human adipose tissue samples were digested in a collagenase 2 buffer to release the stromal vascular fraction (SVF) from mature adipocytes. The SVF cells were stained with fluorescent antibodies specific to CD45, CD31, CD29 and CD34. The human adipocyte precursor cells (APCs) within the SVF were identified in the lineage negative fraction (CD31- CD31-) as CD29+ CD34neg, CD29+ CD34low, CD29+ CD34high cell types and were isolated in a FACS instrument. The isolated cells were frozen immediately, and total RNA was extracted from the frozen cells by using RNeasy Mini kit (Qiagen, Germany). RNA quality of the samples was further assessed by measuring the RNA integrity number (RIN) using the Agilent 2100 Bioanalyzer (Agilent Biosystems) and the RNA concentration was assessed in a Qubit Bioanalyzer (ThermoFisher Scientific).
The RNA samples were first amplified using the Ovation RNA-Seq system V2 kit (NuGEN, protocol M01206v5, 2013) in a thermocycler and then subjected to cDNA synthesis. Single Primer Isothermal strand-displacement Amplification (SPIA) technology was adopted to synthesize cDNA. A total of 15 cDNA libraries were constructed from the RNA samples by this process. The RNA-seq libraries were then constructed from the cDNA samples by using the Ovation Ultralow System V2 (NuGEN) as per the product instructions. An equimolar pool (12 pM) of the all the ligated sample libraries, ~274 bp in size on an average, were pooled and hybridized onto two lanes of the HiSeq 1500 high-output flowcell per sample.

value: Adipose tissue

tag: cell type

value: Adipocyte Progenitor Cell

tag: anatomical location

value: omental

tag: cd34 status


title: P10_Neg

description:
sample name in processed data file:
16-01799


title: PCGF1356fl_TAM_XInput_rep1


title: AR3ZT18

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT18

tag: strain

tag: genotype

tag: Sex


title: P9_High

description:
sample name in processed data file:
16-01798

tag: tissue


title: P9_Low

description:
sample name in processed data file:
16-01797


title: PCGF1356fl_UNT_XInput_rep3


title: P9_Neg

description:
sample name in processed data file:
16-01796


title: AR3ZT10

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT10


title: P8_High

description:
sample name in processed data file:
16-01795


title: P8_Low

description:
sample name in processed data file:
16-01794


title: PCGF1356fl_UNT_XInput_rep2


title: AR3ZT06

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT06


title: P8_Neg

description:
sample name in processed data file:
16-01793


title: P7_High

description:
sample name in processed data file:
16-01792


title: AR3ZT02

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT02


title: P7_Neg

description:
sample name in processed data file:
16-01790


title: PCGF1356fl_UNT_XInput_rep1


title: P7_Low

description:
sample name in processed data file:
16-01791


title: AR2ZT22

description:
RAW_Table.txt
TPM_Table.txt


title: P10_High

description:
sample name in processed data file:
16-01801


title: P1_High

description:
sample name in processed data file:
16-01789


title: AR2ZT18

description:
RAW_Table.txt
TPM_Table.txt


title: P1_Low

description:
sample name in processed data file:
16-01788


title: PCGF1356fl_TAM_XInput_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), gDNA-seq


title: AR3ZT14

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT14


title: P1_Neg

description:
sample name in processed data file:
16-01787


title: AR2ZT14

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF1356fl_TAM_SUZ12_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), SUZ12 ChIP-seq

value: Cell Signaling Technology(#D39F6 )


title: PCGF1356fl_UNT_SUZ12_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, SUZ12 ChIP-seq


title: PCGF1356fl_UNT_SUZ12_rep2


title: PCGF2fl_TAM_NatInput_rep2

organism:
Drosophila melanogaster
Mus musculus

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), gDNA-seq

value: Drosophila melanogaster


title: AR2ZT06

description:
RAW_Table.txt
TPM_Table.txt

value: Wild-type


title: PCGF2fl_TAM_NatInput_rep3


title: PCGF2fl_TAM_NatInput_rep1


title: AR2ZT02

description:
RAW_Table.txt
TPM_Table.txt

value: male


title: PCGF1356fl_UNT_SUZ12_rep1


title: PCGF2fl_UNT_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq


title: PCGF1356fl_TAM_SUZ12_rep3


title: PCGF2fl_UNT_NatInput_rep2


title: PCGF1356fl_TAM_RING1B_rep3


title: PCGF1356fl_TAM_SUZ12_rep2


title: PCGF2fl_UNT_NatInput_rep1


title: PCGF1356fl_TAM_RING1B_rep2


title: AR1ZT18

description:
RAW_Table.txt
TPM_Table.txt

value: Liver


title: PCGF2fl_TAM_H3K27me3_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H3K27me3 ChIP-seq

value: In house (Rose, 2016)


title: PCGF2fl_TAM_H3K27me3_rep2


title: PCGF2fl_TAM_H3K27me3_rep3


title: PCGF2fl_UNT_H3K27me3_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq


title: AR1ZT14

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF3/5fl_UNT_H2AK119ub1_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

value: Cell Signaling Technology(#D27C4 )


title: PCGF1356fl_TAM_RING1B_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), RING1B ChIP-seq


title: AR2ZT10

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF2fl_UNT_H3K27me3_rep2


title: PCGF2fl_UNT_H3K27me3_rep1


title: AR1ZT10

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF1356fl_UNT_RING1B_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq


title: PCGF2fl_TAM_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H2AK119ub1 ChIP-seq


title: PCGF1356fl_UNT_RING1B_rep2


title: PCGF2fl_TAM_H2AK119ub1_rep2


title: AR1ZT02

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF2fl_UNT_H2AK119ub1_rep2


title: AR1ZT22

description:
RAW_Table.txt
TPM_Table.txt

source_name: Fed under arrhythmic feeding paradigm; sacrificed at ZT22


title: AR1ZT06

description:
RAW_Table.txt
TPM_Table.txt


title: PCGF2fl_UNT_H2AK119ub1_rep3


title: PCGF1356fl_UNT_RING1B_rep1


title: PCGF1352fl_TAM_XInput_rep3


title: PCGF2fl_UNT_H2AK119ub1_rep1


title: Mus_Day-14_rep4

city: Gainesville

first: Jason

middle: Orr

last: Brant

state: FL

address: 2197 Mowry Rd

department: Biostatistics

institute: University of Florida

description:
Day 14 wound.
musDay14_6
mus14.6

data_processing:
Raw reads were quality assessed pre- and post-filtering using FastQC [fastqc/0.11.4] and trimmed using Trimmomatic [trimmomatic/0.32, ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40]. Trimmed reads were merged using SeqPrep [seqprep/1.1, -L 40 -n 0.95 -o 25] resulting in both unmerged paired-end reads and merged reads.
Acomys merged and paired-end RNA-Seq reads from all three time-points, plus the DSN library, were assembled using Trinity [trinity/2.0.4, --SS_lib_type FR --min_contig_length 500], with in silico normalization at 50X coverage to remove systemic variation.
Trinotate [trinotate/2.0.1], which utilizes a variety of homology searches to publicly available data to identify homologous sequences (SwissProt/UniRef90), protein domains (HMMER/PFAM), rRNA (RNAMMER), protein signal peptides and transmembrane domains (signalp/tmHMM). The annotation report only includes hits meeting a minimum E-value cutoff of 1E-5.
Transcript abundance estimates were obtained using RSEM [rsem/1.2.28, --paired-end --bowtie2 --estimate-rspd --append-names].
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: aco_vs_mus_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for the COREs between Mus and Acomys for each time-point.
Supplementary_files_format_and_content: aco_per_se_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for Acomys for days 0, 7 and 14.
Supplementary_files_format_and_content: mus_per_se_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for Mus for days 0, 7 and 14.
Supplementary_files_format_and_content: Trinity.fasta: FASTA file includes the Acomys cahirinus transcriptome assembly with Trinity IDs.
Supplementary_files_format_and_content: acomys_annotation.txt: Tab-delimited text file lists the Trinity IDs and annotations.

