title: aB_wt_Brg1

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
MNaseI-Seq_density: quality and adapter trimming: fqtrim-v0.94/fqtrim -A 125 -q 20  -f adapters -p22 -P33
MNaseI-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --local --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 22
MNaseI-Seq_density: filtering and sorting(uniquely aligned reads): samtools-0.1.19/samtools view -Sb | samtools sort -@ 20 -m 1G
MNaseI-Seq_density: merging: samtools-1.1/samtools merge
MNaseI-Seq_density: raw tag density: custom program, density estimate of nucleosome dyads genome wide, wigToBigWig -fixedSummaries -keepAllChromosomes
MNaseI-Seq_density: tag ratio between input and control: ucsc-314/wiggletools ratio input.bw control.bw | wigToBigWig
MNaseI-Seq_density: aB_minus_rB density: ucsc-314/wiggletools diff aB_ratio.bw rb_ratio.bw | wigToBigWig
ATAC-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --end-to-end --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 16
ATAC-Seq_density: filtering (remove random contigs): sed '/random/d;/chrUn/d'
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19/samtools view -S -b -F4
ATAC-Seq_density: merging: samtools-0.1.19/samtools merge && samtools sort -m 10G
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: contact_matrix: 5kb contact matrix was generated from the filtered alignment
HiC-Seq: loop call: juicebox hiccups -m 500 -r 5000 -k KR -f 0.1 -p 4 -i 10 -t 0.01,1.5,1.75,2 -d 20000
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: Gro-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: MNaseI-Seq: .wig files tag density ratio difference between activated and resting B cells (ratio)
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: HiC-Seq: tab seperated loop coordinates with other information

source_name: activated B cell

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing.  Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).                                                                                HiC-Seq:  we used the same protocol for situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)                                                                                ATAC-Seq: we followed the protocol at Buenrostri J.D. et al. (Nat Methods, 2013 Dec; 10(12):1213-8)                 Gro-seq:  Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the  RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated  with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and  purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was  dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation.  Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz  Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis  was performed the next day as described in (Wang et al., 2011). However, for reverse  transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT  GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA  TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England  Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and  RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA  fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel  (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The  final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA  clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                MNase-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina)                                                        ATAC-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                   HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                    Gro-seq: 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).

treatment_protocol: Gro-seq: Myc floxed allele was obtained from Douglas Green (St. Jude Children’s research hospital). Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice). The deletion of floxed allele was checked by PCR or intracellular staining of Myc protein.

tag: genotype

value: WT

value: spleen

tag: chip antibody

value: abcam, ab110641

tag: activation time


title: rB_wt_Brg1

status: Public on Aug 10 2017

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: resting B cell

tag: tissue


title: rB_wt_H3K4me1

value: abcam, ab8895


title: aB_wt_GCN5

value: Santa Cruz, sc-20698


title: mPC_1.2h

city: Frankfurt am Main

first: Christoph

middle: Michael

last: Zehendner

address: Theodor Stern Kai 7

country: Germany

institute: Goethe University

description:
total RNA ribosomal depleted
Hypoxic conditions
mouse PC hypox vs normox_FPKM.txt
mPC_2h

library_source: transcriptomic

data_processing:
(RNA-SEQ) Reads were mapped with Tophat default parameters to MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes).  Afterwards Cufflinks was utilized with the default attributes for gene quantification.
Genome_build: MM10 (mouse brain primary pericytes), or GRCH38 (human primary pericytes)
Supplementary_files_format_and_content: Tab delimited text file which includes FPKM values for each sample

molecule: total RNA

source_name: mouse brain primary pericytes

growth_protocol: Human pericytes (passages 2-9; from ScienCell, Carlsbad, CA, USA) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Pericyte medium consisted of DMEM Glutamax (Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with Penicillin/Streptomycin (Roche Diagnostics) and 10% fetal calf serum. Primary mouse brain pericytes were isolated and cultured as documented in detail (Tigges et al. Microvascular Research 84 (2012) 74–80).

extract_protocol:
RNA deep sequencing was performed by analyzing ribosomal depleted total RNA from human pericytes. RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including DNA digestion.
RNA was fragmented and primed for cDNA synthesis. Human samples: Libraries were created using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer. Mouse sample libraries were created using a Scriptseq v2 Kit from Illumina SSV21124 as recommended by the manufacturer.

treatment_protocol: Hypoxia was induced using a hypoxic incubator (Labotect, Göttingen, Germany). Cell culture medium was pre-equilibrated overnight at 1% O2, 5% CO2 in a humidified atmosphere. Normoxic cell culture medium was carefully switched to hypoxic medium and hypoxic pO2 levels were verified by measuring VEGFA induction by qPCR and pO2 levels with a hypoxia sensing probe from Oxford Optronix (Oxford, UK) as described in detail before (Zehendner et al. Plos One 2013). Cells were transfected after reaching a confluency of 60-80% using Opti-MEM Medium, Lipofectamine RNAiMAX (both from Life technologies, Carlsbad, CA, USA) and 50 nmol/l of LNA GapmeR (Exiqon, Vedbaek, Denmark). After 4h transfection medium was exchanged to the appropriate cell culture medium. 48h upon transfection RNA was isolated and processed for RNA Sequencing.

tag: cell type

value: mouse brain primary pericytes

tag: passage

value: passage 8

tag: treatment

value: Hypoxia 1% O2, 5% CO2 humidified atmosphere


title: rB_wt_H3K27Ac

value: abcam, ab4729


title: Pool_1328_AD008_indexed

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
genome build: hg19
For multiplexed single nucleus methylome samples, reads were first trimmed to remove sequencing adaptors using Cutadapt 1.11 with the following parameters in paired ends mode: -f fastq -q 20 -m 62 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. For singleplex samples, -m parameter was set to 40. For multiplexed samples, 16bp was further trimmed from both 5’- and 3’- ends of R1 and R2 reads to remove random primer index sequence and C/T tail introduced by Adaptase, with the following parameters: -f fastq -u 16 -u -16 -m 30. For singleplex samples, 10bp was trimmed from both 5’- and 3’- ends of R1 and R2 reads with the following parameters: -f fastq -u 10 -u -10 -m 30. Trimmed reads for mouse and human single nuclei were mapped to mm10 and hg19 reference genome, respectively. R1 and R2 reads were mapped separately as single-ended reads using Bismark v0.15.0 with parameter --bowtie2. --pbat option was activated for mapping R1 reads. Resulted bam files were sorted using samtools 1.3 sort, followed by removal of duplicate reads using Picard 1.141 MarkDuplicates with the option REMOVE_DUPLICATES=true. Non-clonal reads were further filtered for minimal MAPQ = 30 using samtools view with option -q30. To prevent regional mCH level estimation from being skewed by rare reads failed to be bisulfite converted, reads with read-level mCH level greater than 0.7 were excluded. The calling of unmethylated and methylated base calls were performed by call_methylated_sites of Methylpy (https://github.com/yupenghe/methylpy/) (1–3).
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

organism: Homo sapiens

source_name: Human frontal cortex

growth_protocol: For the production of single neuron methylomes from layer dissected mouse frontal cortex tissue, eight week old C57BL/6J male mice were purchased from Jackson Laboratories, Bar Harbor ME, and allowed a week of acclimation in our animal facility with 12 h light/dark cycles and food ad libitum, before dissections. The human brain specimen was obtained from the NICHD Brain and Tissue Bank for Developmental disorders at the University of Maryland, Baltimore, MD. The frozen middle frontal gyrus tissue belonged to a 25-year-old Caucasian male (UMB#4540) with a PMI of 23 h.

extract_protocol:
A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.
Nuclei isolation from mouse and human cortical tissues was performed as described in (Lister et al., 2013) with the following modifications: Proteinase inhibitor (11836153001, Roche) and RNAse Inhibitor (30 U/ml, PRN2611 from Promega) was added to the lysis buffer and sucrose gradients. After centrifugation, nuclei were resupended in 0.5% BSA (AM2616, Ambion) PBS (Ca2+ and Mg2+ free, 14190-144 from Life Technologies,) with protein and RNAse inhibitors. Isolated nuclei from mouse and human tissues were labeled by incubation with 1:1000 dilution of AlexaFluor488 conjugated anti-NeuN antibody (MAB377X, Millipore) at 4°C for 1 hour. Nuclei isolated from CLSun1-G35-Cre line were incubated with AlexaFluor647 conjugated anti-NeuN antibody (anti-NeuN antibody MAB377 labeled using Apex Alexa Fluor 647. A10475, Life Technologies) and AlexaFluor488 conjugated anti-GFP antibody (A21311, Life Technologies). Fluorescence activated sorting of single nuclei was performed using a BD Influx sorter with an 85 µm nozzle at 22.5 PSI sheath pressure. Single nuclei were sorted into each well of a 384-well plate preloaded with 2 µl of Proteinase K digestion buffer (1 µl M-Digestion Buffer, 0.1 µl 20 µg/µl Proteinase K and 0.9 µl H2O). The alignment of receiving 384-well plate was performed by sorting sheath flow into wells of an empty plate and making adjustment based on the liquid drop position. Single cell (1 drop single) mode was selected to ensure the stringency of sorting.
Steps of library preparation prior to SPRI purification were performed in a horizontal laminar flow hood to minimize environmental DNA contamination. Bisulfite conversion of single nuclei was carried out using Zymo EZ-96 DNA Methylation-DirectTM Kit (Deep Well Format, cat. #D5023) following the product’s manual with reduced reaction volume. 384-well plate (ThermoFisher Armadillo PCR Plate cat. # AB2384) containing FACS isolated single nuclei were heated at 50°C for 20 min. 25 µl CT Conversion Reagent was added to each well followed by pipetting up-and-down to mix. Plates were treated with a following program using a thermocycler: 98°C for 8 min, 64°C for 3.5 hours and 4°C. Each well of Zymo-Spin™ I-96 Binding Plates was preloaded with 150 µl M-binding buffer. Bisulfite conversion reactions were transferred from 384-well plates to I-96 Binding Plates followed by pipetting up-and-down to mix. I-96 Binding Plates were centrifuged at 5,000g for 5 min. Wells were washed with 400 µl of M-Wash Buffer followed by centrifugation at 5,000g for 5 min. 200 µl of M-Desulphonation Buffer was added to each well and was incubated for 15 min at room temperature before removed by centrifugation at 5,000g for 5 min. Each well was then washed with 400 µl of M-Wash Buffer for two rounds. 12 µl of M-Elution Buffer was added to each well and was incubated for 5 min at room temperature. I-96 Binding Plate was placed above a 96-well PCR plate (Applied Biosystems MicroAmp® EnduraPlateTM cat. # 4483348) and was centrifuged at 5,000g for 3min. 9 µl of eluted DNA was commonly collected in each well of the PCR plate. 1 µl of 5 µM P5L-AD002-N9, P5L-AD006-N9, P5L-AD008-N9 or P5L-AD010-N9 indexed random primer was added to each well of 96-well plate followed by mixing with vortexing. All DNA oligos were purchased from Integrated DNA Technologies (IDT). Plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10 µl enzyme mix containing 2 µl of Blue Buffer (Enzymatics cat. # B0110), 1 µl of  10mM dNTP (NEB cat. # N0447L), 1 µl of Klenow exo- (50U/µl, Enzymatics cat. # P7010-HC-L) and 6 µl H2O. After mixing with vortexing, plate was treated with a following program: 4°C for 5 min, ramp up to 25°C at 0.1°C/sec, 25°C for 5 min, ramp up to 37°C at 0.1°C/sec, 37°C for 60 min, 4°C. 2 µl of Exonuclease 1 (20U/µl, Enzymatics cat. # X8010L) was added to each well followed by mixing with vortexing. Plate was incubated at 37°C for 30 min and then 4°C. 17.6 µl of home-made SPRI beads was added to each well. Sample/bead mixture from four plates indexed using distinct indexed random primers were combined followed by pipetting up-and-down to mix. Sample/bead mixture was incubated at room temperature for 5 min before placed on a 96-well magnetic separator. Supernatant was removed from each well followed by three rounds of washing with 180 µl of 80% ethanol. After air drying beads at room temperature, 10 µl M-Elution buffer was added to each well to fully resuspend the beads. Eluted sample was transferred to a new 96-well PCR plate. PCR plate was heated at 95°C for 3 min to denature the sample and was immediately chilled on ice for more than 2 min. 10.5 µl Adaptase (Swift Biosciences) mix (2 µl Buffer G1, 2 µl Reagent G2, 1.25 µl Reagent G3, 0.5 µl Enzyme G5, 0.5 µl Enzyme G6 and 4.25 µl M-Elution buffer) was added into each well followed by mixing with vortexing. Plates was incubated at 37°C at 30 min and then 4°C. 30 µl PCR mix (25 µl KAPA HiFi HotStart ReadyMix, KAPA BIOSYSTEMS, cat. # KK2602, 1 µl 30 µM P5 indexing primer and 5 µl 10 µM P7 indexing primer) was added into each well followed by mixing with vortexing. PCR plate was treated with the following program: 95 °C for 2 min, 98°C for 30 sec, 17 cycles of (98°C for 15 sec, 64°C for 30 sec, 72°C for 2min), 72°C for 5 min then 4°C. PCR products were cleaned up using 0.8x SPRI beads and was combined into one tube for each 96–well plate. Pooled PCR product was resolved on 2% agarose gel, smear between 400 bp and 2 Kb were excised and purified using QIAquick Gel Extraction Kit (Qiagen cat. # 28706). Library concentration was determined using Qubit® dsDNA HS (High Sensitivity) Assay Kit (Invitrogen cat. # Q32851).

