title: J1_shP400-3_H2AZ ChIP-seq

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_24.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

value: P400 Knock Down


title: J1_shNT_H2AZ ChIP-seq

status: Public on Jul 01 2018

type: SRA

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

country: USA

institute: University of California Irvine

description: side-by-side control of J1_shP400-3_H2AZ and J1_shZnhit1-3_H2AZ ChIP

library_source: genomic

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the mm9 genome using Bowtie v1.1.0; RNA-seq reads were aligned to mm9 genome using tophat v2.0.10
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples. The ChIP-seq profiles were normalized to 20,000,000 total tag numbers, and peaks were called at P ≤ 1 × 10−8.

molecule: genomic DNA

organism: Mus musculus

source_name: J1 cells

growth_protocol: J1 mouse ES cells were maintained in cell cultured dishes coated with 0.1 % (w/v) gelatin (Sigma) without feeders in ESC media [Dulbecco’s modified Eagle’s medium (DMEM, Cellgro) supplemented with 15 % Stasis™ Stem Cell Qualified Fetal Bovine Serum (Gemini), 100 U/ml penicillin, 100 µg/ml streptomycin, 292 µg/ml L-glutamine, 0.1 mM β-mercaptoethanol and 1000 U/mL leukemia inhibitory factor (LIF, ESGRO, Millipore, USA)]. mESCs were plated on 96 well ultra-low attachment round bottom plate (Corning) at 1,000 cells /well in ES cell medium without LIF. Media was changed every other day and every day before and after day 9, respectively. Undifferentiated mESCs cultured in with LIF on gelatin-coated dish, are considered as EB day 0.

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_23.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

treatment_protocol: For infections, J1 cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene for 14 hr. After 48 hr, the infected cells were selected with puromycin (1 µg/ml) or blasticidin (5 µg/ml) for knockdown or overexpression experiments, respectively. All knockdown samples were harvested 8 days after infected with shRNA viruses.

tag: cell line

value: J1 mouse ES cells

tag: treatment

value: control vector

tag: antibody

value: H2AZ, Abcam, ab4174


title: Smad3-knockout bone marrow-derived macrophage [S3KO-M5]

city: Hong Kong

first: Hui-Yao

last: Lan

address: Prince of Wales Hospital, Shatin, N.T.

department: Li Ka Shing Institute of Health Sciences, Department of Medicine & Therapeutics, CUHK-Shenzhen Research Institute

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Processed data file: Expression.matrix.RSEM.TPM.txt

library_source: transcriptomic

data_processing:
The raw reads were quality-checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Low quality reads and adapters were removed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
TPM were calculated for genes defined by the Ensembl (release 67) annotation using RSEM.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Expression.matrix.RSEM.TPM.txt: Tab-separated text file; expression matrix (TPM) for each sample.

molecule: total RNA

growth_protocol: The macrophages were differentiated from bone marrow cells by 50ng/ml M-CSF in DMEM/F12 medium with 10% FBS for 7 days.

extract_protocol:
Total RNA from a single-cell suspension was extracted by RNeasy Plus mini kit (Qiagen), and then prepared the cDNA following the SMART-seq2 protocol according to manufacturer’s instruction.
A total of 2 ng amplified cDNA products purified by 1 x Agencourt AMPure XP beads (Beckman Coulter) were subjected for library construction by TruePrepTM Mini DNA Sample Prep Kit (Vazyme Biotech).

treatment_protocol: The bone marrow-derived macrophages were further stimulated with 5ng/ml of TGF-beta1 in the above medium to undergo MMT process for additional 5 days.

tag: strain/background

tag: genotype/variation

tag: cell type

value: bone marrow-derived macrophages

value: Control


title: J1_Flag_Gas41_W93A ChIP-seq

description: ChIP-seq of Gas41 W93A mutant

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_21.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

value: No treatment

value: Flag, Sigma, F1804


title: Smad3-knockout bone marrow-derived macrophage [S3KO-M4]


title: Smad3-knockout bone marrow-derived macrophage [S3KO-M2]


title: Smad3-knockout bone marrow-derived macrophage [S3KO-M3]


title: TGF-beta1-treated Smad3-wildtype bone marrow-derived macrophage [S3WT-MMT4]


title: Smad3-knockout bone marrow-derived macrophage [S3KO-M1]


title: TGF-beta1-treated Smad3-wildtype bone marrow-derived macrophage [S3WT-MMT2]


title: TGF-beta1-treated Smad3-wildtype bone marrow-derived macrophage [S3WT-MMT1]


title: TGF-beta1-treated Smad3-wildtype bone marrow-derived macrophage [S3WT-MMT3]


title: Smad3-wildtype bone marrow-derived macrophage [S3WT-M5]


title: Smad3-wildtype bone marrow-derived macrophage [S3WT-M2]


title: Smad3-wildtype bone marrow-derived macrophage [S3WT-M3]


title: Smad3-wildtype bone marrow-derived macrophage [S3WT-M1]


title: Smad3-wildtype bone marrow-derived macrophage [S3WT-M4]


title: shCon_EB_D0_Rep2 RNA-seq

description: edgeR_shCon_EB_Day6_vs_shCon_EB_Day0.tsv

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the mm9 genome using Bowtie2 v2.1.0; RNA-seq reads were aligned to mm9 genome using tophat v2.0.10
Genome_build: mm9
ChIP-seq wig files were generated using MACS-1.4.2; Scores represent the ChIP-seq tag numbers; RNA-seq htseq file include differential significance across treatment and control and the tag numbers in all samples
Supplementary_files_format_and_content: ChIP-seq bigwig files reporting tag numbers. RNA-seq tsv files reporting differential significance and tag numbers.

source_name: shCon_EB_D0_Rep2, J1 cells

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit (Invitrogen). Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufactory manual.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

tag: genoype/variation

value: control


title: shCon_EB_D6_Rep3 RNA-seq

source_name: shCon_EB_D6_Rep3, J1 cells

tag: tissue

value: Embryoid Body Day 6 (differentiated from J1)


title: shCon_EB_D0_Rep3 RNA-seq

source_name: shCon_EB_D0_Rep3, J1 cells


title: shGas41-2_Rep2 RNA-seq

source_name: shGas41-2_Rep2, J1 cells

value: Gas41 Knock Down with shGas41-2

value: Gas41 KD


title: shCon_EB_D6_Rep2 RNA-seq

source_name: shCon_EB_D6_Rep2, J1 cells


title: shGas41-2_Rep1 RNA-seq

source_name: shGas41-2_Rep1, J1 cells


title: J1-shG4-H3K27me3 ChIP-seq

source_name: J1-shG4-H3K27me3, J1 cells

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

value: Gas41 Knock Down

tag: chip antibody

value: Millipore, 07-449


title: shCon_Rep2 RNA-seq

description:
edgeR_shGas41-1_vs_shCon.tsv
edgeR_shGas41-2_vs_shCon.tsv

source_name: shCon_Rep2, J1 cells


title: shGas41-1_Rep3 RNA-seq

source_name: shGas41-1_Rep3, J1 cells

value: Gas41 Knock Down with shGas41-1


title: J1-Flag-Gas41 ChIP-seq

source_name: J1-Flag-Gas41, J1 cells

value: Sigma, F1804


title: shGas41-1_Rep1 RNA-seq

source_name: shGas41-1_Rep1, J1 cells


title: J1-H3K14Ac ChIP-seq

source_name: J1-H3K14Ac, J1 cells

extract_protocol:
ChIP-seq were performed following the protocol: Using ChIP-seq technology to generate high-resolution profiles of histone modifications. O'Geen H, Echipare L, Farnham PJ. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_22.
ChIP analysis was performed as described previously (Li et al., 2014) with minor modification. In brief, cells were cross-linked with 1% formaldehyde for 10 min and stopped with 125 mM glycine for 5 min. Fixed cells were scraped from dishes and washed with PBS for 2 times. Cell pellets were resuspended with cell lysis buffer (5 mM PIEPES pH 8.0, 85 mM KCl, 1% NP-40) with protease inhibitor cocktail (Roche) and 10 mM phenylmethanesulfonyl fluoride (PMSF). After 20 min rotation in 4 °C, cell nuclei were pelleted by centrifugation. The nuclei were resuspended with nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) containing protease inhibitors and sonicated using Bioruptor Sonicator (Diagenode). Length of most sheared DNA fragments were between 100-400 base pairs. Sonicated chromatin contains approximately 20-30 μg of DNA were diluted 4 fold with dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.01% SDS) and were subjected to immunoprecipitation with 2–3 μg of antibodies overnight at 4 °C. Protein A/G beads (Millipore) were then added and incubated for 2 hr. The immunoprecipitates were washed twice with low-salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and high-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS) and then once with LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na-Deoxycholate). DNA was eluted with vigorously shaking in elution buffer (50 mM NaHCO3, 1% SDS) for 15 min and then reverse crosslink in the presence of 0.3M NaCl at 67 °C for 12 hr. DNA was purified using PCR purification kit (Qiagen) and analyzed by quantitative real-time PCR on the ABI 7500-FAST System using the Power SYBR Green PCR Master Mix (Applied Biosystems).
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000 or NextSeq 500.

value: Abcam, ab52946


title: J1-shG4-H3K4me3 ChIP-seq

source_name: J1-shG4-H3K4me3, J1 cells

value: Abcam, ab5850


title: shCon_Rep1 RNA-seq

source_name: shCon_Rep1, J1 cells

value: J1 mouse ES cells


title: J1-shG4-H2AZ ChIP-seq

source_name: J1-shG4-H2AZ, J1 cells

value: Abcam, ab4174


title: J1-shNT-H2AZ ChIP-seq

source_name: J1-shNT-H2AZ, J1 cells

value: control vector


title: J1-shNT-H3K4me3 ChIP-seq

source_name: J1-shNT-H3K4me3, J1 cells


title: J1-shNT-H3K27Ac ChIP-seq

source_name: J1-shNT-H3K27Ac, J1 cells

value: Abcam, ab4729


title: 691-A007412_1_1

city: New York

first: Angela

last: Yoon

state: NY

address: 630 West 168th Street, PH15W-1562

institute: Columbia University Medical Center

description: Passed Quality Control

data_processing:
Library strategy: HTG Edge-Seq
Illumina CASAVA is used for base calling and generation of FASTQ files
HTG EdgeSeq Parser software (version 10196100G) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using negative process control probes (ANT plant gene).  Counts are transformed to log2(counts per million) following Law et al. 2004.  Samples are removed if the average expression of negative process control probes is greater than 1.77 after log2 cpm tranformation.
Genome_build: The FASTA file used for read alignment is proprietary to HTG and was not available at the time of submission of the GEO records. The submitter states that this file will be included on the GEO records upon publication of the manuscript.
Supplementary_files_format_and_content: csv file with raw counts.

