title: WT2 input

city: 西安

first: Jun

last: Yu

state: Shaanxi

address: North of Wei 32nd Road, and east of Xitai Road, High-tech Zone

department: Clinical Experimental Center

institute: Xi'an International Medical Center Hospital

description: Biological replicate 2 of 5

hyb_protocol: 2.5 ug of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 uL 10 Blocking Agent and 1 uL of 25 Fragmentation Buffer, add water to 25uL then heated at 60°C for 30 min, and combined with 25 uL 2 Hybridization buffer. 50 uL hybridization solution was dispensed into the gasket slide and assembled to the m6A Single Nucleotide resolution Microarray slide. The slides were incubated at 60°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of Modified (IP enriched MazF digested RNA, Cy5-labelled) and Input (total RNA, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 10 samples were retained as All Targets Value in the Excel sheet for further m6A methylation stoichiometry and m6A quantity analyses. m6A methylation stoichiometry was calculated for the percentage of modification based on the Modified (Cy5-labelled) and Input (Cy3-labelled) normalized intensities. m6A quantity was calculated for the m6A methylation amount based on the Modified (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.

source_name: Input, myocardium, NPRA+/+, replicate 2

label_protocol: Input and IP enriched MazF digested RNAs(denoted as Modified) were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for Input) and Cy5 (for Modified) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific activity (pmol dye/ug cRNA) were measured with NanoDrop ND-1000.

growth_protocol: The NPRA conditional knockout mouse model (NprAflox/flox) was generated by Shanghai Model Organisms Center, Inc (Shanghai, China). All mice were euthanized by inhaling oxygen with 5% isoflurane at a rate of 1 L/min. The mice were confirmed to be deeply anaesthetized after they were immobile for 1 min. A 25% volume of CO2 gas was constantly flowed into the chamber to bring the mice to the point of clinical death (lack of respiration and heartbeat), and the hearts were subsequently removed to obtain the myocardium.

extract_protocol: 1-4 ug total RNA was digested with 2uL 5MazF Buffer, 2uL MazF and 0.5uL RNase inhibtor in a 10uL reaction system at 37°C for 15 mins. Another 1ug total RNA was also processed with 2uL 5MazF Buffer,and 0.5uL RNase inhibtor in a 10uL reaction system at 37°C for 15 mins(without MazF), this fraction denoted as Input. The digested RNA were added to 300 uL 1Digestion buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/uL RNase Inhibitor) containing 2 ug anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 mL Dynabeads M-280 Sheep Anti-Mouse IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 uL 1Digested buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 uL 1Digestion buffer and twice with 500 uL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/uL RNase Inhibitor). The enriched RNA was eluted with 200 uL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K, 1uL RNase inhibtor) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

treatment_protocol: None.

tag: gender

value: male

value: myocardium


title: WT4 input

status: Public on Jul 01 2022

type: RNA

country: China

description: Biological replicate 4 of 5

molecule: total RNA

organism: Mus musculus

source_name: Input, myocardium, NPRA+/+, replicate 4

tag: tissue

tag: treatment


title: WT5 input

description: Biological replicate 5 of 5

source_name: Input, myocardium, NPRA+/+, replicate 5


title: control_169 850k methylation

type: genomic

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
For DNA, Illumina idat signal intensity files were processed using SeSAMe; within-sample normalization with out-of-band probes and dye bias correction were performed {Zhou, 2018, 30085201}. Probes containing a SNP site in our genetic dataset as well as probes with non-unique mapping and off-target hybridization were removed. Additionally, probes with an average detection P value >= .05 across samples and sex chromosome probes were removed prior to analysis.
For DNA methylation, final methylation beta values are included as a processed data file.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: tissue-Explant

label_protocol: not provided

extract_protocol:
DNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen).  DNA integrity number (DIN) >5 were used.
1 ug of DNA was bisulfite treated using the Zymo EZ DNA Methylation kit, labeled and hybridized to Illumina Infinium Human MethylationEPIC BeadChip using standard protocols.

value: lung

tag: center

value: LTRC

tag: dx

value: other

value: control

tag: methylationid

tag: age

tag: Sex

value: f

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: N


title: SAM81_m10_probing_4_igg

type: protein

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

hyb_protocol: Each serum sample was diluted in protein array blocking buffer (GVS, Sanford, ME) supplemented with E. coli lysate (GenScript, Piscataway, NJ) to a final concentration of 10 mg/mL, and pre-incubated at room temperature (RT) for 30 minutes. Concurrently, arrays were rehydrated in blocking buffer (without lysate) for 30 minutes. Blocking buffer was removed, and arrays were probed with pre-incubated serum samples using sealed chambers to ensure no cross-contamination of sample between pads. Arrays were incubated over-night at 4 °C with gentle agitation. Arrays were then washed at RT five times with TBS-0.05% Tween 20 (T-TBS), followed by incubation with QDot®-conjugated goat anti-human IgG/ IgA diluted 1:200 in blocking buffer for 2 hours at RT. After incubation in secondary antibodies, arrays were then washed three times with TTBS and once with water.

scan_protocol: Chips were air dried by centrifugation at 1,000 g for 5 minutes and scanned on a ArrayCamTM 400-S Microarray Imaging System from Grace Bio-Labs (Bend, OR) for QDot.

data_processing:
Spot and background intensities were measured using an annotated grid (gal) file. For ArrayCamTM a number of different settings were used to attempt to obtain readings. Microarray spot intensities were quantified using software ArrayCamTM (Grace Bio-Labs) utilizing automatic local background subtraction for each spot. The generated signal intensity values were considered raw values.
Prior to the analysis, systematic intensity differences in background reactivity as measured by phosphate buffered saline with tween 20 (PBST) were corrected. This was achieved by subtracting the median raw intensity signal for the 24 PBST intensity measurements for a certain array from the array’s non-PBST antigen intensities. Following background correction, for intensities < 1, an intensity value of 1 was imputed. Global outliers based on PCA and MDS plots were removed.

molecule: protein

source_name: serum

label_protocol: No labeling

extract_protocol: The serum samples originated from future-use consenting participants of parallel avian A(H5N1)/Indonesia/05/2005 influenza vaccine mix and match studies involving MF59® and AS03 adjuvant, also known as DMID Protocols 10-0016 and 10-0017.

treatment_protocol: Only the participants that received the 15 µg dose of H5 vaccine were selected for the microarray analysis; three timepoints from each participant were selected and represent baseline (day 0 or pre-vaccination), day 21 (post-first dose of vaccine), and day 42 (21 days post-second dose of vaccine).

tag: subject id

value: A/H5N1 HA + MF59

tag: day

tag: blocking

value: Mini HA-10ug/ml


title: case_168 850k methylation

source_name: tissue-Biopsy

value: ipf

value: case

value: m

value: Y


title: control_170 850k methylation

value: normal


title: SAM65_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM65_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM81_m50_probing_4_igg


title: case_167 850k methylation

extract_protocol:
DNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen). Samples with RNA integrity number (RIN) and DNA integrity number (DIN) >5 were used.
1 ug of DNA was bisulfite treated using the Zymo EZ DNA Methylation kit, labeled and hybridized to Illumina Infinium Human MethylationEPIC BeadChip using standard protocols.

value: lung


title: control_166 850k methylation

value: LTRC


title: 212 input

description: Biological replicate 5 of 5

source_name: Input, myocardium, NPRA-/-,replicate 5

value: male

value: myocardium


title: SAM65_m10_probing_4_igg


title: case_165 850k methylation

source_name: tissue-Unknown


title: WT3 IP

description: Biological replicate 3 of 5

source_name: Modified, myocardium, NPRA+/+, replicate 3

value: m6A modification


title: 224 input

description: Biological replicate 4 of 5

source_name: Input, myocardium, NPRA-/-,replicate 4


title: WT1 input

description: Biological replicate 1 of 5

source_name: Input, myocardium, NPRA+/+, replicate 1


title: WT5 IP

description: Biological replicate 5 of 5

source_name: Modified, myocardium, NPRA+/+, replicate 5


title: 198 input

description: Biological replicate 2 of 5

source_name: Input, myocardium, NPRA-/-,replicate 2


title: WT4 IP

description: Biological replicate 4 of 5

source_name: Modified, myocardium, NPRA+/+, replicate 4


title: 210 input

description: Biological replicate 3 of 5

source_name: Input, myocardium, NPRA-/-,replicate 3


title: 209 input

description: Biological replicate 1 of 5

source_name: Input, myocardium, NPRA-/-,replicate 1


title: WT1 IP

description: Biological replicate 1 of 5

source_name: Modified, myocardium, NPRA+/+, replicate 1


title: WT2 IP

description: Biological replicate 2 of 5

source_name: Modified, myocardium, NPRA+/+, replicate 2


title: 212 IP

description: Biological replicate 5 of 5

source_name: Modified, myocardium, NPRA-/-,replicate 5


title: WT3 input

description: Biological replicate 3 of 5

source_name: Input, myocardium, NPRA+/+, replicate 3


title: 210 IP

description: Biological replicate 3 of 5

source_name: Modified, myocardium, NPRA-/-,replicate 3


title: 224 IP

description: Biological replicate 4 of 5

source_name: Modified, myocardium, NPRA-/-,replicate 4


title: control_164 850k methylation

value: other

value: control

value: f

value: white


title: SAM65_nop_probing_4_igg

source_name: serum

value: N

value: no peptide


title: SAM65_r10_probing_4_igg


title: control_162 850k methylation

source_name: tissue-Explant

value: not hispanic or latino


title: case_163 850k methylation

source_name: tissue-Biopsy

value: ipf

value: case

value: m


title: SAM33_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: 209 IP

description: Biological replicate 1 of 5

source_name: Modified, myocardium, NPRA-/-,replicate 1


title: case_161 850k methylation

value: lung


title: SAM33_nop_probing_4_igg


title: kidney_Bailing Capsule-treated_rep3

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: gene expression data from kidney of Bailing Capsule-treated rat

hyb_protocol: The sample preparation and hybridation of each cDNAs on Agilent Rat 4 x 44K arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the Agilent DNA Microarray Scanner

data_processing: All arrays were uploaded into Genespring v12.1 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

organism: Rattus norvegicus

source_name: Bailing Capsule-treated rats, 21week

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (Rneasy, Qiagen).