value: frontal cortex

tag: Sex

value: Male

tag: age

value: 25 yr


title: aB_wt_H3K4me1


title: Pool_132_AD010_indexed


title: rB_wt_H3K27me3

value: Millipore, 07-449


title: Pool_1328_AD010_indexed


title: rB_wt_GCN5


title: aB48h_wt_H3K27Ac


title: aB_wt_H3K27Ac


title: TYKRIL LNA#2l_n3

description: processed data file: Gene_Expression_Tykril.tsv

data_processing:
10bp were trimmed from the reads. Demultiplexing was done with the following index sequences: norm_n1 TTAGGC, norm_n2:GCCAAT,norm_n3:GTGAAA,hypo_n1:ACAGTG,hypo_n2:CAGATC,hypo_n3:ATTCCT. Reads were mapped by tophat2 (v.2.0.9) to GRCH38. Afterwards Cufflinks was utilized with the default attributes for gene quantification.
Genome_build: GRCH38
Supplementary_files_format_and_content: Tab delimited text file wich includes FPKM values for each sample

source_name: human primary pericytes_TYKRIL LNA

growth_protocol: Human pericytes (passages 2-9; from ScienCell, Carlsbad, CA, USA) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Pericytes medium consisted of DMEM Glutamax (Gibco, Life Technologies, Carlsbad, CA, USA) supplemented with Penicillin/Streptomycin (Roche Diagnostics) and 10% fetal calf serum.

extract_protocol:
RNA deep sequencing was performed by analyzing ribosomal depleted total RNA from human pericytes. RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including DNA digestion. Subsequently RNA was fragmented and primed for cDNA synthesis. Libraries were created using a TruSeq RNA Ribo-Zero Globin kit (from Illumina) as recommended by the manufacturer. An Illumina HiSeq 2000 flowcell was used for sequencing. lncRNA annotation was done based on the NONCODE database (noncode.org).
Libraries were created using a TruSeq RNA Ribo-Zero Globin kit (from Illumina) as recommended by the manufacturer.

treatment_protocol: Hypoxia was induced using a hypoxic incubator (Labotect, Göttingen, Germany). Cell culture medium was pre-equilibrated overnight at 1% O2, 5% CO2 in a humidified atmosphere. Normoxic cell culture medium was carefully switched to hypoxic medium and hypoxic pO2 levels were verified by measuring VEGFA induction by qPCR and pO2 levels with a hypoxia sensing probe from Oxford Optronix (Oxford, UK) as described in detail before (Zehendner et al. 2013).

value: human primary pericytes

value: passage 2-9

tag: genotype/variation

value: TYKRIL knockdown LNA GapmeR LNA#2


title: aB3h_wt_H3K27Ac


title: Ctrl_n3

source_name: human primary pericytes_CTRL LNA

value: Scramble Control GapmeR


title: Pool_1327_AD010_indexed


title: Pool_1328_AD002_indexed


title: TYKRIL LNA#1l_n3

value: TYKRIL knockdown LNA GapmeR LNA#1


title: Ctrl_n2


title: Pool_1327_AD006_indexed


title: aB_wt_Medica_H3K27Ac

description: Medica treatment

value: WT

value: spleen


title: Pool_1327_AD008_indexed


title: TYKRIL LNA#2_n2


title: TYKRIL LNA#1_n2


title: Pool_1326_AD010_indexed


title: Pool_1326_AD006_indexed


title: Pool_1325_AD010_indexed


title: CTRL_n1_R2.fastq


title: TYKRIL LNA#1_n1


title: TYKRIL LNA#2_n1


title: norm_n3

description:
Normoxic conditions
processed data file: Gene_Expression.tsv

source_name: human primary pericytes_normaxia

tag: exposed to

value: Normoxia 20% O2, 5% CO2 humidified atmosphere


title: Pool_1325_AD008_indexed


title: norm_n1


title: norm_n2


title: Pool_1325_AD002_indexed


title: MCF7_ZF_DNMT3A_noDox_rep4_RNAseq

city: Crawley

first: Ethan

middle: Edward

last: Ford

state: WA

address: 35 Stirling Highway

department: Plant Energy Biology

country: Australia

institute: University of Western Australia

description: RNA-seq

data_processing:
Whole Genome Bisulfite Sequencing by MethylC-seq and TAB-seq. Reads were mapped to the human genome (hg19) with the Bowtie alignment algorithm (Langmead et al. 2009) with the following parameters: -e 1120 –O 20 –n 1 as previously reported (Lister et al. 2011).
RAN-seq. Reads were mapped to the human genome assembly hg19 and transcriptome using TopHat2 (Kim et al. 2013). Uniquely mapped reads were assigned to genes with HTseq-count and differentially expressed genes and fold-change of expression was called with DESeq2 (Love et al. 2014). FPKM values were calculated with CuffDiff2 (Trapnell et al. 2013). For all analyses only genes with greater than 20 uniquely mapped reads were used.
ChIP-seq and ChIP-bisulfite seq. For ChIP-seq reads were mapped with the bowtie software package (Langmead et al. 2009) and non-uniquely mapped reads were discarded. For ChIP-bisulfite-seq reads were mapped and methylation was called as described for MethylC-seq. Peaks were called using MACS1.4 (Feng et al. 2011).
Genome_build: hg19
Supplementary_files_format_and_content: For the WGBS data the 'allC' file format is a tab-delimited text file with the following columns: 1) chromosome, 2) position, 3) strand, 4) context, 5) cytosine base calls, and 6) all base calls. For the ChIP-BS-seq data  the 'allC' file format is a tab-delimited text file with the following columns: 1) chromosome, 2) position, 3) position, 4) strand, 5) context, 6) cytosine base calls, and 7) all base calls.

molecule: polyA RNA

growth_protocol: The MCF-7 ZF-DNMT3A and MCF-7 empty vector cell lines are previously described (Stolzenburg et al., Oncogene, 2015). Cells were grown in MEM α nucleosides (Life Technologies) supplemented with 0.075% sodium bicarbonate and 10% tetracycline-free fetal bovine serum (Clonetech).

extract_protocol: Whole Genome Bisulfite Sequencing by MethylC-seq libraries were constructed as follows. Genomic DNA was extracted from cells using the Qiagen Blood and Tissue Kit according to the manufacturer's instructions. 1 ug of genomic DNA was spiked with 0.5% (w/w) of unmethylated lambda phage DNA for the calculations of the non-conversion rate and sheared with a Covaris S2 sonicator to an average length of 200 bp. The sheared DNA was end-repaired, A-tailed and ligated to methylated Illumina TruSeq adapters and subjected to 4 cycles of PCR amplification using KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems). TAB-seq libraries were constructed as follows. Genomic DNA was isolated as described for MethylC-seq. TAB-seq libraries were generated using the 5hmC TAB-seq kit (WiseGene) according to the manufacturer’s instructions. 5-hydroxymethylated pUC19 DNA (WiseGene) was used to estimate the protection of 5hmC by β-glucosyltransferase and unmethylated lambda phage DNA was used to estimate the bisulfite conversion rate. RNA-seq libraries were constructed as follows. RNA was extracted from cells using the Qiagen RNeasy kit. 330 ng of total RNA was used to generate libraries using the Illumina TruSeq Stranded mRNA kit according to the manufacturer's instruction, except one-third of all reaction volumes were used and the final amplification used 10 cycles of PCR. ChIP-seq libraries were constructed as follows. cells were harvested at 72 h by crosslinking in a final concentration of 1% formaldehyde. Crosslinking was stopped after 5 min by adding glycine to a final concentration of 125 mM. Crosslinked cells were washed in cold phosphate buffered saline, lysed using 1 ml low-salt IP buffer (150 mM NaCl, 50 mM Tris-HCl (pH7.5), 5 mM EDTA, NP-40 (0.5%), Triton X-100 (1%) containing protease inhibitors) and aliquoted at 1 × 10∧7 cells/ml. Cells are then sonicated to a fragment size range of 500–800 bp. Samples were then diluted in 1 ml low-salt buffer and incubated with 3 μl of anti-HA antibody (Covance, Princeton, NJ). Three-hundred microliter Sepharose A beads (GE Healthcare Life Science) were used for pull-down. ChIP-bisulfite sequening libraries were constructed as follows. Two 15 cm plates of cells were grown and doxycycline induced for three days. Cells were washed two times with 10 ml of PBS and crosslinked for 5 minutes in 50 mM HEPES-KOH, pH 7.5, 100 mM NaCl, 1mM EDTA, 1% formaldehyde. The crosslinking reaction was quenched by the addition of glycine to a final concentration of 125 mM and washed two times with phosphate buffered saline (PBS). All subsequent solutions were supplemented with a protease inhibitor cocktail from Sigma (Cat. # P8340). Cells were scraped off the plates with a rubber policeman in 10 ml of PBS and spun at 3,000 rpm for 5 minutes in a swinging bucket rotor. The cell pellets were resuspended in 10 ml of 50 mM HEPES-KOH, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, incubated on ice for 10 minutes and centrifuged at 3,000 rpm for 10 minutes in a swinging bucket rotor. Cell pellets were washed two times by adding gently adding 10 mM Tris-HCl, pH 8.1, 200 mM NaCl, 1 mM EDTA to the cell pellets trying not to disturb the pellets and centrifuged at 3,000 rpm for 5 min. Finally the cell pellets were resuspended in 0.1% SDS, 1 mM EDTA and transferred to a Covaris TC12x12 tube. The chromatin was sheared with a Covaris S2 sonicator with the following settings: Time 12 min, duty cycle 5%, intensity 4, cycles per burst 200, temperature 4˚C, power mode frequency sweeping. Triton X-100 and NaCl were added to a final concentration of 1% and 150 mM respectively. The sheared chromatin was centrifuged at maximum speed in a microfuge for 15 minutes at 4˚C and the supernatant was transferred to a new tube. 2 ul of anti-H3K4me3 (Diagenode, Cat. # C15410003) or 4 ul of anti-phospho-Ser5 RNA polymerase antibody (Active Motif, Cat. # 39233) was added and incubated overnight at 4˚C. 30 ul of Protein G Dynabeads (Life Technologies) was added and incubated on a tube rotator for 90 minutes at 4˚C. The beads were washed two times with 20 mM HEPES-KOH, pH 7.9, 0.1% SDS, 150 mM NaCl, 1% Triton X-100 2 mM EDTA, two times with 20 mM HEPES-KOH, pH 7.9, 0.1% SDS, 500 mM NaCl, 1% Triton X-100 2 mM EDTA, one time with 100 mM Tris-HCl pH 7.5, 0.5 M LiCl, 1% NP-40, 1% Sodium Deoxycholate and one time with 10 mM Tris-HCl, pH 8.0, 1 mM EDTA. The DNA was eluted twice by incubating for 30 minutes in 25 ul of 20 mM HEPES-KOH, pH 7.9, 1 mM EDTA, 0.5% SDS, 0.5 mg/ml Proteinase K. To the 50 ul of eluted DNA, 3 ul of 3M Sodium Acetate, pH 5.3 and 0.5 ul 30 mg/ml RNase A was added and incubated overnight at 65˚C in a hybridization oven. 1.5 ul of 20 mg/ml proteinase K was added and incubated for 1 hour at 50˚C and the DNA was purified with a 2X volume of a homemade version of AMPure XP beads and eluted in 20 ul Tris-HCl, pH 8.0, 0.1 mM EDTA. Libraries were made with the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer’s instructions.