organism: Homo sapiens

source_name: Oral cancer tissue

extract_protocol:
HTG EdgeSeq WT-miRNA Assay (Tucson, Arizona)
Tumor samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples were quantified in triplicate.

value: Oral Mucosa

tag: diagnosis

value: OSCC

tag: poor vs favorable prognosis

value: Poor Px


title: 691-A007411_1_1

description: Passed Quality Control


title: 691-A007410_1_1

description: Passed Quality Control


title: 691-A007409_1_1

description: Passed Quality Control


title: 691-A007408_1_1

description: Passed Quality Control


title: 691-A007406_1_1

description: Passed Quality Control


title: 691-A007404_1_1

description: Passed Quality Control


title: 691-A007405_1_1

description: Passed Quality Control


title: 691-A007407_1_1

description: Passed Quality Control


title: shGas41-1_Rep2 RNA-seq

source_name: shGas41-1_Rep2, J1 cells


title: 691-A007401_1_1

description: Failed Quality Control


title: 691-A007403_1_1

description: Passed Quality Control


title: 691-A007402_1_1

description: Passed Quality Control


title: 691-A007399_1_1

description: Passed Quality Control


title: shCon_Rep3 RNA-seq

source_name: shCon_Rep3, J1 cells

value: control


title: J1-shNT-H3K27me3 ChIP-seq

source_name: J1-shNT-H3K27me3, J1 cells


title: 691-A007392_1_1

description: Passed Quality Control


title: 691-A007391_1_1

description: Passed Quality Control


title: 691-A007395_1_1

description: Passed Quality Control


title: 691-A007394_1_1

description: Failed Quality Control


title: 691-A007400_1_1

description: Passed Quality Control


title: 691-A007398_1_1

description: Passed Quality Control


title: 691-A007387_1_1

description: Passed Quality Control


title: 691-A007396_1_1

description: Passed Quality Control


title: 691-A007390_1_1

description: Passed Quality Control


title: 691-A007397_1_1

description: Passed Quality Control


title: 691-A007389_1_1

description: Failed Quality Control


title: 691-A007384_1_1

description: Failed Quality Control


title: 691-A007385_1_1

description: Passed Quality Control


title: 691-A007388_1_1

description: Passed Quality Control


title: 691-A007386_1_1

description: Failed Quality Control


title: 691-A007382_1_1

description: Passed Quality Control


title: 691-A007379_1_1

description: Passed Quality Control


title: 691-A007393_1_1

description: Passed Quality Control


title: 691-A007377_1_1

description: Passed Quality Control


title: 691-A007378_1_1

description: Passed Quality Control


title: 691-A007375_1_1

description: Passed Quality Control


title: 691-A007371_1_1

description: Passed Quality Control


title: 691-A007376_1_1

description: Passed Quality Control


title: 691-A007374_1_1

description: Passed Quality Control


title: 691-A007383_1_1

description: Passed Quality Control


title: 691-A007369_1_1

description: Passed Quality Control


title: 691-A007372_1_1

description: Passed Quality Control


title: 691-A007373_1_1

description: Passed Quality Control


title: 691-A007370_1_1

description: Passed Quality Control


title: 691-A007367_1_1

description: Passed Quality Control


title: 691-A007368_1_1

description: Passed Quality Control


title: 691-A007366_1_1

description: Passed Quality Control


title: 691-A007364_1_1

description: Passed Quality Control


title: 690-A007462_1_1

description: Passed Quality Control

value: Favorable Px


title: 691-A007380_1_1

description: Failed Quality Control


title: 691-A007381_1_1

description: Passed Quality Control


title: 691-A007363_1_1

description: Passed Quality Control


title: 690-A007458_1_1

description: Passed Quality Control


title: 690-A007461_1_1

description: Failed Quality Control


title: 690-A007457_1_1

description: Passed Quality Control


title: 690-A007459_1_1

description: Passed Quality Control


title: 691-A007365_1_1

description: Passed Quality Control


title: 690-A007454_1_1

description: Passed Quality Control


title: 690-A007453_1_1

description: Passed Quality Control


title: 690-A007452_1_1

description: Passed Quality Control


title: 690-A007449_1_1

description: Passed Quality Control


title: 690-A007448_1_1

description: Passed Quality Control


title: 690-A007450_1_1

description: Passed Quality Control


title: 690-A007456_1_1

description: Passed Quality Control


title: 690-A007447_1_1

description: Passed Quality Control


title: 690-A007451_1_1

description: Passed Quality Control


title: 690-A007442_1_1

description: Passed Quality Control


title: 690-A007443_1_1

description: Passed Quality Control


title: 690-A007460_1_1

description: Passed Quality Control


title: 690-A007446_1_1

description: Passed Quality Control


title: 690-A007441_1_1

description: Passed Quality Control


title: 690-A007445_1_1

description: Passed Quality Control


title: 690-A007440_1_1

description: Passed Quality Control


title: 690-A007436_1_1

description: Passed Quality Control


title: 690-A007437_1_1

description: Passed Quality Control


title: 690-A007438_1_1

description: Passed Quality Control


title: 690-A007434_1_1

description: Passed Quality Control


title: 690-A007435_1_1

description: Failed Quality Control


title: 690-A007455_1_1

description: Passed Quality Control


title: 690-A007427_1_1

description: Passed Quality Control


title: 690-A007444_1_1

description: Passed Quality Control


title: 690-A007428_1_1

description: Passed Quality Control


title: 690-A007425_1_1

description: Passed Quality Control


title: 690-A007426_1_1

description: Passed Quality Control


title: 690-A007429_1_1

description: Passed Quality Control


title: 690-A007423_1_1

description: Passed Quality Control


title: 690-A007422_1_1

description: Passed Quality Control


title: 690-A007421_1_1

description: Passed Quality Control


title: OHara_sample_141

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: adaptors: PrefixNX/1: AGATGTGTATAAGAGACAG; PrefixNX/2: AGATGTGTATAAGAGACAG; Transposase1: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG; Transposase2: GTCTCGTGGGCTCGGAGATGTGTATAAGAGAC

data_processing:
Sequences were trimmed of adaptor sequences using Trimmomatic version 0.34, allowing for 2 mismatches and a palindromic clip threshold of 30. In addition, we trimmed off leading and trailing bases with quality < 3, as well as read trimming based on a sliding window of length 4 and average quality < 15. Any trimmed read < 36 bases was excluded. We then aligned against a de novo transcriptome (generated using the Trinity assembler) using the salmon aligner, version 0.6.1, in quasi-mapping mode with the variational Bayesian EM algorithm.
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per transcript for each sample. The first column contains the Trinity transcript identifier, and the remaining columns are counts for each transcript per sample.

organism: Eumetopias jubatus

source_name: Whole blood

extract_protocol:
Whole blood collected in PaxGene™ RNA tubes were placed in a cooler with ice until transport back to the ship, at which point they were kept in the freezer at approximately -15°C. Upon return to UAF the samples were placed in a -80°C freezer and then shipped to the University of Washington Center for Exposures, Diseases, Genomics and Environment in insulated shipping containers with dry ice and subsequently stored at -80°C until extraction. Total RNA was extracted using the PaxGene™ Blood RNA Kit according to the manufacturer’s protocol. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California).  RNA quantity was determined by measuring OD260 with a Thermo Scientific NanoDrop™ 1000 Spectrophotometer (Thermo Fisher Scientific, Inc.; Wilmington, DE).
Total RNA is quantified using the Quanti-iT RNA Assay Kit and RIN scores are confirmed using the Agilent 2100 Bioanalyzer.  A Perkin Elmer Janus workstation is used to normalize library construction input to 1ug per sample.  Next-generation sequencing libraries are prepared in an automated, high-throughput format using the TruSeq Stranded mRNA kit.  All the steps required for library construction have been automated and are performed on a Sciclone NGSx Workstation. During library construction, ribosomal RNA is depleted by means of poly-A enrichment and first and second strand cDNA syntheses are performed.  Each library is then uniquely barcoded using the Illumina adapters and amplified using a total of 13 cycles of PCR. After amplification and cleanup, library concentrations are determined using the Quant-iT dsDNA High Sensitivity Assay.  Library fragment lengths are confirmed using the Agilent 2100 Bioanalzyer.  Barcoded libraries are subsequently normalized and pooled based on quantification values.  Clustering, followed by massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides are carried out on the NextSeq instrument, achieving PE100 reads on a High Output flow cell.  Base calls are generated in real-time by the instrument.  Our read processing pipeline demultiplexes the reads and fastq files are produced by Picard.

value: whole blood

tag: mercury level

value: Low THg

tag: Sex

value: Male

tag: [thg] (ppb, ww)

tag: body condition

tag: mass (kg)


title: OHara_sample_154


title: OHara_sample_115


title: 690-A007419_1_1

description: Passed Quality Control


title: 690-A007417_1_1

description: Passed Quality Control


title: 690-A007439_1_1

description: Passed Quality Control


title: 690-A007420_1_1

description: Passed Quality Control


title: OHara_sample_139

value: High THg


title: OHara_sample_113


title: 690-A007418_1_1

description: Passed Quality Control


title: 690-A007433_1_1

description: Passed Quality Control


title: 690-A007416_1_1

description: Passed Quality Control


title: 690-A007431_1_1

description: Passed Quality Control


title: 690-A007432_1_1

description: Passed Quality Control


title: 690-A007430_1_1

description: Passed Quality Control


title: OHara_sample_145


title: 690-A007424_1_1

description: Passed Quality Control


title: OHara_sample_121


title: 690-A007415_1_1

description: Passed Quality Control


title: 690-A007414_1_1

description: Passed Quality Control


title: 690-A007413_1_1

description: Passed Quality Control


title: OHara_sample_122


title: control pt 33

city: Gent

first: Gloria

last: Milani

address: Pintelaan 185

country: Belgium

institute: Gent University

data_processing:
Samples were aligned to GRCh38 using STAR2.4.2a with default parameters
Reads were count using STAR2.4.2a with default parameters and Ensembl v84 as reference
Counts were normalized using the DESeq2 algorithm.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files include raw counts per gene.

