title: Mouse_RNA_Lysate_Rep4

source_name: brain lysate

extract_protocol: Following lysis 100,000 to 150,000 cells were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was then performed. RNA/DNA samples in 10 l of water were incubated for 2.5 hours at 16 C with 5 l the following mix (3x Blue Buffer (Enzymatics), 1.0 l PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 l Sera-Mag SpeedBeads (Thermo Scientific, 651520505025) resuspended in 30 l 20%PEG 8000/2.5 M NaCl and incubation at RT for 15 min and placed on magnet for two rounds of bead washing with 80% EtOH. Beads were then air-dried for 10-12 min and DNA was eluted off the beads by adding 40 l of water. Supernatant was then collected on magnet and placed on ice or stored at -20 C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.      Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was then pe


title: Mouse_Input_ExVivo_Rep3

status: Public on May 26 2017

type: SRA

city: La Jolla

first: Dylan

middle: Derik

last: Skola

state: CA

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

country: USA

institute: UCSD

library_source: genomic

data_processing:
Tag directories for the ChIP-seq experiments were combined into an ex vivo and in vitro pool for each target in both mouse and human. The tag directories for the input DNA were likewise combined. Peaks were then called on the pooled tags with the pooled input DNA as background using HOMER’s findPeaks command with the following parameters for the PU.1 ChIP-seq: “-style factor -size 200 -minDist 200” and the following parameters for the H3K27ac and H3K4me2 ChIP-seq: “-style histone -size 500 -minDist 1000 -region.” The “-tbp” parameter was set to the number of replicates in the pool.   For identifying regions that are deacetylated in vitro, peaks for H3K27ac replicates were called individually, then merged using bedtools. A matrix containing the number of reads in each merged peak in each replicate was generated using HOMER’s annotatePeaks command with the following parameters: “-size given -noadj -tbp 1”. The read count matrix was then loaded into R and the limma package with voom normalization was used to identify peaks where the reads were reduced more than two-fold in vitro at an FDR of 0.05.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
For ChIP-Seq experiments, a cross-linking step with paraformaldehyde was performed immediately after staining but before microglia sorting. Briefly, a subset of human cells, and mouse cells to be used for ChIP-Seq, were washed once after staining, fixed at RT with 1% paraformaldehyde in PBS (Affymetrix 19943 1 LT) for 10 minutes, incubated for 5 min at RT with glycine to a final concentration of 0.125 M for PFA quenching, and washed twice with cold staining buffer. Microglia were then sorted as described above. After sorting, microglia were pelleted and snap-frozen in liquid nitrogen and stored at -80 C until chromatin immunoprecipitation.   Chromatin immunoprecipitation for histone modification H3K4me2, H3K27ac and transcription factor PU.1 was performed as followed, using 500,000 to 2 million microglia per assay. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in water) for 10 min on ice. Lysate were centrifuge at 800 x rcf for 5 min at 4°C, and pellets were resuspended in 200 l of sonication/immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 15 min each, alternating stages of 30 sec “sonication-on” with 60 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 x rcf at 4°C. Two microliters of supernatant were then set aside for input library sequencing controls. Supernatants were then immunoprecipitated on a rotator for 2 h at 4°C with antibody pre-bound to 20 l Protein A Dynabeads (Life Technologies 10001D). The following antibodies were used: H3k4me2 (Millipore, 07030), 2.0 l from stock per sample; H3K27ac (Active Motif, 39135), 1.5 l from stock per sample; and PU.1 (Santa Cruz, sc-352), 3.0 g per sample.   Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in water) and eluted with 1% SDS/TE at room temperature in a final volume of 100 l.   Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 l of 5 M NaCl (final concentration 300 mM) was added to each samples immersed in 100 l SDS/TE. Crosslinking was then reversed by overnight incubation at 65°C in a hot air oven. Potentially contaminated RNA was then digested for 1 h at 37°C with 0.33 mg/ml RNase A, proteins digested for 1 h at 55°C with 0.5 mg/ml proteinase K, and DNA extracted using Sera-Mag SpeedBeads (Thermo Scientific, 6515205050250).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.
Mice were euthanized with CO2 and quickly perfused intracardially with ice-cold DPBS (Mediatech 21-031CV). Whole brains were removed and gently mechanically homogenized on ice as described above. Cells were fractionated by Percoll gradient centrifugation, washed, FC blocked with CD16/32 antibody (1:50, eBioscience 14-0161, clone 93) on ice for 15 min, stained 1:100 with CD11b-APC (BioLegend 101212, clone M1/70) and CD45-Alexa Fluor 488 (BioLegend 103122, clone 30-F11). Microglia were then purified by cell sorting as specified above, with microglia defined as live-CD11b+CD45Low single cells. Typical yield was roughly 250,000 microglia per mouse brain.

tag: strain

tag: culture protocol

tag: time in culture

value: ex vivo

tag: ligands in culture


title: Male dexamethasone treatment, hypothalamus, biological replicate 3

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Sample K

library_source: transcriptomic

data_processing:
Reads were aligned to the GRCm38 genome using Tophat v 2.0.13 (default parameters) for cerebral cortex samples and Tophat v 2.0.9 (default parameters) for hypothalamus samples
Gene expression values were quantified using HTSeq with the union method
Differential expression was performed for genes with >1 CPM in at least 3 samples
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx file contains results for all genes from differential expression analysis

molecule: total RNA

source_name: Male dexamethasone treatment, Hypothalamus

growth_protocol: Hypothalamus or cortex dissected from embryonic day 14.5 fetal mouse brain were dissociated into single cells and then cultured as neurospheres

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library according to the manufacturer's instructions

treatment_protocol: Neurospheres at third passage were treated with 100 nM dexamethasone or equivalent volumes of ethanol vehicle for 4 hours

tag: age

value: embryonic day E14.5

tag: gender

value: Male

tag: treatment

value: Dexamethasone

tag: tissue

value: brain

tag: tissue region

value: Hypothalamus

tag: cell type

value: neural progenitor/stem cells


title: Female Control 7 day exposure replicate 3

city: Athens

first: Adrian

middle: J.

last: Wolstenholme

state: GA

address: 501 DW Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

data_processing:
Read mapping: was performed using TopHat v2.0.14
Raw count extraction: was performed using HTSEQ v0.6.1p1
Genome_build: Brugia malayi wormbase assembly WS253
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix

organism: Brugia malayi

source_name: total RNA

growth_protocol: Mongolian gerbils (Meriones unguiculatus) were infected with L3 larvae of Brugia malayi ip. Infected animals were maintained for four months until infections were patent.

extract_protocol: RNA-Seq for the Illumina' TruSeq strand-specific kit

treatment_protocol: Infected gerbils were treated with either 6mg/kg DEC, 0.2 mg/kg Ivermectin or 1mg/kg albendazole, or left untreated. The adult worms and microfilariae were isolated 1 day or 7 days after treatment.

tag: sex/stage

value: Female worm

tag: isolation time, post treatment

value: Day 7

tag: replicate

tag: drug treatment

value: Control (DMSO)


title: Male dexamethasone treatment, hypothalamus, biological replicate 2

description: Sample I


title: Female Control 7 day exposure replicate 1


title: Mouse_RNA_Lysate_Rep2

data_processing:
The “analyzeRepeats” function of HOMER was used to generate a table of read counts for each experiment using the parameters “-raw -count exons -strand both -condenseGenes” as well as a table of reads per kilobase per million reads (RPKM) values using “-rpkm -normMatrix 1e7 -count exons -strand both -condenseGenes.” The RPKM values were converted to transcripts per million (TPM) by normalizing the expression values in each experiment to a total count of one million. The base-2 logarithm of the TPM values was taken after adding a pseudocount of 1 TPM to each gene.The raw count data from HOMER analyzerepeat.pl program were imported in R (version 3.3.1) and preprocessed with Bioconductor packages. Expression data was filtered with average logTPM value > 2.0.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq


title: Female Control 1 day exposure replicate 3

value: Day 1


title: Mouse_RNA_Lysate_Rep3


title: Female ethanol vehicle treatment, hypothalamus, biological replicate 1

description: Sample H

source_name: Female ethanol vehicle treatment, Hypothalamus

value: Female

value: Vehicle


title: Female dexamethasone treatment, hypothalamus, biological replicate 1

description: Sample G

source_name: Female dexamethasone treatment, Hypothalamus


title: Mouse_RNA_Lysate_Rep1


title: Female ethanol vehicle treatment, hypothalamus, biological replicate 3

description: Sample F


title: Female dexamethasone treatment, hypothalamus, biological replicate 3

description: Sample E


title: Microfilaria Albendazole 7 day exposure replicate 2

value: Microfilaria

value: Albendazole


title: Female Control 1 day exposure replicate 2


title: Mouse_RNA_ExVivo_Rep3

description:
mouse_rna_read_counts_sample_ids.csv
mouse_rna_tpm_trimmed_sample_ids.csv