source_name: Dermal skin (dorsal) - Wound

extract_protocol:
RNA was extracted following Trizol protocol and cleaned using Qiagen's RNeasy mini kit.
Libraries were prepared using Illumina's TruSeq RNA Sample Preparation kits.
2x150bp paired-end.

treatment_protocol: 8mm full-thickness excisional dorsal dermal wounds. Wounds collected days 7 and 14 after wounding. Wounds compared to day 0, unwounded, normal skin samples for each species.

tag: strain/background

tag: age

value: Adult

value: Dermal skin (dorsal)

tag: treatment

value: Wounded

tag: time point

value: Day 14


title: PCGF1352fl_TAM_XInput_rep2

tag: cell line

tag: replicate

tag: treatment agent

value: tamoxifen (OHT)

tag: treatment time point

value: 72 hr

value: Homo sapiens


title: PCGF6fl_TAM_NatInput_rep3

tag: spike-in reference organism

tag: spike-in cell line

tag: ChIP


title: PCGF6fl_TAM_NatInput_rep2

tag: antibody


title: Mus_Day-14_rep3

description:
Day 14 wound.
musDay14_5
mus14.5


title: PCGF6fl_TAM_NatInput_rep1


title: PCGF1352fl_UNT_XInput_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq

value: 0 hr

tag: clone


title: PCGF6fl_UNT_NatInput_rep3


title: PCGF6fl_UNT_NatInput_rep2


title: PCGF1352fl_UNT_XInput_rep2


title: PCGF6fl_UNT_NatInput_rep1


title: Mus_Day-14_rep1

description:
Day 14 wound.
musDay14_1
mus14.1


title: Mus_Day-14_rep2

description:
Day 14 wound.
musDay14_4
mus14.4


title: Mus_Day-7_rep4

description:
Day 7 wound.
musDay7_6
mus7.6

value: Day 7


title: PCGF6fl_TAM_H2AK119ub1_rep3


title: PCGF1352fl_TAM_XInput_rep1


title: PCGF2fl_TAM_H2AK119ub1_rep1


title: PCGF1352fl_UNT_XInput_rep1


title: PCGF6fl_UNT_H2AK119ub1_rep3


title: PCGF6fl_TAM_H2AK119ub1_rep1


title: PCGF6fl_UNT_H2AK119ub1_rep2


title: Mus_Day-7_rep3

description:
Day 7 wound.
musDay7_5
mus7.5


title: PCGF1352fl_TAM_SUZ12_rep3


title: Mus_Day-7_rep2

description:
Day 7 wound.
musDay7_4
mus7.4


title: PCGF5fl_TAM_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), Input-seq


title: PCGF5fl_TAM_NatInput_rep4


title: PCGF1352fl_TAM_SUZ12_rep2


title: Mus_Day-7_rep1

description:
Day 7 wound.
musDay7_1
mus7.1


title: PCGF1352fl_TAM_SUZ12_rep1


title: PCGF6fl_TAM_H2AK119ub1_rep2


title: PCGF5fl_TAM_NatInput_rep1


title: PCGF5fl_UNT_NatInput_rep4

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, Input-seq


title: Mus_Day-0_rep4

description:
Day 0 normal unwounded skin.
musDay0_6
mus0.6

source_name: Dermal skin (dorsal)

value: Unwounded

value: Day 0


title: PCGF5fl_UNT_NatInput_rep3

value: Drosophila melanogaster


title: Mus_Day-0_rep2

description:
Day 0 normal unwounded skin.
musDay0_4
mus0.4


title: PCGF1352fl_UNT_SUZ12_rep3

value: Cell Signaling Technology(#D39F6 )


title: PCGF5fl_UNT_NatInput_rep1


title: PCGF1352fl_UNT_SUZ12_rep1


title: PCGF5fl_TAM_H2AK119ub1_rep4


title: PCGF1352fl_UNT_SUZ12_rep2


title: Mus_Day-0_rep1

description:
Day 0 normal unwounded skin.
musDay0_1
mus0.1


title: PCGF5fl_TAM_H2AK119ub1_rep3


title: PCGF5fl_TAM_H2AK119ub1_rep2


title: PCGF5fl_TAM_H2AK119ub1_rep1


title: PCGF5fl_UNT_H2AK119ub1_rep4


title: PCGF6fl_UNT_H2AK119ub1_rep1


title: PCGF1352fl_TAM_RING1B_rep3

value: Cell Signaling Technology(#D22F2 )


title: PCGF1352fl_TAM_RING1B_rep2


title: PCGF5fl_UNT_H2AK119ub1_rep2


title: PCGF5fl_UNT_H2AK119ub1_rep1


title: PCGF1352fl_TAM_RING1B_rep1


title: PCGF3fl_TAM_NatInput_rep2


title: PCGF1352fl_UNT_RING1B_rep3


title: PCGF5fl_UNT_NatInput_rep2


title: PCGF3fl_TAM_NatInput_rep1


title: PCGF1352fl_UNT_RING1B_rep2


title: PCGF3fl_UNT_NatInput_rep2


title: PCGF3fl_UNT_NatInput_rep1


title: PCGF1352fl_UNT_RING1B_rep1


title: PCGF3fl_TAM_H2AK119ub1_rep2


title: PCGF3fl_UNT_H2AK119ub1_rep2


title: PCGF5fl_UNT_H2AK119ub1_rep3


title: PCGF3fl_TAM_H2AK119ub1_rep1


title: ovarian secondary follicles_32 weeks old mouse, biological rep3

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: No.1095 Jie Fang Avenue

country: China

institute: Huazhong University of Science and Technology

description: Gene expression data from ovarian secondary follicles extracted from 32 weeks old mouse

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console Software.

data_processing: The raw data from microarray analysis was normalized using robust multi-array average (RMA) algorithm.

source_name: ovarian secondary follicles (32 weeks old mouse)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The 9 weeks old and 32 weeks old, specific pathogen-free (SPF), female C57BL/6J mice were obtained from Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, PR China)

extract_protocol: RNAiso plus reagent extraction of total RNA was performed according to the manufacturer's instructions.

value: ovarian secondary follicles

tag: strain

value: 32 weeks old


title: PCGF5fl_TAM_NatInput_rep2


title: PCGF3fl_UNT_H2AK119ub1_rep1

value: Cell Signaling Technology(#D27C4 )


title: PCGF1fl_TAM_NatInput_rep3


title: PCGF135fl_TAM_XInput_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), gDNA-seq


title: PCGF1fl_TAM_NatInput_rep2


title: ovarian secondary follicles_32 weeks old mouse, biological rep1


title: ovarian secondary follicles_9 weeks old mouse, biological rep2

description: Gene expression data from ovarian secondary follicles extracted from 9 weeks old mouse

source_name: ovarian secondary follicles (9 weeks old mouse)

value: 9 weeks old


title: ovarian secondary follicles_9 weeks old mouse, biological rep3


title: ovarian secondary follicles_9 weeks old mouse, biological rep1


title: PCGF1fl_TAM_NatInput_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), gDNA-seq


title: PCGF1fl_UNT_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq


title: PCGF135fl_TAM_XInput_rep2


title: PCGF1fl_UNT_NatInput_rep2


title: 3346_IRF2-Rep3

city: Houston

first: Guocan

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

hyb_protocol: Standard hyb protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

scan_protocol: Standard scan protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

