title: SAM054_probing_1_igg


title: SAM280_probing_1_igg

status: Public on Jul 01 2022

type: protein

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

country: USA

institute: The Emmes Company

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

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

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

molecule: protein

organism: Homo sapiens

source_name: serum

label_protocol: No labeling

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

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

tag: subject id

tag: treatment

value: A/H5N1 HA + MF59

tag: day

value: N


title: SAM106_probing_1_igg


title: SAM188_probing_1_igg


title: SAM149_probing_1_igg

value: A/H5N1 HA + PBS


title: SAM169_probing_1_igg


title: SAM363_probing_1_igg


title: SAM122_probing_1_igg

value: Y


title: SAM230_probing_1_igg


title: SAM069_probing_1_igg


title: SAM291_probing_1_igg


title: SAM293_probing_1_igg


title: SAM329_probing_1_igg


title: SAM214_probing_1_igg


title: SAM204_probing_1_igg


title: SAM061_probing_1_igg


title: SAM328_probing_1_igg


title: SAM155_probing_1_igg


title: SAM031_probing_1_igg


title: SAM109_probing_1_igg


title: SAM192_probing_1_igg


title: SAM153_probing_1_igg


title: SAM142_probing_1_igg


title: SAM115_probing_1_igg


title: SAM173_probing_1_igg


title: SAM114_probing_1_igg


title: SAM086_probing_1_igg


title: SAM390_probing_1_igg


title: SAM117_probing_1_igg


title: SAM226_probing_1_igg


title: SAM046_probing_1_igg


title: SAM137_probing_1_igg


title: SAM076_probing_1_igg


title: SAM183_probing_1_igg


title: SAM070_probing_1_igg


title: SAM372_probing_1_igg


title: SAM326_probing_1_igg


title: SAM089_probing_1_igg


title: SAM348_probing_1_igg


title: SAM338_probing_1_igg


title: SAM030_probing_1_igg


title: SAM133_probing_1_igg


title: SAM095_probing_1_igg


title: SAM196_probing_1_igg


title: SAM055_probing_1_igg


title: SAM123_probing_1_igg


title: SAM148_probing_1_igg


title: SAM100_probing_1_igg


title: SAM320_probing_1_igg


title: SAM382_probing_1_igg


title: SAM282_probing_1_igg


title: SAM300_probing_1_igg


title: SAM166_probing_1_igg


title: SAM385_probing_1_igg


title: SAM309_probing_1_igg


title: SAM360_probing_1_igg


title: SAM003_probing_1_igg


title: SAM366_probing_1_igg


title: SAM236_probing_1_igg


title: SAM065_probing_1_igg


title: SAM105_probing_1_igg


title: SAM201_probing_1_igg


title: SAM234_probing_1_igg


title: SAM298_probing_1_igg


title: SAM286_probing_1_igg


title: SAM110_probing_1_igg


title: SAM356_probing_1_igg


title: SAM367_probing_1_igg


title: SAM243_probing_1_igg


title: SAM048_probing_1_igg


title: SAM096_probing_1_igg


title: SAM285_probing_1_igg


title: SAM205_probing_1_igg


title: SAM038_probing_1_igg


title: SAM264_probing_1_igg


title: SAM321_probing_1_igg


title: SAM104_probing_1_igg


title: SAM359_probing_1_igg


title: SAM281_probing_1_igg


title: SAM185_probing_1_igg