extract_protocol: Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was then performed. RNA/DNA samples in 10 l of water were incubated for 2.5 hours at 16 C with 5 l the following mix (3x Blue Buffer (Enzymatics), 1.0 l PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 l Sera-Mag SpeedBeads (Thermo Scientific, 651520505025) resuspended in 30 l 20%PEG 8000/2.5 M NaCl and incubation at RT for 15 min and placed on magnet for two rounds of bead washing with 80% EtOH. Beads were then air-dried for 10-12 min and DNA was eluted off the beads by adding 40 l of water. Supernatant was then collected on magnet and placed on ice or stored at -20 C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.      Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was


title: Female Control 1 day exposure replicate 1


title: Female ethanol vehicle treatment, hypothalamus, biological replicate 2

description: Sample D


title: Mouse_RNA_ExVivo_Rep2


title: Mouse_RNA_7day_TGFB_2

value: Isolated microglia were plated in 48-, 24, or 6-well plates at the following numbers, respectively:80,000 to 125,000, 150,000 to 200,000, and 1.5 million. Culture media consisted of DMEM/F12 (Life Technologies, 113300-032) supplemented with 5% FBS (heat inactivated, Omega Scientific, FB-12) and 1x Anti-Anti (Life Technologies, 152240-062). No media changes were performed for the duration of the culture experiments. Interleukin-34 (R&D, human 5265-IL-010; mouse 5195-ML-010) was supplemented daily at a concentration of 20 ng/ml. Recombinant human or mouse TGF-b1 cytokine (R&D, human 240-B-002; mouse 7666-MB-005) was supplements daily as a concentration of 10 ng/ml. At the end of the culture experiments, microglia were washed once with cold PBS and either lysed with 150 ml Oligo d(t) beads lysis/binding buffer (100 mM Tris-HCl ph 7.5, 500 mM LiCl, 10 mM EDTA ph 8.0, 1% LiDS, 5 mM DTT, in water) or 150 ml ATAC-Seq lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water; see below), or cross-linked, scraped off the wells and pelleted in preparation of ChIP-Seq experiments (see below).

value: 7 d

value: IL34 + TGFβ


title: Microfilaria Albendazole 1 day exposure replicate 3


title: Male ethanol vehicle treatment, hypothalamus, biological replicate 1

description: Sample B

source_name: Male ethanol vehicle treatment, Hypothalamus

value: embryonic day E14.5


title: Female dexamethasone treatment, hypothalamus, biological replicate 2

description: Sample C


title: Microfilaria Albendazole 7 day exposure replicate 1


title: Male dexamethasone treatment, hypothalamus, biological replicate 1

description: Sample A

value: Male


title: Mouse_RNA_ExVivo_Rep1

value: ex vivo


title: Male ethanol vehicle treatment, hypothalamus, biological replicate 2

description: Sample J

value: brain


title: Mouse_RNA_7day_TGFB_1


title: Male dexamethasone treatment, cortex, biological replicate 3

source_name: Male dexamethasone treatment, Cortex

value: Dexamethasone

value: Cortex


title: Microfilaria Albendazole 1 day exposure replicate 2


title: Female Control 7 day exposure replicate 2

value: Female worm


title: Mouse_RNA_7day_Rep5


title: Male ethanol vehicle treatment, cortex, biological replicate 3

source_name: Male ethanol vehicle treatment, Cortex

value: neural progenitor/stem cells


title: Microfilaria Albendazole 1 day exposure replicate 1


title: Mouse_RNA_7day_Rep4


title: Male Albendazole 7 day exposure replicate 3

value: Male worm

value: Day 7


title: Mouse_RNA_7day_Rep3


title: Male Albendazole 7 day exposure replicate 1


title: Male Albendazole 7 day exposure replicate 2


title: Male ethanol vehicle treatment, cortex, biological replicate 2


title: Mouse_RNA_7day_Rep1


title: Male Albendazole 1 day exposure replicate 3

value: Day 1


title: Mouse_RNA_7day_Rep2


title: Mouse_RNA_6hr_Rep2

value: 6 h


title: Male ethanol vehicle treatment, cortex, biological replicate 1

value: Vehicle


title: Male dexamethasone treatment, cortex, biological replicate 1


title: Female dexamethasone treatment, cortex, biological replicate 3

source_name: Female dexamethasone treatment, Cortex

value: Female


title: Male Albendazole 1 day exposure replicate 1

value: Albendazole


title: Female Albendazole 7 day exposure replicate 3


title: Female ethanol vehicle treatment, cortex, biological replicate 3

source_name: Female ethanol vehicle treatment, Cortex


title: Mouse_RNA_24hr_Rep3

value: Isolated microglia were plated in 48-, 24, or 6-well plates at the following numbers, respectively:80,000 to 125,000, 150,000 to 200,000, and 1.5 million. Culture media consisted of DMEM/F12 (Life Technologies, 113300-032) supplemented with 5% FBS (heat inactivated, Omega Scientific, FB-12) and 1x Anti-Anti (Life Technologies, 152240-062). No media changes were performed for the duration of the culture experiments. Interleukin-34 (R&D, human 5265-IL-010; mouse 5195-ML-010) was supplemented daily at a concentration of 20 ng/ml. Recombinant human or mouse TGF-b1 cytokine (R&D, human 240-B-002; mouse 7666-MB-005) was supplements daily as a concentration of 10 ng/ml. At the end of the culture experiments, microglia were washed once with cold PBS and either lysed with 150 ml Oligo d(t) beads lysis/binding buffer (100 mM Tris-HCl ph 7.5, 500 mM LiCl, 10 mM EDTA ph 8.0, 1% LiDS, 5 mM DTT, in water) or 150 ml ATAC-Seq lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water; see below), or cross-linked, scraped off the wells and pelleted in preparation of ChIP-Seq experiments (see below).


title: Female Albendazole 7 day exposure replicate 2


title: Mouse_RNA_24hr_Rep1

value: Isolated microglia were plated in 48, 24, or 6-well plates at the following numbers, respectively:80,000 to 125,000, 150,000 to 200,000, and 1.5 million. Culture media consisted of DMEM/F12 (Life Technologies, 113300-032) supplemented with 5% FBS (heat inactivated, Omega Scientific, FB-12) and 1x Anti-Anti (Life Technologies, 152240-062). No media changes were performed for the duration of the culture experiments. Interleukin-34 (R&D, human 5265-IL-010; mouse 5195-ML-010) was supplemented daily at a concentration of 20 ng/ml. Recombinant human or mouse TGF-b1 cytokine (R&D, human 240-B-002; mouse 7666-MB-005) was supplements daily as a concentration of 10 ng/ml. At the end of the culture experiments, microglia were washed once with cold PBS and either lysed with 150 ml Oligo d(t) beads lysis/binding buffer (100 mM Tris-HCl ph 7.5, 500 mM LiCl, 10 mM EDTA ph 8.0, 1% LiDS, 5 mM DTT, in water) or 150 ml ATAC-Seq lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water; see below), or cross-linked, scraped off the wells and pelleted in preparation of ChIP-Seq experiments (see below).


title: Male dexamethasone treatment, cortex, biological replicate 2

value: embryonic day E14.5


title: Female Albendazole 7 day exposure replicate 1


title: Female dexamethasone treatment, cortex, biological replicate 2


title: Female ethanol vehicle treatment, cortex, biological replicate 2


title: HS5 stromal cells grown in monoculture

city: San Francisco

first: Arun

middle: P.

last: Wiita

address: 185 Berry St., Suite 290

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Unprocessed reads were adapter-trimmed and quality filtered using an in-house python script and aligned to hg19 using Bowtie version 0.12.8.
Raw read counts and normalized read counts in RPKM were obtained using in-house C++ scripts as in Wiita et al. eLife (2013) 2:01236.
Genome_build: hg19
Supplementary_files_format_and_content: The attached Excel file give the raw reads mapping to each UCSC identified transcript as well as the normalized read count in RPKM.  Processed data from all three samples is included in this file

molecule: polyA RNA

organism: Homo sapiens

source_name: HS5 bone marrow stromal cells

growth_protocol: See title for each sample

extract_protocol:
Performed as described in methods of Wiita et al eLife (2013) 2:01236.  Briefly, cells were lysed in Trizol and total RNA extracted.  Poly(A) mRNA was then isolated using New England Biolabs poly(dT) kit and quality and concentration evaluated by Nanodrop spectrophotometry.
Performed as described in methods of Wiita et al eLife (2013) 2:01236.  Briefly, poly(A) mRNA was fragmented in alkaline buffer and then size-selected for 50-100 bp fragments on TBE-Urea gels.  These fragments were then ligated to a small RNA linker, reverse transcribed, circularized, and PCR amplified for final library construction.