treatment_protocol: Doxycycline inductions were performed by adding doxycycline to a final concentration of 100 ng/ml.

tag: cell line

value: human brest cancer cell line


title: Pool_1329_AD002_indexed


title: hypo_n3

description:
Hypoxic conditions
processed data file: Gene_Expression.tsv

source_name: human primary pericytes_hypoxia


title: Pool_1324_AD008_indexed


title: hypo_n1


title: Pool_1324_AD006_indexed


title: MCF7_ZF_DNMT3A_noDox_rep1_RNAseq

description: RNA-seq


title: hypo_n2


title: MCF7_ZF_DNMT3A_doxInduced_rep4_RNAseq

description: RNA-seq


title: Exp 2_IP sample

city: Pushchino

first: Olga

middle: N

last: Ozoline

state: Moscow Region

address: Institutskaya

department: Functional Genomics and Cellular Stress

country: Russia

institute: Institute of Cell Biophysics of Russian Academy of Sciences

description:
Experimental sample
Experiment_2_CLC_GW_peaks.txt
Experiment_2_Matcher_peaks.txt

data_processing:
Raw data were quality filtered on the Galaxy server (Filter by Quality tool, Q≥20) providing 99% probability of correct sequencing for all nucleotides in each read. As a result, the sets contain 31,656,551 and 45,396,252 sequences in the control and immunoprecipitated samples of the first experiment, and, respectively, 7,493,528 and 8,214,737 reads for the second experiment.
Two different approaches were used to align sequence reads to the genome of E. coli K-12 MG1655 (U00096.3). First, quality controlled reads were mapped using the CLC Genomics Workbench version 7.5.1 (CLC GW, Bio-Qiagen, Aarhus, Denmark) with either default settings for the length and similarity fractions (0.5 and 0.8, respectively, see supplemental Table 2 of the paper) or with the most stringent criteria (1.0 and 1.0, respectively, deposited). Reads with sequences aligned to multiple genomic regions were ignored.
To apply the second approach variable in length reads from Illumina MiSeq were first trimmed from both sides to obtain a set of standard 50 nt sequences taken from the middle of longer reads. Reads shorter than 50 nt were discarded. Then, all four sets from both experiments were aligned to the genome using the Matcher program (available at: http://www.mathcell.ru/DnaRnaTools/Matcher.zip). This software maps only 5’-ends if the reads correspond to the top strand of genomic DNA, or only 3’-ends, if they are aligned to the bottom strand. As such, the signals from fully complementary reads will match the same (left) position. Reporting the distribution of matching reads across the genome the program also evaluates reads with multiple occurrence and their positions.
Only ideal correspondence of sequence reads to the genome in both cases was permitted. The profiles obtained for experimental and control samples were normalized by the scaling method initially offered by Affymetrix for microarray data analysis and later implemented in several other approaches. This method assumes unaffected protein occupancy at most genomic positions and quantifies the scaling factor on the basis of corrected mean values obtained after removal of 2% signals with highest and lowest intensities from both control and experimental sets.
After normalization, the read counts were estimated in the running windows of 35 bp, and the ratios R between values obtained for experimental and control libraries were calculated. Peaks were localized requiring R≥1.5 for at least 50% positions of at least 60 bp genomic region in length.
Genome_build: E. coli K-12 MG1655 (U00096.3)
Supplementary_files_format_and_content: Processed data include read pileups obtained in two ChIP-seq experiments by two different approaches (files 1-4), the set of regions bound by Dps in both experiments (file 5) and the set of regions unbound by Dps in both experiments (file 6). All processed data are provided as tab-delimited .txt files.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacterial cells

growth_protocol: Bacterial cells were grown aerobically in M9 medium supplemented with 0.2% glucose and 5% LB at 37°C under constant shaking (~120 rpm) in a water bath and harvested at OD ~0.6.

extract_protocol:
For immunoprecipitation, 800 μl of collected chromatin (~1000 μg of protein) were incubated on a rotating wheel over night at 4°C with 10 μg of either rabbit anti-Dps antibodies (experimental sample) or rabbit pre-immune IgG (negative control). Next day 30 μl of Ultra Link Protein A/G beads (Thermo Scientific, USA) were added to the samples, and incubation was allowed for a further 2 hours at 4°C on a rotating wheel. The beads were washed 3 times with 1 ml of the low-salt buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton X-100, 1xPIC) and then with 1ml of the high-salt buffer (500 mM NaCl). Immunoprecipitated DNA-protein complexes were removed from the beads by 3 h shaking at 65°C and 1000 rpm in 110 μl of freshly prepared elution buffer, containing 100 mM NaHCO3 and 1% SDS. After centrifugation at 3000 rpm for 5 minutes, 100 μl of the supernatant was transferred to a new tube, and the DNA was purified with a PCR Purification Kit (Qiagen, Germany). The DNA concentration was measured on Qubit 2.0 using Qubit dsDNA HS Assay kit. A total of 8-10 identical samples were combined and concentrated to a volume of 30-50 μl containing 5-10 ng of the DNA.
ChIP-seq libraries were prepared from 5-10 ng of the DNA samples with the NebNext® Ultra™ DNA Library Prep Kit for Illumina (New England Biolabs, MA, USA) following the manufacturer’s instructions. For the final amplification of the library 15 PCR cycles were used. Size distribution and concentration of the amplicons was checked on the Bioanalyzer 2100 (Agilent, USA). In the first experiment, the maximum was at about 300 bp, and ChIP libraries were sequenced using 50 nt single-end read protocol on the Illumina HiSeq system (Illumina, USA) of the Genomics Facility in the Centre for Genomic Regulation (Barcelona). In the second experiment, the maximum was at about 450 bp, and samples were sequenced using standard paired-end 2*150 nt protocol on the MiSeq system (Illumina, USA) in the Immanuel Kant Baltic Federal University (Kaliningrad).

treatment_protocol: ChIP-seq experiments were performed in duplicate using similar growth condition and protocols for chromatin immunoprecipitation. The first experiment was done in the Centre for Genomic Regulation (CRG, Barcelona, Spain), while the second one in the Immanuel Kant Baltic Federal University (Kaliningrad, Russia). In both cases, bacterial cells were grown aerobically at 37°C until OD600~0.6 were treated with formaldehyde (final concentration of 1%, 20 min incubation). Cross-linking was stopped with glycine (final concentration of 450 mM). After 5 minutes of incubation the cells were pelleted by centrifugation at 14,000 rpm for 15 minutes (+4°C), washed twice with 5 ml of PBS and resuspended in 1.3 ml of ice-cold immunoprecipitation buffer prepared from 50 ml of buffer containing 100 mM NaCl, 50 mM Tris-HCl (pH 8.1), 5 mM EDTA, 0.2% NaN3, 0.5% SDS, and 25 ml of buffer containing 100 mM Tris-HCl (pH 8.6); 100 mM NaCl; 5 mM EDTA; 0,2% NaN3, 5% Triton-X-100. Then phenylmethylsulfonyl fluoride (final concentration of 1 mM) or 20 μl of Protease Inhibitor Cocktail (PIC, Sigma) for the first and the second experiment, respectively, were added followed by incubation for 30 min at +4°C.

tag: growth stage

value: log-phase

tag: medium

tag: antibody

value: Anti-Dps antibodies

tag: ngs platform

value: Illumina MiSeq

tag: sequencing mode

value: paired-end 2*150 nt protocol


title: Pool_1324_AD002_indexed

value: frontal cortex


title: Pool_1328_AD006_indexed

value: Male


title: Pool_1326_AD002_indexed

value: 25 yr


title: MCF7_ZF_DNMT3A_doxInduced_rep3_RNAseq

description: RNA-seq


title: Pool_1323_AD008_indexed


title: Pool_1323_AD010_indexed


title: Pool_1325_AD006_indexed


title: Pool_1323_AD006_indexed


title: MCF7_ZF_DNMT3A_noDox_rep2_RNAseq

description: RNA-seq


title: CD34+ na MACS donor 4

city: Gent

first: Annelynn

last: Wallaert

address: De Pintelaan 185

country: Belgium

institute: UGent

data_processing:
Raw sequencing data was downloaded from Illumina's BaseSpace cloud
Reads were filtered based on stringent read quality control.
After adapter trimming, reads were collapsed and mapped to the reference genome using Bowtie
Mapped reads were annotated to mature miRNAs and different contaminants (tRNA, rRNA …)  using genome annotation data from Ensembl 78, UCSC hg38 and miRBase v21.
Genome_build: GRCh38
Supplementary_files_format_and_content: miRNA read counts

source_name: headthy donor_thymocyte subset CD34+

extract_protocol:
Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.
Libraries were prepared using the TruSeq small RNA library kitt from Illumina according to the manufacturer's use.