title: SAM171_probing_1_igg


title: SAM308_probing_1_igg


title: SAM093_probing_1_igg


title: SAM189_probing_1_igg


title: SAM349_probing_1_igg


title: SAM075_probing_1_igg


title: SAM350_probing_1_igg


title: SAM132_probing_1_igg


title: SAM128_probing_1_igg


title: SAM279_probing_1_igg


title: SAM090_probing_1_igg


title: SAM042_probing_1_igg


title: SAM058_probing_1_igg


title: SAM289_probing_1_igg


title: SAM200_probing_1_igg


title: SAM312_probing_1_igg


title: SAM138_probing_1_igg


title: SAM021_probing_1_igg


title: SAM258_probing_1_igg


title: SAM197_probing_1_igg


title: SAM294_probing_1_igg


title: SAM049_probing_1_igg


title: SAM337_probing_1_igg


title: SAM005_probing_1_igg


title: SAM012_probing_1_igg


title: SAM081_probing_1_igg


title: SAM355_probing_1_igg


title: SAM225_probing_1_igg


title: SAM135_probing_1_igg


title: SAM064_probing_1_igg


title: SAM250_probing_1_igg


title: SAM017_probing_1_igg


title: SAM239_probing_1_igg


title: SAM299_probing_1_igg


title: SAM316_probing_1_igg


title: SAM190_probing_1_igg


title: SAM231_probing_1_igg


title: SAM130_probing_1_igg


title: SAM389_probing_1_igg


title: SAM152_probing_1_igg


title: SAM097_probing_1_igg


title: SAM248_probing_1_igg


title: SAM213_probing_1_igg


title: SAM257_probing_1_igg


title: SAM158_probing_1_igg


title: SAM160_probing_1_igg


title: SAM287_probing_1_igg


title: SAM066_probing_1_igg


title: SAM124_probing_1_igg


title: SAM307_probing_1_igg


title: SAM050_probing_1_igg


title: SAM371_probing_1_igg


title: SAM332_probing_1_igg


title: SAM094_probing_1_igg


title: SAM019_probing_1_igg


title: SAM351_probing_1_igg


title: SAM319_probing_1_igg


title: SAM310_probing_1_igg


title: SAM191_probing_1_igg


title: SAM159_probing_1_igg


title: SAM164_probing_1_igg


title: SAM027_probing_1_igg


title: SAM266_probing_1_igg


title: SAM141_probing_1_igg


title: SAM198_probing_1_igg


title: SAM352_probing_1_igg


title: SAM259_probing_1_igg


title: SAM249_probing_1_igg


title: SAM304_probing_1_igg


title: SAM324_probing_1_igg


title: SAM315_probing_1_igg


title: SAM235_probing_1_igg


title: SAM269_probing_1_igg

value: A/H5N1 HA + AS03


title: SAM154_probing_1_igg


title: SAM088_probing_1_igg


title: SAM378_probing_1_igg


title: SAM162_probing_1_igg


title: SAM388_probing_1_igg


title: SAM242_probing_1_igg


title: SAM346_probing_1_igg


title: SAM127_probing_1_igg


title: SAM043_probing_1_igg


title: SAM001_probing_1_igg


title: SAM228_probing_1_igg


title: SAM078_probing_1_igg


title: SAM384_probing_1_igg


title: SAM083_probing_1_igg


title: SAM217_probing_1_igg


title: SAM369_probing_1_igg


title: SAM067_probing_1_igg


title: SAM199_probing_1_igg


title: SAM303_probing_1_igg


title: SAM292_probing_1_igg


title: SAM253_probing_1_igg


title: SAM181_probing_1_igg


title: SAM297_probing_1_igg


title: SAM194_probing_1_igg


title: SAM284_probing_1_igg


title: SAM026_probing_1_igg