molecule: polyA RNA

source_name: TAL-LMO T-ALL patient

extract_protocol:
RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (Lexogen)
The QuantSeq FWD Kit is a library preparation protocol designed to generate Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA. QuantSeq FWD contains the Illumina Read 1 linker sequence in the second strand synthesis primer, hence NGS reads are generated towards the poly(A) tail, directly reflecting the mRNA sequence.

tag: tumor type

value: TAL-LMO T-ALL

value: PB

tag: age

tag: gender

value: Female


title: MOLT16 H3K27ac

description: T cell acute lymphoblastic leukemia (T-ALL) cell line established from the peripheral blood of a 5-year-old girl at relapse in 1985

data_processing:
quality control of fastq files with FastQC
alignment to hg38 using Bowtie2 v2.3.3.1
peak calling with MACS2, --broad, input as control
Superenhancer analysis using Rose (Young lab), default settings, excluding promoter regions
Genome_build: hg38
Supplementary_files_format_and_content: one tsv file, containing Rose SE output

source_name: MOLT16 cell line DSMZ Acc 29

extract_protocol:
2x10^7 cells crosslinked with methanol-free formaldehyde (1% final concentration) RT for 7 min, reaction quenched with glycine . Nuclei isolation performed using truChIP Chromatin Shearing Reagent KIT (Covaris, PN520154). Purified chromatin fragmented by sonication (Covaris, M220, Focused-ultrasonicator). Chromatin fraction ON IP incubation with 40 μl of Protein A UltraLink™ Resin (Thermo-Scientific, 53139) and 4 μg Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (Abcam, ab4729). Day after, bead wash and ON reverse cross-linking by incubation at 65 °C. Input sample was also included (from 1.6x10^6 cells). DNA purified by Chromatin IP DNA Purification Kit (Active-Motif, 58002).
library prepared using NEBNext Ultra DNA library Prep Kit (New England Biolabs,E73370S) and sequenced by NextSeq 500 (Illumina).
DNA fragmentation, End repair, 5' Phosphorilation, dA-Tailing, Adaptor Ligation with U Excision, Size selection/CleanUp, PCR enrichment, Final CleanUp

tag: antibody

value: H3K27ac (Abcam, ab4729)

tag: sorted cells

value: CD2 +, CD3 +, CD4 -, CD5 +, CD6 +, CD7 +, CD8 -, CD13 -, CD19 -, CD34 -, TCRalpha/beta +, TCRgamma/delta -

tag: sample type


title: MOLT16 input

description: T cell acute lymphoblastic leukemia (T-ALL) cell line established from the peripheral blood of a 5-year-old girl at relapse in 1986


title: control pt 26

value: BM


title: control pt 27


title: control pt 29


title: control pt 18


title: control pt 17


title: OHara_sample_135


title: c-Myc-t pt 46

source_name: MYC-TCR translocated T-ALL patient

value: MYC-TCRAD translocated T-ALL


title: control pt 16


title: c-Myc-t pt 47


title: HeLa-Cellular Extraction

city: Jerusalem

first: Shelly

last: Mahlab-Aviv

address: The Edmond J. Safra Campus - Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Illumina NextSeq 500 Analyzer for small RNA sequencing
Adapter sequnces were trimmed and reads were filtered according to their quality
The reads were aligned to the pre-miRNA genome loctions using TopHat
Mapped reads longer than 17 nucleotides and with no more than two possible mapping hits were considered
Total reads of spliceosome fraction alignend to each microRNA were considered. Total reads of cellular extraction (CE) was proceessed using miRexpress tool.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file of reads count per each miRNA in each sample is provided

source_name: HeLa_Cellular extraction small RNA

growth_protocol: All isolation steps were conducted at 4°C. Supraspliceosomes were prepared from nuclear supernatants enriched in supraspliceosomes

extract_protocol:
nuclear supernatants were prepared from purified cell nuclei by microsonication of the nuclei and precipitation of the chromatin in the presence of excess of tRNAs. The nuclear supernatant was fractionated on 10-45% (vol/vol) glycerol gradients. Centrifugations were carried out at 4°C in an SW41 rotor run at 41 krpm for 90 min [or an equivalent w2t = 2500 (w is in krpm; t is in hr)].  The gradients were calibrated using tobacco mosaic virus as a 200S sedimentation marker. Supraspliceosome peak fractions were confirmed by Western Blot (WB) and by electron microscopy visualization. WB analyses were performed, using anti-hnRNP G, kindly provided by Prof. Stefan Stamm (University of Kentucky, Lexington), visualized with horseradish peroxidase conjugated to affinity-pure Goat anti-Rabbit IgG (H+L; Jackson Immunoreaserch) diluted 1:5000. MAb-104, directed against the phosphorylated epitopes of the SR proteins was used as previously described. RNA was extracted from supraspliceosomes prepared from HeLa cells. The integrity of the RNA was evaluated by an Agilent 2100 bioAnalyzer
For small RNA library construction, ~1 µg of RNA was used. After phosphatase and PNK treatments, the RNA was ethanol precipitated to enrich for small RNA, and small RNA libraries (in triplicates) were prepared according to NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible) Library Preparation Manual. Adaptors were then ligated to the 5’ and 3’ ends of the RNA, and cDNA was prepared from the ligated RNA and amplified to prepare the sequencing library. The amplified sequences were purified on E-Gel® EX 4% Agarose gels (ThermoFisher # G401004), and sequences representing RNA smaller than 200 nt were extracted from the gel. The library was sequenced using the Illumina NextSeq 500 Analyzer.

tag: cell line

value: HeLa


title: HeLa5

data_processing:
Illumina NextSeq 500 Analyzer for small RNA sequencing
Adapter sequnces were trimmed and reads were filtered according to their quality
The reads were aligned to the pre-miRNA genome loctions using TopHat
Mapped reads longer than 17 nucleotides and with no more than two possible mapping hits were considered
Total reads alignend to each microRNA were considered
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file of reads count per each miRNA in each sample is provided

source_name: HeLa_nuclear supernatants enriched in supraspliceosomes


title: HeLa3


title: HeLa6


title: HeLa1


title: HeLa4


title: OHara_sample_80

description: adaptors: common adaptor: GGCCAAGGCG

data_processing:
Sequences were trimmed of adaptor sequences using cutadapt version 1.14 and then aligned against a de novo transcriptome (generated using the Trinity assembler) using the salmon aligner, version 0.6.1, in quasi-mapping mode with the variational Bayesian EM algorithm.
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per transcript for each sample. The first column contains the Trinity transcript identifier, and the remaining columns are counts for each transcript per sample.

extract_protocol:
Whole blood collected in PaxGene™ RNA tubes were placed in a cooler with ice until transport back to the ship, at which point they were kept in the freezer at approximately -15°C. Upon return to UAF the samples were placed in a -80°C freezer and then shipped to the University of Washington Center for Exposures, Diseases, Genomics and Environment in insulated shipping containers with dry ice and subsequently stored at -80°C until extraction. Total RNA was extracted using the PaxGene™ Blood RNA Kit according to the manufacturer’s protocol. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, California).  RNA quantity was determined by measuring OD260 with a Thermo Scientific NanoDrop™ 1000 Spectrophotometer (Thermo Fisher Scientific, Inc.; Wilmington, DE).
RNA samples were depleted of ribosomal RNA using the Low Input RiboMinus Eukaryotic System v2 kit (Thermo Fisher Scientific). The cDNA library was then created with the ribosomal depleted RNA using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific). This included fragmentation via RNase III, hybridizing and ligating the RNA, performing reverse transcription, and amplification.  Samples were labeled with the Ion Xpress RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific) to enable multiplexing 4 samples per run.  Templating, loading and sequencing were carried out using the Ion PI Template OT2 200 Kit v2, the Ion PI Chip Kit v2, and the Ion PI Sequencing 200 Kit v2 respectively (all from Thermo Fisher Scientific).


title: HeLa2


title: OHara_sample_61

description: adaptors: common adaptor: GGCCAAGGCG


title: c-Myc-t pt 48


title: PAO1 DMSO-3 (Control)

city: Granada

first: Matilde

last: Fernández

address: Profesor Albareda 1

department: Estación Experimental del Zaidín

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description: Processed data file: PAO1-100_VS_PAO1-DMSO.xls

data_processing:
A first sequencing data quality control on the raw sequences was performed by FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping and quantification were carried out with the EDGE-pro program (Magoc et al., 2013) which uses bowtie2 software (Langmead and Salzberg, 2012).
Different quality parameters on the mapped sequences were evaluated by QualiMap program (Okonechnikov et al., 2015).
Before proceeding with the differential expression analysis, data were normalized with the trimmed mean of M values (TMM) method.
Genome_build: Sequences were aligned with the reference genome Pseudomonas aeruginosa PAO1 (NC_002516.2).
Supplementary_files_format_and_content: *rpkm: Tab-delimited text files include RPKM values for each Sample.
Supplementary_files_format_and_content: PAO1-100_VS_PAO1-DMSO.xls: Excel file includes final results.