tag: enrichment


title: Female Albendazole 1 day exposure replicate 3


title: MM1S myeloma cells grown for 24h in coculture with HS5 bone marrow stromal cells

source_name: MM.1S myeloma cell line

value: MM1S cells were isolated from HS5 using Accutase and CD138+ magnetic beads


title: Female dexamethasone treatment, cortex, biological replicate 1


title: MM1S myeloma cells grown in monoculture


title: Female Albendazole 1 day exposure replicate 1


title: Female ethanol vehicle treatment, cortex, biological replicate 1


title: Wnt1-Cre; mirflox/flox_21

status: Public on May 25 2017

city: Stockholm

first: Patrik

last: Ernfors

address: Solnavägen 9

department: Medical Biochemestry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Reads were mapped with Tophat/2.0.4 to the mouse genome assembly, bam files from samples run on different lanes were merged with samtools, and FPKM values were calculated using the Cufflinks program with ENSEMBL annotation of genes and transcripts for each sample.
Raw counts for genes were generated using htseq/0.6.1 on bam files with duplicates included and analyzed using DEseq2 (Love et al., 2014) to get the log2 fold change, base mean and P value for comparisons of CKO Ctl VS WT Ctl, WT SNI VS WT Ctl and CKO SNI VS WT Ctl. The fold change of CKO SNI VS WT SNI was calculated by comparing the fold change of CKO SNI VS WT Ctl to the fold change of WT SNI VS WT Ctl.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text including read counts values for each sample and gene

source_name: Wnt1-Cre; mirflox/flox_bulk DRG

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen)
TruSeq Stranded mRNA Sample Prep Kit (Illumina/USA) to get the cDNA library according to the manual.

treatment_protocol: Spared nerve injury (SNI) surgical procedures were performed under anesthesia with isoflurane (1.8%) as previously described (Decosterd and Woolf, 2000; Pertin et al., 2012). Briefly, the skin of the mid-thigh from left lateral surface was incised and a separation was made directly through the biceps femoris muscle exposing three terminal branches of the sciatic nerve: common peroneal, tibial and sural nerves; The common peroneal and tibial nerves were tightly ligated with 6-0 silk (Ethicon), transected together distally to the ligation and a piece of 1-2 mm of the nerve was removed from the distal stump avoiding any contact with or stretching of the intact sural nerve during the surgery process. Finally, muscle and skin were closed in two layers with 5-0 silk.

tag: strain background

value: Mixed with prevalence of C57bl6

tag: animal id

tag: genotype

value: Wnt1-Cre; mirflox/flox

value: 3-6 month

value: Lumber 4-6 DRG (bulk dorsal root ganglia)

tag: condition

value: Spared nerve injury (SNI)


title: wt_23

source_name: wt_bulk DRG

value: wt


title: Mouse_RNA_6hr_Rep1

tag: strain

tag: culture protocol

tag: time in culture


title: Wnt1-Cre_15

source_name: Wnt1-Cre_bulk DRG

tag: age


title: Wnt1-Cre; mirflox/flox_19


title: wt_18


title: Mouse_RNA_24hr_Rep2

tag: ligands in culture


title: Wnt1-Cre; mirflox/flox_8

tag: tissue

value: naïve; control


title: Wnt1-Cre; mirflox/flox_9


title: Wnt1-Cre; mirflox/flox_5


title: Wnt1-Cre_3


title: Wnt1-Cre_2


title: Wnt1-Cre; mirflox/flox_4


title: Wnt1-Cre_1


title: Female Albendazole 1 day exposure replicate 2

value: Female worm


title: DECPLZRAPA24h_2

city: New York

first: Luka

last: Mesin

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
DE_exp2+1.xlsx
DPR_exp2_TCCTGAGC-TATCCTCT

data_processing:
The samples were sequenced on HiSeq 2500. Image analysis and base calling was done in real time by the instrument using default parameters.
40-bp single-end reads were pseudo-aligned using Kallisto version 0.43.0 against mouse transcriptome (Ensembl GRCm38 - release 79). Gene expression was inferred from transcript expression levels using the tximport R package as transcripts per million reads (TPM). Enrichment analysis was performed using GSEA software v2.2.3 (Broad Institute).
Supplementary_files_format_and_content: excel file with TPM and statistical analysis

source_name: Popliteal lymph node

extract_protocol:
Sorted cells were lysed in a guanidine thiocyanate buffer (Qiagen) supplemented with 1% β-mercaptoethanol. RNA isolated by SPRI bead cleanup (Agencourt RNAClean XP Kit) was reversely transcribed into cDNA.
Nextera XT (Illumina) was used to prepare a pooled library of fragmented and uniquely indexed samples, totaling six independent conditions in three biological replicates.

treatment_protocol: Rapamycin-treated samples were harvested from animals that received 2.5mg/kg of rapamycin at the same time of anti-DEC205-OVA injection.

value: Popliteal lymph node

value: Germinal center B cell

tag: cell markers

value: B220+ CD38- CD95+ CD45.1+ CD45.2- CD83hi CXCR4lo (DECPLZ)

tag: cell phenotype


title: DECPLZRAPA24h_3

description:
DE_exp2+1.xlsx
DPR_exp2_TAAGGCGA-AGAGTAGA

tag: cell type


title: DECPLZRAPA24h_4

description:
DE_exp2+1.xlsx
DPR_exp2_CGTACTAG-AGAGTAGA


title: DECNLZ24h_3

description:
DE_exp2+1.xlsx
DN_exp2_GGACTCCT-TATCCTCT

value: B220+ CD38- CD95+ CD45.1+ CD45.2+ CD83hi CXCR4lo (DECNLZ)


title: DECNLZ24h_4

description:
DE_exp2+1.xlsx
DN_exp2_TAGGCATG-TATCCTCT


title: DECPLZRAPA24h_1

description:
DE_exp2+1.xlsx
DPR_exp2_AGGCAGAA-TATCCTCT


title: DECNLZ24h_1

description:
DE_exp2+1.xlsx
DN_exp2_GGACTCCT-AGAGTAGA


title: Wnt1-Cre; mirflox/flox_13


title: DECPLZ24h_1

description:
DE_exp2+1.xlsx
DP_exp2_TAAGGCGA-TATCCTCT


title: DECPLZ24h_2

description:
DE_exp2+1.xlsx
DP_exp2_CGTACTAG-TATCCTCT


title: DECNLZ12h_3

description:
DE_exp1+1.xlsx
DN_exp1_CGTACT


title: Male Albendazole 1 day exposure replicate 2

tag: sex/stage

value: Male worm

tag: isolation time, post treatment

value: Day 1

value: Albendazole


title: DECPLZ24h_3

description:
DE_exp2+1.xlsx
DP_exp2_AGGCAGAA-AGAGTAGA


title: DECPLZ12h_3

description:
DE_exp1+1.xlsx
DP_exp1_TAAGGC


title: DECNLZ12h_2

description:
DE_exp1+1.xlsx
DN_exp1_TCCTGA


title: DECPLZ12h_2

description:
DE_exp1+1.xlsx
DP_exp1_GGACTC


title: DECNLZ12h_1

description:
DE_exp1+1.xlsx
DN_exp1_TAGGCA


title: wt_7


title: DECPLZ12h_1

description:
DE_exp1+1.xlsx
DP_exp1_AGGCAG


title: CTCF_ChIP-exo_WT-untagged_auxin2days_rep1

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

description: ChIP-exo

data_processing:
ChIP-seq and ChIP-exo. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out. for CTCF peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm. For H3K27me3 peaks that are broader we used a threshold-based method.
RNA-seq. Alignment was produced using STAR version 2.5.0a , aligned to mm9. Cufflinks version 2.2.1  with Bedtools version 2.17.0 were used as to produce input for differential expression analysis with Cuffdiff . Genes with an FPKM below 1.1 in all conditions were not considered in the differential expression analysis
Hi-C. We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in  (Imakaev et al., 2012; Lajoie et al., 2015). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs into 20kb and 100kb genomic bins to produce Hi-C contact matrices. To remove the short-range Hi-C artifacts - unligated and self-ligated Hi-C molecules - we ignored the contacts mapping to the same or adjacent genomic bins in all downstream analyses.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with anchor filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.
Supplementary_files_format_and_content: ChIP-seq and ChIP-exo. _Peaks.bed: position of the peaks. _Footprints.bed: position of ChIP-exo footprint. _tagDensity.bw: ChIP signal.
Supplementary_files_format_and_content: RNA-seq. .bw: tagDensity of signal.

source_name: mouse ES cells E14Tg2a

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative. mouse ES cells were targeted to insert an Auxin-Inducible Degron (AID) tag together with an eGFP cassette, and the auxin receptor OsTir1 was expressed from a transgene. ChIP-seq, Hi-C, 5C and RNA-seq were performed at different timepoints after adding auxin to the culture medium.

extract_protocol:
For ChIP-seq cells were  trypsinized and fixed in suspension; For Chromosome Conformation Capture cells were fixed in tissue culture plates and scrapped off; For RNA-seq cells werre washed once with PBS and lysed in Trizol in the tissue culture plate.
ChIP libraries were prepared using standard Illumina protocols; RNA-seq libraries were assembled using the non-stranded kit E7530L from NEB; 5C (in-situ ligation) and Hi-C (dilution ligation) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of Nora et al. 2017 Cell
ChIP-seq, ChIP-exo, RNA-seq, Hi-C, 5C

treatment_protocol: For induction of the auxin-inducible degron indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500µM from a 1000X stock diluted in sterile water and kept at 4°C up to 4 weeks or -20°C for long term storage.