title: SAM387_probing_1_igg


title: SAM056_probing_1_igg


title: SAM210_probing_1_igg


title: SAM126_probing_1_igg


title: SAM099_probing_1_igg


title: SAM313_probing_1_igg


title: SAM116_probing_1_igg


title: SAM079_probing_1_igg


title: SAM336_probing_1_igg


title: SAM261_probing_1_igg


title: SAM362_probing_1_igg


title: SAM260_probing_1_igg


title: SAM072_probing_1_igg


title: SAM345_probing_1_igg


title: SAM013_probing_1_igg


title: SAM305_probing_1_igg


title: SAM271_probing_1_igg


title: SAM262_probing_1_igg


title: SAM245_probing_1_igg


title: SAM015_probing_1_igg


title: SAM365_probing_1_igg


title: SAM022_probing_1_igg


title: SAM251_probing_1_igg


title: SAM016_probing_1_igg


title: SAM145_probing_1_igg


title: SAM174_probing_1_igg


title: SAM244_probing_1_igg


title: SAM357_probing_1_igg


title: SAM373_probing_1_igg


title: SAM029_probing_1_igg


title: SAM268_probing_1_igg


title: SAM073_probing_1_igg


title: SAM040_probing_1_igg


title: SAM238_probing_1_igg


title: SAM103_probing_1_igg


title: SAM085_probing_1_igg


title: SAM278_probing_1_igg


title: SAM180_probing_1_igg


title: SAM275_probing_1_igg


title: SAM041_probing_1_igg


title: SAM118_probing_1_igg


title: SAM376_probing_1_igg


title: SAM302_probing_1_igg


title: SAM218_probing_1_igg


title: SAM168_probing_1_igg


title: SAM334_probing_1_igg


title: SAM246_probing_1_igg


title: SAM129_probing_1_igg


title: SAM024_probing_1_igg


title: SAM010_probing_1_igg


title: SAM341_probing_1_igg


title: SAM112_probing_1_igg


title: SAM151_probing_1_igg


title: SAM161_probing_1_igg


title: Ax3(Rep orf+) cells, rnp1A knockdown 2, biol rep3

type: SRA

city: Baltimore

first: Yinan

last: Liu

address: 725 North Wolfe Street, Physiology Builiding Rm.100

department: Cell Biology

institute: Johns Hopkins University School of Medicine

description:
R1AHPG2vsPLD1G2_DEG.txt
R1AG2_3

library_source: transcriptomic

data_processing:
fastp to remove reads containing adapter and poly-N sequences and reads with low  quality from raw data.
HISAT2 to map to reference genome
Featurecounts to count the read numbers mapped of each gene
DESeq2 to perform differential expression analysis
Assembly: dicty2.7
Supplementary files format and content: Tab-delimited files include gene ID, gene name, read counts and fpkm for each sample, log2 fold change for differential expression (rnp1A KD 1/ WT control 1,rnp1A KD 2/ WT control 2),  p value and p adjusted value for differential expression analysis

molecule: total RNA

organism: Dictyostelium discoideum

source_name: Ax3(Rep orf+) :: rnp1A hp-pLD1

growth_protocol: Cells were maintained in Hans’ enriched HL-5 media (1.4X HL-5 media with 8% FM, penicillin and streptomycin) at 22°C in petri dishes (Fisher Scientific; FB0875712).

extract_protocol:
RNA extraction was done with TRIzolTM reagent (Thermo Fisher 15596026), following manufacturer's instruction.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: cell line