tag: subject status

value: healthy donor

value: Thymocyte subset CD34+

tag: subtype


title: MCF7_ZF_DNMT3A_noDox_rep3_RNAseq

description: RNA-seq


title: Pool_1323_AD002_indexed


title: Pool_1324_AD010_indexed


title: CD4+CD8+CD3+ donor 3

source_name: headthy donor_thymocyte subset CD4+CD8+

value: Thymocyte subset CD4+CD8+


title: CD4+CD8+CD3+ donor 5


title: MCF7_ZF_DNMT3A_DoxWithdrawn_rep3_RNAseq

description: RNA-seq


title: MCF7_ZF_DNMT3A_DoxWithdrawn_rep2_RNAseq

description: RNA-seq


title: Pool_1322_AD006_indexed


title: ALL-SIL

source_name: T-ALL cell line

value: ALL-SIL

value: T-ALL cell line

value: TLX


title: DND-41


title: Pool_1322_AD002_indexed


title: Exp 2_control

description:
Control sample
Experiment_2_CLC_GW_peaks.txt
Experiment_2_Matcher_peaks.txt

value: M9 medium supplemented with 0.2% glucose and 5% LB

value: rabbit pre-immune IgG


title: MCF7_emptyVector_noDox_rep4_RNAseq

description: RNA-seq

value: empty vector


title: MCF7_emptyVector_noDox_rep3_RNAseq

description: RNA-seq

value: human brest cancer cell line


title: HPB-ALL

value: HPB-ALL


title: MCF7_ZF_DNMT3A_doxInduced_rep2_RNAseq

description: RNA-seq


title: JURKAT

value: JURKAT

value: TAL


title: Pool_1321_AD010_indexed


title: Pool_1321_AD008_indexed


title: MCF7_emptyVector_noDox_rep1_RNAseq

description: RNA-seq


title: Pool_1321_AD006_indexed


title: KE-37


title: CD34+ na MACS donor 5


title: MCF7_emptyVector_doxInduced_rep3_RNAseq

description: RNA-seq


title: Pool_1322_AD008_indexed


title: Pool_1321_AD002_indexed


title: PF382


title: MCF7_emptyVector_doxInduced_rep4_RNAseq

description: RNA-seq


title: MCF7_ZF_DNMT3A_DoxWithdrawn_rep1_RNAseq

description: RNA-seq


title: LOUCY

value: LOUCY

value: IMM


title: Pool_1320_AD008_indexed

value: frontal cortex

value: Male


title: Pool_1320_AD010_indexed

value: 25 yr


title: MCF7_emptyVector_doxInduced_rep1_RNAseq

description: RNA-seq


title: MCF7_emptyVector_doxInduced_rep2_RNAseq

description: RNA-seq


title: TALL_JS_63

source_name: T-ALL patient_bone marrow

value: T-cell acute lymphoblastic leukemia (T-ALL) patient

value: bone marrow


title: Pool_1320_AD002_indexed


title: MCF7_emptyVector_doxWithdrawn_rep3_RNAseq

description: RNA-seq


title: MCF7_emptyVector_doxWithdrawn_rep2_RNAseq

description: RNA-seq


title: TALL_JS_62


title: Pool_131_AD010_indexed


title: TALL_JS_61

source_name: T-ALL patient_blood

value: blood

value: HOXA


title: TALL_JS_59

value: TLX


title: MCF7_emptyVector_doxWithdrawn_rep1_RNAseq

description: RNA-seq


title: MCF7_emptyVector_noDox_rep2_RNAseq

description: RNA-seq


title: Pool_1320_AD006_indexed


title: MCF7_ZF_PolII_phospho_ser5_noDOX_ChIP_BS

description: chromatin immunoprecipitaiton bisulfite sequencing (ChIP-BS-seq)

value: anti-RNA polymerase II phospho serine 5


title: Pool_1319_AD008_indexed


title: TALL_JS_56


title: TALL_JS_57


title: TALL_JS_55


title: Pool_1319_AD010_indexed


title: MCF7_ZF_H3K4me3_doxInduced_ChIP_BS


title: MCF7_ZF_H3K4me3_noDox_ChIP_BS


title: TALL_JS_54


title: TALL_JS_60


title: TALL_JS_46


title: TALL_JS_50


title: TALL_JS_43


title: MCF7_ZF_DNMT3A_noDox_H3K4me3_ChIP

description: chromatin immunoprecipitaiton sequencing (ChIP-seq)


title: Pool_1318_AD002_indexed


title: MCF7_ZF_DNMT3A_doxInduced_HA_ChIP

value: anti-HA.11 (Biolegend, cat# MMS-101P)


title: Pool_1317_AD010_indexed


title: Pool_131_AD008_indexed


title: Pool_1318_AD010_indexed


title: TALL_JS_42


title: MCF7_ZF_DNMT3A_doxInduced_TABseq

description: TET-assisted bisulfite sequenicng (TAB-seq)


title: MCF7_emptyVector_doxInduced_HA_ChIP

value: empty vector


title: TALL_JS_39


title: MCF7_ZF_DNMT3A_doxInduced_H3K4me3_ChIP

value: human brest cancer cell line


title: Pool_1318_AD006_indexed


title: MCF7_ZF_DNMT3A_PolII_phospho_ser5_doxInduced_ChIP_BS

value: anti-RNA polymerase II phospho serine 6 (Active Motif, Cat. # 39233)


title: Pool_1317_AD006_indexed


title: TALL_JS_35


title: Pool_1319_AD006_indexed


title: MCF7_emptyVector_doxInduced_TABseq


title: Pool_1316_AD010_indexed


title: MCF7_ZF_DNMT3A_noDox_rep1_WGBS

description: whole genome bisulfite sequencing (WGBS)


title: Pool_1317_AD002_indexed


title: MCF7_ZF_DNMT3A_doxWithdrawn_rep2_WGBS


title: MCF7_ZF_DNMT3A_doxWithdrawn_rep1_WGBS


title: Pool_1316_AD006_indexed


title: TALL_JS_31


title: Pool_1316_AD008_indexed


title: Pool_1316_AD002_indexed


title: Pool_1315_AD010_indexed


title: TALL_JS_34


title: TALL_JS_29


title: MCF7_ZF_DNMT3A_doxInduced_rep2_WGBS


title: Pool_1315_AD008_indexed


title: MCF7_ZF_DNMT3A_doxInduced_rep1_WGBS


title: MCF7_emptyVector_doxInduced_rep1_WGBS


title: MCF7_empytVector_doxWithdrawn_rep1_WGBS


title: TALL_JS_37


title: Pool_1315_AD006_indexed


title: TALL_JS_26


title: TALL_JS_30


title: Pool_1315_AD002_indexed


title: TALL_JS_27


title: TALL_JS_25


title: TALL_JS_24


title: Pool_1314_AD006_indexed


title: Pool_1314_AD008_indexed


title: TALL_JS_23


title: MCF7_ZF_DNMT3A_doxInduced_rep3_WGBS


title: TALL_JS_32


title: TALL_JS_21


title: Pool_1313_AD010_indexed


title: TALL_JS_22


title: TALL_JS_20


title: Pool_1313_AD008_indexed


title: Pool_1313_AD006_indexed


title: Pool_1312_AD008_indexed


title: Pool_1312_AD010_indexed


title: TALL_JS_17


title: TALL_JS_18


title: Pool_1312_AD006_indexed


title: Pool_1313_AD002_indexed


title: Pool_1312_AD002_indexed


title: Pool_1322_AD010_indexed


title: TALL_JS_16


title: Pool_1311_AD010_indexed


title: TALL_JS_14


title: TALL_JS_13


title: TALL_JS_15


title: Pool_1311_AD006_indexed


title: TALL_JS_12


title: Pool_1310_AD006_indexed


title: Pool_1310_AD010_indexed


title: TALL_JS_11


title: Pool_1310_AD002_indexed


title: TALL_JS_10


title: TALL_JS_19


title: TALL_JS_9


title: Pool_130_AD008_indexed


title: TALL_JS_8


title: TALL_JS_6


title: Pool_1309_AD010_indexed


title: TALL_JS_7


title: TALL_JS_5


title: Pool_1309_AD006_indexed


title: Pool_1309_AD008_indexed


title: TALL_JS_4


title: TALL_JS_3


title: Pool_1309_AD002_indexed


title: Pool_130_AD010_indexed


title: Pool_1308_AD008_indexed


title: sonication INPUT_ChIPseq

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

country: United Kingdom

institute: University of Oxford

data_processing:
Data were analysed using in-house pipeline that automatically assesses the quality of data, trims adaptors, merges short reads, maps reads to the reference genome, and filters data for duplicates :
mapping : bowtie -m 2 --maxIns 350
for un-mapping reads : trim_galore -- length 10, flash -m 9 -x 0.125
combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
removing read pairs overlapping Duke Blacklisted regions
removing duplicates : samtools rmdup
reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
pileup of fragments (bedtools genomecov -counts)
generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig : un-normalised coverage of filtered fragments (reconstructing fragments, filtering : see above)

source_name: hES H1

growth_protocol: H1 hES cells were expanded in mTeSR1 medium (Stem Cell Technologies) on Matrigel

extract_protocol:
ChIP was performed with the Millipore ChIP Assay Kit (Millipore, 17-295)
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370S) and sequenced on NextSeq500

tag: chip antibody


title: TALL_JS_1

tag: tissue


title: Pool_1307_AD008_indexed


title: Pool_1307_AD006_indexed


title: Pool_1308_AD002_indexed


title: Pool_1307_AD010_indexed


title: H3K36me3_ChIPseq

value: H3K36me3, Abcam, ab9050


title: Pool_1307_AD002_indexed


title: Duodenum_2_refed_RNA

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description: 5h fasting and 2h refeeding

data_processing:
bcl2fastq 1.8.4 for demultiplexing
Raw read files of ribosome profiling libraries and corresponding mRNA libraries were analyzed and quantified with Ribomap 1.1 by making use of the following flags:--min_fplen 28 --max_fplen 34 --adapter CTGTAGGCACCATCAAT.
Processed data files are stat-file outputs from Ribomap, PMID: 27153676 (https://github.com/Kingsford-Group/ribomap) and show the summarized statistics for each transcripts. Each entry of a specific transcript looks like this:  refID: The transcript fai index in the transcriptome fasta file.   tid: Transcript header name in the transcriptome fasta file.   rabd: Ribosome loads, which is the total number of ribosome reads that are esimated from this transcript.   tabd: Relative transcript abundance from Sailfish’s result.   te: Relative translational efficiency, which is the ratio between rabd and tabd.
Genome_build: Mus_musculus.GRCm38.rel84
Supplementary_files_format_and_content: Ribomap output

source_name: mouse duodenum

extract_protocol:
Duodenum was split into two equal parts. RNA for mRNA-Seq was extracted with the RNeasy mini kit (Qiagen, 74104) according to the manufacturers’ instructions.  Split duodenum for Ribo-Seq was briefly rinsed in PBS supplemented with 100μg/ml Cycloheximide (Sigma C4859-1ML) and flash frozen. Flash frozen duodenum tissue fragments were ground by pestle and mortar while being submersed in liquid nitrogen. The resulting powder was rapidly dissolved in ribosome profiling lysis buffer (PMID 23180859), Ribosome protected fragments were generated as previously described (PMID 22836135).
Messenger RNA was isolated with NEBNext Poly(A) beads (New England Biolabs, E7490S) and sequencing libraries were created with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, E7420S). Ribosome profiling libraries were generated according to a published potocol (PMID 22836135). Briefly, size-selected ribosome protected RNA fragments were dephosphorylated with T4 polynucleotide kinase (New England Biolabs M0201S), reverse transcribed with SuperScript III (ThermoFisher Scientific, 18080093), circularized with CircLigase (Epicentre CL4111K), and PCR-amplified with Phusion polymerase (New England Biolabs M0530S).