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial culture, control

growth_protocol: Three independent cultures of P. aeruginosa PAO1 were grown in LB medium overnight at 37 °C and used to inoculate three 500 ml Erlenmeyer flasks containing 60 mL of LB medium to an initial OD660 of 0.05. Cultures were grown to early exponential phase at OD660 0.5-0.6 at which point 20 ml aliquots were transferred to six 200 mL Erlenmeyer flasks and the corresponding treatment was applied. Cultures were then grown for two more hours before RNA extraction.

extract_protocol:
Ribonucleic acids were extracted using the High Pure RNA Isolation Kit (Roche Life Science) and dissolved in 50 µl of elution buffer. RNA samples for RNA sequencing were additionally purified on NucleoSpin RNA II columns (Macherey Nagel) according to the manufacturer's instructions. Resulting samples were analyzed spectrophotometrically using a NanoDrop instrument for quantification and assessment of purity. Prior to the RNA library preparation, ribosomal RNAs were removed form the samples using the RiboZeroTM kit (Epicentre, Gram-Negative-Bacteria#MRZGN126) following the manufacturers’ instructions.
Samples were processed with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) following the Sample Preparation Guide. The final library (adapter and index included) was validated using the DNA-specific chip Agilent DNA 1000. The final products were fragments between 265-300 bp.
RNA-seq libraries were sequenced on the Illumina NextSeq 500 sequencer.

treatment_protocol: To three of these flasks, RA (72 mM in DMSO) was added to a final concentration of 100 µM, whereas the corresponding amount of DMSO was added to the remaining three flasks.

tag: strain/background

tag: genotype/variation

value: Wild type

tag: growth phase

value: Late exponential phase

tag: treatment

value: DMSO added to culture medium


title: OHara_sample_60

description: adaptors: common adaptor: GGCCAAGGCG

tag: tissue


title: PAO1 DMSO-2 (Control)


title: OHara_sample_72

description: adaptors: common adaptor: GGCCAAGGCG

tag: mercury level


title: PAO1-100UMRA-2

source_name: Bacterial culture, Rosmarinic acid

value: Rosmarinic acid 100 mM (dissolved in DMSO) added to culture medium


title: c-Myc-t pt 44


title: PAO1-100UMRA-3


title: PAO1-100UMRA-1


title: control pt 30


title: MCF7_shRenilla_H3K4me1

status: Public on Jun 30 2018

first: Kinisha

last: Gala

address: 417 E. 68th Street

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA seqeuncing was done on the Illumina HiSeq2500 sequence as 50bp paried-read with 30-40 million reads per sample
Raw RNA seq reads were aligned to the transcriptiome derived from UCSC genome assembly hg19 using STAR55 with default parameters
Read counts for each mRNA transcript were measured using featureCounts
Differential expressed genes were determined using DESeq2 and a cut-off of 0.05 on adjusted p-value was used
ChIP sequencing raw data were trimmed using trim_galore to remove low-quality ends from reads and adapter sequences
The trimmed ChIP sequencing data was aligned using Bowtie2 to UCSC genome assembly hg19
Duplicate reads were removed using Picard and bigwig files were created and peaks were identified with Mac1.4
Genome_build: hg19

source_name: MCF7 cells

growth_protocol: Cultured in DMEM:F12 with 10%FBS and 1%pennicilin/ streptavidin and 1%glutamine

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using 5ng of DNA and KAPA Hyper Prep Kit for Illumina, according to the manufacturer’s protocol. Libraries were validated using the Agilent 2200 Tapestation and KAPA library quantification qPCR assay

tag: cell type

value: metastatic ER+ breast cancer

value: H3K4me1 antibody (abcam 8895)

tag: knockdown

value: shRenilla


title: MCF7_shRenilla_input


title: MCF7_shRenilla_input_forK27ac


title: MCF7_shKMT2C_R_H3K4me1_rep2_input

growth_protocol: Cutured in phenol-free DMEM:F12 with 10% charcoal stripped serum and 1% pennicilin/ streptavidin and 1%glutamine


title: IBU+ACE

city: Montpellier

first: Brigitte

last: Boizet-Bonhoure

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: CNRS

data_processing:
Sequencing Analysis with Bcl2fastq v2.17  (Illumina)
FastQC tool
Genome_build: Mus_musculus.GRCm38.84
SAMtools v1.3 , Bowtie v2.2.6, TopHat v2.1 and Cufflinks v2.2.1
R package CummeRbund
Supplementary_files_format_and_content: output of all differentially expressed genes

source_name: testis

growth_protocol: All animal work was performed under Institute of Human Genetics Animal Ethics approval (BBB 34-366). Microdissected gonads were separated from mesonephros of E13.5 embryos, snap frozen and stored at −80°C.

extract_protocol:
RNA was extracted using the TRIZOL technique
Libraries were generated using the kit TruSeq Stranded Total RNA Sample preparation with Ribo-Zero Gold depletion (Illumina)
1.2 pM of bar-coded libraries per lane were sequenced using the Illumina NextSeq500. Paired-end RNA sequencing chemistry, using 75 nt read lengths, at 40 million reads per sample was performed.

tag: strain

tag: genotype

value: wildtype

tag: developmental stage

value: gonads

value: ibuprofen+acetaminophen


title: Control


title: ASP+ACE

value: aspirin+acetaminophen


title: ACE+ACE

value: acetaminophen


title: c-Myc-t pt 45

tag: tumor type

tag: age

value: Female


title: MCF7_shRenilla_H3K27Ac

tag: antibody

value: H3K27ac antibody (abcam 4729)


title: MCF7_shKMT2C_R_H3K4me1_rep1


title: MCF7_shKMT2C_R_ER_rep2_input


title: MCF7_shKMT2C_R_ER_rep1_input


title: MCF7_shRenilla_ERa

value: ER antibody (Santa Cruz HC-20)


title: MCF7_shKMT2C_R_H3K4me1_rep2


title: MCF7_shKMT2C_R_ER_rep2


title: MCF7_shKMT2C_R_H3K4me1_rep1_input


title: MCF7_shKMT2C_R_ER_rep1


title: MCF7_shKMT2C_2_input


title: PAO1-DMSO-1 (Control)


title: MCF7_shKMT2C_2_H3K4me1


title: MCF7_shKMT2C_2_ERa


title: JIMT-1

city: Nanjing

first: Chunxiao

last: Sun

address: Guangzhou Road,300

country: China

institute: Nanjing Medical University

data_processing:
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the analysis.
Trimmed reads (with 5’, 3’-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences getting from GtRNAdb using NovoAlign software (v2.07.11).
The alignment statistical analysis was applied to retain the valid sequences for subsequent tDR expression profiling and differential expression analysis.
Supplementary_files_format_and_content: TagCount

source_name: breast

growth_protocol: Trastuzumab-sensitive cell lines SKBR3 and trastuzumab primary resistant cell lines JIMT-1 were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) . The normal breast epithelial cells lines HBL-100 was obtained from Cell bank of Chinese Academy of Sciences (Shanghai, China). SKBR3 cells were cultured in RPMI-1640 (Multicell, USA), and JIMT-1 along with HBL-100 cells were cultured in DMEM (Gibco, UK) with 10% fetal bovine serum (FBS, Gibco), containing 100 U/ml penicillin and 100 μg/ml streptomycin(Multicell, USA). Cells were cultured at 37°C in 5% CO2, and the cell medium was replaced every 48 h.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Life Technologies, USA). We do the following treatments before library preparation for total RNA samples:  3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.
Sequencing libraries are size-selected for the RNA biotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100.

value: trastuzumab-resistant cells

value: breast adenocarcinoma


title: HBL-100

value: normal breast epithelial cells

value: breast epithelial


title: MCF7_shKMT2C_1_H3K4me1


title: SKBR3

value: trastuzumab-sensitive cells


title: MCF7_shKMT2C#2_input_forK27ac


title: MCF7_shKMT2C#2_H3K27Ac


title: MCF7_shKMT2C_1_input


title: MCF7_shKMT2C_1_ERa


title: MCF7_shKMT2C#1_input_forK27ac


title: T47D_shRenilla_rep1

source_name: T47D cells

growth_protocol: Cultured in RPMI with 10%FBS and 1%pennicilin/ streptavidin and 1%glutamine

extract_protocol:
Qiagen RNeasy Kit (74106)
Libraries were generated using Illumina’s TruSeq RNA sample Prep Kit v2, following the maufacturer’s protocol


title: T47D_shKMT2C#2_rep1


title: T47D_shKMT2C#2_rep2


title: RNA E16.5 midbrain r2

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
RNA-seq data was processed using the ENCODE RNA-seq uniform processing pipeline.
Briefly, RNA-seq reads were mapped to the mm10 mouse reference using STAR aligner (version 2.4.0k) with Gencode M4 annotation.
We quantified gene expression levels using RSEM (version 1.2.23), expressed as transcripts per million (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: A matrix of TPM values of each gene in each sample

source_name: fetal midbrain

extract_protocol:
We first extracted total RNA using RNeasy Lipid tissue mini kit from Qiagen (cat no.#74804).
We used Truseq Stranded mRNA LT kit (Illumina, RS-122-2101 and RS-122-2102) to constructed stranded RNA-seq libraries on 4ug of the extracted total RNA.

value: midbrain


title: MCF7_shKMT2C#1_H3K27Ac

value: metastatic ER+ breast cancer


title: ES cells RC ASO replicate2

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

country: United Kingdom

institute: MRC Laboratory of Medical Sciences

data_processing:
Reads were quality and adaptor trimmed using UC Davis tools Sickle (v7667f147e6) and Scythe (vc128b19), and standard parameters
Trimmed reads were aligned to mm9 (Thermo Fisher Scientific) using tophat2 v2.0.9, using standard parameters. Setting g-1 was used for aligning repeats to one location in the genome
Bam files were used to generate count data using htseq-count v0.6.1p1, parameters: -f bam -s reverse -t exon -i gene_id -m union
Count data was analyzed in R v3.3.0, using Bioconductor v3.3, Deseq2 v.1.12.3
Genome_build: mm9
Supplementary_files_format_and_content: Percharde_ASOexpt1_raw-reads.xlsx, excel spreadsheet file

source_name: Mouse E14 ES cells

growth_protocol: E14 ES cells were cultured in DMEM GlutaMAX with Na Pyruvate (Thermo Fisher Scientific), 15% FBS (Atlanta Biologicals), 0.1 mM Non-essential amino acids, 50 U/ml Penicillin/Streptomycin (UCSF Cell Culture Facility), 0.1 mM EmbryoMax 2-Mercaptoethanol (Millipore) and 2000 U/ml ESGRO supplement (LIF, Millipore).

extract_protocol:
RNA was extracted using QiaGen Mini purifcation kit, according to standard protocols, including on-column DNAse I digestion
Libraries were generated using the NEBnext Ultra Directional mRNA-seq kit using 1ug total DNAse-1 treated RNA per sample, using NEBNex index primers

treatment_protocol: ASOs were introduced into cells by nucleofection, utilizing an Amaxa Nucleofector 2b device and ES nucleofection kit (Lonza), according to the manufacturer’s instructions. 4-5 million cells were used per nucleofection together with 5 nmol of the indicated ASO. Cells were plated in ES media immediately following electroporation and left to recover for 48 hours. 300,000 ES cells were purified by Lissamine fluorescence by flow cytometry after 2 days and used for RNA extraction.