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

source_name: iKAP primary cultured cells (#3346)

label_protocol: Standard label protocol per the Sequencing & Non-coding RNA facility at MD Anderson Cancer Center. For more details, please contact Chang-Gong Liu <cgliu@mdanderson.org>

growth_protocol: 3346 cells were cultured in Gibco DMEM Medium with 5% Tetracycline-Free.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: expression

value: IRF2 ORF


title: ovarian secondary follicles_32 weeks old mouse, biological rep2


title: PCGF1fl_UNT_NatInput_rep1


title: 3346_IRF2-Rep2


title: 3346_IRF2-Rep1


title: PCGF135fl_TAM_XInput_rep4


title: PCGF1fl_TAM_H3K27me3_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H3K27me3 ChIP-seq

value: In house (Rose, 2016)


title: PCGF1fl_TAM_H3K27me3_rep3


title: 3346_GFP control-Rep3

value: GFP control


title: PCGF135fl_UNT_XInput_rep4


title: PCGF1fl_UNT_H3K27me3_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq


title: organoid_9M_3

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

data_processing:
Illumina Casava software used for basecalling.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflelink
Read count profile were analyzed for the differential expression analysis using DESeq2 (version 1.10.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

source_name: retinal organoid

growth_protocol: Retinal cell differentiation from H1 hESCs was performed. Briefly, cysts and adherent cultures were generated as described previously, with the starting day of cell differentiation designated as day 0. On day 15, adherent cultures were partially lifted at edges via one-minute dispase treatment (1 mg/ml in DMEM/F12), rinsed with DMEM/F12 medium, and then grown in a B27 medium (DMEM/F12 (3:1), 2% B27, NEAA). In a few hours, the adherent cultures were spontaneously detached as floating aggregates. In about one week, retinal organoids with a bright ring under an inverted microscope spontaneously formed, and were grown in a serum medium (DMEM/F12 (3:1), 8% fetal calf serum (Gibco), 2% B27, NEAA, 100 mM Taurine (Sigma), and 2mM GlutaMAX) on an orbital shaker. The medium was changed every three days unless stated otherwise.Retinal organoids and adherent cultures were fixed in 4% PFA for 15-30 minutes at room temperature and then processed for cryosectioning at 9 month.

extract_protocol:
RNA was harvested using Trizol reagent from retinal organoids/cultures at the time points.
RNA libraries were prepared from ∼500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina).

value: retinal organoid

tag: culture time

value: 259 days


title: PCGF135fl_UNT_XInput_rep2

value: Homo sapiens


title: PCGF135fl_UNT_XInput_rep3

value: 0 hr


title: PCGF1fl_UNT_H3K27me3_rep2


title: PCGF135fl_UNT_XInput_rep1


title: PCGF1fl_UNT_H3K27me3_rep3


title: PCGF1fl_TAM_H3K27me3_rep1

value: tamoxifen (OHT)

value: 72 hr


title: PCGF135fl_TAM_XInput_rep1


title: organoid_9M_2

tag: tissue


title: organoid_9M_1

value: 258 days


title: PCGF135fl_TAM_SUZ12_rep4

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), SUZ12 ChIP-seq


title: PCGF1fl_UNT_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

value: Drosophila melanogaster


title: 3346_GFP control-Rep2


title: PCGF1fl_TAM_H2AK119ub1_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H2AK119ub1 ChIP-seq


title: PCGF1fl_TAM_H2AK119ub1_rep2


title: organoid_6.5M_3

value: 195 days


title: PCGF135fl_TAM_SUZ12_rep2

value: Cell Signaling Technology(#D39F6 )


title: PCGF135fl_TAM_SUZ12_rep1


title: PCGF1fl_TAM_H2AK119ub1_rep3


title: organoid_6.5M_1

value: 194 days


title: PCGF135fl_UNT_SUZ12_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, SUZ12 ChIP-seq


title: organoid_3M_3

value: 94 days


title: RING1Bfl_TAM_NatInput_rep3


title: PCGF1fl_UNT_H2AK119ub1_rep2

value: Cell Signaling Technology(#D27C4 )


title: PCGF1fl_UNT_H2AK119ub1_rep1


title: RING1Bfl_UNT_NatInput_rep1


title: RING1Bfl_UNT_NatInput_rep3


title: organoid_3M_2


title: organoid_3M_1

value: 85 days


title: RING1Bfl_TAM_NatInput_rep2


title: RING1Bfl_TAM_H2AK119ub1_rep2


title: RING1Bfl_UNT_NatInput_rep2


title: RING1Bfl_TAM_H2AK119ub1_rep1


title: RING1Bfl_UNT_H2AK119ub1_rep3


title: RING1Bfl_TAM_H2AK119ub1_rep3


title: organoid_6.5M_2


title: PCGF135fl_TAM_RING1B_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), RING1B ChIP-seq

value: Cell Signaling Technology(#D22F2 )


title: 3346_GFP control-Rep1


title: PCGF135fl_UNT_SUZ12_rep1


title: RING1Bfl_TAM_NatInput_rep1


title: PCGF135fl_TAM_RING1B_rep2


title: organoid_1M_3

value: 30 days


title: Acomys_DSN

description:
day 0, 7 and 14 skin and wounds.
DSN

organism: Acomys cahirinus

source_name: Dermal Skin and Wounds (Dorsal)

value: Adult

value: Dermal skin (dorsal)

value: Pool of unwounded and wounded

value: Pool of days 0, 7 and 14


title: organoid_1M_2

value: retinal organoid


title: PCGF135fl_TAM_RING1B_rep1

value: tamoxifen (OHT)

value: Homo sapiens


title: Acomys_Day-14_rep4

description:
Day 14 wound.
AcomysDay14_7
aco14.7

source_name: Dermal skin (dorsal) - Wound

value: Wounded

value: Day 14


title: PCGF135fl_UNT_SUZ12_rep4

value: 0 hr


title: organoid_1M_1


title: RING1Bfl_UNT_H2AK119ub1_rep1

value: Drosophila melanogaster


title: RING1Bfl_UNT_H2AK119ub1_rep2


title: Acomys_Day-14_rep1

description:
Day 14 wound.
AcomysDay14_2
aco14.2


title: organoid_D15_3

value: 15 days


title: Acomys_Day-7_rep4

description:
Day 7 wound.
AcomysDay7_7
aco7.7

value: Day 7


title: organoid_D15_2


title: Acomys_Day-7_rep3

description:
Day 7 wound.
AcomysDay7_6
aco7.6


title: Acomys_Day-7_rep2

description:
Day 7 wound.
AcomysDay7_3
aco7.3


title: Acomys_Day-7_rep1

description:
Day 7 wound.
AcomysDay7_2
aco7.2


title: organoid_D15_1


title: Acomys_Day-0_rep3

description:
Day 0 normal unwounded skin.
AcomysDay0_6
aco0.6

source_name: Dermal skin (dorsal)

value: Unwounded

value: Day 0


title: PCGF135fl_UNT_RING1B_rep2

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq

value: Cell Signaling Technology(#D22F2 )


title: PCGF135fl_UNT_RING1B_rep3


title: PCGF2fl_TAM_XInput_rep4

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, tamoxifen-treated (72hr), gDNA-seq

value: 72 hr


title: Cancer [CA14]