treatment_protocol: Fasted mice had their food removed just before onset of the dark phase and 5h prior to sacrificing them, refed mice were had free access to food after the 5h fasting period for 2h of refeeding time

tag: strain

value: 8 weeks

value: duodenum


title: MCF7_ZF_DNMT3A_doxInduced_rep1_RNAseq

description: RNA-seq

tag: cell type


title: Pool_1306_AD010_indexed


title: Duodenum_1_refed_RNA

description: 5h fasting and 2h refeeding


title: Duodenum_3_refed_RNA

description: 5h fasting and 2h refeeding


title: Duodenum_2_fasting_RNA

description: 5h fasting


title: Pool_1308_AD006_indexed


title: TALL_JS_2

value: IMM


title: Pool_1306_AD002_indexed

value: frontal cortex


title: Duodenum_1_fasting_RNA

description: 5h fasting


title: Pool_1306_AD008_indexed

value: Male


title: Pool_1306_AD006_indexed

value: 25 yr


title: Pool_1305_AD008_indexed


title: Reck vKO subcortex rep2

city: Baltimore

first: Jeremy

last: Nathans

address: 725 North Wolfe Street, 805 PCTB

institute: Johns Hopkins University School of Medicine

data_processing:
Illumina NextSeq instrument RTA v2.4.11 was used for base calling
Sequenced reads were aligned to the mouse genome (mm10) using HISAT2 v2.0.1.
Fragments Per Kilobase of transcript per Million mapped reads (FPKMs) and differentially expressed genes in the cortex and subcortex (between WT and Reck vascular KO genotypes) was determined using the Cuffdiff program (Cufflinks v.2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the following for each gene: FPKMs for WT (sample_1) and vascular Reck KO (sample_2); the (base 2) log of the fold change (sample_2/sample_1); test statstic value, uncorrected p_value, the FDR-adjusted q_value, and significance.

source_name: Reck flex2/Δex1; Tie2Cre Brain

extract_protocol:
Dissected tissue was flash frozen in liquid nitrogen, and total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific 15596026) and purified using an Rneasy Mini Kit (Qiagen 74104). Libraries were constructed using a TruSeq Stranded Total RNA Library Prep Kit (Illumina RS-122-2201). 250ng of total purified RNA was used for the construction of each library.
Libraries were constructed following the standard Illumina protocol.

value: Mixed

value: subcortex

tag: genotype

value: Reck vascular KO


title: Reck vKO subcortex rep3


title: Reck vKO subcortex rep1


title: Pool_1305_AD006_indexed

tag: Sex


title: Reck vKO cortex rep3

value: cortex

tag: age


title: Pool_1304_AD010_indexed


title: Pool_1305_AD002_indexed


title: Pool_1304_AD002_indexed


title: WT subcortex rep3

source_name: WT Brain

value: Wild type


title: Reck vKO cortex rep1


title: Pool_1304_AD008_indexed


title: Reck vKO cortex rep2


title: WT subcortex rep2


title: WT subcortex rep1


title: Pool_1303_AD010_indexed


title: WT cortex rep3


title: Pool_1303_AD006_indexed


title: Pool_1305_AD010_indexed


title: Pool_1303_AD002_indexed


title: WT cortex rep2


title: WT cortex rep1


title: Duodenum_3_fasting_RNA

description: 5h fasting


title: NDGA8_2_miRNA

city: Hangzhou

first: Dongdong

last: Li

state: Zhejiang

address: Yuhangtang Road

department: Food Science and Nutrition

country: China

institute: Zhejiang University

description: known-miRNA expression.xls; known-miRNA.fa; novel-miRNA expression.xls; novel-miRNA.fa; Table S5.xlsx; Table S6.xlsx; Table S7.xlsx

data_processing:
Raw reads were filtered before assembly to exclude low quality reads, including adaptors, low quality sequences (reads with more than 5% ambiguous bases) and reads with a Phred quality score Q ≤ 20 using the NGS QC toolkit (Patel & Jain 2012). The resulting clean reads were assembled with Trinity program (Grabherr et al. 2011). Assembled unigenes, which can not be extended on either end, were aligned against the NCBI non-redundant (NR) protein database using the BLASTx with an E-value cut-off of 10−5. All the unigenes also compared with protein databases of Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), euKaryotic Ortholog Groups (KOG) and Pfam using the BLASTx algorithm with E-value cut-off of 10−5. Gene expression levels in each sample were normalized with the read counts per kilobase of exon model per million reads (RPKM) method (Mortazavi et al. 2008). Differential expressed genes (DEGs, P <0.05) were analysed among groups according to the method described by Yu et al. (2012).
sRNA sequencing data were processed as described previously by Li et al. (2013). In addition, the recently released miRbase v 21.0 was applied to indentify conserved miRNAs in strawberry. The differential expression levels of miRNAs based on normalized deep-sequencing counts, was analyzed by Chi-squared nXn test among groups.

organism: Fragaria x ananassa

source_name: strawberry fruit

growth_protocol: Octaploid strawberry plants (Fragaria ananassa ‘Toyonoka’) were planted in a greenhouse (60%-80% relative humidity) with cycles of 14 h light at 25 oC followed by 10 h dark at 20 oC.

extract_protocol:
transcriptome sequencing: Total RNA was isolated using Trizol Reagent (Invitrogen Life Technologies, USA) according to the manufacturer’s instructions. RNA samples were treated with RNase free DNase I (Takara, Japan) to avoid genomic DNA contamination. For each group, samples from 10 individual fruits were randomly selected and RNA was extracted separately. Before equal amount pooling, the total RNA quantity and concentration were tested on Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RNA integrity number (RIN) higher than 8.0.
transcriptome sequencing: Paired-end Illumina mRNA libraries were generated in accordance with the manufacturer’s instructions for mRNA-Seq Sample Preparation (Illumina Inc., San Diego, CA, USA). The 7 libraries were subjected to sequencing on an Illumina Hiseq 4000 platform and 100 bp paired-end reads were generated.
miRNA sequencing: fourteen small RNA libraries of samples as mentioned above were prepared for sRNA analysis according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA).
miRNA sequencing: Single end sequencing (50 bp) was performed on an Illumina Hiseq 4000 at 1GENE (Hangzhou, China) following the vendor’s recommended protocol.

treatment_protocol: 100 μL chemical solutions of ABA (1 μM), ABA biosynthesis blocker nordihydroguaiaretic acid (NDGA, 100 μM) or distilled water (served as control) were injected into each fruit receptacle core through the pedicel with a sterile 100 μL microsyringe.

tag: cultivar

value: Toyonoka

value: Strawberry receptacle

tag: treatment

value: fruit treated with NDGA, samples collected 8 days later after the treatment


title: Pool_1302_AD010_indexed


title: Pool_1302_AD002_indexed


title: NDGA5_1_miRNA

value: fruit treated with NDGA, samples collected 5 days later after the treatment


title: Pool_1301_AD010_indexed


title: NDGA5_2_miRNA


title: Pool_1302_AD006_indexed


title: Pool_1304_AD006_indexed


title: Pool_1301_AD008_indexed


title: ABA8_1_miRNA

value: fruit treated with ABA, samples collected 8 days later after the treatment


title: Pool_1300_AD008_indexed


title: Pool_1300_AD006_indexed


title: Pool_1301_AD002_indexed


title: ABA5_2_miRNA

value: fruit treated with ABA, samples collected 5 days later after the treatment


title: Pool_1300_AD002_indexed


title: CK8_1_miRNA

value: fruit treated with water, samples collected 8 days later after the treatment


title: CK8_2_miRNA


title: Pool_1303_AD008_indexed


title: CK5_2_miRNA

value: fruit treated with water, samples collected 5 days later after the treatment


title: Pool_12_AD010_indexed


title: ABA5_1_miRNA


title: NDGA8_1_miRNA


title: Pool_12_AD008_indexed


title: CK5_1_miRNA


title: Pool_129_AD010_indexed


title: Pool_129_AD008_indexed


title: NDGA8_2_transcriptome

description: Table S1.xlsx; Table S2.xlsx; Table S3.xlsx; Table S4.xlsx; Gene RPKM expression of two replicates and annotation.xlsx; Trinity.fasta


title: ABA8_2_miRNA


title: Pool_1301_AD006_indexed


title: Pool_1299_AD008_indexed


title: Pool_1299_AD006_indexed


title: NDGA8_1_transcriptome


title: Pool_1299_AD002_indexed


title: NDGA5_2_transcriptome


title: Pool_1317_AD008_indexed


title: NDGA5_1_transcriptome


title: Pool_1298_AD010_indexed


title: ABA8_2_transcriptome


title: Pool_1298_AD008_indexed


title: ABA8_1_transcriptome


title: ABA5_2_transcriptome


title: Pool_1297_AD010_indexed


title: CK8_2_transcriptome


title: ABA5_1_transcriptome


title: CK0_2_miRNA

value: fruit treated with water two weeks after athesis, set as day 0


title: Pool_1297_AD008_indexed

value: frontal cortex


title: CK8_1_transcriptome


title: Pool_1297_AD006_indexed

value: Male


title: CK0_1_miRNA


title: Pool_1299_AD010_indexed

value: 25 yr


title: CK5_2_transcriptome


title: CK5_1_transcriptome


title: Pool_128_AD010_indexed


title: Pool_1297_AD002_indexed


title: CK0_2_transcriptome


title: Pool_128_AD008_indexed


title: Pool_125_AD010_indexed


title: Pool_125_AD008_indexed


title: CK0_1_transcriptome


title: Pool_126_AD008_indexed


title: Pool_124_AD010_indexed


title: Pool_123_AD010_indexed


title: Pool_123_AD008_indexed


title: Pool_1298_AD006_indexed


title: Pool_121_AD008_indexed


title: Pool_121_AD010_indexed


title: Pool_122_AD008_indexed


title: Pool_120_AD008_indexed


title: Pool_120_AD010_indexed


title: Pool_11_AD008_indexed


title: Pool_1298_AD002_indexed


title: Pool_11_AD010_indexed


title: Pool_119_AD010_indexed


title: Pool_118_AD008_indexed


title: Pool_116_AD008_indexed


title: Pool_117_AD010_indexed


title: Pool_116_AD010_indexed


title: Pool_117_AD008_indexed


title: Pool_119_AD008_indexed


title: Pool_114_AD008_indexed


title: Pool_115_AD008_indexed


title: Pool_113_AD008_indexed


title: Pool_124_AD008_indexed


title: Pool_113_AD010_indexed


title: Pool_112_AD010_indexed


title: Pool_111_AD010_indexed


title: Pool_110_AD010_indexed


title: Pool_110_AD008_indexed


title: Pool_111_AD008_indexed


title: Pool_1104_AD006_indexed


title: Pool_1103_AD002_indexed


title: Pool_1102_AD006_indexed


title: Pool_1101_AD006_indexed


title: Pool_1101_AD002_indexed


title: Pool_1100_AD002_indexed


title: Pool_112_AD008_indexed


title: Pool_10_AD010_indexed


title: Pool_10_AD008_indexed


title: Pool_109_AD008_indexed


title: Pool_109_AD010_indexed


title: Pool_1098_AD002_indexed


title: Pool_1097_AD006_indexed


title: Pool_1098_AD006_indexed


title: Pool_1099_AD006_indexed


title: Pool_1096_AD006_indexed


title: Pool_1096_AD002_indexed


title: Pool_1095_AD006_indexed


title: Pool_1095_AD002_indexed


title: Pool_1094_AD006_indexed


title: Pool_1104_AD002_indexed


title: Pool_1102_AD002_indexed


title: Pool_1094_AD002_indexed


title: Pool_1093_AD006_indexed


title: Pool_1100_AD006_indexed


title: Pool_1091_AD002_indexed


title: Pool_1090_AD006_indexed


title: Pool_1092_AD002_indexed


title: Pool_1091_AD006_indexed


title: Pool_1090_AD002_indexed


title: Pool_108_AD010_indexed


title: Pool_1089_AD002_indexed


title: Pool_108_AD008_indexed


title: Pool_1099_AD002_indexed


title: Pool_1088_AD006_indexed


title: Pool_1097_AD002_indexed


title: Pool_1089_AD006_indexed


title: Pool_1087_AD002_indexed


title: Pool_1086_AD006_indexed


title: Pool_1085_AD002_indexed


title: Pool_1084_AD006_indexed


title: Pool_1085_AD006_indexed


title: Pool_1086_AD002_indexed


title: Pool_1083_AD006_indexed


title: Pool_1084_AD002_indexed


title: Pool_1092_AD006_indexed


title: Pool_1093_AD002_indexed


title: Pool_1082_AD006_indexed


title: Pool_1083_AD002_indexed


title: Pool_1081_AD006_indexed


title: Pool_1082_AD002_indexed


title: Pool_1081_AD002_indexed


title: Sample_27_2Dcultured_GCB_d6_R3

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
CPM were obtained using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression CPM