value: ES cells


title: T47D_shRenilla_rep2

value: shRenilla


title: T47D_shKMT2C#1_rep1


title: ES cells RC ASO replicate3


title: ES cells LINE1 ASO replicate3


title: ES cells RC ASO replicate1


title: T47D_shKMT2C#1_rep2


title: RNA P0 midbrain r2


title: RNA E15.5 midbrain r2


title: ES cells LINE1 ASO replicate2


title: MCF7_shRenilla_3


title: MCF7_shRenilla_CSS_2

treatment_protocol: Cutured in phenol-free DMEM:F12 with 10% charcoal stripped serum and 1% pennicilin/ streptavidin and 1%glutamine for five days


title: MCF7_shRenilla_CSS_1


title: RNA E14.5 midbrain r2


title: RNA E13.5 midbrain r2


title: MCF7_shRenilla_1


title: MCF7_shRenilla_2


title: RNA E12.5 midbrain r2


title: MCF7_shKMT2C_R_2


title: MCF7_shKMT2C_R_3


title: RNA E11.5 midbrain r2


title: ES cells LINE1 ASO replicate1


title: MCF7_shKMT2C_2_3


title: MCF7_shKMT2C_R_1


title: RNA P0 midbrain r1


title: MCF7_shKMT2C_1_3


title: RNA E10.5 midbrain r1


title: RNA E14.5 midbrain r1


title: RNA E16.5 midbrain r1


title: RNA E15.5 midbrain r1


title: RNA E13.5 midbrain r1


title: MCF7_shRenilla_CSS_3


title: MCF7_shKMT2C_2_2


title: MCF7_shKMT2C_2_1


title: MCF7_shKMT2C_1_1


title: MCF7_shKMT2C_1_2


title: RNA P0 liver r2

source_name: fetal liver

value: liver


title: RNA E11.5 midbrain r1


title: MCF7_shKMT2C#2_CSS_2


title: RNA E16.5 liver r2


title: RNA E10.5 midbrain r2


title: Sperm_PCE_4

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Raw sequence reads from WBGS libraries were trimmed to remove poor quality reads and adapter contamination, using Trim Galore (v0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The remaining sequences were mapped using Bismark (v0.18.1) (Krueger and Andrews, 2011) with default parameters to the mouse reference genome GRCm38 in paired-end mode. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor in paired-end mode.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol: WGBS libraries were prepared by sonicating genomic DNA using a Covaris Sonicator, followed by end-repair, A-tailing and methylated adapter (Illumina) ligation using NEB-Next reagents. Subsequently, libraries were bisulfite treated using EZ DNA Methylation-Direct Kit (Zymo), followed by library amplification with indexed primers using KAPA HiFi Uracil HotStart DNA Polymerase (KAPA Biosystems).

tag: background strain

value: Sperm

value: cold stimulation


title: Sperm_PCE_6


title: Sperm_PCE_5


title: MCF7_shKMT2C#2_CSS_1


title: RNA E15.5 liver r2


title: Sperm_PCE_2


title: Sperm_PCE_3


title: Sperm_PCE_1


title: RNA E12.5 midbrain r1


title: MCF7_shKMT2C#2_CSS_3


title: RNA E14.5 liver r2


title: pmr1/pmr1 mutant

city: Zibo

first: Linghuo

last: Jiang

address: 266 West Road Xincun

institute: Shandong University of Technology

description: Sample T03

data_processing:
Raw reads from mRNA sequencing were filtered by discarding the reads with adaptor contamination, masking low-quality reads with ambiguous ‘N’ bases and removing reads in which more than 10% bases had a Q-value <20.
Clean reads were assembled into full-length transcriptome from RNA-Seq data with the reference genome (http://www.candidagenome.org/).
Gene expression levels were measured as numbers of reads, and normalized with FPKM
Differentially expressed genes were identified in pair-wise comparison with the IDEG6 software
All statistical test results were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR<0.01)
Genome_build: Assembly 21
Supplementary_files_format_and_content: FPKMs. DEGs

organism: Candida albicans

source_name: Log-phase cells in SD-URA medium at 30oC.

growth_protocol: Four strains were grown to log phase in SD-URA medium at 30oC.

extract_protocol:
Total RNA samples were extracted using the TRIzol total RNA reagent (Tiangen Inc., Beijing, China) according to the manufacturer’s instructions. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were constructed using Illumina’s TruSeq RNA Sample Preparation Kit (Illumina Inc, San Diego, CA, USA). RNA sequencing, data analysis and sequence assembly were performed by Beijing BioMarker Technologies (Beijing, China). Preparation of the paired-end libraries and sequencing were performed following standard Illumina methods and protocols. The mRNA-seq library was sequenced on the Illumina Hiseq 2500 system.

treatment_protocol: No treatment

value: CAI4 pmr1/pmr1


title: gdt1/gdt1 pmr1/pmr1 mutant

description: Sample T04

value: CAI4 gdt1/gdt1 pmr1/pmr1


title: Sperm_CTRL_6

value: control


title: RNA E13.5 liver r2


title: Sperm_CTRL_3


title: Sperm_CTRL_5


title: RNA E12.5 liver r2


title: RNA E11.5 liver r2


title: Sperm_CTRL_4


title: RNA P0 liver r1


title: Sperm_CTRL_1


title: RNA E15.5 liver r1


title: wild type CAI4

description: Sample T01


title: RNA E14.5 liver r1


title: RNA E12.5 liver r1


title: JCLIA002C

city: Berkeley

first: Ligia

last: Acosta-Sampson

address: 2151 Berkeley Way, Room 320, MC 5230

department: MCB/EBI

institute: UC Berkeley

description: The_transcriptome_profiles-lacostasampson.xlsx

data_processing:
Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence.
For footprint analysis, trimmed sequencing reads without the linker were aligned to the S. cerevisiae ribosomal sequences using Bowtie (Langmead et al., 2009).  These reads were removed, and the non-rRNA reads were then mapped to the S. cerevisiae genome using Tophat (Trapnell et al., 2009).  The sequence for the pRS316-NC/OPT plasmids were manually annotated and added to separate genome fasta files created for each condition and designated as new chromosomes. Only uniquely aligned reads were used for subsequent analyses. Most of the reads were between 27-32 nt long and these reads were mapped onto their respective coding sequences as described previously (Ingolia et al., 2012; Ingolia et al., 2009).
For RNA-seq data, sequence reads were assembled and analyzed in CLC Genomics Workbench 6.5 (CLC Bio, Aarhus, Denmark).  The genome for S. cerevisiae S288C (version R64.2.1), the parent strain of D452-2 , was downloaded from Refseq at the NCBI (http://www.ncbi.nlm.nih.gov/refseq/); the mitochondrial genome was included.  The sequence for pRS316-NC and -OPT were manually annotated and added to this file.  Expression values were normalized by calculating the reads per kb of mRNA per million mapped reads (RPKM), and normalized further by using the option of “By totals”.
Genome_build: Saccharomyces cerevisiae S288C (version R64.2.1)

organism: Saccharomyces cerevisiae

source_name: Mid-exponentially grown cells expressing NC

extract_protocol:
(1) Extraction of ribosome-protected mRNA: Frozen cell pellets were lysed by low-frequency cryogenic mixer milling.  Lysate was clarified of cell debris and 25 A260 units of extract were treated with 450 U of RNase I (Ambion) for 1 h at room temperature with gentle rotation; digestion was stopped by addition of 120 U of Superase-IN.  Ribosomes were pelleted using high-speed centrifugation through a 1 M sucrose cushion.  miRNeasy Mini kit (Qiagen) was used to purifiy ribosome-protected mRNA fragments following the manufacturer’s instructions. (2) Extraction of total RNA: Total RNA was extracted using the RiboPure Yeast kit (Ambion, Austin, TX, USA), according to manufacturer's instructions, except cells were disrupted by bead-beating 3 times for 30 sec, with a 30 sec pause between runs.
(1) Ribosome profiling library: Preparation of ribosome profiling libraries followed similar protocols as those in (Ingolia et al., 2012; Ingolia et al., 2009). (2) RNA-seq library: 4 µg of total RNA were used to prepare the multiplexing libraries with barcodes following the standard instructions of the Illumina TruSeq RNA Sample Prep Kit.

tag: strains

value: Engineered D452-2 containing the plasmid pRS316-NC


title: JCLIA002F

source_name: Mid-exponentially grown cells expressing OPT

value: Engineered D452-2 containing the plasmid pRS316-OPT


title: siRNA-Control

city: White Plains

first: Mary

middle: E

last: Donohoe

state: New York

address: 785 Mamaroneck Ave

department: Burke Medical Research Institute

institute: Weill Cornell Medical Colledge

data_processing:
Reads were mapped to mm9 using TopHat (Trapnell et.al., Bioinfromatics (2009)).
Differentially expressed genes were identified using SeqMonk (Babraham Institute, http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ ).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Tab-delimited text file includes the values of RPKM (log2) for all genes and differentially expressed genes (p<0.075)

source_name: Extraembryonic endoderm stem (XEN) cells

growth_protocol: PS10 XEN cells were cultured as described in the related publication.

extract_protocol:
RNA was extracted by TRIzol geagent and purified by RNeasy Mini Kit.
Illumina TrueSeq library prep kit

treatment_protocol: Gata6-AS targeting (siRNA-Gata6AS) or control (siRNA-Control) locked nucleic acid was transfected using Lipofectamine RNAiMax.

tag: gender

value: female

value: ICR

tag: cell line


title: JCLIA002E


title: JCLIA002D


title: RNA E13.5 liver r1


title: JCLIA002A


title: JCLIA002B


title: gdt1/gdt1 mutant

description: Sample T02

value: CAI4 gdt1/gdt1


title: JCLIA001E

description: Ribosome-protected mRNA


title: siRNA-Gata6AS

value: Extraembryonic endoderm stem (XEN) cells


title: Input visceral Repl2

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human genome hg19 or hg38 using bowtie 1.0 with n = 1 and m = 3 as parameter
Bigwig files were created using Galaxy/deepTools, duplicated tags were ignored
Genome_build: hg19, hg38
Supplementary_files_format_and_content: bigwig

source_name: visceral adipocytes

growth_protocol: Human primary preadipocytes were obtained from Innoprot and cultured in complete preadipocyte Medium (Innoprot).