value: 129/Ola, XY

value: WT-untagged

tag: chip epitope

value: CTCF (Active Motif 61311)


title: CTCF_ChIP-exo_WT-untagged_untreated_rep1

description: ChIP-exo


title: 4C-CTCF-delCDE-rep2

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
Trimmed reads were mapped to DpnII enzyme based reduced mm10 genome using Bowtie2.
Mapped reads were processed with 4Cker R package to generate bedgraph files
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated by 4Cker R package

source_name: mammary gland

growth_protocol: Mammary gland is harvested from lactating day1 female mouse

extract_protocol:
The 4C protocol was adapted from published methods 2,3. Frozen-stored mammary tissues collected at lactation day 1 (L1) were ground into powder. Chromatin was fixed with formaldehyde (final 1%) for 15 min at room temperature, and then was quenched with glycine (final 0.125 M). Pellets were lysed in lysis buffer (10 mM Tris HCI pH 8.0, 10 mM NaCl, 0.5% Nonidet P-40) containing Phenylmethylsulfonyl fluoride (PMSF) and protease inhibitors, incubated on ice for 30 min, and dounced using pre-chilled glass homogenizer, followed by another 10 min incubation on ice. After removal of supernatant, nuclei pellets were re-suspended in DpnIII buffer (New England Biolabs). SDS was added to a final concentration of 0.2% and samples was incubated for 1 hr at 37°C. 2% Triton X-100 was added, followed incubation for 1 hr at 37°C. Samples were incubated with 400 units each of restriction enzymes DpnII (New England Biolabs) and were incubated overnight at 37°C. To enzyme inactivation SDS was added (final 1%) and incubated for 30 min at 65°C, followed by SDS-sequestration with 1% Triton X-100 at 37°C for 1 hr, T4 ligase (New England Biolabs) was added to each sample and incubated for 1 hr at 16°C. Ligated samples were treated overnight with proteinase K (20 mg/mL, Invitrogen) at 65°C and 1 hr at 37°C with RNase A (10 mg/mL, Thermo Fisher Scientific), and DNA fragments were purified by phenol-chloroform method. DNA fragments from 3C were digested with MseI (New England Biolabs) overnight at 37°C and ligated using T4 ligase overnight at 16°C. DNA was purified by phenol/chloroform method and then amplified with site-specific primers linked to the Illumina DNA adaptors. Libraries for next generation sequencing were prepared and sequenced with HiSeq 2500 (Illumina).
4C-seq

value: mammary gland

tag: developmental stage

value: lactating day 1

value: CTCF site A mutant


title: 4C-CTCF-delCDE-rep1


title: CTCF_ChIP-exo_WT-untagged_untreated_rep2

description: ChIP-exo


title: CTCF_ChIP-exo_CTCF-AID_untreated_rep1

description: ChIP-exo

value: CTCF-AID, Tir1


title: 4C-STAT5A-delS3-rep1

value: STAT5A enhancer 3 mutant


title: 4C-WT-rep2

value: wild type


title: 4C-STAT5A-delS3-rep2


title: 4C-WT-rep1


title: ChIP-seq-Mammary-delD-L1-CTCF-rep1

data_processing:
ChIP-seq signals were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) to filter low-quality reads and subsequently  aligned to the mouse reference genome (mm10) using Bowtie aligner (Langmead et al., Nature methods, 2012) with the -m 1 parameter to obtain only uniquely mapped reads, except for CTCF samples where the -m 3 and --best parameters were used. HOMER software (Heinz et al., Mol. Cell, 2010) was applied for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Mammary

growth_protocol: CRISPR/Cas9 targeted mice were generated by the transgenic core of the National Heart, Lung, and Blood Institute (NHLBI). Mice carrying loxP sites flanking CTCF sites A and B were generated by InGenious using homologous recombination. The sequences between loxP sites were deleted using the germline Figla-Cre delete mice (gift from Jurrien Dean, NIDDK, NIH). All animal procedures were in accordance with NIH, NIDDK guidelines for the care and use of laboratory animals.

extract_protocol:
All tissues were snap frozen and stored at -80°C. Tissues were pulverized in liquid nitrogen followed by chromatin fixation with 1% formaldehyde final concentration. Washed chromatin (PBS) was homogenized using a dounce tissue grinder in Farnham’s lysis buffer and followed by chromatin fragmentation through sonication. Fragmentation efficiency in the range of 200 bp - 500 bp was controlled by gel electrophoresis and ChIP was performed using Dynabeads Protein A (Invitrogen) and the following antibodies: CTCF (Abcam ab70303 / Millipore 07-729) and H3K27ac (Abcam ab4729). Indexed libraries were produced using the NEBNext Ultra II DNA Library Prep Kit and NEBNext Index Primer Set for Illumina according to the manufacturer’s protocol. Fragments between 200 bp and 500 bp were selected by gel electrophoresis and 50 bp single-end sequencing was performed on an Illumina HiSeq 2500.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: state

value: day one of lactation

value: CTCF-delD

tag: chip antibody

value: CTCF (Abcam ab70303 / Millipore 07-729)


title: ChIP-seq-Mammary-delC-L1-CTCF-rep2

tag: genotype

value: CTCF-delC


title: ChIP-seq-Mammary-delD-L1-CTCF-rep2


title: ChIP-seq-Mammary-delCDE-L1-H3K27ac-rep1

value: CTCF-delCDE

value: H3K27ac (Abcam ab4729)


title: ChIP-seq-Mammary-delCDE-L1-H3K27me3-rep1

value: H3K27me3 (Abcam ab6002)


title: ChIP-seq-Cerebellum-delCDE-L1-H3K27me3-rep2

source_name: Cerebellum

value: Cerebellum


title: ChIP-seq-Cerebellum-delE-L1-H3K27me3-rep1

value: CTCF-delE


title: ChIP-seq-Mammary-delCDE-L1-CTCF-rep2


title: ChIP-seq-Mammary-delCDE-L1-H3K27me3-rep2


title: ChIP-seq-Mammary-delE-L1-CTCF-rep2


title: ChIP-seq-Cerebellum-WT-L1-H3K27me3-rep1

value: wild-type


title: ChIP-seq-Mammary-delAB-L1-CTCF-rep2

value: CTCF-delAB


title: ChIP-seq-Cerebellum-delCDE-L1-H3K27me3-rep1


title: ChIP-seq-Cerebellum-delE-L1-H3K27me3-rep2


title: ChIP-seq-Mammary-WT-L1-CTCF-rep2


title: ChIP-seq-Mammary-delCDE-L1-CTCF-rep1


title: ChIP-seq-Cerebellum-WT-L1-H3K27me3-rep2


title: ChIP-seq-Mammary-delE-L1-H3K27ac-rep1


title: ChIP-seq-Mammary-delE-L1-H3K27ac-rep2


title: ChIP-seq-Mammary-WT-L1-CTCF-rep1


title: ChIP-seq-Mammary-delE-L1-CTCF-rep1


title: ChIP-seq-Mammary-delCDE-L1-H3K27ac-rep2


title: ChIP-seq-Mammary-delD-L1-H3K27ac-rep1


title: ChIP-seq-Mammary-delD-L1-H3K27ac-rep2


title: Wnt1-Cre_6

tag: strain background

value: Mixed with prevalence of C57bl6

tag: animal id

value: 3-6 month

value: Lumber 4-6 DRG (bulk dorsal root ganglia)

tag: condition

value: naïve; control


title: ChIP-seq-Mammary-delC-L1-H3K27ac-rep2

tag: strain


title: ChIP-seq-Mammary-delC-L1-CTCF-rep1


title: ChIP-seq-Mammary-delAB-L1-CTCF-rep1


title: ChIP-seq-Mammary-WT-L1-H3K27me3-rep1


title: ChIP-seq-Mammary-delC-L1-H3K27ac-rep1


title: E7107 PHF5A Y36C 6

city: Cambridge

first: Silvia

last: Buonamici

state: MA

address: 300 Technology Square #5

institute: H3 Biomedicine

description: Sample name: GS002884

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Junction counts and reads across exon-intron boundaries are converted to percent spliced-in (PSI)
Genome_build: hg19
Supplementary_files_format_and_content: PSI values for each junction within each sample

source_name: Colon colorectal carcinoma

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: mutation

value: PHF5A Y36C


title: E7107 PHF5A Y36C 5

description: Sample name: GS002883


title: E7107 PHF5A Y36C 4

description: Sample name: GS002882


title: DECNLZ24h_2

description:
DE_exp2+1.xlsx
DN_exp2_TAGGCATG-AGAGTAGA

tag: tissue

value: Popliteal lymph node

value: Germinal center B cell

value: B220+ CD38- CD95+ CD45.1+ CD45.2+ CD83hi CXCR4lo (DECNLZ)