source_name: splenic B cells

growth_protocol:
Naïve B cells were isolated using sorting markers: FAS-GL7-IgD+B220+
GCB cells were isolated using sorting markers: FAS+GL7+B220+
2D culture GCB were differentiatedusing !L4 interspersed among cultured 40LB cells

extract_protocol: RNA-seq libraries were prepared using the TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

tag: background strain

value: activated GC B cell

tag: sample type

value: 2D cultured

tag: time


title: Sample_26_2Dcultured_GCB_d6_R2


title: Pool_1080_AD006_indexed

source_name: Human frontal cortex


title: Sample_24_2Dcultured_GCB_d4_R4


title: Sample_25_2Dcultured_GCB_d6_R1


title: Pool_1103_AD006_indexed


title: Pool_1087_AD006_indexed


title: Sample_23_2Dcultured_GCB_d4_R3


title: Sample_21_2Dcultured_GCB_d4_R1


title: Pool_107_AD008_indexed


title: Pool_1079_AD002_indexed


title: Sample_19_GC_B_cells_Cdkn1aKO_Ezh2KO_R3

value: GC B cell

tag: genotype/variation

value: in vivo sample


title: Pool_107_AD010_indexed


title: Sample_22_2Dcultured_GCB_d4_R2


title: Pool_1078_AD006_indexed


title: Pool_1078_AD002_indexed


title: Sample_16_GC_B_cells_Cdkn1aKO_R5


title: Sample_15_GC_B_cells_Cdkn1aKO_R4


title: Pool_1076_AD002_indexed


title: Pool_1079_AD006_indexed


title: Sample_20_GC_B_cells_Cdkn1aKO_Ezh2KO_R4


title: Sample_13_GC_B_cells_Cdkn1aKO_R2


title: Pool_1075_AD006_indexed


title: Sample_18_GC_B_cells_Cdkn1aKO_Ezh2KO_R2


title: Sample_17_GC_B_cells_Cdkn1aKO_Ezh2KO_R1


title: Sample_11_GC_B_cells_WT_R5

value: WT


title: Pool_1076_AD006_indexed


title: Pool_1074_AD006_indexed


title: Sample_10_GC_B_cells_WT_R4


title: Pool_1080_AD002_indexed


title: Pool_1074_AD002_indexed


title: Pool_1073_AD006_indexed


title: Sample_9_GC_B_cells_WT_R3


title: Sample_8_GC_B_cells_WT_R2


title: Pool_1072_AD006_indexed


title: Pool_1077_AD002_indexed


title: Sample_7_GC_B_cells_WT_R1


title: Sample_6_naive_B_cells_Cdkn1aKO_Ezh2KO_R2

value: Naive B cell


title: Pool_1072_AD002_indexed


title: Pool_1071_AD006_indexed


title: Sample_14_GC_B_cells_Cdkn1aKO_R3


title: Sample_5_naive_B_cells_Cdkn1aKO_Ezh2KO_R1


title: Pool_1071_AD002_indexed


title: Sample_4_naive_B_cells_Cdkn1aKO_R2


title: Sample_3_naive_B_cells_Cdkn1aKO_R1


title: Pool_1070_AD002_indexed


title: Pool_106_AD008_indexed


title: Pool_1070_AD006_indexed


title: Sample_12_GC_B_cells_Cdkn1aKO_R1


title: Pool_1075_AD002_indexed


title: Sample_1_naive_B_cells_WT_R1


title: Sample_2_naive_B_cells_WT_R2


title: Pool_1069_AD006_indexed


title: Pool_1068_AD006_indexed


title: Pool_1069_AD002_indexed


title: Atg7_cKO_rep4

first: Paolo

last: Guarnieri

address: 1130 St. Nicholas Avenue

department: Systems Biology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming
We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Genome_build: mm9
Supplementary_files_format_and_content: We estimate the relative abundance (expression level) of genes and splice isoforms using cufflinks (version 2.0.2) with default settings. We generate and provide FPKM and counts data matrices.

source_name: Lumbar spinal cord

extract_protocol:
Lumbar spinal cords were dissected, flash frozen on dry ice, and RNA was extracted using Trizol (Thermo Fisher) and the RNeasy mini kit (Qiagen). Poly-A pulldown was used to enrich for mRNA.
Libraries were prepared using Illumina TruSeq RNA prep kit.

value: Lumbar spinal cord

value: 150 days

value: Atg7 cKO


title: Pool_1067_AD006_indexed


title: Pool_1073_AD002_indexed


title: Pool_1068_AD002_indexed


title: Atg7_cWT_SOD1_rep4

value: Atg7 cWT; SOD1G93A


title: Atg7_cKO_SOD1_rep4

value: Atg7 cKO; SOD1G93A


title: Atg7_cWT_rep4

value: Atg7 cWT


title: Pool_1067_AD002_indexed


title: Atg7_cWT_SOD1_rep3


title: Atg7_cKO_SOD1_rep3


title: Pool_1066_AD006_indexed


title: Atg7_cWT_rep3


title: Atg7_cKO_rep3


title: Pool_1066_AD002_indexed


title: Pool_1065_AD006_indexed


title: Atg7_cKO_SOD1_rep2


title: Pool_1065_AD002_indexed


title: Pool_1064_AD006_indexed


title: Atg7_cWT_SOD1_rep2


title: Pool_1064_AD002_indexed


title: Atg7_cWT_rep2


title: Pool_1063_AD006_indexed


title: Atg7_cWT_SOD1_rep1


title: Pool_1063_AD002_indexed


title: Atg7_cKO_rep2


title: Atg7_cKO_rep1


title: Pool_1062_AD006_indexed


title: Pool_1062_AD002_indexed


title: B16BL6

city: Houston

first: Spencer

last: Wei

state: TX

address: 7455 Fannin St.

department: Immunology

institute: MD Anderson Cancer Center

description: Mouse cell line 1

data_processing:
Library strategy: Whole Exome Sequencing
WES data was aligned to GRCm38 using Burrows-Wheeler Alignment Tool (BWA)
Picard was used to convert SAM files to BAM files, sort and mark duplicates.
Bam files were then realigned and recalibrated using Genome Analysis Toolkit (GATK). The Mouse Genomes Project SNP and indel Release Version 5 were used as the known indels and SNPs for realignment and recalibration.  These VCF files were downloaded from Sanger Institute FTP
VarScan2 was used to call the mutations without matched normal samples
Data were annotated by ANNOVAR using NCBI Reference Sequence Database
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files containing the detailed information of mutations in samples

source_name: murine melanoma cells

extract_protocol:
Genomic DNA was extracted from tumor cell line pellets using DNeasy Blood and Tissue kit (Qiagen).  Samples libraries were prepared using NimbleGen SeqCap EZ Developer library murine whole exome capture kit (Roche, design: 110624_MM9_Exome L2R_D02_EZ, catalog # 06471706001).
Indexed sample libraries were sequenced by 76-nucleotide pair end sequencing on a HiSeq2000 sequencer (Illumina).

tag: cell line

value: murine melanoma cells


title: Pool_1061_AD002_indexed


title: Pool_1060_AD002_indexed


title: Pool_1060_AD006_indexed


title: MC38

description: Mouse cell line 2

source_name: murine colon carcinoma cells

value: murine colon carcinoma cells


title: aB_wt_CTCF_rep5

source_name: activated B cell

value: spleen

value: abcam, ab70303

tag: activation time


title: Pool_105_AD010_indexed

value: frontal cortex

value: Male

value: 25 yr


title: Pool_105_AD008_indexed


title: Pool_1059_AD006_indexed


title: rB_wt_CTCF_rep5

source_name: resting B cell


title: Pool_1059_AD002_indexed


title: rB_wt_CTCF_rep4


title: aB_wt_Rad21_rep2

value: abcam, ab992


title: Pool_1058_AD006_indexed


title: rB_wt_Rad21_rep5


title: Pool_1058_AD002_indexed


title: Pool_1057_AD006_indexed


title: Pool_1057_AD002_indexed


title: Pool_1061_AD006_indexed


title: Sample_21_in_vivo_PC_R5

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mm10 using STAR with default parameters
CPM were obtained using Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

growth_protocol:
Naïve B cells were isolated using sorting markers: FAS-GL7-IgD+B220+
In vivo GCB cells were isolated using sorting markers: FAS+GL7+B220+
In vivo plasma cells were isolated using sorting markers: CD138+ B220dim
Organoid GCB were differentiated using protocol from PMID: 28005068

extract_protocol: RNA-seq libraries were prepared using the Illumina ChIP-Seq and TruSeq RNA sample kits, respectively, according to the manufacturer. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT™ dsDNA HS Assay (Life Technologies)