value: kidney

value: 21 week


title: kidney_Bailing Capsule-treated_rep2


title: SAM33_r10_probing_4_igg


title: kidney_DN_rep3

description: gene expression data from kidney of diabetic rat

source_name: diabetic, 21 weeks


title: SAM33_r50_probing_4_igg


title: case_160 850k methylation

source_name: tissue-Unknown

value: LTRC

value: Y


title: SAM33_m50_probing_4_igg

value: Mini HA -50ug/ml


title: kidney_Bailing Capsule-treated_rep1


title: control_159 850k methylation

value: other

value: control


title: case_158 850k methylation

value: National Jewish

value: white


title: 198 IP

description: Biological replicate 2 of 5

source_name: Modified, myocardium, NPRA-/-,replicate 2

value: male

value: myocardium

value: m6A modification


title: SAM16_r10_probing_4_igg

value: A/H5N1 HA + PBS

value: N


title: control_157 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: m

value: not hispanic or latino


title: kidney_DN_rep1

value: kidney

value: 21 week


title: 227

description: Biological repetition 5 of 5

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 5 out of 10 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: myocardium, NPRA+/+, replicate 3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The myocardium samples were collected and the total RNA extraction was carried out using TRI Reagent（Sigma: T9424）according to manufacturer’s instructions. RNA concentration was then measured by the NanoDrop® ND-1000 (BioTek, Vermont, USA).RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: genotype/variation

value: NPRA+/+


title: SAM16_m50_probing_4_igg

value: Mini HA -50ug/ml


title: High-throughput high-multiplexed first screening for splicing factors

type: SRA

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

description: RASL-seq

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed by using cutadapt program (version 1.2.1). Trimmed reads smaller than 16 nt were discarded.
Reads were mapped to the human genome by using Bowtie (version 0.12.7), with parameters "--best --strata -l25 -n2'. Only uniquely mapped reads were kept.
For RASL-seq, the reads were mapped to targetd exon-exon junctions with up to two mismatches.
Assembly: hg18
Supplementary files format and content: readcounts
Library strategy: RASL-seq

source_name: Hela S3 cell

growth_protocol: HeLa S3 cells were from ATCC (Cat# CCL-2.2) and cultured in DMEM, high glucose (GIBCO, Cat# 11965) with 10% fetal bovine serum (Omega Scientific, Cat# FB-01) and 1 x penicillin-streptomycin (GIBCO, Cat# 15140122) at 37 °C in a 5% of CO2 incubator. V6.5 murine embryonic stem cells (mESCs) were cultured in 2i + LIF conditions at 37 °C in a 5% of CO2 incubator. Cells were tested every month negative for mycoplasma contamination.

extract_protocol: Qiagen RNA kit and was used For RNA extraction from isolated cardiac myocytes by following manufacturer's instructions. 1 µg total RNA was mixed with 100 fmol of mouse RASL oligos, 2 pmol of biotinylated-oligo-dT and 5 µl of streptavidin magenetic beads. Followed by one hour of annealing at 45ºC, magnetic beads were washed 3 times by washing buffer. Then ligation was achieved by adding 5U of T4 DNA ligase for 1 hour at 37ºC. After 3 times of wash, ligated oligos were eluted to water by heating at 65ºC for 5 minutes, and then PCR amplified using primers containing sequencing adaptor and barcode sequences. PCR products were purified and sequenced.

treatment_protocol: 384-well plates with optical bottom (Greiner Bio-One, Monroe, NC) were spotted with 1 μl of 0.5 μM siRNA. Reverse transfection was next performed using Lipofectamine RNAiMAX at the final siRNA concentration of 10 nM. Culture medium was replaced with DMEM 24 hrs after transfection and cells were incubated for additional 48 hrs before lysis in SDS buffer for downstream analysis.

tag: cell line

value: HeLa S3


title: High-throughput high-multiplexed second screening for splicing factors

description: RASL-seq


title: SAM16_r50_probing_4_igg


title: case_156 850k methylation

value: lung

value: ipf

value: case

value: f

value: unknown


title: 9-36-4

city: nanjing

first: Ying

last: Zhou

address: 101 longmian street

institute: Nanjing Medical university

data_processing:
g NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)  used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample,Matrix table with raw gene counts for every gene and every sample

source_name: induced pluripotent stem cells-derived cardiomyocytes (iPSC-CMs)

growth_protocol: The ultra-pure cryopreserved human iPSC-derived cardiomyocytes were thawed at 37°C and resuspended in culture medium, consisting of RPMI Media 1640 (11875168, GIBCO) and B27 (17504044, GIBCO) supplement. 72-hour prior to experiments, cells were cultured in maturation medium (MM), which contains fatty acids as previously reported.

extract_protocol:
Cells were collected with TRI reagent (AM9728, Life Technologies), stored in −80 °C and transported on dry ice. Total RNA was extracted using RNA Kit according to the manufacturer’s recommended procedure. Affymetrix microarray performed by GeneChem (Shanghai Genechem Co., Ltd.) was used for mRNA profiling.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: After 72-hour maturation, iPSC-CMs were cultured with diabetogenic medium (DM) (10 mM glucose, 10 nM h-endothelin-1, and 1 μM cortisol) to mimic the chemical environment of diabetes mellitus for 48-hour. 1000 nM of GLP-1(7-36 and 9-36 peptide) were applied for 12-hour to evaluate the potential therapeutic effects on DCM model.

tag: cell type

value: cardiomyocytes

value: diabetic cardiomyocytes modeling+GLP-19-36 treatment


title: case_155 850k methylation

value: National Jewish

value: white

value: Y


title: kidney_DN_rep2


title: 9-36-3


title: 9-36-2


title: SAM16_nop_probing_4_igg

value: A/H5N1 HA + PBS

value: N

value: no peptide


title: 217

description: Biological repetition 4 of 5

source_name: myocardium, NPRA+/+, replicate 2

value: male

value: myocardium


title: SAM16_m10_probing_4_igg

value: Mini HA-10ug/ml


title: 242

description: Biological repetition 1 of 3

source_name: myocardium, NPRA-/-,replicate 1

value: NPRA-/-


title: 240

description: Biological repetition 3 of 5

source_name: myocardium, NPRA+/+, replicate 1

value: NPRA+/+


title: 230

description: Biological repetition 3 of 3

source_name: myocardium, NPRA-/-,replicate 3


title: 241

description: Biological repetition 1 of 5


title: SAM83_nop_probing_4_igg


title: 7-36-2

value: diabetic cardiomyocytes modeling+GLP-17-36 treatment


title: 9-36-1


title: 7-36-4


title: control_154 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m

value: not hispanic or latino


title: case_153 850k methylation

value: National Jewish

value: ipf

value: case

value: multiple-unspecified

value: hispanic


title: control_152 850k methylation

value: white

value: N


title: SAM83_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: 7-36-1

value: cardiomyocytes


title: DCM4

value: diabetic cardiomyocytes modeling


title: 231

description: Biological repetition 2 of 5

value: male

value: myocardium

value: NPRA+/+


title: DCM3


title: 228

description: Biological repetition 2 of 3

source_name: myocardium, NPRA-/-,replicate 2

value: NPRA-/-


title: DCM2


title: 7-36-3

value: diabetic cardiomyocytes modeling+GLP-17-36 treatment


title: case_151 850k methylation

value: lung

value: m

value: Y


title: CM4

value: untreated


title: CM3


title: DCM1


title: SAM83_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM83_r50_probing_4_igg


title: SAM38_nop_probing_4_igg

value: A/H5N1 HA + MF59

value: no peptide


title: SAM38_m50_probing_4_igg


title: control_147 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino


title: SAM83_m10_probing_4_igg

value: A/H5N1 HA + PBS

value: N

value: Mini HA-10ug/ml


title: CM1

value: cardiomyocytes


title: control_149 850k methylation

value: f


title: PF3_Input

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

library_source: genomic

data_processing:
ChIP-seq data was aligned to reference genome hg19 using bowtie (1.2) with the following parameters (-p 4 --best -k 1 -m 1 -S). Sam file ouput was converted to bam format using samtools (0.1.19) view with the following parameters (-b -h -S -F 4) and then sorted using samtools sort. For genome browser visualization of data, sorted bam files were converted into tdf files using igvtools (version 2.3.7) count and visualized using IGV (2.3.88). For ChIP-seq read counting, bam files for ChIP-seq data were converted to bed files using bedtools (v2.17.0) bamToBed function, followed by counting within TSS +/- 1kb for all refseq genes using bemap (2.4.1) bases function. All counts were then normalized to the number of reads for each data set.
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: Posterior Fossa Ependymoma

extract_protocol:
Ependymoma samples were homogenized and fixed in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with the addition of 125 mM glycine for 5 min. Samples were then lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl) and sonicated with Bioruptor (Diagenode) to 200-500 bp fragments. After centrifugation, the lysates were diluted with dilution buffer (167 mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl) and incubated with 10 µg of anti-H3K27me3 antibody (9733, Cell Signaling Technology) bound to Dynal magnetic beads (Invitrogen) overnight at 4¡C. Magnetic beads were washed with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl) and TE buffer (1 mM EDTA; 10 mM Tris-HCl). ChIP DNA was eluted and recovered using Qiagen PCR purification kit.
ChIP sequencing libraries were prepared according to the Illumina TruSeq protocol and were sequenced on the HiSeq 2000.

value: Posterior Fossa Ependymoma

tag: antibody


title: PF2_Input


title: ST2_Input

source_name: Supratentorial Ependymoma

value: Supratentorial Ependymoma


title: PF1_Input


title: ST3_Input


title: PF3_H3K27ac

value: anti-H3K27ac chip-grade antibody (8173, Cell Signaling Technology)


title: case_146 850k methylation

value: lung

value: National Jewish

value: ipf

value: case


title: case_150 850k methylation

value: m

value: U


title: SAM38_r10_probing_4_igg

source_name: serum

value: A/H5N1 HA + MF59


title: ST1_Input


title: SAM38_r50_probing_4_igg


title: case_148 850k methylation

value: white

value: unknown


title: ST1_H3K27ac


title: control_145 850k methylation

source_name: tissue-Explant

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino

value: Y


title: PF2_H3K27ac

value: Posterior Fossa Ependymoma


title: SAM11_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: control_140 850k methylation

value: lung

value: f

value: N


title: case_141 850k methylation

value: National Jewish

value: ipf

value: case


title: SAM38_m10_probing_4_igg

value: A/H5N1 HA + MF59

value: Mini HA-10ug/ml


title: case_144 850k methylation

value: m

value: white


title: PF1_H3K27ac

value: anti-H3K27ac chip-grade antibody (8173, Cell Signaling Technology)


title: S24

city: Wuhan

first: Shengqing

last: Hu

state: China

address: NO.1277, jiefang road

institute: wuhan union hospital

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: According to the manufacturer’s recommendations.

data_processing:
Raw data was extracted as pair files by NimbleScan software. We perform Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data was created for each sample. From the normalized log2-ratio data, a sliding-window (750bp) peak-finding algorithm provided by NimbleScan v2.6 (Roche-NimbleGen) is applied to analysis the MeDIP-chip data. A one-sided Kolmogorov-Smirnov (KS) test is applied to determine whether the probes are drawn from a significantly more positive distribution of intensity log2-ratios than those in the rest of the array. Each probe receives a -log10 p-value score from the windowed KS test around that probe (*_pvalues.gff).
If several adjacent probes rise significantly above a set threshold, the region is assigned to an enrichment peak (EP). The peak data files (*_peaks.gff) are generated from the p-value data files (*_pvalues.gff). NimbleScan detects peaks by searching for at least 2 probes above a p-value minimum cutoff (-log10) of 2. Peaks within 500bp of each other are merged.
normalized data file contains: log2 [MeDIP]/[Input]

source_name: CVD

label_protocol: For DNA labelling, the NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled DNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Genomic DNA (gDNA) was extracted from 9 cell samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA). The purified gDNA was then quantified and quality assessed by nanodrop ND-1000. Genomic DNA of each sample was sonicated to ~200 – 1000 bp with a Bioruptor sonicator (Diagenode) on “Low” mode for 10 cycles of 30 seconds “ON” & 30 seconds “OFF”. The gDNA and each sheared DNA were aragrose analyzed.