title: DMSO PHF5A Y36C 2

description: Sample name: GS002874


title: E7107 PHF5A Y36C 3

description: Sample name: GS002881


title: E7107 PHF5A Y36C 2

description: Sample name: GS002880


title: DMSO PHF5A Y36C 5

description: Sample name: GS002877


title: DMSO PHF5A Y36C 4

description: Sample name: GS002876


title: DMSO PHF5A Y36C 3

description: Sample name: GS002875


title: E7107 PHF5A WT 6

description: Sample name: GS002860

value: none (wildtype)


title: E7107 PHF5A WT 2

description: Sample name: GS002856


title: DMSO PHF5A Y36C 1

description: Sample name: GS002873


title: E7107 PHF5A WT 5

description: Sample name: GS002859


title: E7107 PHF5A WT 3

description: Sample name: GS002857


title: DMSO PHF5A WT 6

description: Sample name: GS002854


title: E7107 PHF5A WT 1

description: Sample name: GS002855


title: DMSO PHF5A WT 5

description: Sample name: GS002853


title: DMSO PHF5A WT 3

description: Sample name: GS002851


title: DMSO PHF5A WT 1

description: Sample name: GS002849


title: DMSO PHF5A WT 4

description: Sample name: GS002852


title: E7107 PHF5A Y36C 1

description: Sample name: GS002879


title: DMSO PHF5A Y36C 6

description: Sample name: GS002878


title: PC3 TSA 2

city: Carlsbad

first: Joanne

last: Yeakley

address: 1945 Camino Vida Roble Ste i

institute: BioSpyder Technologies, Inc.

description:
processed data file:
Pan-Cell TSA Response Read Counts.xlsx

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

source_name: PC3 TSA

growth_protocol: for the TSA response experiment, cells were grown in DMEM with 10% FBS

extract_protocol:
for the TSA response experiment, cells were washed once with PBS, then lysed using TempO-Seq Lysis Buffer
TempO-Seq targeted expression assay. Addition of adapters by amplification.

treatment_protocol: for the TSA response experiment, cells were treated with 0.1% DMSO or 1 uM Trichostatin A in 0.1% DMSO for 6 hours

tag: sample preparation

value: purified total RNA

tag: input


title: PC3 DMSO 3

source_name: PC3 DMSO


title: PC3 TSA 3


title: E7107 PHF5A WT 4

description: Sample name: GS002858


title: PC3 TSA 1


title: DMSO PHF5A WT 2

description: Sample name: GS002850


title: PC3 DMSO 1


title: MCF7 TSA 3

source_name: MCF7 TSA


title: PC3 DMSO 2


title: MCF7 TSA 2


title: MCF7 DMSO 3

source_name: MCF7 DMSO


title: HL60 diff DMSO TSA 3

source_name: HL60 diff DMSO TSA


title: MCF7 TSA 1


title: HL60 diff DMSO TSA 1


title: HL60 diff DMSO DMSO 3

source_name: HL60 diff DMSO DMSO


title: HL60 diff ATRA TSA 2

source_name: HL60 diff ATRA TSA


title: HL60 diff DMSO DMSO 1


title: HL60 diff ATRA TSA 1


title: HL60 diff DMSO DMSO 2


title: HL60 diff DMSO TSA 2


title: HL60 diff ATRA DMSO 2

source_name: HL60 diff ATRA DMSO


title: HL60 undiff TSA 3

source_name: HL60 undiff TSA

value: 50 ng


title: HL60 undiff TSA 2


title: HL60 diff ATRA DMSO 1


title: HL60 undiff DMSO 3

source_name: HL60 undiff DMSO

value: 30 ng


title: HL60 undiff TSA 1


title: Attenuation URR2

description:
processed data file:
Attenuation Read Counts.xlsx

source_name: Attenuation URR

tag: sample type

value: pooled donors

tag: source material manufacturer

value: Thermo Fisher


title: MCF7 DMSO 2


title: Attenuation URR3


title: HL60 undiff DMSO 2


title: MCF7 DMSO 1


title: Seq Run 2 URR4

description: processed data file: Seq Run Repeatability Read Counts.xlsx

source_name: pooled donors

extract_protocol: TempO-Seq targeted expression assay. Addition of adapters by amplification.

tag: manufacturer


title: Seq Run 2 URR5


title: Seq Run 2 URR3


title: Attenuation URR1


title: No Attenuation URR3

source_name: No Attenuation URR


title: Seq Run 2 URR2


title: HL60 undiff DMSO 1


title: Seq Run 1 URR3


title: Seq Run 1 URR5


title: Dose Response Vehicle rep 2

description: processed data file: Dose Response Read Counts.xlsx

data_processing:
base calling on instrument with RTA
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
then bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing and generating fastqs
fastqs were aligned to a pseudo transcriptome using Bowtie, allowing up to 2 mis-matches.
Genome_build: Multiple pseudo transcriptomes and hg38 (for GSM2422725 to GSM2422736). Processed data files include the sequences used for alignment in column "Probe_Sequence".
Supplementary_files_format_and_content: Probe_ID (genes) in column 1, Probe_Sequence used for alignment in column 2, Accession Number in column 3. Sample Names in row 1.

source_name: MCF-7 cell line

growth_protocol: Cell lines were grown in DME with 10% FBS under 5% CO2 in 96-well plates.

extract_protocol:
Cells were washed with 1X PBS, then lysed in 1X Lysis Buffer (BioSpyder Technologies, Inc.) at ~2,000 cells/uL, and stored at -80C.
TempO-Seq targeted expression assay. Addition of adapters by amplification.

value: homogeneous cell lysate

value: 4000 cells

value: BioSpyder


title: Seq Run 1 URR1


title: No Attenuation URR2


title: Dose Response Vehicle rep 1


title: Dose Response TSA 10 uM rep 3

treatment_protocol: Cells were either untreated, or treated with from 0.033 uM to 10 uM Trichostatin A diluted in 0.1% DMSO


title: Dose Response Vehicle rep 3


title: Dose Response TSA 10 uM rep 1


title: Dose Response TSA 3.3 uM rep 3


title: Dose Response TSA 10 uM rep 2


title: No Attenuation URR1


title: Dose Response TSA 3.3 uM rep 2


title: Dose Response TSA 1 uM rep 2


title: Dose Response TSA 1 uM rep 3


title: Dose Response TSA 3.3 uM rep 1


title: Dose Response TSA 1 uM rep 1


title: Seq Run 2 URR1


title: Dose Response TSA 0.03 uM rep 3


title: Dose Response TSA 0.1 uM rep 2


title: Dose Response TSA 0.1 uM rep 1


title: Dose Response TSA 0.1 uM rep 3


title: Seq Run 1 URR4


title: Dose Response TSA 0.3 uM rep 1


title: Dose Response TSA 0.3 uM rep 3


title: Seq Run 1 URR2


title: Platform RNAseq MDA rep 4

description:
processed data file: Platform Comparison RNAseq Read Counts.xlsx
genome build: hg38

source_name: MDA MB 231 cell line

value: MDA MB 231


title: Platform RNAseq MDA rep 6


title: Platform RNAseq MDA rep 5


title: Platform RNAseq MDA rep 3


title: Dose Response TSA 0.03 uM rep 1


title: Platform RNAseq MDA rep 2


title: Platform RNAseq MDA rep 1


title: Platform RNAseq MCF7 rep 3


title: Platform RNAseq MCF7 rep 6


title: Dose Response TSA 0.3 uM rep 2


title: Platform RNAseq MCF7 rep 4


title: Dose Response TSA 0.03 uM rep 2


title: Platform RNAseq MCF7 rep 1


title: Platform RNAseq MCF7 rep 2


title: Platform TempO-Seq MDA RNA  rep 12

description: processed data file: Platform Comparison TempO-Seq Read Counts.xlsx


title: Platform TempO-Seq MDA RNA  rep 10


title: Platform TempO-Seq MDA RNA  rep 3


title: Platform TempO-Seq MDA RNA  rep 6


title: Platform TempO-Seq MDA RNA  rep 8


title: Platform TempO-Seq MDA RNA  rep 1


title: Platform TempO-Seq MDA RNA  rep 7


title: Platform TempO-Seq MDA RNA  rep 4


title: Platform TempO-Seq MCF-7 RNA rep 12


title: Platform TempO-Seq MCF-7 RNA rep 8


title: Platform TempO-Seq MCF-7 RNA rep 11


title: Platform TempO-Seq MDA RNA  rep 9


title: Platform TempO-Seq MCF-7 RNA rep 9


title: Platform TempO-Seq MCF-7 RNA rep 7


title: Platform TempO-Seq MCF-7 RNA rep 5


title: Platform TempO-Seq MCF-7 RNA rep 6


title: Platform RNAseq MCF7 rep 5


title: Platform TempO-Seq MCF-7 RNA rep 4


title: Platform TempO-Seq MCF-7 RNA rep 3


title: Platform TempO-Seq MCF-7 RNA rep 2


title: Platform TempO-Seq MCF-7 RNA rep 1


title: TSN3 [run2]