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA14

data_processing:
Illumina Casava1.7 software used for basecalling?
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: HG19, GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw reads values for each Sample

source_name: Cervix

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

tag: disease

value: Cancer

value: HPV-positive  Cervix tissue


title: Acomys_Day-0_rep4

description:
Day 0 normal unwounded skin.
AcomysDay0_7
aco0.7

tag: age

value: Adult

value: Dermal skin (dorsal)


title: Cancer [CA13]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA13


title: Acomys_Day-0_rep2

description:
Day 0 normal unwounded skin.
AcomysDay0_3
aco0.3

tag: treatment


title: PCGF2fl_TAM_XInput_rep3


title: PCGF2fl_TAM_XInput_rep2


title: Cancer [CA12]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA12


title: Acomys_Day-14_rep3

description:
Day 14 wound.
AcomysDay14_6
aco14.6

tag: time point


title: PCGF2fl_TAM_XInput_rep1

tag: cell line


title: Cancer [CA11]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA11


title: RING1Bfl_TAM_H3K27me3_rep2

tag: replicate

value: In house (Rose, 2016)


title: RING1Bfl_TAM_H3K27me3_rep3

tag: treatment agent

value: tamoxifen (OHT)


title: Normal [N10]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N10

value: Normal

value: HPV-negative Cervix tissue


title: RING1Bfl_UNT_H3K27me3_rep2

tag: treatment time point


title: Acomys_Day-14_rep2

description:
Day 14 wound.
AcomysDay14_3
aco14.3

value: Wounded

value: Day 14


title: PCGF2fl_UNT_XInput_rep3

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, gDNA-seq

value: 0 hr

tag: spike-in reference organism

value: Homo sapiens


title: RING1Bfl_UNT_H3K27me3_rep1

value: Drosophila melanogaster

tag: spike-in cell line


title: Acomys_Day-0_rep1

description:
Day 0 normal unwounded skin.
AcomysDay0_2
aco0.2

value: Unwounded


title: Normal [N8]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N8


title: Normal [N7]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N7


title: Cancer [CA6]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA6


title: PCGF2fl_UNT_XInput_rep2

tag: ChIP


title: PCGF2fl_TAM_SUZ12_rep3

tag: antibody

value: Cell Signaling Technology(#D39F6 )


title: PCGF2fl_UNT_XInput_rep1

tag: clone


title: Cancer [CA5]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA5


title: Normal [N9]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N9


title: Cancer [CA4]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
CA4


title: PCGF2fl_UNT_SUZ12_rep3


title: PCGF2fl_TAM_SUZ12_rep1


title: PCGF2fl_TAM_SUZ12_rep2


title: RING1Bfl_TAM_H3K27me3_rep1


title: Normal [N3]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N3


title: PCGF2fl_UNT_SUZ12_rep2


title: PCGF2fl_UNT_XInput_rep4


title: Normal [N2]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N2


title: Normal [N1]

description:
High risk HPV infection was determined by Digene HPV Genotyping Kits
N1


title: PCGF2fl_TAM_RING1B_rep4

value: Cell Signaling Technology(#D22F2 )


title: PCGF2fl_UNT_SUZ12_rep1


title: RING1Bfl_UNT_H3K27me3_rep3


title: PCGF2fl_TAM_RING1B_rep3

value: 72 hr


title: PCGF2fl_TAM_RING1B_rep2


title: PCGF2fl_TAM_RING1B_rep1


title: PCGF2fl_UNT_RING1B_rep4


title: PCGF2fl_UNT_RING1B_rep3


title: PCGF2fl_UNT_RING1B_rep1


title: day5

city: Basel

first: Denise

last: Serra

address: Maulbeerstrasse 14

country: Switzerland

institute: FMI

data_processing:
The CellRanger suite (1.3.0) was used to generate the aggregated gene expression matrix from the BCL files generated by the sequencer based on the mm10 Cell Ranger mouse genome annotation files.
Single-cell expression profiles (raw UMI counts) were analysed using Griph (https://github.com/ppapasaikas/Griph), which yields a graph encoding cell to cell relationships along with a 2D embedding. The graph represents cells as nodes and similar cells are connected by weighted edges. This graph was also used to identify the k-nearest-neighbours of each cell for smoothing of expression values in visualizations as indicated.
In order to control for variable cell size and quality, marker gene expression in individual cells were normalized as follows: For a given set of marker genes, the log2 scaled UMI counts were first smoothed by calculating the average over 10-nearest-neighbor cells and then summed up (eobs). Then, 200 control gene sets, containing equal numbers of genes as the marker genes and having a similar average expression distribution over all cells were randomly sampled. The mean of the expression of these control gene sets was calculated (eexp) and used to generate a normalized marker gene expression score as ns = (eobs – eexp) for mapping to colors.
For all the day 3 cells and for day 3 cells not expressing Paneth, Goblet, Enteroendocrine, Enterocyte or Stem cell markers, Spearman correlation coefficients between the normalized expression scores of Yap1 target genes and Notch receiving cell marker genes (Dll1, Dll4, Jag1, Jag2, Atoh1) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: comma-seperated text files with raw and log2 scaled UMI counts for genes and cells used in the analysis

source_name: intestinal organoids day 5

growth_protocol: Organoids were kept in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin for amplification and maintenance. From day 0 to day 1, we supplemented ENR (advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin-Streptomycin, 1×Glutamax (Thermo Scientific), 1×B27 (Thermo Scientific), 1xN2 (Thermo Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (Thermo Scientific))  with 20% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (GSK3B inhibitor, STEMCELL Technologies). From day 1 to 3 we supplemented ENR with 20% Wnt3a-CM and 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies). From day 3 to 5, only ENR was added to the cells. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis)

extract_protocol:
Cellular suspensions were loaded on a 10x Genomics Chromium Single Cell instrument to generate single cell GEMs.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit according to CG00052_SingleCell3'ReagentKitv2UserGuide_RevB.

value: intestinal organoids day 5

tag: strain

tag: genotype

value: wild type

value: 10 weeks


title: XU1_R1

city: Xi'an

first: WENQIN

last: XU

state: Shaanxi

address: 15 Changle West Road

department: Ophthalmology

institute: The Fourth Military Medical University

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,

source_name: exosomes from microglia

extract_protocol:
The preparation and sequencing of exosome miRNA were performed by Ribobio (Guangzhou, China). First, total RNA samples were fractionated by using 15% Tris-borate-EDTA (TBE) polyacrylamide gel (Invitrogen), then small RNAs ranging from 18 to 30 nucleotides were used for library preparation. Amplification of these small RNAs was then accomplished by PCR
RNA libraries were prepared for sequencing using standard illumina protocols

value: microglial cells


title: day3

source_name: intestinal organoids day 3

value: intestinal organoids day 3


title: d4_mouse3_rep3

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were mapped to the UCSC mouse genome mm10 using STAR (version 2.5.2b, 8) with parameters --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1.
Genes expression level were quantified with the QuasR Bioconductor package 9, using gene annotations from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package.
Log2(CountsPerMillion) (log2(cpm)) of uniquely mapped genes were used to describe similarities and differences among the samples by Principal Component Analysis (PCA).
Differentially expressed genes were determined with the package edgeR (version 3.20.5, 10) by fitting a three-factor model (timepoint + mouse + dnase treatment ) to the counts of genes that were detected in 2 or more samples with at least one read per million reads. Genes with an FDR less than 0.01 and an absolute log2 fold-change of at least 1 were identified as differentially expressed. For visualization of gene expression profiles and calculation of between gene correlations, averages of mean-centered log2(cpm) were used.
The gene correlation matrix was then hierarchically clustered using Euclidian distances between correlation profiles. To display clusters profiles, clusters averages and quantiles were calculated.
Transcription Factor Binding Site Analysis was done applying an elastic net regression model (package glmnet, 12) to the differential gene expression day 1 versus day 0 as follows: First, promoter regions were defined as a windows of 1500 bp centered on the transcript start site, only retaining a single region per gene. Transcription factor binding sites (TFBS) for 519 vertebrate motifs from the JASPAR2016 Bioconductor package (version 1.6) were predicted by converting the positional frequency matrices to log2-odds matrices (using a pseudocount of 1.0 per position and base and a unform base frequencies as background), and then scanning the promoter regions with a cut-off score of 10.0 or the maximal motif score if less than 10. For each promoter region, the fraction G+C bases (fGC) and the CpG observed over expected ratio (oeCpG), defined as fraction of CG dinucleotides divided by the product of the fractions of C and G mononucleotides, were calculated and used in the linear model as regressors in addition to the predicted numbers of TFBS to control for sequence composition. The elastic net model was fit using alpha of 0.2 and lambda of 0.0588 identified based on a 10-fold cross-validation grid search over combinations of alpha and lambda values. The fitted model coefficients (beta values) represent the magnitude of contributions of each transcription factor to the differential gene expression between the two time-points. For visualization, only transcription factors with positive beta values (TFBS in the promoter is predicted to increase the transcription of the target gene from day 0 to day 1) and positive log2FoldChange (log2FC) between day 1 and day 0 were considered.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file with RPKM values for each Sample (columns)