value: Blood Cell

tag: group id

value: CVD

tag: sample type

value: input

value: IP


title: S23


title: S78


title: S187

source_name: NC

value: NC


title: case_139 850k methylation

tag: tissue

value: unknown


title: ST3_H3K27ac

value: Supratentorial Ependymoma


title: CM2

value: cardiomyocytes

tag: treatment

value: untreated


title: SAM11_r10_probing_4_igg

value: A/H5N1 HA + PBS

value: Y


title: control_143 850k methylation

value: lung

tag: center

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control

value: not hispanic or latino

value: N


title: case_136 850k methylation

value: National Jewish

value: ipf

value: case

tag: methylationid

tag: age

value: f

value: white


title: SAM18_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: case_135 850k methylation

tag: Sex

value: m

tag: race


title: SAM11_nop_probing_4_igg

tag: subject id

value: no peptide


title: case_142 850k methylation

tag: ethnicity


title: SAM18_nop_probing_4_igg

tag: day

tag: blocking


title: S130

source_name: DM

value: Blood Cell

value: DM

value: input

value: IP


title: S102


title: MemoryB  B.1.1.529-1

city: West Haven

first: Sidi

last: Chen

state: CT

address: 850 West Campus Drive

institute: Yale University

description:
LNP-mRNA
10x Genomics
vloupe.vloupe

data_processing:
Single-cell sequencing data was processed using the Cellranger v6.0.1 (10x Genomics) pipeline and aligned to customized germline V and J gene references.
Assembly: Customized germline V and J gene references
Supplementary files format and content: Cell Ranger Loupe-formatted output

source_name: Spleen and lymph nodes

extract_protocol:
Omicron RBD-specific memory B cells were isolated from pre-enriched memory B cells by magnetic positive selection according to the manufacturer’s protocol (Miltenyi Biotec, 130-095-838). Briefly, spleen and lymph nodes were gently homogenized and red blood cells were lysed in ACK lysis buffer (Lonza). The remaining cells were washed by PBS with 2%FBS and filtered through with a 50ml falcon tube. Thereafter, memory B cells were labeled with memory B cell biotin-antibody cocktail combined with anti-biotin microbeads and isolated using a magnetic rack. Enriched memory B cells were eluted and mixed with 25ug of Omicron RBD recombinant protein with his tag and incubated for 30mins on ice. After incubation, the complex was washed and respectively incubated with anti-his-APC antibody and anti-APC microbeads. The final antigen-enrichment B cells were eluted in PBS and stored on ice until use.                Plasma B cells were collected by fragmenting and rinsing bone marrows with PBS containing 2% FBS. Non-plasma cells were labeled with a biotin-conjugated antibody cocktail combined with anti-biotin microbeads and separated using a magnetic rack according to the manufacturer’s protocol (Miltenyi Biotec, 130-092-530). Purified plasma B cells were eluted and sequentially incubated with CD138 microbeads for an additional 15 minutes at 4℃. The final CD138+ plasma B cells were eluted in PBS and stored on ice until use.                PBMC cells were isolated from fresh whole blood by using SepMate-15 tubes with Lymphoprep gradient medium (StemCell Technologies) after centrifugation at 1200g for 20 minutes. Poured top layer solution that contained PBMCs from SepMate tubes to a new falcon tube and washed once with PBS+2%FBS, resuspended with PBS and stored on ice until use.
Cell suspension were normalized to 1000 cells/ml and loaded to achieve targeted cell recovery to 10000 cells. The samples were subjected to 14 cycles of cDNA amplification. Following this, BCR-enriched libraries were prepared according to the manufacturer’s protocol (10x Genomics). All libraries were sequenced using a Miseq (Illumina) with 26X91 read length.
scVDJ-seq

value: Spleen and lymph nodes

tag: cell line

value: Memory B cell

tag: genotype

value: human IgG and IgK knock-in


title: control_137 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino

value: Y


title: S91

tag: cell type


title: SAM11_m10_probing_4_igg

value: A/H5N1 HA + PBS


title: S278

tag: group id

value: NC


title: case_138 850k methylation

source_name: tissue-Unknown

value: National Jewish

value: ipf

value: case

value: m

value: black


title: S69

value: Blood Cell

tag: sample type

value: input

value: IP


title: ST2_H3K27ac

tag: tissue

value: Supratentorial Ependymoma

tag: antibody

value: anti-H3K27ac chip-grade antibody (8173, Cell Signaling Technology)


title: case_132 850k methylation

value: lung

tag: center

value: UCSF

value: white


title: Control Ad-C infected mouse articular chondrocytes_rep 1

city: Suwon

first: Jimin

last: Jeon

address: 206, World cup-ro, Yeongtong-gu

department: Biomedical Sciences

country: South Korea

institute: Ajou University Graduate School of Medicine

description: Gene expression data from Ad-C infected mouse articular chondrocytes

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Cultured were maintained at 37 °C in an humidified atmosphere containing 5% CO2 as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum and antibiotics (penicillin G and streptomycin). 37 °C, 5% CO2

extract_protocol: Total RNA was extracted from mouse articular chondrocytes using a Purelink RNA mini kit (Ambion). The concentration, purity, and integrity of the extracted RNA were determined by spectrophotometry.

treatment_protocol: mouse articular chondrocytes were infected with Ad-Rip3 or Ad-C. The cells were harvested for total RNA extraction at 36 h post treatment.

value: articular chondrocytes

tag: treatment

value: Ad-C infection


title: SAM18_r10_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: SAM11_r50_probing_4_igg

value: A/H5N1 HA + PBS

value: Y


title: case_131 850k methylation

tag: dx

value: ipf

value: case

tag: methylationid

value: not hispanic or latino


title: SAM18_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_129 850k methylation

tag: age

tag: Sex

value: m

value: unknown

value: hispanic


title: SAM85_m50_probing_4_igg

tag: subject id


title: SAM18_r50_probing_4_igg


title: PBMC  B.1.1.529-1

description:
LNP-mRNA
10x Genomics
vloupe.vloupe

source_name: Peripheral Blood

value: Peripheral Blood

value: Peripheral blood mononuclear cell

value: human IgG and IgK knock-in


title: SAM36_r10_probing_4_igg


title: case_134 850k methylation

value: lung

value: National Jewish

value: f

tag: race

value: white

tag: ethnicity


title: control_133 850k methylation

value: normal

value: control


title: case_126 850k methylation

value: UCSF

value: N


title: SAM85_nop_probing_4_igg

value: A/H5N1 HA + AS03

tag: day

tag: blocking

value: no peptide


title: SAM36_nop_probing_4_igg


title: Ad-Rip3 infected mouse articular chondrocytes_rep 2

description: Gene expression data from Ad-Rip3 infected mouse articular chondrocytes

value: articular chondrocytes

value: Ad-Rip3 infection


title: SAM85_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM85_r10_probing_4_igg


title: Control Ad-C infected mouse articular chondrocytes_rep 2

value: Ad-C infection


title: case_130 850k methylation

value: ipf

value: case

value: m

value: not hispanic or latino

value: Y


title: SAM36_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM70_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: Ad-Rip3 infected mouse articular chondrocytes_rep 1


title: control_128 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: f

value: white


title: PlasmaB  B.1.1.529-1

description:
LNP-mRNA
10x Genomics
vloupe.vloupe

source_name: Bone marrows

value: Bone marrows

tag: cell line

value: Plasma B cell

tag: genotype

value: human IgG and IgK knock-in


title: case_123 850k methylation

value: UCSF


title: SAM85_r50_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: case_127 850k methylation

value: ipf

value: case


title: SAM36_r50_probing_4_igg


title: case_121 850k methylation

value: m

value: not hispanic or latino


title: SAM36_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_124 850k methylation


title: control_125 850k methylation

value: control


title: MG_MACS_MIA_STR_LPS_Rep3_excluded

city: Baltimore

first: Lindsay

middle: N

last: Hayes

state: Maryland

address: 600 North Wolfe Street, Meyer 4-136

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Alignment: FASTQ files aligned and assembled with RSEM and STAR: rsem-calculate-expression -p 4 --paired-end --star --star-output-genome-bam --calc-ci --forward-prob 0.5
Counts: Count matrix was assembled using tximport in R  files <- list.files(path = "../1.align/genes.results/")  names(files) <- strtrim(files, 4)  txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)  txi.rsem$length[txi.rsem$length == 0] <- 1  table(txi.rsem$length == 0)  save(txi.rsem, file = "txi.rsem.RData")
Differential expression was performed with DESeq2.
Assembly: GRCm38vM25
Supplementary files format and content: Adult_MACS_counts.csv: Comma-separated file of raw counts from RSEM output.

source_name: brain striatum

extract_protocol:
Male mice (8-10 wk) were deeply anesthetized with ether, perfused with PBS, and brains extracted. The meninges were removed and then the frontal cortex and striatum were collected into 2 mL tubes with HBSS on ice. The frontal cortex was collected from a coronal slice anterior to 1.7 mm bregma and dorsal of the corpus callosum, and the anterior striatum was excised from this slice by collecting the tissue surrounding the nucleus accumbens. The next coronal slice was cut at -0.5 bregma and the dorsal and ventral striatum was excised from this slice, excluding the olfactory tubercle, and all striatum pieces were pooled together. The brain pieces were diced with scissors and then homogenized with papain according to the adult neural dissociation kit (Miltenyi). Briefly, the tissue was treated with papain and DNase at 37°C for 30 min with rotation. The homogenates were pipetted gently and filtered with a 70 µm strainer. The cell pellet was resuspended in debris removal solution (300 µL debris removal, 700 µL PBS), overlaid with 300 µL of PBS, centrifuged at 3000xg for 10 min, debris aspirated, washed with PBS, and centrifuged at 1000xg for 10 min. The cells were resuspended in 0.5% BSA in HBSS. For magnetic sorting anti-CD11b magnetic beads were added for 30 min at 4C. The cells were washed with buffer and isolated on the magnetic column before final collection into RNA lysis buffer. RNA was collected according to the kit instructions (Qiagen, Micro-RNeasy, PicoPure RNA isolation Kits).
Bulk cell RNA sequencing libraries were prepared using a modified Smart-Seq2 protocol. 5 ng of purified RNA were mixed with 2.5 mM dNTP mix, 2.5 µM oligo-dT30VN, and 1 U/µL RNasin and incubated at 72°C for 3 min. Then 5.7 µL of the single-cell reverse transcription mix (1x superscript II buffer, 1 M betaine, 5 mM DTT, 100 U superscript II, 10 U RNasin, 1 µM TSO oligo, 6 mM MgCl2) was added to each sample for reverse transcription. The cDNA was amplified with the KAPA HF Ready mix with 9 PCR cycles. The cDNA was cleaned up with AMPure XP beads (Beckman Coulter) at a ratio of 0.7:1, washed with 80% ethanol, and resuspended in 17.5 µL water. The libraries were tagmented for sequencing using the Illumina Nextera XT DNA sample preparation kit. 200-250 pg of cDNA was added to 2.5 µL tagment DNA buffer (Illumina) and 1.25 µL of amplicon tagment mix (Illumina) and incubated at 55°C for 5 min to tagment cDNA. The reaction was neutralized with 1.25 µL of neutralize tagment buffer and incubated at room temperature for 5 min. Then the tagmented DNA was indexed and amplified with 3.75 µL of PCR master mix (Illumina) and 1.25 µL each of i5 and i7 indexing primers (Illumina, diluted 1:5). The samples were indexed with the following PCR cycles: 1 cycle of 72°C for 3 min and 95°C for 30 sec; 12 cycles of 95°C for 10 sec, 55°C for 30 sec, and 72°C for 30sec, and 1 cycle of 72°C for 5 min. The final libraries were purified using AMPure XP beads (Beckman Coulter) at a 0.6:1 ratio, washed with 80% ethanol and resuspended in 12 µL water.