city: Rochester

first: Lynne

last: Maquat

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

description: miRNA fractions enriched from Total RNA

data_processing:
For each read, the insert sequence 5' to the Illumina adaptor TGGAATTCTCGGGTGCCAAGGAACTCCA was extracted with the program cutadapt. Only inserts in the range of 18-25 nt were used.
BOWTIE2 was used to map them to mature miRNAs
The DESeq2 package was used for data normalization and differential expression analysis.
Raw reads where also normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: miRBase Release 21
Supplementary_files_format_and_content: EXCEL spreadsheet format. Raw reads mapped to miRNA, DESeq output, and RPM

source_name: HEK293T cells

growth_protocol: HEK293T cells were propagated in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was purified from cell pellets using miRNeasy Kits (Qiagen).
cDNA libraries were generated using the TruSeq Small RNA library preparation protocol (Illumina). After addition of the TruSeq 3' adapter (5' adenylated) using truncated T4 RNA ligase II (New England Biolabs) and, subsequently, the 5' adapter using T4 RNA ligase I (New England Biolabs), RNA was reverse-transcribed using a 3' adapter-specific primer. The resulting cDNA was then amplified using 12 cycles of PCR and a universal forward primer and a reverse primer, the latter harboring a bar code. cDNA libraries were purified using the Pippin Prep system (Sage Sicence) and quantified first using an Agilent Bioanalyzer and subsequently using qPCR analysis. Barcoded libraries were mixed at equimolar concentrations and sequenced using an Illumina HISeq2500v4 sequencer (Illumina) by single-end 50nt sequencing.

value: HEK293T cells

tag: transfected with

value: Tudor-SN siRNA


title: Context Indep URR in 2363 plex rep 2

description: processed data file: Context Independence Read Counts.xlsx

source_name: pooled cell lines

value: mixture

value: Agilent


title: Context Indep URR in 2363 plex rep 3


title: TSN2 [run2]

description: miRNA fractions enriched from Total RNA


title: Platform TempO-Seq MDA RNA  rep 5


title: TSN1 [run2]

description: miRNA fractions enriched from Total RNA


title: control3 [run2]

description: miRNA fractions enriched from Total RNA

value: Control (Ctl) siRNA


title: Context Indep URR in 2363 plex rep 1


title: Context Indep URR in 2941 plex rep 3


title: Platform TempO-Seq MDA RNA  rep 11


title: Platform TempO-Seq MCF-7 RNA rep 10


title: control2 [run2]

description: miRNA fractions enriched from Total RNA


title: control1 [run2]

description: miRNA fractions enriched from Total RNA


title: Context Indep URR in 2941 plex rep 1


title: Subject P25, time point 1, severe dysplasia

city: Boston

first: Jennifer

last: Beane

address: 72 East Concord Street, E6

department: School of Medicine

institute: Boston University

data_processing:
Demultiplexing and creation of FASTQ files was performed using Illumina CASAVA v1.8.2 software.
The FASTQ files were aligned to hg19 using TopHat v2.0.4 software and default parameters in addition to the mean insert size and standard deviation determined using MISO based on an initial TopHat alignment.
Alignment and quality metrics, including genebody ratio, were calculated using RSeQC v2.3.3.
Gene count estimates were derived using RSEM v1.2.1, Bowtie v1.0.0, and the Ensembl v74 GTF annotation file.
Gene filtering was conducted on normalized counts per million (cpm) calculated using R v3.0.0 and edgeR v3.4.2 using a modified version of the mixture model in the SCAN.UPC Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: matrix of raw count values for each Sample and each filtered Gene

source_name: Bronchial brushing

extract_protocol:
Bronchial airway brushings were obtained during autofluorescence bronchoscopy. Autofluorescence bronchoscopy and endobronchial biopsy were used to identify and sample PMLs (if present). The pathological grade of the lesions with the worst histology present was recorded. Total RNA was extracted from samples using miRNeasy Mini kit (Qiagen) according to manufacturer's protocol.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2. The libraries from individual samples were pooled in groups of 10 for cluster generation on the Illumina® cBot® using Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on the Illumina® HiSeq® 2500 to generate 100 nucleotide single-end reads.

value: Bronchial brushing

tag: patient id

tag: time point

tag: age

tag: Sex

value: Female

tag: smoking status

value: Ever smoker

tag: pack years

tag: copd status

value: COPD

tag: max histology

value: Severe dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P14, time point 1, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

value: Male

value: Moderate dysplasia


title: Cell Mix MDA DOs MCF-7 Lysate 4000 cells rep 3

description: processed data file: Cell Titration Read Counts.xlsx

tag: cell line

tag: sample preparation

value: homogeneous cell lysate

tag: input

tag: source material manufacturer


title: Cell Mix MDA DOs MCF-7 Lysate 4000 cells rep 2

value: 4000 cells


title: Subject P29, time point 1, moderate dysplasia

tag: smoking status

tag: pack years

tag: copd status

value: Unknown

tag: max histology

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment


title: Cell Mix MDA DOs 0.00001% MDA in MCF rep 3

source_name: MCF-7 and MDA MB 231 cell lines

value: MCF-7 and MDA MB 231

value: BioSpyder


title: Cell Mix MDA DOs 0.00001% MDA in MCF rep 2


title: Subject P1, time point 2, metaplasia

tag: tissue

tag: patient id

value: Metaplasia

value: Normal

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P11, time point 1, severe dysplasia

tag: time point

tag: age

tag: Sex

tag: smoking status

tag: pack years


title: Subject P22, time point 2, metaplasia

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments

tag: unique alignments


title: Cell Mix MDA DOs 0.00001% MDA in MCF rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Cell Mix MDA DOs 0.0001% MDA in MCF rep 2


title: Context Indep URR in 2941 plex rep 2

value: mixture

value: purified total RNA

value: Agilent


title: Cell Mix MDA DOs 0.0001% MDA in MCF rep 1


title: Subject P26, time point 2, normal

tag: tissue

value: Bronchial brushing

tag: patient id

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Subject P31, time point 3, mild dysplasia

tag: time point

tag: age

tag: Sex

tag: smoking status

value: Ever smoker

tag: pack years

tag: copd status

tag: max histology

value: Mild dysplasia

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MDA DOs 0.001% MDA in MCF rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Subject P9, time point 2, metaplasia

tag: tissue

tag: patient id

value: COPD

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Subject P17, time point 3, metaplasia

tag: time point

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MDA DOs 0.001% MDA in MCF rep 2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: DECPLZ24h_4

description:
DE_exp2+1.xlsx
DP_exp2_TCCTGAGC-AGAGTAGA

source_name: Popliteal lymph node

tag: strain

tag: tissue

value: Popliteal lymph node

tag: cell type

value: Germinal center B cell

tag: cell markers

value: B220+ CD38- CD95+ CD45.1+ CD45.2- CD83hi CXCR4lo (DECPLZ)

tag: cell phenotype


title: Cell Mix MDA DOs 0.01% MDA in MCF rep 3

value: homogeneous cell lysate


title: Cell Mix MDA DOs 0.0001% MDA in MCF rep 3

value: 4000 cells


title: ChIP-seq-Mammary-WT-L1-H3K27me3-rep2

source_name: Mammary

value: Mammary gland

tag: state

value: day one of lactation

tag: genotype

value: wild-type

tag: chip antibody

value: H3K27me3 (Abcam ab6002)


title: Subject P8, time point 2, moderate dysplasia

tag: patient id

tag: time point

tag: age

tag: Sex

value: Male

tag: smoking status

tag: pack years

tag: max histology

value: Moderate dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MDA DOs 0.001% MDA in MCF rep 3

tag: cell line

value: MCF-7 and MDA MB 231

tag: sample preparation

tag: input

tag: source material manufacturer

value: BioSpyder


title: Subject P29, time point 3, moderate dysplasia

tag: tissue

value: Bronchial brushing

tag: patient id

tag: time point

tag: age

tag: Sex

value: Female

value: Ever smoker

tag: copd status

value: Unknown

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Subject P20, time point 2, normal

tag: smoking status

tag: pack years

tag: max histology

value: Normal

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments


title: Cell Mix MDA DOs MCF-7 Lysate 4000 cells rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Cell Mix MDA DOs 0.01% MDA in MCF rep 2


title: Subject P24, time point 2, normal

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: copd status

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P20, time point 1, metaplasia

tag: smoking status

tag: pack years

tag: max histology

value: Metaplasia

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MDA DOs 0.01% MDA in MCF rep 1

tag: cell line

tag: sample preparation

value: homogeneous cell lysate

tag: input

tag: source material manufacturer


title: Subject P28, time point 2, hyperplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: copd status

value: COPD

value: Hyperplasia

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments


title: Cell Mix MDA DOs 0.1% MDA in MCF rep 3

value: 4000 cells


title: Subject P14, time point 2, severe dysplasia

tag: smoking status

tag: pack years

tag: max histology

value: Severe dysplasia

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P26, time point 1, hyperplasia

tag: tissue

tag: patient id

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Subject P21, time point 3, hyperplasia

tag: time point

tag: age

tag: Sex

tag: copd status

tag: read 1 alignment


title: Cell Mix MDA DOs 1% MDA in MCF rep 2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Th2-1st_MeninKO_RNA

city: Chiba

first: Atsushi

last: Onodera

address: Chuo-ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Five-day cultured Th2 cells generated from primary splenic CD4_T cells

growth_protocol: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro.