extract_protocol:
For ChIP mature adipocyte cells were crosslinked with 1% formaldehyd for 10 min and sonicated to 200 bps. Genomic DNA was extracted using antibodies for H3K4me3, H3K9me3 and H3K27ac.
The libraries for ChIP-Seq were preparated using the MicroPlex Library preparation kit (Diagenode) and purified with Agencourt AMPure XP beads (Beckman Coulter Life Sciences, Krefeld, Germany).

treatment_protocol: For differentiation, the preadipocytes were seeded with preadipocyte medium into poly-L-lysine coated 15 cm petri dishes and grown until they were confluent. Then, cells were differentiated with complete preadipocyte differentation medium (Innoprot) for 12 days to mature adipocytes. Medium was changed every 2-3 days.

tag: chip antibody

value: input


title: Sperm_CTRL_2


title: JCLIA001D

description: Ribosome-protected mRNA


title: Input visceral Repl1


title: RNA E16.5 hindbrain r2

source_name: fetal hindbrain

value: hindbrain


title: RNA E15.5 hindbrain r2


title: H3K27ac visceral Repl2

value: H3K27ac, Diagenode C15410196


title: H3K27ac visceral Repl1


title: JCLIA001B

description: Ribosome-protected mRNA


title: H3K9me3 visceral Repl2

value: H3K9me3, abcam ab8898


title: H3K9me3 visceral Repl1


title: RNA E14.5 hindbrain r2


title: JCLIA001C

description: Ribosome-protected mRNA


title: H3K4me3 visceral Repl2

value: H3K4me3, abcam ab8580


title: H3K4me3 visceral Repl1


title: RNA P0 hindbrain r1


title: RNA E10.5 hindbrain r2


title: RNA E12.5 hindbrain r2


title: RNA E11.5 hindbrain r2


title: RNA E16.5 hindbrain r1


title: Input subcutaneous Repl2

source_name: subcutaneous adipocytes


title: RNA P0 hindbrain r2


title: Input subcutaneous Repl1


title: H3K27ac subcutaneous Repl2


title: JCLIA001A

description: Ribosome-protected mRNA


title: RNA E11.5 liver r1

value: liver


title: H3K9me3 subcutaneous Repl2


title: H3K27ac subcutaneous Repl1


title: RNA E13.5 hindbrain r2


title: RNA E13.5 hindbrain r1


title: H3K4me3 subcutaneous Repl2


title: RNA E11.5 hindbrain r1


title: RNA E15.5 hindbrain r1


title: RNA E12.5 hindbrain r1


title: RNA E14.5 hindbrain r1


title: H3K9me3 subcutaneous Repl1


title: H3K4me3 subcutaneous Repl1


title: RNA E10.5 hindbrain r1


title: RNA E16.5 forebrain r2

source_name: fetal forebrain

value: forebrain


title: RNA P0 forebrain r2


title: RNA E15.5 forebrain r2


title: RNA P0 forebrain r1


title: RNA E13.5 forebrain r2


title: RNA E14.5 forebrain r2


title: RNA E12.5 forebrain r2


title: RNA E10.5 forebrain r2


title: ES cells RC ASO + siNcl replicate2

data_processing:
Reads were quality and adaptor trimmed using trim_galore v0.4.0, and standard parameters
Trimmed reads were aligned to mm9 (Thermo Fisher Scientific) using tophat2 v2.0.9, using standard parameters. Setting g-1 was used for aligning repeats to one location in the genome
Bam files were used to generate count data using Rsubread package feature-counts v1.22.3, parameters: -t exon -T 4 -s 2 -g gene_id
Count data was analyzed in R v3.3.0, using Bioconductor v3.3, Deseq2 v.1.12.3
Genome_build: mm9
Supplementary_files_format_and_content: Percharde_ASOexpt2_raw-reads.xlsx, excel spreadsheet file

treatment_protocol: ASOs were introduced into cells by nucleofection, utilizing an Amaxa Nucleofector 2b device and ES nucleofection kit (Lonza), according to the manufacturer’s instructions. 4-5 million cells were used per nucleofection together with 5 nmol of the indicated ASO. Cells were plated in ES media immediately following electroporation and left to recover for 7 hours. Then, ES cells were transfected with 100 pmol per well of siRNA according to standard Lipofectamine 2000 protocol. Media was changed the next day and cells harvested after 2 days without sorting and used for RNA extraction.

value: ES cells


title: ES cells LINE1 ASO + siDux replicate3


title: RNA E16.5 liver r1


title: RNA E16.5 forebrain r1


title: ES cells RC ASO + siNcl replicate1


title: ES cells RC ASO + siNcl replicate3


title: RNA E11.5 forebrain r1


title: RNA E13.5 forebrain r1


title: RNA E14.5 forebrain r1


title: ES cells LINE1 ASO + siDux replicate1


title: ES cells LINE1 ASO + siControl replicate3


title: ES cells LINE1 ASO + siControl replicate2


title: ES cells LINE1 ASO + siControl replicate1


title: FAD MeDIP-Seq

city: Beijing

first: Wei

last: Li

address: NO.2, Yabao road

institute: Capital of Pediatrics Institute

data_processing:
Raw sequencing data were first processed to filter out low-quality reads that contained more than five ‘N’s or over 50% of the sequence with low quality values (Phred score < 5).
The MeDIP-seq data were aligned to the mouse reference genome (UCSC Genome Browser mm10), allowing up to two mismatches, using SOAP2 (Version 2.21).
Raw sequencing data were first processed to filter out low-quality reads that contained more than five ‘N’s or over 50% of the sequence with low quality values (Phred score < 5).
For each sample, the distribution of MeDIP-Seq the reads on the mouse genome were analyzed in CpG islands (CGIs), gene region and different CG density regions.
The distribution of the peaks in different genome components in each group, including the upstream 2 kb, 5´-untranslated region (UTR), 3´-UTR, CDS, intron, and downstream 2 kb was also analyzed.
Genome_build: mm10
Supplementary_files_format_and_content: bed files include the distribution of the peaks in different genome components in each group.

source_name: HFD supplemented with folic acid (FAD)

growth_protocol: Male 6-week-old C57BL/6J mice were obtained from Beijing HFK Bioscience Co. Ltd. (Beijing, China) and housed in a temperature-controlled room (23±2°C) with 12-h light-dark cycles. Mice were enabled ad libitum access to food and water. Animals were randomly assigned to a normal diet (ND; ~10% energy as fat), a high-fat diet (HFD; ~60% energy as fat) or a HFD supplemented with folic acid (FAD, 20 μg/mL, Sigma) in the drinking water for 10 weeks.

extract_protocol:
Genomic DNA samples were extracted from the epdidymal adipose tissues using a DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).
MeDIP DNA libraries were prepared using the TruSeq DNA Sample Preparation Guide (Illumina, San Diego, CA, USA).

value: epididymal adipose tissue

tag: development stage

value: 16 weeks


title: ND MeDIP-Seq

source_name: normal diet (ND)


title: ES cells RC ASO + siDux replicate3


title: ES cells RC ASO + siDux replicate1


title: ES cells RC ASO + siDux replicate2


title: ES cells RC ASO + siControl replicate1


title: ES cells RC ASO + siControl replicate2


title: RNA E12.5 forebrain r1


title: ES cells LINE1 ASO + siDux replicate2


title: HFD MeDIP-Seq

source_name: high-fat diet (HFD)


title: r01.1

city: Moscow

first: Pavel

last: Mazin

address: Skolkovo Innovation Center, Building 3

department: Biomed

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
read mapping by tophat2. Parameters: "“--read-mismatches 4 --read-edit-dist 4 --read-realign-edit-dist 0 --min-intron-length 10 --max-intron-length 3000000 --coverage-search --microexon-search --max-segment-intron 3000000"
read counting by SAJR (http://storage.bioinf.fbb.msu.ru/~mazin/)
Genome_build: v0.9 from http://bertone.nises-f.affrc.go.jp/midgebase/
Supplementary_files_format_and_content: gtf file and tab-delimited text file with gene read counts for all samples

organism: Polypedilum vanderplanki

source_name: whole larva

growth_protocol: Highly inbred lines of these sibling species that differ in their ability to resist complete desiccation were used for RNA extraction. P. vanderplanki and P. nubifer larvae were reared on a 1% agar diet containing 2% commercial milk under controlled photoperiod (13 h light: 11 h dark) and temperature (27–28 °C) conditions

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) and the RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s recommendations.
TruSeq RNA Sample Preparation kit v.2 (Illumina) was used for preparation of RNA-seq libraries.

tag: Stage

value: rehydration

tag: duration (hours)

tag: batch


title: r12.1


title: d48.1

value: dehydration


title: r00


title: d48


title: r01


title: d40.3


title: d40


title: RNA E11.5 forebrain r2

tag: tissue


title: r03.1


title: r48.1


title: r00.1


title: d36


title: d24


title: ES cells RC ASO + siControl replicate3

tag: cell type


title: d24.3


title: d24.1


title: d16


title: d16.3


title: r24.1


title: d12


title: r03


title: d12.3


title: d12.1


title: r06.1


title: d40.1


title: RNA E15.5 forebrain r1


title: d08


title: d32


title: d01.1


title: d01.2


title: d00.1


title: d00.2


title: d08.1


title: FABGPL2

city: Blacksburg

first: Stephen

last: Melville

state: Virginia

address: 217 LS1, Washington St.

department: Biological Sciences

institute: Virginia Tech

description: FABG plates

data_processing:
Geneious version 9 with low sensitivity
Relative expression levels of annotated coding regions were calculated with units of transcripts per million (TPM). TPM, as proposed by Wagner (3) is calculated as: TPM= (coding Sequence read count x Mean read length x 106)/(Coding sequence length x Total transcript count). Differentially expressed genes were identified by a stringent cutoff of fold-change >4 when media conditions were compared against one another for each gene.
Genome_build: NC_003366
Supplementary_files_format_and_content: excel, raw and average RNA-seq data and compiled sRNA values

organism: Clostridium perfringens

source_name: Bacteria

growth_protocol: C. perfringens HN13 cells were grown in duplicate in six conditions: liquid culture to mid-log phase and 1% agar plates of PGY, BHI, and FABG media for 24 hours.  Liquid cultures were standardized to OD600=0.500 and cells were scraped from the outer edges of plate grown colonies and resuspended in DPBS to OD600=0.500.  Bacteria were pelleted and frozen in liquid nitrogen prior to RNA purification.