treatment_protocol: Lipopolysaccharide (LPS) was delivered by intraperitoneal injection to mice at a dose of 4500 endotoxin units / gram body weight. Microglia were extracted 18 hours after LPS or saline treatment.

value: brain striatum

tag: cell type

value: microglia

tag: group

value: MIA

value: LPS

value: male


title: control_122 850k methylation

tag: tissue

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: f

value: white


title: MG_MACS_MIA_STR_SAL_Rep2

value: SAL


title: control_119 850k methylation

value: black

value: unknown

value: U


title: MG_MACS_MIA_STR_LPS_Rep2


title: MG_MACS_MIA_CTX_SAL_Rep3

source_name: brain frontal cortex

value: brain frontal cortex


title: SAM70_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Y

value: Mini HA -50ug/ml


title: MG_MACS_MIA_CTX_LPS_Rep3

value: microglia


title: SAM70_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM84_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: MG_MACS_MIA_STR_SAL_Rep1

value: brain striatum

value: MIA

value: male


title: control_116 850k methylation

value: lung

value: National Jewish

value: normal

value: control

value: not hispanic or latino


title: case_117 850k methylation

value: ipf

value: case

value: m

value: white


title: SAM70_r50_probing_4_igg

value: A/H5N1 HA + PBS

value: Y


title: MG_MACS_MIA_STR_SAL_Rep3

value: microglia

value: SAL


title: case_120 850k methylation

value: UCSF

value: N


title: case_118 850k methylation

value: unknown


title: SAM70_nop_probing_4_igg

value: no peptide


title: SAM84_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: MG_MACS_CON_STR_SAL_Rep2

value: brain striatum

value: CON

value: male


title: MG_MACS_CON_STR_SAL_Rep3


title: MG_MACS_MIA_CTX_SAL_Rep2

value: brain frontal cortex

value: MIA


title: case_115 850k methylation

value: lung

value: National Jewish

value: ipf

value: case

value: multiple-unspecified

value: hispanic


title: MG_MACS_CON_STR_SAL_Rep1

value: microglia

value: SAL


title: SAM84_r50_probing_4_igg

value: Y


title: MG_MACS_MIA_STR_LPS_Rep1

value: LPS


title: SAM84_m50_probing_4_igg

value: Mini HA -50ug/ml


title: MG_MACS_CON_STR_LPS_Rep2


title: case_114 850k methylation

value: m

value: N


title: MG_MACS_CON_STR_LPS_Rep3

value: brain striatum

value: CON


title: MG_MACS_MIA_CTX_SAL_Rep1

value: brain frontal cortex

value: male


title: SAM03_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: MG_MACS_CON_CTX_SAL_Rep2


title: case_111 850k methylation

value: lung

value: UCSF

value: white

value: not hispanic or latino


title: control_113 850k methylation

value: National Jewish

value: normal

value: control

value: multiple-unspecified

value: hispanic


title: MG_MACS_MIA_CTX_LPS_Rep2

value: microglia

value: MIA

value: LPS


title: MG_MACS_CON_CTX_LPS_Rep3


title: MG_MACS_CON_STR_LPS_Rep1

value: brain striatum


title: SAM84_m10_probing_4_igg

value: A/H5N1 HA + MF59

value: Y

value: Mini HA-10ug/ml


title: case_112 850k methylation

value: ipf

value: case

value: m

value: unknown


title: SAM03_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: MG_MACS_CON_CTX_SAL_Rep3

value: brain frontal cortex

value: CON

value: SAL

value: male


title: SAM03_nop_probing_4_igg

value: no peptide


title: MG_MACS_CON_CTX_LPS_Rep2

value: microglia


title: case_109 850k methylation

value: lung

value: UCSF

value: white

value: not hispanic or latino


title: SAM03_m50_probing_4_igg

value: Y

value: Mini HA -50ug/ml


title: MG_MACS_CON_CTX_LPS_Rep1

value: LPS


title: MG_MACS_CON_CTX_SAL_Rep1


title: MG_MACS_MIA_P4_Rep5

data_processing:
Alignment: FASTQ files aligned and assembled with RSEM and STAR: rsem-calculate-expression -p 4 --paired-end --star --star-output-genome-bam --calc-ci --forward-prob 0.5
Counts: Count matrix was assembled using tximport in R  files <- list.files(path = "../1.align/genes.results/")  names(files) <- strtrim(files, 4)  txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)  txi.rsem$length[txi.rsem$length == 0] <- 1  table(txi.rsem$length == 0)  save(txi.rsem, file = "txi.rsem.RData")
Differential expression was performed with DESeq2.
Assembly: GRCm38vM25
Supplementary files format and content: Neonatal_MACS_counts.csv: Comma-separated file of raw counts from RSEM output.

source_name: whole brain

extract_protocol:
P4 mice were not perfused but blood was drained by decapitation, and brains extracted. The meninges were removed and the whole brain collected into 2 mL tubes with HBSS on ice. The brain pieces were diced with scissors and then homogenized with papain according to the adult neural dissociation kit (Miltenyi). Briefly, the tissue was treated with papain and DNase at 37°C for 30 min with rotation. The homogenates were pipetted gently and filtered with a 70 µm strainer. The cell pellet was resuspended in debris removal solution (300 µL debris removal, 700 µL PBS), overlaid with 300 µL of PBS, centrifuged at 3000xg for 10 min, debris aspirated, washed with PBS, and centrifuged at 1000xg for 10 min. The cells were resuspended in 0.5% BSA in HBSS. For magnetic sorting anti-CD11b magnetic beads were added for 30 min at 4C. The cells were washed with buffer and isolated on the magnetic column before final collection into RNA lysis buffer. RNA was collected according to the kit instructions (Qiagen, Micro-RNeasy, PicoPure RNA isolation Kits).
Bulk cell RNA sequencing libraries were prepared using a modified Smart-Seq2 protocol. 5 ng of purified RNA were mixed with 2.5 mM dNTP mix, 2.5 µM oligo-dT30VN, and 1 U/µL RNasin and incubated at 72°C for 3 min. Then 5.7 µL of the single-cell reverse transcription mix (1x superscript II buffer, 1 M betaine, 5 mM DTT, 100 U superscript II, 10 U RNasin, 1 µM TSO oligo, 6 mM MgCl2) was added to each sample for reverse transcription. The cDNA was amplified with the KAPA HF Ready mix with 9 PCR cycles. The cDNA was cleaned up with AMPure XP beads (Beckman Coulter) at a ratio of 0.7:1, washed with 80% ethanol, and resuspended in 17.5 µL water. The libraries were tagmented for sequencing using the Illumina Nextera XT DNA sample preparation kit. 200-250 pg of cDNA was added to 2.5 µL tagment DNA buffer (Illumina) and 1.25 µL of amplicon tagment mix (Illumina) and incubated at 55°C for 5 min to tagment cDNA. The reaction was neutralized with 1.25 µL of neutralize tagment buffer and incubated at room temperature for 5 min. Then the tagmented DNA was indexed and amplified with 3.75 µL of PCR master mix (Illumina) and 1.25 µL each of i5 and i7 indexing primers (Illumina, diluted 1:5). The samples were indexed with the following PCR cycles: 1 cycle of 72°C for 3 min and 95°C for 30 sec; 12 cycles of 95°C for 10 sec, 55°C for 30 sec, and 72°C for 30sec, and 1 cycle of 72°C for 5 min. The final libraries were purified using AMPure XP beads (Beckman Coulter) at a 0.6:1 ratio, washed with 80% ethanol and resuspended in 12 µL water.

value: whole brain

value: MIA


title: MG_MACS_MIA_P4_Rep7_excluded


title: MG_MACS_MIA_P4_Rep3


title: MG_MACS_MIA_P4_Rep6_excluded


title: case_107 850k methylation

value: ipf

value: case

value: f

value: N


title: control_110 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: MG_MACS_MIA_P4_Rep2

value: microglia


title: SAM35_r50_probing_4_igg

value: A/H5N1 HA + AS03


title: MG_MACS_MIA_P4_Rep4


title: MG_MACS_MIA_P4_Rep1


title: SAM35_r10_probing_4_igg


title: control_108 850k methylation

value: lung

value: m


title: MG_MACS_CON_P4_Rep6_excluded

value: CON


title: SAM35_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM35_nop_probing_4_igg

value: no peptide


title: SAM03_m10_probing_4_igg

value: A/H5N1 HA + PBS

value: Y


title: case_105 850k methylation

value: UCSF

value: unknown


title: MG_MACS_CON_P4_Rep4

value: whole brain


title: MG_MACS_CON_P4_Rep2


title: MG_MACS_CON_P4_Rep3


title: control_104 850k methylation

value: black


title: SAM35_m50_probing_4_igg

value: N

value: Mini HA -50ug/ml


title: KO_pro-B_63

city: Freiburg im Breisgau

first: Marc

last: Bayer

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description: matrix column name: KO_pro-B_63

data_processing:
Reads were mapped to the mouse genome (GRCm38 – mm10) using STAR (v2.7.4a).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with RPKM normalization.
The expression level of the annotated genes (UCSC, mm10) was calculated by featureCounts (subread v2.0.0).
The differential gene expression was calculated between conditions by DESeq2. Genes with a total read count < 10 across all samples were excluded. Genes with a q-value < 0.05 were considered significant and a fold change > 2 was used as a cut-off.
Assembly: mm10
Supplementary files format and content: The raw count matrix of sequencing reads obtained from featureCounts is provided in tab-delimited txt format.
Supplementary files format and content: The normalized gene expression values calculated by DESeq2 is provided in tab-delimited txt format.
Supplementary files format and content: An RPKM-normalized bigwig file is provided for each sample.

source_name: bone marrow

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Libraries were prepared using the NEBNext Low Input RNA Library preparation kit (NEB, E6420) according to the manufacturer's protocol.