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
TruSeq Stranded mRNA Library Preparation Kit (Illumina) was used according to the manufacturer's protocol.

tag: cell type

value: Th2 cells

tag: strain

tag: genotype/variation

value: Menin KO


title: Th2-3rd_WT_RNA

source_name: Three-week cultured Th2 cells generated from primary splenic CD4_T cells

growth_protocol: Splenic CD4_T cells were stimulated under Th2 culture conditions (15 ng/ml IL-2, 10 ng/ml IL-4) for 5 days in vitro. The Th2 cells were further cultured in vitro for another 2 days in the absence of any exogenous cytokines. The cultured CD4 T cells were then restimulated with immobilized anti-TCR mAbs with IL-2 and anti-IL-4 mAbs for 5 days.

value: wild type


title: Subject P10, time point 2, moderate dysplasia

tag: tissue

value: Male

tag: smoking status

value: Never smoker

tag: pack years

tag: max histology

value: Moderate dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: unique alignments

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MDA DOs 10% MDA in MCF rep 3

tag: cell line

value: MCF-7 and MDA MB 231

tag: sample preparation

tag: input

value: BioSpyder


title: Subject P5, time point 2, hyperplasia

value: Bronchial brushing

tag: patient id

tag: time point

tag: age

tag: Sex

value: Female

value: Ever smoker

tag: copd status

tag: read 1 alignment

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Th2-3rd_MeninKO_RNA

tag: cell type

tag: strain

tag: genotype/variation


title: Cell Mix MDA DOs 1% MDA in MCF rep 3

value: homogeneous cell lysate

tag: source material manufacturer


title: Th2-1st_WT_Menin_rep2

data_processing:
Illumina Casava software used for basecalling and making Fastq files.
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8).
Each aligned read sequence was extended to 120 bp in order to efficiently detect duplicate reads aligned to identical locations. These 120 bp tags were used for further analysis (Bed files)
Genome_build: mm10
Supplementary_files_format_and_content: Bed files

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Antibody-specific immunoprecipitates and total input DNA samples were prepared using a NEBNext ChIP-Seq Library Prep Reagent Set for Illumina.  Adaptor-ligated DNA was recovered using AMPure XP Beads.  This DNA was then amplified by 15 cycles of PCR and again recovered using AMPure XP Beads. Fifty cycles of sequencing reaction were preformed on an Illumina HiSeq1500.

tag: chip antibody

value: Menin (bethyl:A300-105A)


title: Th2-1st_WT_RNA


title: Subject P3, time point 2, severe dysplasia

tag: tissue

tag: smoking status

tag: pack years

value: COPD

tag: max histology

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P31, time point 2, moderate dysplasia

tag: patient id

tag: time point

tag: age

tag: Sex

tag: copd status

tag: read 1 alignment

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MDA DOs 0.1% MDA in MCF rep 1

tag: cell line

tag: sample preparation

tag: input

value: 4000 cells

tag: source material manufacturer


title: Cell Mix MDA DOs 10% MDA in MCF rep 2


title: Th2-3rd_WT_Input_rep1

tag: cell type

tag: strain

tag: chip antibody

tag: genotype/variation


title: Th2-1st_WT_Input_rep1


title: Cell Mix MDA DOs No Input rep 3

organism: unidentified

value: 0 ng


title: Subject P16, time point 2, metaplasia

tag: tissue

tag: patient id

tag: smoking status

tag: pack years

tag: max histology

value: Metaplasia

tag: dysplasia status

value: Normal

tag: total alignments

tag: unique alignments

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MDA DOs 10% MDA in MCF rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Th2-3rd_WT_Menin_rep1

tag: cell type

value: Th2 cells

tag: strain

tag: chip antibody

tag: genotype/variation

value: wild type


title: Subject P18, time point 2, hyperplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

value: Hyperplasia

tag: read 1 alignment

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MDA DOs MDA Lysate 4000 cells rep 3

tag: cell line

value: MDA MB 231

tag: sample preparation

tag: input

tag: source material manufacturer


title: Th2-1st_WT_Menin_rep1

tag: cell type

tag: strain

tag: chip antibody

tag: genotype/variation


title: Cell Mix MDA DOs No Input rep 2


title: Cell Mix MDA DOs 0.1% MDA in MCF rep 2


title: Cell Mix MDA DOs 1% MDA in MCF rep 1


title: Th2-3rd_WT_Menin_rep2


title: Cell Mix MDA DOs MDA Lysate 4000 cells rep 2


title: Cell Mix MDA DOs No Input rep 1


title: Cell Mix MCF DOs No Input rep 2


title: Cell Mix MCF DOs No Input rep 1


title: Subject P15, time point 2, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

value: Male

value: Unknown

value: Moderate dysplasia

tag: dysplasia status

value: Dysplasia

tag: total alignments

tag: unique alignments

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P25, time point 3, moderate dysplasia

value: Bronchial brushing

value: Female

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: read 1 alignment

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MCF DOs MDA Lysate 4000 cells rep 3

tag: cell line

tag: sample preparation

value: homogeneous cell lysate

tag: input

tag: source material manufacturer

value: BioSpyder


title: Cell Mix MCF DOs No Input rep 3


title: Cell Mix MDA DOs MDA Lysate 4000 cells rep 1


title: Repeatability No Input rep 3

description: processed data file: Repeatability Read Counts.xlsx


title: Subject P5, time point 1, metaplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

value: Ever smoker

value: COPD

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 2 alignment


title: RNA Input No Input Control rep 2

description: processed data file: RNA Input Titration Read Counts.xlsx

value: 0 ng


title: Subject P9, time point 1, moderate dysplasia

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: read 1 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: RNA Input No Input Control rep 3

tag: sample preparation

tag: input

tag: source material manufacturer


title: Repeatability No Input rep 1


title: Cell Mix MCF DOs MDA Lysate 4000 cells rep 1

tag: cell line

value: 4000 cells


title: Repeatability No Input rep 2


title: Subject P25, time point 2, normal

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

value: Normal

tag: dysplasia status

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MCF DOs 0.00001% MCF in MDA rep 2


title: PG1

city: Beijing

first: Yang

last: Yang

address: No. 17 Tsing Hua East Road，HaiDian District

department: College of Food Science and Nutritional Engineering

country: China

institute: China Agricultural University

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq R package v1.18.0. DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed.
Genome_build: NC_999999999.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Lactiplantibacillus plantarum

source_name: cells

growth_protocol: Samples of control group and H2O2-treated group were cultrued in MRS media at 37℃ until OD600 ~ 0.8

extract_protocol:
Cells were harvested by centrifugation, flash frozen by liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Samples of H2O2-treated group were further cultrued in 5mM H2O2-contained MRS media at 37℃ for 30 min

tag: strain

tag: growth condition

tag: treatment

value: treated by 5mM H2O2-contained MRS media for 30 min


title: Subject P31, time point 1, moderate dysplasia

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: CK3

value: untreated


title: Subject P29, time point 2, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: dysplasia status

tag: non-splice alignments

tag: splice alignments


title: Subject P7, time point 2, hyperplasia

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

value: Hyperplasia

tag: properly paired alignments


title: CK2

tag: strain

tag: growth condition

tag: treatment


title: Subject P16, time point 1, moderate dysplasia

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MCF DOs 0.0001% MCF in MDA rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Cell Mix MCF DOs 0.00001% MCF in MDA rep 3


title: Cell Mix MCF DOs 0.0001% MCF in MDA rep 2


title: CK1


title: PG2


title: Cell Mix MCF DOs 0.001% MCF in MDA rep 3


title: RNA Input No Input Control rep 1


title: Subject P24, time point 1, metaplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

value: Metaplasia

tag: dysplasia status

tag: non-splice alignments

tag: splice alignments


title: Cell Mix MCF DOs 0.0001% MCF in MDA rep 3


title: Cell Mix MCF DOs 0.01% MCF in MDA rep 3


title: Cell Mix MCF DOs 0.01% MCF in MDA rep 2


title: Subject P17, time point 1, metaplasia

value: Male

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P2, time point 1, severe dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

value: Unknown

value: Severe dysplasia


title: Subject P1, time point 1, severe dysplasia

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

value: Dysplasia


title: Cell Mix MCF DOs 0.01% MCF in MDA rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Subject P28, time point 1, normal

value: Bronchial brushing

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MCF DOs MDA Lysate 4000 cells rep 2