value: Plasma cell

value: wild type C57BL/6


title: Sample_19_in_vivo_PC_R3


title: Sample_20_in_vivo_PC_R4


title: Sample_22_in_vivo_PC_R6


title: Pool_1056_AD002_indexed


title: Sample_18_in_vivo_PC_R2


title: Pool_1055_AD006_indexed


title: rB_wt_Rad21_rep4

value: WT


title: Sample_17_in_vivo_PC_R1


title: Atg7_cKO_SOD1_rep1

value: Lumbar spinal cord


title: aB_wt_CTCF_rep4


title: Pool_1056_AD006_indexed


title: Sample_16_in_vivo_GCB_R6

value: GC B cell


title: aB_wt_Rad21_rep3


title: Pool_1054_AD002_indexed


title: Pool_1055_AD002_indexed


title: Pool_1053_AD006_indexed


title: Sample_14_in_vivo_GCB_R4


title: Sample_15_in_vivo_GCB_R5


title: Pool_1053_AD002_indexed


title: Sample_13_in_vivo_GCB_R3


title: Sample_12_in_vivo_GCB_R2


title: Pool_1052_AD006_indexed


title: Sample_11_in_vivo_GCB_R1


title: Pool_1052_AD002_indexed


title: Pool_1051_AD006_indexed


title: Sample_10_organoid_GCB_day6_R3

value: GC organoid activated B cell


title: Pool_1051_AD002_indexed


title: Pool_1050_AD006_indexed


title: Pool_1054_AD006_indexed


title: Sample_9_organoid_GCB_day6_R2


title: Sample_7_organoid_GCB_day4_R4


title: Sample_5_organoid_GCB_day4_R2


title: Pool_104_AD008_indexed


title: Pool_1050_AD002_indexed


title: Sample_6_organoid_GCB_day4_R3


title: Sample_4_organoid_GCB_day4_R1


title: Pool_1049_AD006_indexed


title: Atg7_cWT_rep1

value: 150 days


title: Pool_104_AD010_indexed


title: Pool_1049_AD002_indexed


title: Sample_2_naive_B_cells_R2

value: Naive B cell


title: Sample_3_naive_B_cells_R3


title: Pool_1048_AD006_indexed


title: Pool_1048_AD002_indexed


title: Sample_1_naive_B_cells_R1


title: Pool_1047_AD006_indexed


title: Pool_1047_AD002_indexed


title: Duodenum_1_refed_Ribo

description:
5h fasting and 2h refeeding
ribosomal footprints

data_processing:
Library strategy: Ribo-Seq
bcl2fastq 1.8.4 for demultiplexing
Raw read files of ribosome profiling libraries and corresponding mRNA libraries were analyzed and quantified with Ribomap 1.1 by making use of the following flags:--min_fplen 28 --max_fplen 34 --adapter CTGTAGGCACCATCAAT.
Processed data files are stat-file outputs from Ribomap, PMID: 27153676 (https://github.com/Kingsford-Group/ribomap) and show the summarized statistics for each transcripts. Each entry of a specific transcript looks like this:  refID: The transcript fai index in the transcriptome fasta file.   tid: Transcript header name in the transcriptome fasta file.   rabd: Ribosome loads, which is the total number of ribosome reads that are esimated from this transcript.   tabd: Relative transcript abundance from Sailfish’s result.   te: Relative translational efficiency, which is the ratio between rabd and tabd.
Genome_build: Mus_musculus.GRCm38.rel84
Supplementary_files_format_and_content: Ribomap output

value: 8 weeks

value: duodenum


title: Duodenum_3_refed_Ribo


title: Duodenum_2_refed_Ribo


title: Pool_1046_AD002_indexed


title: Duodenum_3_fasting_Ribo

description:
5h fasting
ribosomal footprints


title: Pool_1045_AD006_indexed


title: Sample_8_organoid_GCB_day6_R1


title: Duodenum_2_fasting_Ribo

description:
5h fasting
ribosomal footprints


title: Pool_1045_AD002_indexed


title: Duodenum_1_fasting_Ribo

description:
5h fasting
ribosomal footprints


title: Pool_1044_AD006_indexed


title: Pool_1044_AD002_indexed


title: Pool_1043_AD002_indexed


title: Pool_1042_AD006_indexed


title: LCM_refed_apical_5

description: 5h fasting, 2h refed, apical cell side

data_processing:
bcl2fastq 1.8.4 for demultiplexing
kallisto 0.42.4 for index creation: kallisto index -i Mus_musculus.GRCm38.rel84.cdna.all.idx Mus_musculus.GRCm38.rel84.cdna.all.fa.gz
kallisto 0.42.4 for pseudoalignment: kallisto quant -i path_to_index/Mus_musculus.GRCm38.rel84.cdna.all.idx -o path_to_output/ --single -l 200 -s 20 -b 50 path_to_fastq/Sample.fastq.gz
Genome_build: Mus_musculus.GRCm38.rel84
Supplementary_files_format_and_content: Tab Separated Values, kallisto output

source_name: subcellular fragment: apical small intestinal epithelium

extract_protocol:
Tissue blocks for microdissection were obtained from 8-week-old male B6 mice.The small intestine was briefly washed in cold PBS and embedded and frozen in OCT without fixation. 8µm thick sections were cut from the frozen block, mounted on polyethylene-naphthalate membrane-coated glass slides (Zeiss, A4151909081000), air-dried for 1m at room temperature, washed in 70% ethanol (30s), incubated in water (Sigma, W4502, 30s), stained with HistoGene Staining Solution (ThermoFisher Scientific, KIT0401, 20s), washed vigorously in water for a total of 30s. The stained sections were dehydrated with subsequent 30s incubations in 70%,95% and 100% ethanol and air dried for 3m before microdissection.  Tissue sections were microdissected on a UV laser-based PALM Microbeam (Zeiss). The system makes use of a pulsed UV laser that cuts the tissue at indicated marks with minimal damage to surrounding cells; the cutting was performed with the following parameters: PALM 40X lens, cut energy 48 (1-100), cut focus 69 (1-100).  Tissue fragments were catapulted and collected in 0.2ml adhesive cap tubes (Zeiss, A4151909191000) with these settings: LPC energy 57 (1-100), LPC focus 67 (1-100). The capturing success was visually confirmed by focusing the PALM on the targeted adhesive cap after each use of the laser-catapult. A total of 15’000 µm2 of subcellular apical or basal tissue areas was collected for RNA sequencing experiments.
Library preparation for microdissected tissues was achieved by resuspension of the fragments in 9.5µl H2O and 1µl of 10x reaction buffer of the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, 634888) in the adhesive cap of the collection tubes. Tissue lysis was achieved by incubation for 5m at room temperature; the lysed samples were flash frozen until library preparation. The RNA was amplified with the SMART-Seq v4 kit according to the manufacturer’s instructions and by using 15 PCR cycles for the cDNA amplification step.

treatment_protocol: Mice were fed regular chow ad libitum and were exposed to phase-reversed circadian cycles. Fasted mice had their food removed just before onset of the dark phase and 5h prior to sacrificing them, refed mice were had free access to food after the 5h fasting period for the indicated amount of refeeding time.


title: Pool_1043_AD006_indexed


title: LCM_refed_basal_3

description: 5h fasting, 2h refed, basal cell side

source_name: subcellular fragment: basal small intestinal epithelium


title: Pool_1042_AD002_indexed


title: LCM_refed_apical_3

description: 5h fasting, 2h refed, apical cell side


title: LCM_refed_basal_4

description: 5h fasting, 2h refed, basal cell side


title: LCM_refed_basal_5

description: 5h fasting, 2h refed, basal cell side


title: Pool_1046_AD006_indexed


title: Pool_1041_AD006_indexed


title: LCM_refed_apical_2

description: 5h fasting, 2h refed, apical cell side


title: Pool_1041_AD002_indexed


title: LCM_refed_basal_2

description: 5h fasting, 2h refed, basal cell side


title: Pool_1040_AD002_indexed


title: Pool_103_AD010_indexed


title: LCM_refed_apical_1

description: 5h fasting, 2h refed, apical cell side


title: LCM_refed_apical_4

description: 5h fasting, 2h refed, apical cell side


title: LCM_refed_basal_1

description: 5h fasting, 2h refed, basal cell side


title: LCM_fasting_apical_5

description: 5h fasting, apical cell side


title: Pool_103_AD008_indexed


title: LCM_fasting_basal_5

description: 5h fasting, basal cell side


title: Pool_1039_AD006_indexed


title: LCM_fasting_basal_4

description: 5h fasting, basal cell side


title: Pool_1038_AD006_indexed


title: LCM_fasting_apical_4

description: 5h fasting, apical cell side


title: LCM_fasting_basal_3

description: 5h fasting, basal cell side


title: Pool_1038_AD002_indexed


title: LCM_fasting_basal_2

description: 5h fasting, basal cell side


title: Pool_1040_AD006_indexed


title: LCM_fasting_apical_3

description: 5h fasting, apical cell side


title: Pool_1037_AD006_indexed


title: LCM_fasting_apical_1

description: 5h fasting, apical cell side


title: Pool_1037_AD002_indexed


title: Pool_1036_AD002_indexed


title: Pool_1035_AD006_indexed


title: Pool_1036_AD006_indexed


title: LCM_fasting_basal_1

description: 5h fasting, basal cell side


title: D4 small-RNAseq

data_processing:
trim fastqs to 25base long reads (saving the 5' end of the reads) - to cut of adaptors
mapping : star --outFilterMultimapNmax 2   --outFilterMatchNmin 40    --outFilterMismatchNmax 4
generating bed file without introns (bedtools bamToBed -split) - for visualisation
counting coverage of reads (bedtools genomecov -counts)
generating bigwig file (ucsctools bedGraphToBigWig)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bigwig of raw read counts (without introns)

source_name: ZFaAS mouse ES-derived day 4 EB

growth_protocol: ES-cell derived EB were obtained by culturing ES cells in the absence of LIF and the presence of transferrin and ascorbic acid as described in Tufarelli et al., 2003 (PMID  12730694)

extract_protocol:
Total RNA was extracted using the Qiagen All prep kit using the conditions indicated for enrichment in small RNAst, and ribo-depleted with Illumina® Ribo-Zero rRNA Removal Kit
Libraries were prepared according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

tag: strain background

value: embryonic stem (ES) cells

value: carrying a transgene including human HBA2

tag: differentiation stage

value: day 4

tag: molecule subtype

value: ribodepleted - total RNA


title: Pool_1034_AD006_indexed

tag: tissue

value: frontal cortex

value: Male


title: D6 small-RNAseq

source_name: ZFaAS mouse ES-derived day 6 EB

value: day 6


title: Pool_1033_AD006_indexed

value: 25 yr


title: Pool_1034_AD002_indexed


title: Pool_1033_AD002_indexed


title: Pool_1035_AD002_indexed


title: Pool_1039_AD002_indexed


title: D0 small-RNAseq

source_name: ZFaAS mouse ES cell clone 2A3

value: day 0 (undifferentiated)


title: Pool_1031_AD006_indexed


title: Pool_1032_AD002_indexed


title: aB_wt_ATAC7

data_processing:
Library strategy: ATAC-seq
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
MNaseI-Seq_density: quality and adapter trimming: fqtrim-v0.94/fqtrim -A 125 -q 20  -f adapters -p22 -P33
MNaseI-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --local --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 22
MNaseI-Seq_density: filtering and sorting(uniquely aligned reads): samtools-0.1.19/samtools view -Sb | samtools sort -@ 20 -m 1G
MNaseI-Seq_density: merging: samtools-1.1/samtools merge
MNaseI-Seq_density: raw tag density: custom program, density estimate of nucleosome dyads genome wide, wigToBigWig -fixedSummaries -keepAllChromosomes
MNaseI-Seq_density: tag ratio between input and control: ucsc-314/wiggletools ratio input.bw control.bw | wigToBigWig
MNaseI-Seq_density: aB_minus_rB density: ucsc-314/wiggletools diff aB_ratio.bw rb_ratio.bw | wigToBigWig
ATAC-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --end-to-end --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 16
ATAC-Seq_density: filtering (remove random contigs): sed '/random/d;/chrUn/d'
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19/samtools view -S -b -F4
ATAC-Seq_density: merging: samtools-0.1.19/samtools merge && samtools sort -m 10G
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: contact_matrix: 5kb contact matrix was generated from the filtered alignment
HiC-Seq: loop call: juicebox hiccups -m 500 -r 5000 -k KR -f 0.1 -p 4 -i 10 -t 0.01,1.5,1.75,2 -d 20000
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: Gro-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: MNaseI-Seq: .wig files tag density ratio difference between activated and resting B cells (ratio)
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: HiC-Seq: tab seperated loop coordinates with other information