extract_protocol:
Cells were lysed in 500 μl Tri Reagent (Zymo Research) using high-impact zirconium beads in a Mini-Beadbeater (Biospec) for one minute and kept on ice.  RNA was then purified from cell lysate using a Direct-Zol RNA Mini-Prep Plus Kit according to the manufacturer’s protocol (Zymo Research), including an on-column DNA digestion. RNA integrity was measured using an Agilent BioAnalyzer 2100 (VBI), and samples with a RIN of 8.3 or greater were used for RNA sequencing.
Library construction was performed for Illumina sequencing by Virginia Bioinformatics Institute. All samples were processed with HiSeq Illumina sequencing (VBI) creating 100-bp paired-end reads, and the resulting data was aligned to C. perfringens strain 13 reference genome (NCBI, accession number NC_003366) using the bioinformatics mapper Geneious version 9 with low sensitivity

tag: strain

tag: growth

value: FABG plates


title: PGYPL2

description: PGY plates

value: PGY plates


title: d08.3


title: FABGPL1

description: FABG plates


title: FABGLI1

description: FABG liquid

value: FABG liquid


title: Phalaenopsis equestris_stem

city: Shenzhen

first: Zhong Jian

last: Liu

address: No.889 Wangtong Road

institute: Shenzhen Key Laboratory for Orchid Conservation and Utilization

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, De novo transcriptome reconstruction was performed using Trinity (version trinityrnaseq_r20140717). Trinity was applied using the inchworm method with a minimum contig length of 200 nucleotides. The default settings for Trinity paired-end assembly were used for the remaining parameters.
Fragment Per Kilobase of exon model per Million mapped reads (FPKM) were calculated using  Bioconductor tools (edgeR and DESeq)
heat shock proteins 20,70 and 90 acquired from the genome sequence of the orchid Phalaenopsis equestris using hmmsearch methods and the expression value from four transcriptomes
Supplementary_files_format_and_content: matrix files including FPKM values for four tissues

organism: Phalaenopsis equestris

source_name: Stem

extract_protocol:
RNA was harvested using RNAprep Pure Plant Kit(Polysaccharides&Polyphenolics-rich (Cat#DP441) was used with 100 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stem

value: three years


title: d16.1


title: PGYLI2

description: PGY liquid

value: PGY liquid


title: FABGLI2

description: FABG liquid


title: Phalaenopsis equestris_root

source_name: Root

value: root


title: Phalaenopsis equestris_leaf

source_name: Leaf

value: leaf


title: Phalaenopsis equestris_flower

source_name: Flower

value: flower


title: BHIPL1

description: BHI plates

value: BHI plates


title: fft2fft3 R3

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC

description:
TC_trimmed_pooled_TPM_chr123.txt
HU2000_meanReplicates_TPM.bw

data_processing:
Base-calling with Illumina CASAVA v1.6
Removing of 5' adapters and trimming of read ends (keeping from bp 12 to bp 36) and filtering for Q30 over 50% remaining length with Fastx Toolkit v0.0.13
Mapping with Bowtie v0.12.7
Clustering of mapped tags with Bedtools v2.15.0
TPM normalization and trimming of tag clusters by both ends simultaneously until 90 percentile TC expression is reached with in-house script
Genome_build: ASM294v2
Supplementary_files_format_and_content: [.bw] bigwig files generated with Bedtools v2.15.0 where score represents TPM-normalized mapped tags.
Supplementary_files_format_and_content: [R#.txt] Expression matrices are tab-delimited file where first column is identifier for TC (chr:start-end,strand) followed by TPM expression in the sample mentioned as header.
Supplementary_files_format_and_content: [chr123.txt] Trimmed TC file is the full collection of detected TC in all samples along with chromosome, coordinates, id, score (TPM of pooled samples), strand and TC summit coordinates.

organism: Schizosaccharomyces pombe

source_name: fft2fft3 cells

growth_protocol: Duplicate liquid cultures were grown in YES media at 30°C and 180 RPM shaking. For all experiments, cells were harvested in mid-log growth (~5×106 cells/ml).

extract_protocol: CAGE libraries were prepared as in Takahashi, H., Lassmann, T., Murata, M. & Carninci, P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7, 542–561 (2012).

value: Hu2000 h- fft2::kan fft3::hph ade6M210 leu1-32 ura4-D18

value: whole cells

tag: genotype/variation

value: fft2fft3 double mutant


title: fft2fft3 R2


title: BHILI3

description: BHI liquid

value: BHI liquid


title: BHILI1

description: BHI liquid


title: fft2fft3 R1


title: wt R3

description:
TC_trimmed_pooled_TPM_chr123.txt
HU0029_meanReplicates_TPM.bw

source_name: wt cells

value: wt


title: PGYPL1

description: PGY plates


title: wt R1


title: wt R2


title: 48hrs treated_3

city: Los Angeles

first: vineela

last: gangalapudi

state: CALIFORNIA

address: 8723 Alden drive

department: Biomedical sciences

institute: Cedars- sinai Medical center

data_processing:
We used the STAR aligner to map the samples, and Qced them using Rseqc then used DEseq2 for DE to get the significantly differentially expressed genes between the control  and  treated samples at each time point
Genome_build: GRCh38 version 23
Supplementary_files_format_and_content: Excel table includes count values for lincRNA and protein-coding genes for each Sample calculated by STAR.

organism: Chlorocebus aethiops

source_name: Vero cell line

growth_protocol: Vero cells from three different time points(12hr,24hr, 48hr) were used.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.

treatment_protocol: Vero cell line was maintained in DMEM medium which was supplemented in 10% fetal bovine serum (FBS), penicillin (100 units/ml), streptomycin (100 mg/ml), 10 mM Hepes, and 2 mM L-glutamine.The following day, Zika viral inoculum was prepared in serum-free base media at an MOI of 1.

tag: treatment

value: zika infected

value: vero


title: 48hrs control_3

value: control


title: 48hrs control_1


title: 12hrs treated_1


title: 48hrs control_2


title: 48hrs treated_2


title: BHIPL2

description: BHI plates


title: 12hrs treated_2


title: HrpL-FLAG-2

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

institute: City University of Hong Kong

data_processing:
Bacterial ChIP-seq reads were mapped to the P. syringae genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A
Supplementary_files_format_and_content: xls file containing comparisons between HrpRSL and control

source_name: liquid culture in minimal medium

growth_protocol: MM with spec

extract_protocol:
ChIP was performed as previously described with slightly modified. An empty pHM2, pHM2-hrpSpsph-FLAG, pHM2-hrpRpsph-FLAG, or pHM2-hrpLpsph-FLAG plasmid was transformed into the wild-type of Psph, then cultured in KB medium until the OD600= 0.4~0.6 before transferring to MM liquid medium with spectinomycin 50μg/ml for 6 h. The strains were treated with 1% formaldehyde for 10 min at 37℃. Subsequently, added 125 mM glycine to stop the crosslinking. After pelleting, bacterial were washed twice by Tris buffer (20-mM Tris-HCl pH 7.5, 150-mM NaCl), and then resuspended in 500 μl IP buffer (50mM Hepes-KOH pH 7.5, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche). Next the DNA was sonicated into fragments ranged from100 to 300 bp. The cellular debris was removed, and the supernatant was saved as the input sample in the IP experiments. Both the control and IP samples were washed by protein A beads (General Electric). Then in the IP buffer, the samples were mixed with 50 μl agarose conjugated anti-FLAG antibodies (Sigma). The subsequent washing, crosslink reversal and purification of ChIP-DNA was following by previously reported protocols. DNA fragments (150 to 250 bp) were selected for library construction and sequencing the libraries using the NEXTflexTM ChIP-Seq Kit (Bio Scientific). The libraries were sequenced using the HiSeq 2000 system (Illumina). ChIP-seq results were mapped to the Psph genome using TopHat (version 2.0.0) with two mismatches allowed. The binding peaks were detected by MACS software (version 2.0.0) and nearly all of them were performed in two experiments and the reported peaks are found in both experiments.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol: grow until mid-log phase in KB, then transfer to MM for 6 h

value: anti-FLAG (Sigma)


title: 12hrs control_2


title: HrpL-FLAG-1

organism: Pseudomonas savastanoi pv. phaseolicola 1448A


title: HrpS-FLAG-2


title: HrpS-FLAG-1


title: (-) mild  IMG1979 [21-P1]

city: State College

first: Sally

middle: A

last: Mackenzie

state: PA

address: 362 North Frear

department: Biology

institute: Penn State University

data_processing:
Illumina for basecalling
The sequences were trimmed using trim_galore 0.4.1 and cutadapt 1.9.1  with cutoff 20
The sequences were aligned using Erne-meth 2.1.1 with default options and set the output as a bismark coverage file
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: SL250 - Solanum_lycopersicum.SL2.50
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic coords with <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated> fields

organism: Solanum lycopersicum

source_name: cultivar Rutgers

growth_protocol: Wild-type tomato (Solanum lycopersicum, cultivar Rutgers) and the corresponding, MSH1-RNAi segregate out (msh1 memory line) were germinated on MetroMix 200 medium (SunGro) and maintained at 26°C to 28°C with a 15-h day length and at 20°C to 22.8°C with a 9-h dark period.