tag: strain

value: bone marrow

value: pro-B

value: Tnpo3fl/fl mb1Cre


title: case_103 850k methylation

tag: center

value: ipf

value: case

value: white

value: not hispanic or latino


title: MG_MACS_CON_P4_Rep1

value: microglia

value: CON


title: case_106 850k methylation

value: lung

value: m

value: hispanic


title: SAM51_m50_probing_4_igg

tag: treatment

value: A/H5N1 HA + MF59

value: Y


title: SAM51_r50_probing_4_igg


title: KO_pro-B_51

description: matrix column name: KO_pro-B_51


title: WT_pro-B_69

description: matrix column name: WT_pro-B_69

value: Tnpo3+/+ mb1Cre


title: SAM51_r10_probing_4_igg


title: case_102 850k methylation

value: UCSF

tag: dx


title: MGE_rep2

city: Bethesda

first: Timothy

last: Petros

address: 35 Convent Drive, Bg 35 Room 3B-1002

institute: NICHD

data_processing:
Libraries were sequenced with paired-end reads of 51 nucleotides
Valid interaction pairs were found by HiC-Pro pipeline and converted into cool and mcool files with higlass
Averages from replicates were used for visualization
Assembly: mm10
Supplementary files format and content: hic per sample

source_name: mouse embryonic forebrain

extract_protocol:
To recover embryonic tissue, dams were anesthetized with isoflurane and then euthanized by cervical dislocation. Embryos were removed from the uterus and kept in chilled artificial cerebrospinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Brains were extracted from E12.5 embryos, hemisected, microdissected to obtain the MGE, LGE, CGE and somatosensory cortex, and kept in ACSF. To collect whole cells, embryonic MGE, LGE, CGE and cortex tissue was incubated in 1 mg/mL Pronase (Roche #10165921001) in ACSF for 20 minutes at RT. Pronase solution was removed and 2 ml of reconstitution solution (1% fetal bovine serum + DNAse (1:10,000, Roche #47167280001)) in oxygenated ACSF was added. DNAse was not included in the reconsititution solution. Cells were triturated sequentially with fire-polished large, medium and small bore Pasteur pipettes to mechanically dissociate tissue.
After cell dissociation, 1 million cells per region were fixed with 1% formaldehyde (Thermo: 28908) made in 1 ml HBSS media. Fixation was carried out at room temperature on a nutator, for 10 mins, protected from light. To stop fixation, glycine was added at a final concentration of 0.13 M and samples were incubated for 5 mins 595 at room temperature followed by 15 mins on ice. Fixed cells were then washed once with ice-cold PBS. After spinning cells at 2500g 4oC for 5 mins, the pellet was flash frozen in liquid nitrogen and stored at -80oC. To perform Hi-C, pellets were first thawed on ice and then incubated with 1 ml lysis buffer (10 mM Tris-HCL pH8, 10 mM NaCl, 0.2% Igepal CA-630, Roche Complete EDTA-free Sigma #11836170001). After lysis, cells were dounced and washed with cold PBS. Nuclei extracted with this method were then collected by centrifugation and subjected to DpnII digest in 50 μl 0.5% SDS and incubated at 62oC for 10 minutes after which 150 μl of 1.5% Triton-X was added and cells incubated for 15 minutes at 37oC while shaking at 900 rpm. 25 μl of 10X DpnII restriction buffer (NEB) was then added, and cells were incubated for 15 minutes while shaking. After that, 200U of DpnII (NEB R0543M) were added and incubated for 2 hours, then 200U more and incubated overnight. Next morning 200U more were added and incubated for 3h (total 600U of DpnII). DpnII was inactivated at 62oC for 20 minutes. For Hi-C, biotin fill-in was done by incubating cells with a mixture of 4.5 μl dCTP dTTP and dGTP at 3.3 mM, 8 μl klenow polymerase (NEB M0210L) and 37.5 μl Biotin-14-dATP (Thermo 19524016) for 4h at RT while shaking at 900 rpm for 10 seconds every 5 minutes. Ligation was done overnight at 16oC also rotating at 900 rpm for 10 seconds every 5 minutes by adding 120 μl of 10X ligation buffer (NEB), 664 μl water, 100 μl 10% Triton-X, 6 μl BSA 20mg/ml, and 2 μl T4 ligase (NEB cat #M0202M). For Capture-C, biotin fill-in step was skipped and 50 μl more of water was added to the ligation mix. Crosslink removal was done overnight with 50 μl of proteinase K in 300 μl of following buffer (10 mM Tris-HCl pH8.0, 0.5 M NaCl, 1%SDS) while shaking at 1400 rpm at 65oC. Following Sodium Acetate and 100% Ethanol -80oC precipitation, DNA was resuspended in 50 μl 10 mM Tris HCL.   Sonication was done using Covaris onetube-10 AFA strips using the following parameters for a 300 bp fragment size (Duration: 10 secs, repeat for 12 times, total time 120 secs, peak power-20W, duty factor 40%, CPB-50). Sonications were performed in a Covaris ME220 sonicator. Sonicated material was then size selected using SPRI beads with the following ratios: 0.55X and 0.75X. Hi-C material was then bound, washed and recovered to 150 μl Streptavidin C1 beads (Thermo 65002) per sample following manufacturers recommendations. Bead-bound DNA was resuspended in 50 μl 10 mM Tris HCl. Library preparation was done using Kapa Hyper Prep KK8502 kit. 10 μl of End-repair buffer and enzyme mix were added to resuspended beads and incubated for 30 minutes at RT and then 30 minutes at 65oC. 1 μl of 15 mM annealed-Illumina adaptors, containing an universal p5 and an indexed p7 oligo, were then incubated with a mixture containing 40 μl of ligase and ligation buffer at RT for 60 minutes. Libraries were then amplified using 4 reactions per sample for a total of 200 μl and 10 cycles, as recommended by manufacturer.

value: Medial ganglionic eminence

value: wild-type

tag: developmental stage


title: LGE_rep2

value: Lateral ganglionic eminence


title: CTX_rep2

value: Cortex


title: control_101 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

tag: methylationid

tag: age


title: CTX_rep1


title: control_100 850k methylation

tag: Sex

value: f

value: white

value: not hispanic or latino

value: N


title: MG_MACS_CON_P4_Rep5

value: whole brain

value: microglia

value: CON


title: CGE_rep1

value: Caudal ganglionic eminence


title: CGE_rep2


title: SAM51_nop_probing_4_igg

tag: subject id

value: A/H5N1 HA + MF59

value: Y

value: no peptide


title: SAM15_r10_probing_4_igg


title: SAM51_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM15_r50_probing_4_igg


title: SAM15_nop_probing_4_igg


title: case_99 850k methylation

value: lung

value: UCSF

value: ipf

value: case

value: m

tag: race

value: unknown

tag: ethnicity

value: hispanic


title: E13.5 wt RLJK CAR151A24

city: London

first: Alessia

last: Caramello

state: London

address: The Francis Crick Institute, 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: E13.5 wt RLJK

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Genome_build: GRCm38 Ensembl release 89
Supplementary_files_format_and_content: table of normalized counts per gene  per sample obtained from DESeq

source_name: dissected archicortex

extract_protocol:
Archicortex were dissected, snap frozen in liquid nitrogen, and RNA was iextracted using RNeasy Plus Micro kit (Qiagen) and quantified with NanoDrop (Thermo Fisher Scientific)
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

value: mixed C57BL/6J;MF1


title: case_97 850k methylation

value: white

value: not hispanic or latino

value: N


title: MGE_rep1

value: Medial ganglionic eminence

value: wild-type


title: SAM15_m50_probing_4_igg

value: A/H5N1 HA + MF59

tag: day

tag: blocking

value: Mini HA -50ug/ml


title: control_94 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: E13.5 wt RLJK CAR151A22

description: E13.5 wt RLJK

tag: genotype


title: E12.5 wt RLFO CAR151A16

description: E12.5 wt RLFO


title: E13.5 mut RLJK CAR151A18

description: E13.5 mut RLJK


title: control_98 850k methylation

value: lung


title: case_96 850k methylation

value: UCSF

value: ipf

value: asian

value: Y


title: E13.5 wt RLJK CAR151A23

description: E13.5 wt RLJK


title: E13.5 mut RLJK CAR151A20

description: E13.5 mut RLJK


title: WT_pro-B_55

description: matrix column name: WT_pro-B_55

value: bone marrow

tag: cell type

value: pro-B

value: Tnpo3+/+ mb1Cre


title: E12.5 wt RLFO CAR151A14

description: E12.5 wt RLFO

value: mixed C57BL/6J;MF1


title: E13.5 wt RLJK CAR151A21

description: E13.5 wt RLJK


title: E12.5 wt RLFO CAR151A13

description: E12.5 wt RLFO


title: SAM24_nop_probing_4_igg

value: N

value: no peptide


title: LGE_rep1

value: Lateral ganglionic eminence

value: wild-type


title: case_93 850k methylation

value: case

value: f

value: white

value: not hispanic or latino


title: E12.5 wt RLFO CAR151A15

description: E12.5 wt RLFO


title: SAM24_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM24_r50_probing_4_igg


title: E12.5 mut RLFO CAR151A9

description: E12.5 mut RLFO


title: control_92 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m


title: SAM24_m50_probing_4_igg

value: Mini HA -50ug/ml


title: E13.5 wt RLFO CAR151A7

description: E13.5 wt RLFO


title: control_89 850k methylation


title: E12.5 mut RLFO CAR151A12

description: E12.5 mut RLFO


title: E13.5 mut RLJK CAR151A19

description: E13.5 mut RLJK


title: E13.5 mut RLJK CAR151A17

description: E13.5 mut RLJK


title: SAM24_m10_probing_4_igg

value: Mini HA-10ug/ml


title: E13.5 wt RLFO CAR151A6

description: E13.5 wt RLFO

value: mixed C57BL/6J;MF1


title: case_95 850k methylation

value: UCSF

value: ipf

value: Y


title: E12.5 mut RLFO CAR151A11

description: E12.5 mut RLFO


title: SAM54_m10_probing_4_igg


title: E12.5 mut RLFO CAR151A10

description: E12.5 mut RLFO


title: E13.5 mut RLFO CAR151A4

description: E13.5 mut RLFO


title: case_88 850k methylation


title: SAM54_r50_probing_4_igg


title: SAM15_m10_probing_4_igg

value: N


title: case_86 850k methylation

value: case


title: case_91 850k methylation

value: f


title: case_90 850k methylation

value: unknown

value: hispanic


title: E13.5 wt RLFO CAR151A8

description: E13.5 wt RLFO


title: MG_MACS_MIA_CTX_LPS_Rep1

value: brain frontal cortex

value: microglia

tag: group

value: MIA

value: LPS

value: male


title: control_85 850k methylation

tag: tissue

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino


title: SAM54_m50_probing_4_igg

value: A/H5N1 HA + MF59

value: Y

value: Mini HA -50ug/ml


title: case_84 850k methylation

value: UCSF

value: ipf

value: case

value: m


title: Trophoblast stem cell OL

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
Raw reads were mapped with vast-tools align v2.5.1
Genome_build: mm10
Supplementary_files_format_and_content: Files with raw read counts to each mouse gene in Ensembl v88 and cRPKMs.

molecule: polyA RNA

source_name: trophoblast stem cell

growth_protocol:
As described Tanaka et al. Science. 1998 Dec 11;282(5396):2072-5
TS were grown as described in Tanaka et al. Science. 1998 Dec 11;282(5396):2072-5 and XEN cells in Kunath et al. Development. 2005 Apr;132(7):1649-61.