source_name: Intestinal organoids day 4

extract_protocol:
RNA was isolated using Single Cell RNA Purification Kit (Norgen Biotek Corporation, Cat #51800) pooling 30 wells of 96-well plates (C57BL/6 wild type) for each sample. A step of DNAse treatment was included (RNase-Free DNase I Kit, Cat #25710) for two replicates of samples (day 0 day 5), as indicated in the sample characteristics.
RNA sequencing libraries were prepared using the TruSeq Illumina mRNA Library Prep

value: Intestinal organoids day 4

value: 8 weeks

tag: dnase treatment

value: Yes


title: d5_mouse2_rep2

source_name: Intestinal organoids day 5

tag: tissue

value: Intestinal organoids day 5


title: d5_mouse1_rep1

value: No


title: d5_mouse3_rep3


title: d4_mouse2_rep2


title: PCGF2fl_UNT_RING1B_rep2

value: 0 hr


title: beta islets from WT pregnant mice, rep 3

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

description: beta islets from WT pregnant mice

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: non-transgenic

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Islets were isolated from bPRLR-KO and non-transgenic pregnant mice using retrograde perfusion of the pancreatic duct with collagenase, purified using density centrifugation, hand-picked and cultured. Islets from pregnant mice were hand-picked in RPMI media containing 2% serum then immediately processed for RNA. For in vitro islet experiments, hand-picked islets were cultured overnight in RPMI supplemented with 10% FBS.

tag: Sex

value: beta islet

tag: gestation

value: Pregnant

tag: gestation day

value: CON


title: d3_mouse3_rep3

source_name: Intestinal organoids day 3

value: Intestinal organoids day 3

tag: age


title: d3_mouse2_rep2


title: D3-8_H3K9ac-ChIP_Rep2

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

data_processing:
Obtained reads were mapped to mouse reference genome mm9 with bowtie2.3.4. Peakcalling was performed with MACS2.1.1 using broadpeaks, merging the two replicas from identical cell lines, and using the merged input samples as control. Differential peaks were determined with the R package DiffBind, again merging the two replicas from the identical cell line and using the peaks from MACS.
Genome_build: mm9
Supplementary_files_format_and_content: excel file with differential bound regions from diffbind

source_name: mESCs-Rb + E2F4 QKO

growth_protocol: mESC lines were maintained feeder-free on 0.2% gelatin-coated (Sigma G9382) plates in Dulbecco’s modified Eagle’s medium (Gibco SH30243.01) containing 15% fetal bovine serum (Hyclone SH30071.03; VWR Seradigm 97068-085), MEM non-essential amino acids (Gibco 11140-050), penicillin-streptomycin-glutamine (Gibco 10378-016), and 0.1 mM beta-mercaptoethanol (Gibco 21985-023), and supplemented with LIF. Cells were passaged enzymatically using 0.05% Trypsin-EDTA (Gibco 15400-054). Single-cell suspensions of 1000 mESCs/mL were cultured in low density assays.

extract_protocol:
Chromatin immunoprecipitation was done according to a published method (O’Geen, H., Nicolet, C.M., Blahnik, K., Green, R. & Farnham, P.J. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques 41, 557-580 (2006). Briefly, mESCs were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature and the reaction was stopped by adding glycine to final concentration of 1.25M for 5 minutes at room temperature. Crosslinked cells were collected with a cell scraper, rinsed twice with PBS, and resuspended at a concentration of 5 x 10^7 cells/mL of swelling buffer (0.1 M Tris pH 7.6, 10 mM KOAc, 15 mM MgOAc, 1% NP40) to remove the cytoplasmic fraction. Nuclei were resuspended at a concentration of 10 x 10^8 cells/mL of nuclei lysis buffer (50 mM Tris-Cl pH 8.0, 10 mM EDTA, 1% SDS), and lysate was sonicated for 90 cycles (30 sec on / 50 sec off) in a Diagenode Bioruptor (Diagenode UCD-300). The sonicated chromatin was precleared by adding washed and blocked StaphA at a concentration of 10 uL/1 x 10^7 cells (Calbiochem 507862). StaphA were prepared as previously described, washed in dialysis buffer (2 mM EDTA, 50 mM Tris-Cl pH 8.0), and blocked in 10 mg/mL salmon sperm DNA (EMD Millipore 16-157) and 10 mg/mL BSA. For each IP, 100 uL of precleared chromatin was diluted in twice the volume of IP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl) and 5 ug of antibody was added. Antibodies against H3K4me3 (Abcam ab8580), H3K9Ac (Active Motif 39137) were used.
Libraries were constructed using the NEBNext DNA Sample Prep Master Mix Set for Illumina (NEBNext E6040) and NEBNext Multiplex Oligos for Illumina (NEBNext E7335 and E7500), according to kit instructions. Libraries were then quantified using the KAPA Library Quantification Kit with Universal qPCR Master Mix (KAPA Biosystems, KK4824) according to kit instructions, and quantitative PCR was performed using the SYBR GreenER MasterMix (Invitrogen) on an ABI 7900HT Detection System. Pooled samples were sequenced on a HiSeq4000.

tag: cell type

value: ESC

value: Rb + E2F4 QKO


title: sP23

description:
F2_P23_S56_L005
processed data file: f2.glyphosate.csv.gz

source_name: F2_PBS control_sperm

tag: strain background

value: an outbred strain Hsd:Sprague Dawley SD (Harlan) strain

tag: generation

tag: treatment

value: PBS control

value: sperm


title: d2_mouse3_rep3

source_name: Intestinal organoids day 2

value: Intestinal organoids day 2

value: wild type


title: beta islets from WT pregnant mice, rep 1

description: beta islets from WT pregnant mice


title: beta islets from bPRLRKO pregnant mice, rep 2

description: beta islets from bPRLR-KO pregnant mice, rep 1

source_name: bPRLRKO

value: bPRLR-KO


title: d3_mouse1_rep1

value: 8 weeks


title: beta islets from bPRLRKO pregnant mice, rep 3


title: D3-8_H3K9ac-ChIP_Rep1


title: D3-8_H3K4me3-ChIP_Rep2


title: beta islets from WT pregnant mice, rep 2

description: beta islets from WT pregnant mice


title: beta islets from bPRLRKO pregnant mice, rep 1


title: D3-8_H3K4me3-ChIP_Rep1


title: ILCs-GS-4

city: Seoul

first: Juri

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Environmental Medical Biology

country: South Korea

institute: Yonsei University

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using HISAT2 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie 1.3.4d software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: G. lamblia incubated ICF cells

growth_protocol: ICFs (1 × 106 cells per well) were seeded in a 24 well culture plate with transwell membranes and incubated for 6 hr for RNA preparation, with G. lamblia having multiplicity of infection (MOI) of 5. The ILCs were harvested for RNA preparation.

extract_protocol:
RNAs were extracted from the cell of Homo Sapiens. Poly(A) mRNA using the Illumina  TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA Sample Prep Kit , according to the manufacturer’s protocol.