value: MDA MB 231


title: Cell Mix MCF DOs 0.1% MCF in MDA rep3

value: homogeneous cell lysate


title: Subject P17, time point 2, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: smoking status

tag: pack years

value: Moderate dysplasia

tag: genebody 80/20 ratio

tag: mean gc content


title: PG3

tag: strain

tag: growth condition

tag: treatment


title: Cell Mix MCF DOs 0.1% MCF in MDA rep2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer

value: BioSpyder


title: Cell Mix MCF DOs 0.001% MCF in MDA rep 2


title: Subject P10, time point 1, moderate dysplasia

value: Never smoker

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Cell Mix MCF DOs 0.001% MCF in MDA rep 1


title: Subject P11, time point 2, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: smoking status

value: Ever smoker

tag: pack years

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MCF DOs 1% MCF in MDA rep 2

tag: cell line

tag: sample preparation

tag: input

value: 4000 cells

tag: source material manufacturer


title: Cell Mix MCF DOs 0.1% MCF in MDA rep1


title: Subject P2, time point 2, moderate dysplasia

value: Female

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Cell Mix MCF DOs 1% MCF in MDA rep 3


title: Subject P21, time point 2, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: age

tag: Sex

tag: smoking status

value: COPD

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Subject P7, time point 1, mild dysplasia

tag: pack years

tag: copd status

tag: max histology

value: Mild dysplasia

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MCF DOs 10% MCF in MDA rep 3

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Cell Mix MCF DOs 1% MCF in MDA rep 1


title: Subject P15, time point 1, moderate dysplasia

tag: tissue

tag: patient id

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Cell Mix MCF DOs 10% MCF in MDA rep 1


title: Subject L82, metaplasia

data_processing:
Demultiplexing and creation of FASTQ files was performed using Illumina CASAVA v1.8.2 software.
The FASTQ files were aligned to hg19 using TopHat v2.0.4 software and default parameters in addition to the mean insert size and standard deviation determined using MISO based on an initial TopHat alignment.
Alignment and quality metrics, including genebody ratio, were calculated using RSeQC v2.3.3.
Gene count estimates were derived using HTSeq-count v0.5.4 with Python v2.7.3 and the Ensembl v64 GTF annotation file.
Gene filtering was conducted on normalized counts per million (cpm) calculated using R v3.0.0 and edgeR v3.4.2 using a modified version of the mixture model in the SCAN.UPC Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited matrices includes raw count values for each Sample and each filtered Gene, CPM values for each Sample and each filtered Gene, RPKM values for each Sample and each filtered Gene, raw count values for each Sample and each filtered Gene, and RPKM values for each Sample and each filtered Gene

extract_protocol:
Bronchial airway brushings were obtained during autofluorescence bronchoscopy. Autofluorescence bronchoscopy and endobronchial biopsy were used to identify and sample PMLs (if present). The pathological grade of the lesions with the worst histology present was recorded. Total RNA was extracted from bronchial brushings using miRNeasy Mini kit (Qiagen) according to manufacturer's protocol.
Sequencing libraries were prepared from total RNA samples using Illumina® TruSeq® RNA Sample Preparation Kit v2. The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina® cBot® using Illumina® TruSeq® Paired-End Cluster Kit. Each sample was sequenced on the Illumina® HiSeq® 2500 to generate paired-end 100 nucleotide reads

tag: age

tag: Sex

tag: smoking status

value: Current smoker

tag: pack years

tag: copd status

tag: non-splice alignments

tag: splice alignments

tag: properly paired alignments


title: Subject P21, time point 1, severe dysplasia

tag: tissue

tag: time point

tag: max histology

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject P8, time point 1, moderate dysplasia

tag: patient id

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment


title: Cell Mix MCF DOs 10% MCF in MDA rep 2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Subject L81, metaplasia

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

value: No COPD

value: Metaplasia

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments


title: Subject P3, time point 1, severe dysplasia

tag: tissue

tag: patient id

tag: time point

tag: max histology

tag: dysplasia status

tag: splice alignments

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Cell Mix MCF DOs MCF-7 Lysate 4000 cells rep 1

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Subject L80, metaplasia

tag: age

tag: Sex

tag: smoking status

value: Former smoker

tag: pack years

tag: copd status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment


title: Cell Mix MCF DOs MCF-7 Lysate 4000 cells rep 3


title: Platform TempO-Seq MDA RNA  rep 2

value: purified total RNA


title: Subject P22, time point 1, moderate dysplasia

tag: tissue

tag: patient id

tag: time point

tag: max histology

tag: dysplasia status

value: Dysplasia

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Cell Mix MCF DOs MCF-7 Lysate 4000 cells rep 2

tag: cell line

tag: sample preparation

tag: input

tag: source material manufacturer


title: Lysate Input 0_004 cell rep 3

description: processed data file: Lysate Input Titration Read Counts.xlsx

value: 0.004 cells


title: Lysate Input 0_004 cell rep 2

value: MDA MB 231


title: Subject L8, dysplasia

value: Bronchial brushing

tag: age

tag: Sex

tag: smoking status

tag: pack years

tag: copd status

tag: total alignments

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject L79, metaplasia

tag: tissue

tag: max histology

tag: dysplasia status

tag: unique alignments

tag: read 1 alignment

tag: read 2 alignment

tag: positive strand alignments


title: Subject L9, dysplasia

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Lysate Input 0_04 cell rep 2

tag: cell line

tag: sample preparation

value: homogeneous cell lysate

tag: input

value: 0.04 cells

tag: source material manufacturer


title: Subject L78, metaplasia

tag: age

tag: Sex

value: Male

tag: smoking status

tag: pack years

tag: copd status

tag: total alignments

tag: properly paired alignments


title: Lysate Input 0_04 cell rep 3

value: BioSpyder


title: Lysate Input 0_004 cell rep 1


title: Subject L77, metaplasia

tag: tissue

tag: max histology

tag: dysplasia status

tag: unique alignments

tag: read 1 alignment

tag: genebody 80/20 ratio

tag: mean gc content


title: Lysate Input 0_04 cell rep 1

tag: cell line

tag: sample preparation


title: Lysate Input 0_4 cell rep 3

tag: input

value: 0.4 cells

tag: source material manufacturer


title: Subject L74, dysplasia

tag: age

tag: Sex

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments

tag: non-splice alignments

tag: splice alignments


title: Subject L76, metaplasia

tag: tissue

value: Female

tag: smoking status

tag: pack years

tag: copd status

tag: max histology

tag: total alignments

tag: properly paired alignments


title: Lysate Input 0_4 cell rep 1

tag: cell line

tag: sample preparation


title: Subject L75, dysplasia

value: COPD

value: Severe dysplasia

tag: dysplasia status

tag: unique alignments

tag: read 1 alignment

tag: genebody 80/20 ratio

tag: mean gc content


title: Subject L73, dysplasia

tag: age

tag: Sex

value: Mild dysplasia

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Lysate Input 0_4 cell rep 2

tag: input

tag: source material manufacturer


title: Subject L71, dysplasia

tag: tissue

tag: smoking status

value: Current smoker

tag: pack years

tag: copd status

tag: max histology

tag: non-splice alignments

tag: splice alignments


title: Lysate Input 4 cells rep 2

tag: cell line

tag: sample preparation

value: 4 cells


title: Subject L72, dysplasia

value: No COPD

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Lysate Input 4 cells rep 3

tag: input

tag: source material manufacturer


title: Subject L70, dysplasia

tag: tissue

tag: age

tag: Sex

tag: smoking status

value: Former smoker

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Subject L7, dysplasia

tag: pack years

tag: copd status

tag: max histology

value: Dysplasia

tag: non-splice alignments

tag: splice alignments


title: Lysate Input 4 cells rep 1

tag: cell line

tag: sample preparation


title: Lysate Input 40 cells rep 3

value: 40 cells


title: Lysate Input 40 cells rep 2

value: MDA MB 231


title: Lysate Input 40 cells rep 1


title: Subject L67, dysplasia

value: Bronchial brushing

tag: dysplasia status

tag: total alignments

tag: unique alignments

tag: read 1 alignment

tag: properly paired alignments

tag: genebody 80/20 ratio

tag: mean gc content


title: Lysate Input 400 cells rep 3

value: homogeneous cell lysate

tag: input

value: 400 cells

tag: source material manufacturer


title: Subject L69, no dysplasia

tag: tissue

tag: age

tag: Sex

value: Male

tag: smoking status

value: Hyperplasia

value: Normal

tag: read 2 alignment

tag: positive strand alignments

tag: negative strand alignments


title: Lysate Input 400 cells rep 2

tag: cell line

tag: sample preparation

value: BioSpyder


title: Lysate Input 400 cells rep 1


title: Subject L66, no dysplasia

value: Female

tag: pack years

tag: copd status

tag: max histology

tag: dysplasia status

tag: total alignments

tag: non-splice alignments

tag: splice alignments


title: Lysate Input 4000 cells rep 2

tag: input

value: 4000 cells

tag: source material manufacturer