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: OL


title: E13.5 mut RLFO CAR151A1

description: E13.5 mut RLFO

tag: strain

value: mixed C57BL/6J;MF1


title: E13.5 wt RLFO CAR151A5

description: E13.5 wt RLFO


title: Extraembryonic endoderm stem (XEN) cells JR

source_name: extraembryonic endoderm stem cell

growth_protocol:
As described Kunath et al. Development. 2005 Apr;132(7):1649-61
TS were grown as described in Tanaka et al. Science. 1998 Dec 11;282(5396):2072-5 and XEN cells in Kunath et al. Development. 2005 Apr;132(7):1649-61.

value: JR


title: E13.5 mut RLFO CAR151A2

description: E13.5 mut RLFO


title: E13.5 mut RLFO CAR151A3

description: E13.5 mut RLFO


title: SAM54_nop_probing_4_igg

source_name: serum

tag: treatment

value: no peptide


title: Placenta E13.5 Mbnl3 KO replicate 2 3'seq (Quantseq Reverse)

source_name: Foetal placenta

extract_protocol:
Rneasy plus Mini Kit (Qiagen)
QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen)

value: Mbnl3 KO


title: Trophoblast stem cell JR


title: Trophoblast stem cell FxL4


title: SAM02_nop_probing_4_igg

extract_protocol: The serum samples originated from future-use consenting participants of parallel avian A(H5N1)/Indonesia/05/2005 influenza vaccine mix and match studies involving MF59® and AS03 adjuvant, also known as DMID Protocols 10-0016 and 10-0017.

value: A/H5N1 HA + AS03

value: N


title: control_87 850k methylation

source_name: tissue-Explant

extract_protocol:
DNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen).  DNA integrity number (DIN) >5 were used.
1 ug of DNA was bisulfite treated using the Zymo EZ DNA Methylation kit, labeled and hybridized to Illumina Infinium Human MethylationEPIC BeadChip using standard protocols.

value: lung

tag: center

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control


title: Placenta E13.5 WT replicate 1 3'seq (Quantseq Reverse)

description: QuantSeq 3’ mRNA-Seq Library Prep Kit REV (Lexogen)

value: WT


title: Extraembryonic endoderm stem (XEN) cells DIZ6


title: Placenta E13.5 Mbnl3 KO replicate 1 3'seq (Quantseq Reverse)


title: case_81 850k methylation

tag: methylationid

value: f

value: unknown

value: hispanic


title: Placenta E13.5 WT replicate 2 3'seq (Quantseq Reverse)


title: SAM02_r50_probing_4_igg


title: Placenta E13.5 Mbnl2 KO replicate 2 3'seq (Quantseq Reverse)

value: Mbnl2 KO


title: SAM02_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_82 850k methylation

extract_protocol:
DNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen). Samples with RNA integrity number (RIN) and DNA integrity number (DIN) >5 were used.
1 ug of DNA was bisulfite treated using the Zymo EZ DNA Methylation kit, labeled and hybridized to Illumina Infinium Human MethylationEPIC BeadChip using standard protocols.

tag: age

value: white

value: not hispanic or latino

value: U


title: control_80 850k methylation

tag: Sex

value: m


title: case_83 850k methylation

value: UCSF

value: ipf

value: case

value: Y


title: Placenta E13.5 Mbnl2 KO replicate 1 3'seq (Quantseq Reverse)


title: Placenta E13.5 Mbnl2+Mbnl3 KO replicate 2 3'seq (Quantseq Reverse)

value: Mbnl2/Mbnl3 DKO


title: case_79 850k methylation

value: lung

value: N


title: SAM02_r10_probing_4_igg

tag: subject id

value: A/H5N1 HA + AS03


title: SAM02_m50_probing_4_igg

value: Mini HA -50ug/ml


title: Labryrinth E18.5 WT replicate 2 3'seq (Quantseq Reverse)

source_name: Labyrinth (placenta)

value: WT


title: Labryrinth E18.5 WT replicate 1 3'seq (Quantseq Reverse)


title: SAM04_nop_probing_4_igg

value: no peptide


title: SAM04_m10_probing_4_igg


title: case_78 850k methylation

value: f

tag: race


title: Labryrinth E18.5 Mbnl2 KO replicate 2 3'seq (Quantseq Reverse)

value: Mbnl2 KO


title: Labryrinth E18.5 Mbnl3 KO replicate 2 3'seq (Quantseq Reverse)

value: Mbnl3 KO


title: case_77 850k methylation

value: white

tag: ethnicity

value: not hispanic or latino


title: SAM04_m50_probing_4_igg

tag: day


title: Labryrinth E18.5 Mbnl3 KO replicate 1 3'seq (Quantseq Reverse)


title: control_76 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m


title: RNA-seq of labyrinth at E18.5 from WT mice, replicate 2


title: Labryrinth E18.5 Mbnl2+Mbnl3 KO replicate 1 3'seq (Quantseq Reverse)


title: SAM04_r10_probing_4_igg

value: Y

tag: blocking


title: RNA-seq of labyrinth at E18.5 from Mbnl3 KO mice, replicate 2

tag: genotype


title: case_75 850k methylation

value: UCSF

value: ipf

value: case

value: other

value: unknown


title: RNA-seq of labyrinth at E18.5 from WT mice, replicate 1

value: WT


title: SAM04_r50_probing_4_igg

value: A/H5N1 HA + AS03


title: control_74 850k methylation

value: lung

value: f

value: N


title: Labryrinth E18.5 Mbnl2+Mbnl3 KO replicate 2 3'seq (Quantseq Reverse)

value: Mbnl2/Mbnl3 DKO


title: Placenta E13.5 Mbnl2+Mbnl3 KO replicate 1 3'seq (Quantseq Reverse)


title: RNA-seq of labyrinth at E18.5 from Mbnl3 KO mice, replicate 1

value: Mbnl3 KO


title: RNA-seq of labyrinth at E18.5 from Mbnl2 KO mice, replicate 2

value: Mbnl2 KO


title: SAM62_m10_probing_4_igg

value: Mini HA-10ug/ml


title: Labryrinth E18.5 Mbnl2 KO replicate 1 3'seq (Quantseq Reverse)


title: case_73 850k methylation

value: white

value: not hispanic or latino


title: RNA-seq of labyrinth at E18.5 from Mbnl2/3 double KO mice, replicate 1


title: control_72 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m

value: Y


title: RNA-seq of labyrinth at E18.5 from Mbnl2 KO mice, replicate 1


title: case_71 850k methylation

value: UCSF

value: ipf

value: case


title: RNA-seq of placenta at E13.5 from WT mice, replicate 2

value: WT


title: SAM62_r50_probing_4_igg

value: A/H5N1 HA + AS03


title: case_70 850k methylation

value: lung


title: SAM62_r10_probing_4_igg


title: RNA-seq of placenta at E13.5 from Mbnl3 KO mice, replicate 1


title: RNA-seq of placenta at E13.5 from Mbnl3 KO mice, replicate 2


title: case_69 850k methylation

value: unknown

value: hispanic


title: SAM62_nop_probing_4_igg

value: no peptide


title: RNA-seq of placenta at E13.5 from Mbnl2 KO mice, replicate 2

value: Mbnl2 KO


title: control_68 850k methylation

value: f

value: white


title: RNA-seq of placenta at E13.5 from Mbnl2/3 double KO mice, replicate 2

value: Mbnl2/Mbnl3 DKO


title: RNA-seq of placenta at E13.5 from Mbnl2 KO mice, replicate 1


title: case_67 850k methylation

value: not hispanic or latino

value: N


title: SAM57_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM57_m10_probing_4_igg

value: Y

value: Mini HA-10ug/ml


title: RNA-seq of placenta at E13.5 from Mbnl2/3 double KO mice, replicate 1


title: RNA-seq of placenta at E11.5 from WT mice, litter PG

description: placentas from two litters


title: RNA-seq of labyrinth at E18.5 from Mbnl2/3 double KO mice, replicate 2


title: SAM62_m50_probing_4_igg

value: Mini HA -50ug/ml


title: RNA-seq of placenta at E11.5 from WT mice, litter MG

description: placentas from one litter


title: RNA-seq of placenta at E11.5 from WT mice, litter EG

description: placentas from one litter


title: SAM57_nop_probing_4_igg


title: RNA-seq of placenta at E13.5 from WT mice, replicate 1


title: RNA-seq of placenta at E11.5 from Mbnl3 KO mice, litter PG

description: placentas from two litters

value: Mbnl3 KO


title: SAM57_r10_probing_4_igg


title: case_65 850k methylation

value: UCSF

value: ipf

value: case

value: m


title: control_66 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: RNA-seq of placenta at E11.5 from Mbnl3 KO mice, litter MG

description: placentas from one litter


title: control_64 850k methylation

value: National Jewish

value: white


title: SAM57_m50_probing_4_igg


title: WT INPUT ChIP-seq biological replicate 1

first: Kayleigh

last: Bozon

address: 1 Midland Road

description: ChIP-seq

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters "-a AGATCGGAAGAGC -A AGATCGGAAGAGC --minimum-length=25 –quality-cutoff=20".
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the mouse mm10 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Duplicate marking was performed using the picard tool MarkDuplicates (version 2.1.1). Filtering was performed to exclude read pairs that were duplicates, discordant, mapped to different chromosomes, ambiguously mapped, insert size > 1kb, and had a mismatch > 1 in any read.
Genome_build: mm10
Supplementary_files_format_and_content: Genome-wide peak calling was performed with  MACS2 callpeak (version 2.1.1.20160309) (Zhang et al., 2008) with the parameters "--format BAMPE --gsize=hs --keep-dup all --cutoff-analysis". The annotatePeaks.pl program from HOMER (version 4.8) (Heinz et al., 2010) was used to annotate peaks relative to mm10 RefSeq features downloaded from the UCSC on 19th February 2016.
Supplementary_files_format_and_content: BedGraph coverage tracks representing the accessibility signal per million mapped paired-reads were generated using BEDTools genomeCoverageBed with the parameters “-bg -pc -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).

source_name: Trophoblast stem cells

growth_protocol: Trophoblast stem cells were maintained in MEF conditioned medium as described in Tanaka et al. 1998 (Science, 282, 2072-5).

extract_protocol:
Approximately 1x10^8 adherent cells were fixed in 4% PFA for 9 min at room temperature, washed in PBS + protease inhibitors and detached using cell scrapers. Processing was performed using a modified Xenopus protocol (Methods Mol Biol. 2017;1507:23-42). Nuclei were isolated in cell lysis buffer (10mM Tris-HCl pH8, 10mM NaCl, 0.2% IGEPAL CA-630) and pelleted. To sheer chromatin, pellets were resuspended in CEWB1 buffer (10mM Tris-HCl pH8, 150mM NaCl, 1mM EDTA, 0.1% SDS, 0.25% sodium deoxycholate, 1% IGEPAL CA-630) and sonicated using a covaris S220 Focused-ultrasonicator: duty cycle = 5%, intensity = 4, cycles/burst = 200, procedure time = 420 seconds, temperature = <8°C.
Reverse cross-linking of ChIP and input samples were performed as described previously (Methods Mol Biol. 2017;1507:23-42), purified using QIAquick PCR purification kit and concentrations determined using the QubitTM dsDNA HS Assay. Paired-end library prep was according to the Gentsch and Smith, 2017 (Methods Mol Biol. 2017;1507:23-42). Libraries were sequenced as paired-end, 101bp reads on the Illumina High-Seq 2500 platform (Francis Crick Institute).