value: Innate lymphoid cells


title: ILCs-only-3

source_name: ILC-containing fraction (ICF)


title: ILCs-only-1


title: ILCs-GS-1


title: ILCs-GS-2


title: ILCs-only-2


title: ILCs-only-4


title: D3-8_input_Rep2


title: d2_mouse1_rep1


title: d4_mouse1_rep1

value: Intestinal organoids day 4


title: D3-8_input_Rep1


title: d1_mouse3_rep3

source_name: Intestinal organoids day 1

value: Intestinal organoids day 1

value: Yes


title: d2_mouse1_rep2


title: PCGF135fl_UNT_RING1B_rep1

source_name: Mouse embryonic stem cells with human HEK293T cells spike-in, untreated control, RING1B ChIP-seq

tag: cell line

tag: replicate

tag: treatment agent

tag: treatment time point

value: 0 hr

tag: spike-in reference organism

value: Homo sapiens

value: Cell Signaling Technology(#D22F2 )


title: D1-9_H3K9ac-ChIP_Rep2


title: D1-9_H3K9ac-ChIP_Rep1


title: d0_mouse3_rep3

source_name: Intestinal organoids day 0

value: Intestinal organoids day 0

tag: strain


title: d0_mouse2_rep2

tag: genotype


title: D1-9_input_Rep2

value: ESC


title: d0_mouse1_rep1

tag: dnase treatment

value: No


title: d1_mouse1_rep1

tag: tissue


title: d1_mouse1_rep2


title: D1-2_H3K4me3-ChIP_Rep2

source_name: mESCs-Rb TKO

value: Rb TKO


title: D1-2_H3K9ac-ChIP_Rep1


title: D1-9_H3K4me3-ChIP_Rep1

value: Rb + E2F4 QKO


title: D1-9_H3K4me3-ChIP_Rep2


title: D1-2_H3K9ac-ChIP_Rep2


title: D1-9_input_Rep1


title: D1-2_input_D1-2-Rep1


title: D1-2_input_D1-2-Rep2


title: D1-2_H3K4me3-ChIP_Rep1


title: Interspecies_Xist_Transgene_DOX_NatInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, doxycycline-treated (72hr), gDNA-seq

value: 129S1 x Cast with randomly integrated full-length Xist transgene

value: doxycycline (DOX)

value: 72 hr

tag: clone

value: Drosophila melanogaster

tag: spike-in cell line

tag: ChIP

tag: antibody


title: Interspecies_Xist_Transgene_DOX_NatInput_rep3


title: Interspecies_Xist_Transgene_DOX_NatInput_rep1


title: D1-10_H3K9ac-ChIP_Rb-TKO_Rep2

tag: cell type


title: Interspecies_Xist_Transgene_UNT_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq


title: Interspecies_Xist_Transgene_UNT_NatInput_rep2


title: Interspecies_Xist_Transgene_UNT_NatInput_rep1


title: D1-10_H3K4me3-ChIP_Rb-TKO_Rep2


title: D1-10_H3K9ac-ChIP_Rb-TKO_Rep1


title: M Chol I vs M Gly II [Mtb]-2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: polarity(-)

hyb_protocol: Commercial-custom M.smegmatis 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

organism: Mycobacterium tuberculosis H37Rv

source_name: M Chol I

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: M. tuberculosis H37Rv (ATCC 27294) was propagated in Middlebrook 7H9 broth supplemented with albumin-dextrose-catalase enrichment (Becton Dickinson, MD, USA) , 0.2% glycerol, and 0.05% Tyloxapol at 37°C with agitation (100 rpm) or on Middlebrook 7H11 agar containing 10% v/v oleic acid-albumin-dextrose-catalase enrichment (Becton Dickinson).

extract_protocol: Total RNA was extracted with TRIzol reagent according to the manufacturer’s instructions. Cell lysis was achieved through three cycles of bead beating in a Mini-Beadbeater (Biospec) at 5,000 rpm for 30 s.

treatment_protocol: Carbon utilization assays were performed using minimal medium and cholesterol (0.01%), ethanol (0.01%–1%) and glycerol.

tag: genotype/variation

value: KO mutant

value: Cholesterol

value: biol. replicate 1

source_name: M Gly II

value: Glycerol

value: biol. replicate 2


title: M Chol I vs WT Chol II [Mtb]-2

description: polarity(-)

source_name: WT Chol II

value: wildtype


title: M Gly I vs M Chol II [Mtb]-2

description: polarity(+)

source_name: M Gly I

source_name: M Chol II


title: WT Chol I vs M Chol II [Mtb]-2

description: polarity(+)

source_name: WT Chol I


title: M EtOH I vs WT EtOH II [Mtb]-2

description: polarity(-)

source_name: M EtOH I

value: Ethanol

source_name: WT EtOH II


title: WT EtOH I vs M EtOH II [Mtb]-2

description: polarity(+)

source_name: WT EtOH I

source_name: M EtOH II


title: WT Gly I vs M Gly II [Mtb]-2

description: polarity(+)

source_name: WT Gly I


title: D1-10_H3K4me3-ChIP_Rb-TKO_Rep1


title: ILCs-GS-3

source_name: G. lamblia incubated ICF cells

value: Innate lymphoid cells


title: Interspecies_Xist_Transgene_UNT_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

value: 0 hr

value: Cell Signaling Technology(#D27C4 )


title: D1-10_input_Rep2

value: ESC


title: Interspecies_Xist_Transgene_UNT_H2AK119ub1_rep2


title: D1-10_input_Rep1

value: Rb TKO


title: PCGF1/3/5/6fl_TAM_NatInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), gDNA-seq

value: tamoxifen (OHT)


title: PCGF1/3/5/6fl_TAM_NatInput_rep3


title: Math1_1140

city: Washington

first: Yanxin

last: Pei

state: DC

address: 111 Michigan Ave NW

department: Center for Cancer and Immunology

institute: Children's National Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads mapping to the reference genome (GRCm38) was performed on quality-checked and trimmed reads using HISAT2. The reference annotation is Ensembl v87.
The overlap of reads with annotation features found in the reference.gtf was calculated using HT-seq v0.6.1. The output computed for each sample (raw read counts) was then used as input for DESeq2 analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file include FPKM values for each samples

source_name: Cerebellar tumor

growth_protocol: Primary cerebellar cells and cerebellar tumors were isolated from mice.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (Life Technologies) according to manufacturer’s instructions.
The cDNA libraries were constructed following the standard Illumina protocols by TruSeq RNA and DNA sample preparation kits (Illumina).

treatment_protocol: No treatment for isolated cells.

value: NSG

value: Cerebellar tumor

value: Immunodeficient

tag: surface markers

value: No sorting


title: Interspecies_Xist_Transgene_UNT_H2AK119ub1_rep1

value: 129S1 x Cast with randomly integrated full-length Xist transgene

value: Drosophila melanogaster


title: PCGF1/3/5/6fl_TAM_NatInput_rep1

value: 72 hr


title: Interspecies_Xist_Transgene_DOX_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, doxycycline-treated (72hr), H2AK119ub1 ChIP-seq

value: doxycycline (DOX)


title: Math1_1139


title: PCGF1/3/5/6fl_UNT_NatInput_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, gDNA-seq


title: PCGF1/3/5/6fl_TAM_H3K27me3_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H3K27me3 ChIP-seq

value: In house (Rose, 2016)


title: PCGF1/3/5/6fl_UNT_NatInput_rep2


title: M Chol I vs WT Chol II [Mtb]

description: polarity(-)

source_name: M Chol I

value: KO mutant

tag: treatment

value: Cholesterol

value: biol. replicate 1

value: wildtype

value: biol. replicate 2


title: PCGF1/3/5/6fl_TAM_H3K27me3_rep3

tag: cell line


title: M Gly I vs WT Gly II [Mtb]-2

description: polarity(-)

value: Glycerol

tag: replicate

source_name: WT Gly II


title: Interspecies_Xist_Transgene_DOX_H2AK119ub1_rep1

tag: treatment agent

value: Cell Signaling Technology(#D27C4 )


title: M Chol I vs M Gly II [Mtb]

description: polarity(-)

source_name: M Gly II


title: M EtOH I vs WT EtOH II [Mtb]

description: polarity(-)