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany). Genomic DNA from three individual plants for both WT and msh1 memory line were used for subsequent Bisulfite methylome sequencing experiment.
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: The top three leaves from each tomato plant (four weeks old) were collected and freeze in liquid nitrogen immediately and put into -80 ℃

tag: genotype

value: msh1 memory line

tag: background cultivar

value: Rutgers


title: (-) mild  IMG1980 [21-P22]


title: HrpR-FLAG-2

tag: antibody


title: 48hrs treated_1


title: 24hrs control_1


title: 24hrs treated_1


title: Mw2012007-3

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

data_processing:
To obtain high-quality clean read data for de novo assembly, the raw reads from mRNA-seq were filtered by stringent standards: 1)Remove reads with adaptors;2) Remove reads with more than 5% unknown nucleotides; 3) Remove low quality reads more than 20% low quality bases(base quality≤10).
Then, clean reads were assembled into contigs using the Trinity software. The result sequences of trinity is called Unigenes.
Unigene expression levels are calculated using FPKM method(Fragments Per kb per Million fragments){Mortazavi, 2008}. The formula is FPKM=(1000000*C)/(N*L*1000)
In the final step, blastx alignment (evalue < 0.00001) between Unigenes and protein databases like NR, Swiss-Prot, KEGG and COG is performed, and all Unigenes will be annoated based on blastx
Genome_build: No reference genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Agropyron mongolicum

source_name: normal condition

growth_protocol: We selected an original A. mongolicum Keng plant (MW2012) from the variety breeding centre of Inner Mongolia Agricultural University and then transplanted it to the artificial intelligence green house.

extract_protocol:
All the tissues containing root, leaf, stem and tassel were extracted for sequencing preparation.After total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) were used to isolate mRNA or by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA was fragmented into short fragments. Then cDNA was synthesized using the mRNA fragments as templates.
RNA libraries were prepared for sequencing using Illumina HiSeq™ 2000 protocols.

treatment_protocol: MW2012 was splited to three equal parts including Control, 5-day drought sress and 15-day drought stress.

tag: stress

value: normal condition

value: whole plant


title: HrpR-FLAG-1


title: Rutgers WT [2-P2]

value: WT


title: 24hrs control_2


title: Rutgers WT [2-P1]

value: leaf


title: CK-2


title: (-) mild  IMG1974 [21-P32]


title: JCLIA001F

description: Ribosome-protected mRNA

source_name: Mid-exponentially grown cells expressing OPT

tag: strains

value: Engineered D452-2 containing the plasmid pRS316-OPT


title: 12hrs control_1

tag: cell line


title: Rutgers WT [1-P1]


title: Mw2012007-2

source_name: drought stress 15 days

value: drought stress 15 days


title: Mw2012007-1

source_name: drought stress 5 days

value: drought stress 5 days


title: CK-1


title: Liver reg diet 20

status: Public on Jun 29 2018

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

description: Liver regular diet 7 weeks

data_processing:
Library strategy: DREAM
Illumina fastq files were aligned to the Rattus norvegicus genome (rn4) using Bowtie2. Uniquely mapped reads were sorted into bam files using samtools.
We used a python script to map aligned sequencing reads to target CCCGGG sites in the Rattus norvegicus genome (rn4) and enumerate signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG for each target site.
We used an R script to calculate methylation levels at each SmaI/XmaI site based on the following formula: let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: rn4
Supplementary_files_format_and_content: tab delimited text file with numbers of reads and percent methylation at individual CCCGGG sites

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
spinal nerve ligation protocol: Spinal nerve ligation (SNL) in male Sprague-Dawley rats (8-9 weeks old, ± 220 g; Harlan Sprague-Dawley, Indianapolis, IN) was used for this study as the neuropathic pain model. Animals were anesthetized with 2-3% isoflurane, and the left L5 and L6 spinal nerves were isolated and ligated tightly with 4.0-silk suture under a surgical microscope. Sham surgery (without nerve ligation) was performed on the contralateral side as the control.
chemotherapy-induced neuropathy: Four intraperitoneal injections of the chemotherapeutic agent paclitaxel (2 mg/kg, every two days) were performed, and vehicle (cremophor ethanol 1:1)-treated rats were used as the control group.
intrathecal cathetrization: Under anesthesia with 2% isoflurane, an intrathecal catheter (a PE-10 tubing) was surgically inserted through an incision made in the cisternal membrane. The catheter is directed to the lumbar region of the spinal cord, and the external opening was sealed. Rats displaying signs of the motor or neurological dysfunction were excluded and terminated immediately with an overdose of phenobarbital (200 mg/kg, i.p.). The animals were allowed to recover for five days before intrathecal injections. Ten micrograms of N-phthaloyl-L-tryptophan (RG108, Tocris Bioscience, Bristol, UK) or vehicle (10% DMSO; saline) were injected intrathecally in a 5 µl volume followed by 10 µl saline flush.(Chestnut et al. 2011). Animals received intrathecal injections for four consecutive days.
neuronal enrichment: To prepare a neuronal nuclear enrichment, fresh whole DRG samples were cut and mashed onto an ice-cold petri dish. Mashed tissue from 3 DRGs was pooled in one 1.5 ml tube. The tissue was resuspended in buffer NAME (20 mM Tris pH8, 20 mM KCl, 1.5 mM MgCl2) with a cocktail of protease and phosphatase inhibitors cocktails (Pierce), 0.5 mM DTT and 1 mM PMSF (Sigma-Aldrich, MO) to obtain a single cell suspension. Cells were incubated on ice for 5 min before to be spincentrifuged at 3,000 rpm at 4 °C for 2 min. The pPellet was resuspended in buffer NAME containing 0.15% NP-40. Cells were incubated on a rotator overnight to isolate nuclei. Neuronal nuclei were immunoprecipitated using anti-Fox3 (neuronal nuclear marker, Abcam #104225) in PBS. Then, classical and genomic DNA extraction was performed. Neuronal nuclei were lysed with lysis buffer (0.1 M Tris pH 8, 5 mM EDTA, 0.2% SDS, 0.2 M NaCl and, proteinase K) overnight and precipitated with isopropanol. Genomic DNA pellet was washed with 75% ethanol, dried and re-suspended in TE buffer (Tris 10 mM pH8, 1 mM EDTA). The isolation purity was validated by western blot analysis. Nuclear proteins were extracted from one batch. Cytoplasm/nucleus separation was validated by western blot using anti-histone H3 (Cell Signaling Technology#9715; 1/4000) and neuronal enrichment was validated by western blot using the neuronal marker anti-Fox3 (Abcam #104225) and the satelite/glia markers anti-g Glutamine sSynthetase (Millipore #MAB302; 1/200) and anti-GFAP (Abcam #7260; 1/4000).
Genomic DNA extracted from tissue samples was spiked with methylation standards and sequentially digested with two restriction endonucleases recognizing CCCGGG sites in DNA. SmaI cleaved only unmethylated sites resulting in blunt ended fragments starting with 5’-GGG. Next, XmaI cleaved the remaining methylated sites creating 5’-CmeCGG overhang sequences. Exonuclease-deficient Klenow fragment DNA polymerase was then used to fill in the 3’ recesses left by XmaI and add 3’-dA overhangs to the ends of all fragments. Thus, specific signatures 5’-GGG and 5’-CCGGG were created at unmethylated and methylated CpG sites, respectively. Illumina sequencing adapters were then ligated to the enzyme-treated DNA; sequencing libraries were generated according to Illumina protocols and run on an Illumina HiSeq 2500 instruments at Fox Chase Cancer Center Genomics facility. Sequencing data were aligned to the rat genome (rn4), and the reads with unmethylated and methylated signatures were counted at individual CCCGGG sites. Methylation levels were calculated as the ratio of reads with the methylated signature to all reads mapping to each respective site. DNA methylation values at individual CpG sites were adjusted based on spiked in standards and filtered for the minimum sequencing depth of 100 reads.

treatment_protocol: modified diet treatment: To manipulate DNA methylation levels, we altered the intake of methyl group donors (folate and vitamin B12) by feeding the rats with modified diets. The original diet AIN-93M (normal folate and vitamin B12 doses are 2.1 ppm and 28 µg/kg, respectively) was modified by Purina Animal Nutrition LLC Technical Services to make a folate and vitamin B12 deficient diet (0.1 ppm and 3 µg/kg respectively) and a diet 5 times enriched in folate and vitamin B12 (10.5 ppm and 140 µg/kg respectively). Five-week-old rats (weighing ~120 g) were randomly placed in new cages with ad libitum regular, deficient and enriched diets, respectively. The animals were kept on the diets for four weeks before SNL surgery, followed by three weeks after SNL.

value: Sprague-Dawley

value: Liver

tag: age

value: adult

tag: procedure

value: regular diet 7 weeks


title: Liver def diet 21

description: Liver deficient diet 7 weeks

value: deficient diet 7 weeks


title: Liver def diet 19

description: Liver deficient diet 7 weeks


title: Liver reg diet 15

description: Liver regular diet 7 weeks


title: Liver rich diet 14

description: Liver rich diet 7 weeks

value: rich diet 7 weeks


title: Liver rich diet 18

description: Liver rich diet 7 weeks


title: Liver def diet 13

description: Liver deficient diet 7 weeks


title: Liver def diet 10

description: Liver deficient diet 4 weeks

value: deficient diet 4 weeks


title: Liver reg diet 07

description: Liver regular diet 4 weeks

value: regular diet 4 weeks


title: Liver def diet 04

description: Liver deficient diet 4 weeks


title: Liver reg diet 03

description: Liver regular diet 4 weeks


title: Liver def diet 09

description: Liver deficient diet 4 weeks


title: Liver reg diet 17

description: Liver regular diet 7 weeks


title: Liver rich diet 02

description: Liver enriched diet 4 weeks

value: enriched diet 4 weeks


title: Liver reg diet 06

description: Liver enriched diet 4 weeks


title: Liver rich diet 08

description: Liver enriched diet 4 weeks


title: Spleen def diet 21

description: Spleen deficient diet 7 weeks

source_name: Spleen

value: Spleen


title: Spleen rich diet 18

description: Spleen rich diet 7 weeks


title: Liver reg diet 01

description: Liver regular diet 4 weeks


title: Spleen reg diet 20

description: Spleen regular diet 7 weeks


title: Spleen def diet 13

description: Spleen deficient diet 7 weeks


title: Spleen rich diet 16

description: Spleen rich diet 7 weeks


title: Spleen def diet 19

description: Spleen deficient diet 7 weeks


title: Spleen reg diet 15

description: Spleen regular diet 7 weeks


title: Liver rich diet 16

description: Liver rich diet 7 weeks


title: Spleen reg diet 17

description: Spleen regular diet 7 weeks


title: Spleen rich diet 14

description: Spleen rich diet 7 weeks