value: wild-type

tag: timepoint


title: SAM48_r50_probing_4_igg

value: N


title: WT CDX2 IP ChIP-seq biological replicate 2

description: ChIP-seq

tag: chip antibody

value: CDX2 (Bethyl Laboratories, A300-691A)


title: WT CDX2 IP ChIP-seq biological replicate 1

description: ChIP-seq


title: case_63 850k methylation

data_processing:
For DNA, Illumina idat signal intensity files were processed using SeSAMe; within-sample normalization with out-of-band probes and dye bias correction were performed {Zhou, 2018, 30085201}. Probes containing a SNP site in our genetic dataset as well as probes with non-unique mapping and off-target hybridization were removed. Additionally, probes with an average detection P value >= .05 across samples and sex chromosome probes were removed prior to analysis.
For DNA methylation, final methylation beta values are included as a processed data file.

tag: tissue

value: not hispanic or latino

value: Y


title: RNA-seq of placenta at E11.5 from Mbnl3 KO mice, litter EG

description: placentas from one litter


title: SAM48_m50_probing_4_igg

data_processing:
Spot and background intensities were measured using an annotated grid (gal) file. For ArrayCamTM a number of different settings were used to attempt to obtain readings. Microarray spot intensities were quantified using software ArrayCamTM (Grace Bio-Labs) utilizing automatic local background subtraction for each spot. The generated signal intensity values were considered raw values.
Prior to the analysis, systematic intensity differences in background reactivity as measured by phosphate buffered saline with tween 20 (PBST) were corrected. This was achieved by subtracting the median raw intensity signal for the 24 PBST intensity measurements for a certain array from the array’s non-PBST antigen intensities. Following background correction, for intensities < 1, an intensity value of 1 was imputed. Global outliers based on PCA and MDS plots were removed.

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: Untransfected biological replicate 3 library 3

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1) (Martin M, 2011) with parameters "-a CTGTCTCTTATA -A CTGTCTCTTATA --minimum-length=25 –quality-cutoff=20".
BWA (version 0.6.2) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the mouse mm10 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Read group addition, duplicate marking and insert size assessment was performed using the picard tools AddOrReplaceReadGroups, MarkDuplicates and CollectMultipleMetrics, respectively (version 2.1.1) (http://broadinstitute.github.io/picard).
Reads mapped to mitochondrial DNA were removed using the pairToBed command from BEDTools (version 2.26.0-foss-2016b) (Quinlan & Hall, 2010). Additional filtering was performed to only include uniquely mapped, properly-paired reads with insert size <= 1kb, and mismatches <= 1 in both reads. SAMtools (version 1.3.1) (Li et al., 2009) was used for bam file sorting and indexing.
The filtered alignments from each library were merged at the condition-level using the picard MergeSamFiles command. Duplicate marking and removal was reperformed on the merged alignments.
Genome_build: mm10
Supplementary_files_format_and_content: Genome-wide peak calling at the condition-level was performed with  MACS2 callpeak (version 2.1.1.20160309) (Zhang et al., 2008) with the parameters "--format BAMPE --gsize=mm --keep-dup all --no-model --broad". The annotatePeaks.pl program from HOMER (version 4.8) (Heinz et al., 2010) was used to annotate peaks relative to mm10 RefSeq features downloaded from the UCSC on 19th February 2016.
Supplementary_files_format_and_content: BedGraph coverage tracks representing the accessibility signal per million mapped reads were generated at the condition-level using BEDTools genomeCoverageBed with the parameters “-bg -pc -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).

extract_protocol:
Cells were dissociated using TrypLE, clumps removed using cell strainers and pelleted. Transfected (mCherry positive) and untransfected (mCherry negative) resuspended cells were isolated by fluorescent activated cell sorting (FACS). Cells were pelleted, washed in PBS and resuspended in lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After a 10min centrifugation at 4 C, nucleic extracts were resuspended in transposition buffer for 1 hour at 37 C and purified using a QIAGEN PCR Purification kit following manufacturer’s instructions.
Eluted transposed DNA was amplified by PCR with Nextera primers to generate single-indexed libraries. A maximum of 12 cycles of PCR was used to prevent saturation biases

treatment_protocol: Cells were incubated with shRNA vectors and jetPRIME transfection reagent for 4 hours; after which the medium was aspirated and fresh medium added and cells cultured for a further 44 hours.

value: Untransfected, sorted by FACs


title: Untransfected biological replicate 3 library 2

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: Untransfected biological replicate 3 library 1

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: case_61 850k methylation

value: ipf

value: f


title: SAM48_m10_probing_4_igg

value: Mini HA-10ug/ml


title: Untransfected biological replicate 2 library 1

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: Untransfected biological replicate 2 library 2

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: SAM48_r10_probing_4_igg


title: control_60 850k methylation

value: lung

value: m


title: Untransfected biological replicate 1 library 3

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: SAM48_nop_probing_4_igg

value: no peptide


title: Untransfected biological replicate 2 library 3

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: Untransfected biological replicate 1 library 2

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig


title: SAM26_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: case_58 850k methylation

value: UCSF

value: case


title: Untransfected biological replicate 1 library 1

description:
ATAC-seq
UT.broadPeak.gz
UT.bigWig

value: wild-type


title: control_57 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white


title: Scrambled positive biological replicate 3 library 3

description:
ATAC-seq
SCR_POS.broadPeak.gz
SCR_POS.bigWig

value: Transfected with scrambled shRNA (mCherry positive), sorted by FACS


title: Scrambled positive biological replicate 3 library 2


title: case_59 850k methylation

value: National Jewish

value: not hispanic or latino

value: N


title: control_62 850k methylation


title: SAM26_r50_probing_4_igg


title: case_56 850k methylation

value: ipf

value: f


title: Scrambled positive biological replicate 3 library 1


title: Scrambled positive biological replicate 2 library 3


title: control_55 850k methylation

value: lung


title: SAM26_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_54 850k methylation

value: m

value: unknown

value: hispanic

value: Y


title: Scrambled positive biological replicate 2 library 1

value: wild-type


title: Scrambled positive biological replicate 1 library 3


title: Scrambled positive biological replicate 1 library 2


title: SAM26_m10_probing_4_igg

value: A/H5N1 HA + MF59

value: Mini HA-10ug/ml


title: Scrambled positive biological replicate 1 library 1


title: Scrambled negative biological replicate 3 library 3

description:
ATAC-seq
SCR_NEG.broadPeak.gz
SCR_NEG.bigWig

value: Non-transfected scrambled shRNA (mCherry negative), sorted by FACS


title: control_53 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: black


title: Scrambled negative biological replicate 3 library 2


title: SAM86_r10_probing_4_igg


title: Scrambled negative biological replicate 3 library 1


title: Scrambled negative biological replicate 2 library 2


title: SAM86_r50_probing_4_igg


title: control_51 850k methylation

value: white

value: not hispanic or latino

value: N


title: Scrambled negative biological replicate 2 library 3


title: Scrambled negative biological replicate 2 library 1


title: case_52 850k methylation

value: lung

value: UCSF

value: ipf

value: case

value: other


title: SAM86_nop_probing_4_igg

value: Y

value: no peptide


title: SAM26_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: Scrambled negative biological replicate 1 library 2

value: wild-type


title: Scrambled negative biological replicate 1 library 1

value: Non-transfected scrambled shRNA (mCherry negative), sorted by FACS


title: Scrambled positive biological replicate 2 library 2

value: Transfected with scrambled shRNA (mCherry positive), sorted by FACS


title: SAM86_m50_probing_4_igg

value: Mini HA -50ug/ml


title: Cdx2 knockdown positive biological replicate 3 library 3

description:
ATAC-seq
KD_POS.broadPeak.gz
KD_POS.bigWig

value: Transfected with shRNA targetting Cdx2 (mCherry postive), sorted by FACS


title: case_49 850k methylation

value: m


title: Scrambled negative biological replicate 1 library 3


title: control_50 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f

value: white


title: SAM86_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_48 850k methylation

value: lung

value: not hispanic or latino

value: N


title: SAM72_m10_probing_4_igg

value: A/H5N1 HA + PBS


title: Cdx2 knockdown positive biological replicate 3 library 1


title: Cdx2 knockdown positive biological replicate 2 library 3


title: case_47 850k methylation

value: UCSF

value: ipf

value: case

value: Y


title: Cdx2 knockdown positive biological replicate 3 library 2

value: wild-type


title: Cdx2 knockdown positive biological replicate 2 library 1

value: Transfected with shRNA targetting Cdx2 (mCherry postive), sorted by FACS


title: Cdx2 knockdown positive biological replicate 2 library 2


title: SAM72_r50_probing_4_igg


title: case_45 850k methylation

value: m

value: other

value: unknown


title: Cdx2 knockdown positive biological replicate 1 library 2


title: SAM72_r10_probing_4_igg


title: Cdx2 knockdown positive biological replicate 1 library 1


title: SAM72_nop_probing_4_igg

value: no peptide


title: control_44 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: SAM72_m50_probing_4_igg

value: Mini HA -50ug/ml


title: T4.Tfh.LCMV.d41.Sp#1

city: La Jolla

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Tophat
HT-Seq Count
DESeq from BioConductor
Genome_build: UCSC mm10
Supplementary_files_format_and_content: gct

source_name: D41 Spleen SMARTA SLAMlo CXCR5hi

extract_protocol:
Total RNA was extracted in TRIZoL reagent
PrepX RNA-seq library preperation kit (Integenex)

value: 6-16 Weeks

value: Spleen


title: T4.Th1.LCMV.d41.Sp#1

source_name: D41 Spleen SMARTA SLAMhi CXCR5lo


title: T4.Th1.LCMV.d41.Sp#2


title: T4.Tfh.LCMV.d41.Sp#2


title: control_42 850k methylation

value: lung

value: white

value: not hispanic or latino


title: SAM49_r10_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: SAM49_m50_probing_4_igg


title: T4.Tfh.LCMV.d21.Sp#4

source_name: D21 Spleen SMARTA SLAMlo CXCR5hi


title: case_43 850k methylation

value: UCSF

value: ipf

value: case

value: Y


title: T4.Tfh.LCMV.d21.Sp#5


title: case_41 850k methylation

value: m

value: unknown

value: hispanic


title: case_46 850k methylation


title: SAM49_r50_probing_4_igg


title: T4.Tfh.LCMV.d21.Sp#2


title: Cdx2 knockdown positive biological replicate 1 library 3

value: wild-type

value: Transfected with shRNA targetting Cdx2 (mCherry postive), sorted by FACS


title: SAM49_nop_probing_4_igg

value: no peptide


title: T4.Tfh.LCMV.d21.Sp#1

value: 6-16 Weeks


title: SAM54_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: T4.Tfh.LCMV.d7.Sp#4

source_name: D7 Spleen SMARTA SLAMlo CXCR5hi

value: Spleen


title: SAM60_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: case_40 850k methylation