value: Ethanol


title: Math1_1065

value: NSG


title: Interspecies_Xist_Transgene_DOX_H2AK119ub1_rep2

tag: treatment time point


title: Math1_1006

value: Cerebellar tumor


title: M Gly I vs M Chol II [Mtb]

description: polarity(+)

source_name: M Gly I

source_name: M Chol II


title: PCGF1/3/5/6fl_UNT_H3K27me3_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H3K27me3 ChIP-seq

value: 0 hr

tag: spike-in reference organism


title: B_2607b

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
Sleuth for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: An Excel file including TPM of each gene for all 28 samples

source_name: interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
TruSeq Stranded LT mRNA kit

value: iPSC-derived interneurons

tag: disease

value: healthy control


title: WT EtOH I vs M EtOH II [Mtb]

description: polarity(+)

source_name: WT EtOH I


title: Math1_1005

tag: strain

tag: genotype

value: Immunodeficient

value: No sorting


title: B_L5a


title: PCGF1/3/5/6fl_UNT_NatInput_rep1

data_processing:
Paired-end reads were aligned to the genome sequence of concatenated mouse and spike-in genomes (mm10+dm6 for native cChIP-seq and mm10+hg19 for cross-linked cChIP-seq) using Bowtie 2 with the “--no-mixed” and “--no-discordant” options specified. Reads that were mapped more than once were discarded, followed by removal of PCR duplicates with SAMTools for native cChIP-seq or Sambamba for cross-linked cChIP-seq.
To internally calibrate cChIP-seq experiments, we spiked-in a fixed number of control cells (Drosophila SG4 cells for native cChIP-seq and human HEK293T cells for cross-linked cChIP-seq) to each experimental sample. For annotation of genomic intervals and data visualisation, mm10 reads were randomly subsampled using factors that reflected the total number of dm6 (or hg19) reads in each sample. To account for any variation in spike-in cell mixing in different biological replicates, the downsampling factors were additionally corrected using the ratio of dm6 (or hg19)/mm10 total read counts in corresponding Input samples.
For each condition, biological replicates were merged for downstream applications. Genome coverage tracks were generated using the pileup function from MACS2 (Zhang et al. 2008).
RING1B and SUZ12 peak sets were generated with MACS2 (--broad) using corresponding Input samples for background normalisation. For each factor, a set of peaks identified in all biological replicates (intersection) was manually curated to remove sequencing artefacts. Classical Polycomb chromatin domains were identified by k-means clustering of ±10 kb windows centred on RING1B peaks based on their RING1B and SUZ12 chromatin occupancy using deeptools (v.3.0.1). This generated three clusters, two of which displayed high enrichment of both RING1B and SUZ12 and were combined into one set of genomic intervals.
Allele-specific analysis of H2AK119ub1 cChIP-seq was performed as described previously (Pintacuda et al. 2017). Briefly, paired-end reads were aligned using STAR (with “--outFilterMultimapNmax 1”, “--outFilterMismatchNmax 2”, “--alignEndsType EndToEnd” parameters) against the concatenated mm10+dm6 genome, in which polymorphic SNPs for 129S1 and CAST mouse strains were N-masked. Reads that were mapped more than once were discarded and PCR duplicates were removed with Sambamba. Reads mapping to mm10 genome were randomly subsampled using downsampling factors calculated based on spike-in calibration as described previously. To separate reads specifically mapping to the 129S1 and CAST alleles, we used SNPsplit (Krueger et al. 2016) with the paired-end mode.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing genome coverage for merged replicates of spike-in normalised cChIP-seq and Input profiles
Supplementary_files_format_and_content: bed files with enrichment peaks for RING1B and SUZ12 generated with MACS2 (--broad) from at least three biological replicates (intersection)

extract_protocol:
For RING1B, SUZ12, PCGF1, PCGF2, CBX7 and PHC1 cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^6 human HEK293T cells. Cells were resuspended in 10 ml phosphate buffered saline (PBS) and crosslinked at 25°C firstly with 2 mM DSG (Thermo Scientific) for 45 mins, and then with 1% formaldehyde (methanol-free, Thermo Scientific) for a further 15 minutes. Reactions were quenched by the addition of 125 mM glycine. Crosslinked cells were incubated in lysis buffer (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton-X100) for 10 min at 4˚C. The released nuclei were then washed (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 5 min at 4˚C. Chromatin was then resuspended in 1 ml of sonication buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine) and sonicated for 30 min using a BioRuptor Pico sonicator (Diagenode), shearing genomic DNA to an average size of approximately 0.5 kb. Following sonication, TritonX-100 was added to a final concentration of 1%. For ChIP, sonicated chromatin was diluted 10-fold in ChIP dilution buffer (1% Triton-X100, 1 mM EDTA, 20 mM Tris-HCl pH 8, 150 mM NaCl) and pre-cleared for 1 hour using Protein A agarose beads (Repligen) blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA. For each ChIP reaction, 1ml of diluted and pre-cleared chromatin was incubated overnight with the appropriate antibody, anti-RING1B (CST D22F2, 3 ul), anti-SUZ12 (CST D39F6, 3 ul), anti-PCGF1 (in-house, 3 ul), anti-PCGF2 (sc-10744, 3 ul), anti-Cbx7 (ab21873, 4 ul), anti-Phc1 (CST 1F3F3, 6 ul). Antibody-bound chromatin was captured using blocked protein A agarose for 2 hours at 4°C and collected by centrifugation. ChIP washes were performed as described previously (Farcas et al. 2013). ChIP DNA was eluted in elution buffer (1% SDS, 0.1 M NaHCO3) and cross-links were reversed overnight at 65°C with 200 mM NaCl and 2 µl of RNase A (Sigma). A matched input sample (corresponding to 10% of original ChIP reaction) was identically treated. The following day ChIP samples and Inputs were incubated with Proteinase K (Sigma) for 1.5 hours at 56°C and purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For H2AK119ub1 and H3K27me3 native cChIP-seq, 5 x 10^7 mouse ESCs (both untreated and following 72 hours tamoxifen treatment) were mixed with 2 x 10^7 Drosophila SG4 cells in PBS. Mixed cells were pelleted and nuclei were released by resuspending in ice cold lysis buffer (10mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM N-ethylmaleimide). Nuclei were then washed, and resuspended in 1 ml of MNase digestion buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25M sucrose, 3mM CaCl2, 10 mM N-ethylmaleimide, 1x protease inhibitors (Sigma)). Each sample was then incubated with 200 units of MNase (Fermentas) at 37°C for 5 min, followed by the addition of 4 mM EDTA to halt MNase digestion. Following centrifugation at 1500 g for 5 min at 4°C, the supernatant (S1) was retained. The remaining pellet was incubated with 300 µl of nucleosome release buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x protease inhibitors, 10 mM N-ethylmaleimide) at 4°C for 1 h, passed five times through a 27G needle using a 1 ml syringe, and spun at 1500 g for 5 min at 4°C. The second supernatant (S2) was collected and combined with corresponding S1 sample from above. A small amount of S1/S2 DNA was purified and visualized on a 1.5% agarose gel to confirm digestion to mostly mono-nucleosomes. For ChIP experiments, S1/S2 nucleosomes were diluted 10-fold in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1% Triton, 1x protease inhibitor cocktail (Roche), 10 mM N-ethylmaleimide (NEM)), and 1 ml aliquots were made. Each ChIP reaction was then incubated overnight at 4°C with 5 ul of anti-H2AK119ub1 (CST D27C4) or anti-H3K27me3 (in-house). Antibody-bound nucleosomes were captured using protein A agarose (Repligen) beads, pre-blocked in native ChIP incubation buffer supplemented with 1 mg/ml BSA and 1 mg/ml yeast tRNA, for 1 hour at 4°C and collected by centrifugation. Immunoprecipitated material was washed four times with Native ChIP wash buffer (20 mM Tris pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1% Triton-X100) and once with Tris-EDTA buffer (10 mM Tris pH 8, 1 mM EDTA). ChIP DNA was eluted using 100 ul of elution buffer (1% SDS, 0.1 M NaHCO3), and then purified using ChIP DNA Clean and Concentrator Kit (Zymo Research). For each individual ChIP sample, DNA from a matched Input control (corresponding to 10% of original ChIP reaction) was also purified.
Libraries for both ChIP and Input samples were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries was analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads on Illumina NextSeq 500 platform in biological triplicate unless otherwise specified. For allele-specific analysis in 129S1 x CAST hybrid ESC line with inducible fill-length Xist transgene, native cChIP-seq libraries were sequenced as 80 bp paired-end reads on Illumina NextSeq 500 platform to increase the number of reads overlapping allele-specific SNPs.