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 1 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. For native chip, chromatin was digested with Mnase (Sigma) in digestion buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100, butyrate 5 mM) for 5’ at  37°C and dialyzed against RIPA buffer for 2hrs at 4°C. Five micrograms of antibody were incubated with 40 μl of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μl of sonicated or Mnase-digested chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  MNase-Seq: 4x107 resting and activated B cells were digested with 24 different concentrations of MnaseI. After an initial RT-qPCR analysis and curve-fitting, the MnaseI concentrations for the most representative nucleosomal fraction was determined. The lowest three nucleosomal fractions (which corresponded to MnaseI concentrations of 0U, 0U, and 0.0026U) were pooled together and used as input control. Nucleosomal fractions 16-18 (which corresponded to enzyme concentrations of 0.068U, 0.045U, and 0.03U) were also pooled for further processing.  Input samples were sonicated to obtain similar fragment sizes as the MnaseI-digested samples. DNA was then concentrated and each sample was spiked with 0.055mg of l DNA (also sonicated to match the sample size as was input DNA).                                                                                HiC-Seq:  we used the same protocol for situ HiC libraries at Rao et al., (Cell, 2014 Dec; 159:1-16)                                                                                ATAC-Seq: we followed the protocol at Buenrostri J.D. et al. (Nat Methods, 2013 Dec; 10(12):1213-8)                 Gro-seq:  Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the  RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated  with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and  purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was  dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation.  Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz  Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis  was performed the next day as described in (Wang et al., 2011). However, for reverse  transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT  GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA  TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England  Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and  RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA  fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel  (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The  final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA  clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                                                                MNase-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina)                                                        ATAC-Seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 50 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                   HiC-seq: DNA was isolated and prepared for paired-end Illumina sequencing following the genomic DNA protocol. 100 cycles of sequencing data were acquired on the HiSeq 2000 or 2500 (Illumina).                                    Gro-seq: 50 cycles of sequencing data were acquired on the HiSeq 2000 (Illumina).

value: WT

value: spleen


title: aB_wt_ATAC6


title: aB_wt_ATAC10


title: aB_wt_ATAC8


title: Pool_1031_AD002_indexed

data_processing:
genome build: hg19
For multiplexed single nucleus methylome samples, reads were first trimmed to remove sequencing adaptors using Cutadapt 1.11 with the following parameters in paired ends mode: -f fastq -q 20 -m 62 -a AGATCGGAAGAGCACACGTCTGAAC -A AGATCGGAAGAGCGTCGTGTAGGGA. For singleplex samples, -m parameter was set to 40. For multiplexed samples, 16bp was further trimmed from both 5’- and 3’- ends of R1 and R2 reads to remove random primer index sequence and C/T tail introduced by Adaptase, with the following parameters: -f fastq -u 16 -u -16 -m 30. For singleplex samples, 10bp was trimmed from both 5’- and 3’- ends of R1 and R2 reads with the following parameters: -f fastq -u 10 -u -10 -m 30. Trimmed reads for mouse and human single nuclei were mapped to mm10 and hg19 reference genome, respectively. R1 and R2 reads were mapped separately as single-ended reads using Bismark v0.15.0 with parameter --bowtie2. --pbat option was activated for mapping R1 reads. Resulted bam files were sorted using samtools 1.3 sort, followed by removal of duplicate reads using Picard 1.141 MarkDuplicates with the option REMOVE_DUPLICATES=true. Non-clonal reads were further filtered for minimal MAPQ = 30 using samtools view with option -q30. To prevent regional mCH level estimation from being skewed by rare reads failed to be bisulfite converted, reads with read-level mCH level greater than 0.7 were excluded. The calling of unmethylated and methylated base calls were performed by call_methylated_sites of Methylpy (https://github.com/yupenghe/methylpy/) (1–3).
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)


title: D2 small-RNAseq

data_processing:
trim fastqs to 25base long reads (saving the 5' end of the reads) - to cut of adaptors
mapping : star --outFilterMultimapNmax 2   --outFilterMatchNmin 40   --outFilterMismatchNmax 4
generating bed file without introns (bedtools bamToBed -split) - for visualisation
counting coverage of reads (bedtools genomecov -counts)
generating bigwig file (ucsctools bedGraphToBigWig)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bigwig of raw read counts (without introns)

source_name: ZFaAS mouse ES-derived day 2 EB

value: day 2


title: Pool_1030_AD006_indexed


title: aB_wt_ATAC5


title: Pool_1030_AD002_indexed


title: aB_wt_ATAC4


title: aB_wt_ATAC3


title: Pool_102_AD010_indexed


title: aB_wt_ATAC9


title: aB_wt_ATAC1


title: Pool_102_AD008_indexed


title: Pool_1029_AD006_indexed


title: aB_wt_ATAC2


title: rB_wt_ATAC11


title: rB_wt_ATAC10


title: Pool_1028_AD006_indexed


title: Pool_1032_AD006_indexed


title: rB_wt_ATAC9


title: Pool_1027_AD006_indexed


title: rB_wt_ATAC7


title: LCM_fasting_apical_2

description: 5h fasting, apical cell side

tag: strain


title: Pool_1026_AD006_indexed


title: rB_wt_ATAC6


title: rB_wt_ATAC5


title: Pool_1025_AD006_indexed


title: Pool_1026_AD002_indexed


title: rB_wt_ATAC4


title: rB_wt_ATAC3


title: Pool_1029_AD002_indexed


title: rB_wt_ATAC2


title: Pool_1023_AD006_indexed


title: Pool_1024_AD002_indexed


title: rB_wt_ATAC1


title: rB_wt_ATAC8


title: Pool_1028_AD002_indexed


title: aBm_wt_MNase3

description: aBminusrB.bw

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
MNaseI-Seq_density: quality and adapter trimming: fqtrim-v0.94/fqtrim -A 125 -q 20  -f adapters -p22 -P33
MNaseI-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --local --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 22
MNaseI-Seq_density: filtering and sorting(uniquely aligned reads): samtools-0.1.19/samtools view -Sb | samtools sort -@ 20 -m 1G
MNaseI-Seq_density: merging: samtools-1.1/samtools merge
MNaseI-Seq_density: raw tag density: custom program, density estimate of nucleosome dyads genome wide, wigToBigWig -fixedSummaries -keepAllChromosomes
MNaseI-Seq_density: tag ratio between input and control: ucsc-314/wiggletools ratio input.bw control.bw | wigToBigWig
MNaseI-Seq_density: aB_minus_rB density: ucsc-314/wiggletools diff aB_ratio.bw rb_ratio.bw | wigToBigWig
ATAC-Seq_density: alignment: bowtie2-2.2.3/bowtie2 --phred 33 --trim3 5 --end-to-end --sensitive-local -I 0 -X 1000 --no-discordant --no-mixed --fr --no-unal -p 16
ATAC-Seq_density: filtering (remove random contigs): sed '/random/d;/chrUn/d'
ATAC-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19/samtools view -S -b -F4
ATAC-Seq_density: merging: samtools-0.1.19/samtools merge && samtools sort -m 10G
ATAC-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
HiC-Seq: alignment: bwa-sw with default parameter (map each read separately)
HiC-Seq: filter: remove duplicates and near duplicates, removes reads that map to the same fragemnt and low quality reads (MAPQ <30)
HiC-Seq: contact_matrix: 5kb contact matrix was generated from the filtered alignment
HiC-Seq: loop call: juicebox hiccups -m 500 -r 5000 -k KR -f 0.1 -p 4 -i 10 -t 0.01,1.5,1.75,2 -d 20000
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: Gro-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: MNaseI-Seq: .wig files tag density ratio difference between activated and resting B cells (ratio)
Supplementary_files_format_and_content: ATAC-Seq: .wig files tag density in 100 nt windows divided by windowsize and library size in millions to obtain normalized read density (rpkm)
Supplementary_files_format_and_content: HiC-Seq: tab seperated loop coordinates with other information


title: aBm_wt_MNase6

description: aBminusrB.bw


title: Pool_101_AD010_indexed


title: aBi_wt_MNase6

description: aBminusrB.bw


title: aBm_wt_MNase5

description: aBminusrB.bw


title: Pool_1020_AD006_indexed


title: aBm_wt_MNase2

description: aBminusrB.bw


title: Pool_1022_AD002_indexed


title: Pool_1021_AD002_indexed


title: Pool_1022_AD006_indexed


title: aBi_wt_MNase5

description: aBminusrB.bw


title: aBm_wt_MNase4

description: aBminusrB.bw


title: Pool_1021_AD006_indexed


title: aBm_wt_MNase1

description: aBminusrB.bw


title: Pool_1019_AD002_indexed


title: aBi_wt_MNase4

description: aBminusrB.bw


title: Pool_1025_AD002_indexed


title: aBi_wt_MNase2

description: aBminusrB.bw


title: Pool_1019_AD006_indexed


title: Pool_1017_AD006_indexed


title: aBi_wt_MNase1

description: aBminusrB.bw


title: Pool_1016_AD006_indexed


title: rBm_wt_MNase5

description: aBminusrB.bw


title: rBm_wt_MNase6

description: aBminusrB.bw


title: Pool_1015_AD006_indexed


title: Pool_1015_AD002_indexed


title: Pool_1014_AD006_indexed


title: Pool_101_AD008_indexed


title: Pool_1014_AD002_indexed


title: Pool_1013_AD002_indexed


title: rBm_wt_MNase4

description: aBminusrB.bw


title: aBi_wt_MNase3

description: aBminusrB.bw


title: rBm_wt_MNase3

description: aBminusrB.bw


title: Pool_1018_AD002_indexed


title: Pool_1012_AD006_indexed


title: Pool_1013_AD006_indexed


title: rBm_wt_MNase2

description: aBminusrB.bw


title: rBm_wt_MNase1

description: aBminusrB.bw


title: rBi_wt_MNase5

description: aBminusrB.bw


title: Pool_1011_AD002_indexed


title: rBi_wt_MNase3

description: aBminusrB.bw


title: rBi_wt_MNase4

description: aBminusrB.bw


title: rBi_wt_MNase2

description: aBminusrB.bw


title: Pool_1010_AD006_indexed


title: rBi_wt_MNase1

description: aBminusrB.bw


title: Pool_1011_AD006_indexed


title: Pool_1010_AD002_indexed


title: Pool_100_AD010_indexed


title: rB_wt_Rad21_rep3

tag: chip antibody

value: abcam, ab992


title: Pool_100_AD008_indexed


title: Pool_1009_AD002_indexed


title: Pool_1008_AD010_indexed


title: Pool_1008_AD008_indexed


title: Pool_1023_AD002_indexed


title: rBi_wt_MNase6

description: aBminusrB.bw

tag: genotype


title: Pool_1007_AD010_indexed

tag: Sex


title: rB_wt_Rad21_rep1


title: Pool_1012_AD002_indexed

tag: age


title: rB_wt_CTCF_rep2

value: abcam, ab70303


title: rB_wt_CTCF_rep3


title: Pool_1007_AD008_indexed


title: aB_wt_Rad21_rep1


title: Pool_1005_AD010_indexed


title: Pool_1006_AD008_indexed


title: Pool_1005_AD008_indexed


title: Pool_1004_AD010_indexed


title: Pool_1004_AD008_indexed


title: rB_wt_GROseq

description: Gro-Seq


title: rB_wt_CTCF_rep1


title: aB_wt_CTCF_rep3


title: aB_wt_CTCF_rep1


title: Pool_1003_AD010_indexed