value: lung


title: T4.Th1.LCMV.d21.Sp#1

source_name: D21 Spleen SMARTA SLAMhi CXCR5lo


title: case_39 850k methylation

value: f

value: other


title: T4.Tfh.LCMV.d7.Sp#2


title: case_38 850k methylation

source_name: tissue-Unknown

value: National Jewish

value: white

value: N


title: case_37 850k methylation

value: ipf

value: case

value: not hispanic or latino

value: Y


title: SAM60_nop_probing_4_igg


title: SAM60_r50_probing_4_igg


title: case_36 850k methylation

value: m


title: T4.Tfh.LCMV.d21.Sp#3


title: case_35 850k methylation


title: T4.Tfh.LCMV.d7.Sp#3


title: T4.Tfh.LCMV.d7.Sp#1


title: T4.Th1.LCMV.d21.Sp#2


title: SAM60_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM60_m10_probing_4_igg

value: Mini HA-10ug/ml


title: T4.Th1.LCMV.d21.Sp#3

value: 6-16 Weeks


title: T4.Th1.LCMV.d7.Sp#2

source_name: D7 Spleen SMARTA SLAMhi CXCR5lo


title: T4.TN.SM.Sp#3

source_name: Naïve SMARTA


title: case_34 850k methylation


title: T4.Th1.LCMV.d7.Sp#1


title: control_33 850k methylation

value: normal

value: control


title: T4.Th1.LCMV.d30.Id3Low.Sp#3

value: Spleen


title: case_32 850k methylation

value: lung

value: Vanderbilt


title: SAM90_m10_probing_4_igg

value: A/H5N1 HA + MF59


title: T4.Th1.LCMV.d7.Sp#5


title: SAM90_nop_probing_4_igg

value: no peptide


title: SAM90_r10_probing_4_igg


title: T4.Th1.LCMV.d30.Id3High.Sp#3


title: T4.Th1.LCMV.d30.Id3Low.Sp#2


title: T4.Th1.LCMV.d7.Sp#4


title: T4.Th1.LCMV.d30.Id3High.Sp#2


title: T4.Th1.LCMV.d7.Sp#3


title: case_31 850k methylation

value: white


title: T4.Th1.LCMV.d30.Id3High.Sp#1


title: T4.TN.SM.Sp#5


title: SAM90_r50_probing_4_igg

value: N


title: T4.Tfh.LCMV.d30.Id3Low.Sp#3


title: T4.Tfh.LCMV.d30.Id3Low.Sp#1


title: SAM90_m50_probing_4_igg


title: T4.Tfh.LCMV.d30.Id3High.Sp#3


title: control_28 850k methylation

value: UCSF

value: black

value: unknown


title: case_29 850k methylation

value: ipf

value: case

value: not hispanic or latino

value: Y


title: SAM47_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: T4.Tfh.LCMV.d30.Id3High.Sp#2

value: 6-16 Weeks


title: T4.Tfh.LCMV.d30.Id3Low.Sp#2

value: Spleen


title: case_27 850k methylation

value: lung

value: m


title: SAM47_nop_probing_4_igg


title: T4.Tfh.LCMV.d30.Id3High.Sp#1


title: T4.Th1.LCMV.d30.Id3Low.Sp#1


title: SAM47_r10_probing_4_igg


title: SAM47_r50_probing_4_igg


title: control_30 850k methylation

value: normal

value: control

value: f


title: case_25 850k methylation

value: Vanderbilt

value: white

value: N


title: control_26 850k methylation

value: UCSF

value: black

value: unknown


title: 25EG2-16B-1001

city: Ramat Gan

first: Avigail

last: Rein

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center

data_processing:
Reads were trimmed using cutadapt
After trimming, the reads were mapped to the Mouse genome (GRCm38) using STAR  v2.4.2a (using options alignEndsType EndToEnd and outFilterMismatchNoverLmax set to 0.04)
Counting proceeded over genes annotated in Ensembl release 92, using htseq-count (version 0.6.1p1)
Normalization and differential expression was performed using DESeq2 (Version 1.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed files include raw counts.

source_name: Fetal liver E14.5 lineage negative cells

extract_protocol:
Femur and tibia of 6-8 week old mice were harvasted and flashed on ice. Fetal livers of 14.5E fetuses were harvasted, purified and crushed into single cells on ice. Lineage negative cells were generated using miltenyi magnetic beads. RNA was obtained using Trizole reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ERG/Gata2 heterozygote


title: 15ERG-5A-2712

value: ERG

value: Fetal liver E14.5 lineage negative cells


title: 18EG2-14B-1001


title: 23EG2-12B-2712


title: SAM47_m10_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA-10ug/ml


title: 22EG2-2A-2712


title: case_24 850k methylation

first: Ivana

last: Yang

value: ipf

value: case

value: not hispanic or latino

value: Y


title: case_23 850k methylation

value: lung

value: m


title: SAM06_m50_probing_4_igg

first: Johannes

last: Goll

value: Mini HA -50ug/ml


title: 16ERG-10B-2712


title: 9G2-19C-2712

value: Gata2 heterozygote (Gata2+/-)


title: control_22 850k methylation

value: normal

value: control

value: f

value: hispanic

value: N


title: SAM06_r10_probing_4_igg


title: SAM06_r50_probing_4_igg


title: 12G2-1A-143


title: 11G2-12B-1001


title: 8G2-9B-2712


title: 26EG2-2A-143

value: ERG/Gata2 heterozygote


title: case_21 850k methylation

value: Vanderbilt

value: white


title: 1WT-16C-2712

value: WT

value: Fetal liver E14.5 lineage negative cells


title: 2WT-18C-2712


title: case_20 850k methylation

value: ipf

value: case


title: 5WT-6A-143


title: 19ERG-4A-143

value: ERG


title: SAM06_m10_probing_4_igg

value: A/H5N1 HA + PBS

value: Y

value: Mini HA-10ug/ml


title: control_19 850k methylation

value: lung

value: UCSF

value: m

value: black

value: unknown


title: 4WT-17B-1001


title: EG2_23_422

source_name: lineage negative bone marrow progenitors

value: 6-8 weeks


title: SAM67_r50_probing_4_igg


title: control_17 850k methylation

value: normal

value: control

value: hispanic


title: EG2_22_402

value: ERG/Gata2 heterozygote

value: lineage negative bone marrow progenitors


title: case_18 850k methylation

value: Vanderbilt

value: ipf

value: white

value: not hispanic or latino


title: SAM67_r10_probing_4_igg

value: A/H5N1 HA + PBS

value: Y


title: EG2_19_390


title: erg_18_420

value: ERG


title: erg_16_421


title: EG2_20_385


title: EG2_21_396


title: SAM67_nop_probing_4_igg

value: no peptide


title: erg_17_419


title: SAM67_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_16 850k methylation

value: lung

value: case

value: m


title: case_15 850k methylation


title: case_14 850k methylation

value: UCSF


title: erg_14_400

value: 6-8 weeks


title: G2_12_807

value: Gata2 heterozygote (Gata2+/-)


title: G2_11_398


title: control_13 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f

value: N


title: SAM55_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM06_nop_probing_4_igg

value: A/H5N1 HA + PBS


title: G2_10_403

value: lineage negative bone marrow progenitors


title: SAM55_r50_probing_4_igg

value: Y


title: G2_9_413


title: case_11 850k methylation

value: ipf

value: white

value: not hispanic or latino


title: control_12 850k methylation

value: lung


title: SAM55_nop_probing_4_igg

value: no peptide


title: G2_7_389


title: SAM67_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_9 850k methylation

value: UCSF

value: case

value: m


title: erg_13_387

value: 6-8 weeks

value: ERG


title: wt_6_457

value: WT


title: erg_15_391


title: SAM55_m50_probing_4_igg

value: Mini HA -50ug/ml


title: G2_8_388

value: Gata2 heterozygote (Gata2+/-)


title: control_10 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: N


title: wt_5_401

value: lineage negative bone marrow progenitors


title: SAM55_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Y


title: case_8 850k methylation

value: lung

value: ipf

value: white

value: not hispanic or latino


title: SAM77_m50_probing_4_igg

value: A/H5N1 HA + PBS


title: wt_1_386

value: 6-8 weeks


title: case_7 850k methylation

value: UCSF

value: case

value: m

value: White


title: mES_1Gy_4h_2

city: Leiden

first: Bharath

last: Sampadi

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description: molecule: BrU-labeled RNA

data_processing:
Illumina Casava v1.8.2 was used for basecalling.
Reads were mapped to the mouse ribosomal DNA complete repeating unit (GenBank BK000964.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1.
Reads that did not map to the ribosomal DNA were mapped to the mm9 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files for gene abundance measurements.  Columns are standard BED6 format columns - (1) chr, (2) start, (3) end, (4) name, (5) score (0 as palceholder), strand (6) - and the following additional columns: (7) gene length, (8) num features (introns/exons) in meta-gene, (9) effective length (sum of feature lengths, for measuring RPKM), (10) read counts, (11) density (reads per kb), (12) RPKM

source_name: mESC

growth_protocol: mESCs were cultured in 10-cm dishes (pre-coated with 0.1%(w/v) gelatin) and maintained in mESC medium – KnockOut DMEM 500 ml [Gibco 10829018] supplemented with  55 ml fetal calf serum, 5.5 ml Pen-strep [Gibco 15140122] , 5.5 ml Sodium Pyruvate [Gibco 11360070], 5.5 ml Glutamax [Gibco 35050061], 1.25 ml b-mercaptoethanol [Gibco 31350010] and 55 ml leukemia inhibitory factor (LIF) [Millipore ESG1107].

extract_protocol:
For Bru-seq experiments, we followed the previously published protocol from Paulsen et al., Methods, 2014. Briefly, bromouridine (BrU) was added to the culture media at a final concentration of 2mM and the dishes were returned to CO2 incubator at 37°C for 30 minutes to label the nascent RNA. Labeling was done in the last 30 minutes of the corresponding incubation times for each experiment. Cells were trypsinized, collected pellets were frozen in liquid nitrogen and stored at -80°C until use. From then on BrU-seq protocol was applied. Cell pellets were then lysed in Trizol, total RNA isolated, BrU-RNA was immunoprecipitated using anti-BrdU antibodies (BD Pharmingen, 555627), strand-specific DNA libraries were prepared with Illumina TruSeq kit [Illumina, RS-122-2001]. Samples were then deep sequenced using Illumina sequencing platform.
Library construction was performed according to the previously published protocol from Paulsen et al., Methods, 2014.
BrU-seq

treatment_protocol: 5-Bromo Uridine [Sigma Aldrich 850187-1G] was directly added to the culture dish with cells 30 minutes prior to trypsinization at a final concentration of 2mM. For BrU-seq experiments, first four passages were done on top of a monolayer of lethally irradiated mouse embryonic fibroblasts and the next three passages were done without feeders for a total of seven passages. Cells were irradiated with X-rays (YXLON  International) for 60 seconds at a dose rate of 0.1 Gy/min for low DNA damage (LD) and at a dose rate of 1 Gy/min for high DNA damage (HD).

tag: cell type

value: embryonic stem cells

tag: labelling agent

value: Bromouridine (BrU)