value: Drosophila melanogaster


title: Math1_1137

tag: tissue


title: PCGF1/3/5/6fl_TAM_H3K27me3_rep1

value: tamoxifen (OHT)

value: 72 hr

tag: clone

value: In house (Rose, 2016)


title: B_2607a


title: M Gly I vs WT Gly II [Mtb]

description: polarity(-)

value: KO mutant

value: biol. replicate 1


title: PCGF1/3/5/6fl_TAM_H2AK119ub1_rep3

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), H2AK119ub1 ChIP-seq

tag: spike-in cell line


title: B_L5d


title: PCGF1/3/5/6fl_TAM_H2AK119ub1_rep1

tag: ChIP


title: PCGF1/3/5/6fl_UNT_H2AK119ub1_rep3

tag: antibody


title: PCGF1/3/5/6fl_UNT_H3K27me3_rep3


title: PCGF1/3/5/6fl_TAM_H2AK119ub1_rep2


title: PCGF1/3/5/6fl_UNT_H2AK119ub1_rep2


title: WT Gly I vs M Gly II [Mtb]

description: polarity(+)

source_name: WT Gly I

value: wildtype

value: biol. replicate 2


title: PCGF1/3/5/6fl_UNT_H2AK119ub1_rep1

value: Cell Signaling Technology(#D27C4 )


title: Sox2_752


title: PCGF1/3/5/2fl_TAM_NatInput_rep3


title: PCGF1/3/5/2fl_TAM_NatInput_rep2


title: PCGF1/3/5/6fl_UNT_H3K27me3_rep1


title: Sox2_1017


title: Sox2_750


title: B_pyaumc

tag: cell type


title: Math1_1004


title: PCGF1/3/5/2fl_UNT_NatInput_rep2


title: PCGF1/3/5/2fl_UNT_NatInput_rep3


title: KO mix

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz10 whole genome using HISAT, mapped to genes using Bowtie2.
fragments per kilo bases per million fragments (FPKM) were calculated using RSEM.
Genome_build: GRCz10
Supplementary_files_format_and_content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.

organism: Danio rerio

source_name: Ovary

extract_protocol:
Ovaries were isolated, frozen on dry ice, and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols.

value: AB

value: Ovary

tag: age

value: Adult


title: PCGF1/3/5/2fl_TAM_NatInput_rep1

first: Nadezda

address: South Parks Rd

institute: University of Oxford


title: PCGF1/3/5/2fl_UNT_NatInput_rep1

value: 0 hr


title: Sox2_727

value: NSG

value: Cerebellar tumor

tag: surface markers


title: PCGF1/3/5/2fl_TAM_H3K27me3_rep2


title: PCGF1/3/5/2fl_TAM_H3K27me3_rep3


title: PCGF1/3/5/2fl_TAM_H3K27me3_rep1


title: Sox2_682

value: Immunodeficient


title: B_L9c

value: iPSC-derived interneurons

value: healthy control


title: B_L9a


title: Sox2_631

value: No sorting


title: PCGF1/3/5/2fl_UNT_H3K27me3_rep2

value: Drosophila melanogaster


title: WT mix


title: PCGF1/3/5/2fl_UNT_H3K27me3_rep3

value: In house (Rose, 2016)


title: B_L7b


title: 12BWL

first: Thanh

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description:
WT LF.AVG_signal
sample name:
12BWL
global knockout of Siah2

data_processing:
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6  Raw data were background-subtracted and normalized using the quantile normalization method using the preprocessCore package in R.
The "Matrix normalized" tab contains quantile normalized and background subtracted gene expression signals.  "Matrix non-normalized" contains background subtracted non-normalized data exported from GenomeStudio.

source_name: brown adipose tissue

extract_protocol: The brown adipose tissue was quickly removed, frozen in liquid nitrogen and stored at -80C.  Total RNA was isolated using Tri-Reagent (Molecular Research Center, Inc. Cincinnati, Ohio) with modifications to remove DNA using Qiagen RNAeasy columns.

value: brown adipose tissue

tag: gender

value: Male

tag: diet

value: low fat diet

value: 20 weeks

value: WT


title: Sox2_598


title: PCGF1/3/5/2fl_TAM_H2AK119ub1_rep3

tag: cell line

tag: replicate

value: tamoxifen (OHT)

value: 72 hr

value: Cell Signaling Technology(#D27C4 )


title: 11BWL

description:
WT LF.AVG_signal
sample name:
11BWL
global knockout of Siah2


title: B_367b


title: 10BWL

description:
WT LF.AVG_signal
sample name:
10BWL
global knockout of Siah2


title: B_pyauma


title: Sox2_728


title: B_L7a


title: Normal_S6

source_name: cerebellar cells

value: Cerebella

value: GFP+


title: PCGF1/3/5/2fl_TAM_H2AK119ub1_rep2

tag: treatment agent

tag: treatment time point


title: 8BWH

description:
WT HF.AVG_signal
sample name:
8BWH
global knockout of Siah2

value: high fat diet


title: B_365a

tag: disease


title: Normal_S5

tag: strain


title: B_367c


title: PCGF1/3/5/2fl_UNT_H2AK119ub1_rep1

source_name: Mouse embryonic stem cells with Drosophila spike-in, untreated control, H2AK119ub1 ChIP-seq

value: 0 hr

tag: spike-in reference organism


title: PCGF1/3/5/2fl_TAM_H2AK119ub1_rep1


title: 7BWH

description:
WT HF.AVG_signal
sample name:
7BWH
global knockout of Siah2

tag: tissue

tag: genotype


title: PCGF1/3/5/2fl_UNT_H2AK119ub1_rep3

tag: clone

tag: spike-in cell line


title: B_365b

value: iPSC-derived interneurons


title: Normal_S4


title: 9BWH

description:
WT HF.AVG_signal
sample name:
9BWH
global knockout of Siah2


title: PCGF1/3/5/2fl_UNT_H2AK119ub1_rep2

tag: ChIP

tag: antibody


title: Normal_M5


title: B_317c

tag: cell type

value: healthy control


title: PCGF1/3/5fl_TAM_K27me3_NatInput_rep2

source_name: Mouse embryonic stem cells with Drosophila spike-in, tamoxifen-treated (72hr), gDNA-seq


title: PCGF1/3/5/2fl_UNT_H3K27me3_rep1


title: PCGF1/3/5fl_TAM_K27me3_NatInput_rep3


title: Normal_M4

tag: surface markers


title: B_317b


title: 4BSL

description:
SKG LF.AVG_signal
sample name:
4BSL
global knockout of Siah2

tag: gender

tag: age

value: Siah2 knockout


title: 6BSL

description:
SKG LF.AVG_signal
sample name:
6BSL
global knockout of Siah2

tag: diet


title: PCGF1/3/5fl_TAM_K27me3_NatInput_rep1

tag: cell line

tag: replicate

value: Drosophila melanogaster


title: Normal_M1


title: 5BSL

description:
SKG LF.AVG_signal
sample name:
5BSL
global knockout of Siah2


title: B_292b