value: Ax3(Rep orf+) ::rnp1A hp-pLD1

tag: genotype

value: rnp1A knockdown


title: SAM163_probing_1_igg


title: SAM028_probing_1_igg


title: SAM111_probing_1_igg


title: SAM101_probing_1_igg


title: SAM377_probing_1_igg


title: SAM380_probing_1_igg


title: SAM240_probing_1_igg


title: Ax3(Rep orf+) cells, RNAi control 2, biol rep3

description:
R1AHPG2vsPLD1G2_DEG.txt
PLD1G2_3

source_name: Ax3(Rep orf+) :: pLD1

value: Ax3(Rep orf+) ::pLD1

value: WT


title: Ax3(Rep orf+) cells, rnp1A knockdown 2, biol rep2

description:
R1AHPG2vsPLD1G2_DEG.txt
R1AG2_2


title: Ax3(Rep orf+) cells, rnp1A knockdown 1, biol rep1

description:
R1AHPG1vsPLD1G1_DEG.txt
R1AG1_1


title: SAM131_probing_1_igg


title: SAM215_probing_1_igg


title: Ax3(Rep orf+) cells, RNAi control 1, biol rep2

description:
R1AHPG1vsPLD1G1_DEG.txt
PLD1G1_2


title: SAM223_probing_1_igg


title: SAM036_probing_1_igg


title: Ax3(Rep orf+) cells, RNAi control 1, biol rep1

description:
R1AHPG1vsPLD1G1_DEG.txt
PLD1G1_1


title: DL1_E271A_GFPpos_rep3

city: Freiburg im Breisgau

first: Marc

last: Bayer

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
matrix column name: DL1_E271A_GFPpos_rep3
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.3), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using STAR (v2.7.4a).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with RPKM normalization.
The expression level of the annotated genes (Gencode, VM23, GRCm38.p6) was calculated by featureCounts (subread v2.0.0).
The differential gene expression in GFP+CD19- cells was calculated between conditions by paired DESeq2 analysis pairing samples of each independent replicate experiment. Genes with a total read count < 10 across all samples were excluded. Genes with a q-value < 0.1 were considered significant.
The differential gene expression in GFP+ cells was calculated between conditions by DESeq2 analysis. Genes with a total read count < 10 across all samples were excluded. Genes with a q-value < 0.1 were considered significant.
Assembly: mm10
Supplementary files format and content: The raw count matrix of sequencing reads obtained from featureCounts is provided for GFP+CD19- or GFP+ cells in tab-delimited txt format.
Supplementary files format and content: The normalized gene expression values calculated by DESeq2 is provided for GFP+CD19- or GFP+ cells in tab-delimited txt format.
Supplementary files format and content: An RPKM-normalized bigwig file is provided for each sample.

organism: Mus musculus

source_name: fetal liver

growth_protocol: E16.5 Ebf1-/- mouse embryos were collected and c-kit+ lymphocyte progenitors were sorted from the fetal liver using standard MACS enrichment. Cells were transduced with corresponding viruses, sorted for GFP expression after 16 hours and co-cultured with OP9-DL1 feeder cells for either 3 or 7 days in Opti-MEM medium with 4% FCS, 1% Penicillin-Streptomycin-Glutamine, 0.06 mM β-mercaptoethanol, 5 ng/ml IL7, 10 ng/ml SCF and 10 ng/ml Flt3 ligand.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
Libraries of GFP+CD19- cells were prepared using the SMART-seq v4 Ultra Low Input RNA library preparation kit (Takara, 634893) according to the manufacturer's instructions. Libraries of GFP+ cells were prepared using the NEBNext Low Input RNA Library preparation kit (NEB, E6420) according to the manufacturer's protocol.

tag: strain

tag: tissue

value: fetal liver

tag: cell type

value: c-kit+ lymphocyte progenitors

tag: transfection


title: SAM080_probing_1_igg


title: SAM074_probing_1_igg


title: SAM381_probing_1_igg


title: Ax3(Rep orf+) cells, RNAi control 2, biol rep2

description:
R1AHPG2vsPLD1G2_DEG.txt
PLD1G2_2


title: SAM033_probing_1_igg


title: DL1_E271A_GFPpos_rep2

description:
matrix column name: DL1_E271A_GFPpos_rep2
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt


title: SAM139_probing_1_igg


title: DL1_E271A_GFPpos_rep1

description:
matrix column name: DL1_E271A_GFPpos_rep1
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt


title: DL1_wt_GFPpos_rep3

description:
matrix column name: DL1_wt_GFPpos_rep3
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt


title: SAM283_probing_1_igg


title: Ax3(Rep orf+) cells, rnp1A knockdown 1, biol rep2

description:
R1AHPG1vsPLD1G1_DEG.txt
R1AG1_2


title: DL1_wt_GFPpos_rep2

description:
matrix column name: DL1_wt_GFPpos_rep2
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt


title: SAM113_probing_1_igg


title: SAM018_probing_1_igg


title: SAM220_probing_1_igg


title: SAM037_probing_1_igg


title: DL1_wt_GFPpos_rep1

description:
matrix column name: DL1_wt_GFPpos_rep1
featureCounts_GFPpos.txt
norm_counts_GFPpos.txt


title: SAM091_probing_1_igg


title: DL1_wt_CD19neg_rep2

description:
matrix column name: DL1_wt_CD19neg_rep2
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: DL1_E271A_CD19neg_rep1

description:
matrix column name: DL1_E271A_CD19neg_rep1
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: DL1_wt_CD19neg_rep3

description:
matrix column name: DL1_wt_CD19neg_rep3
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: DL1_E271A_CD19neg_rep3

description:
matrix column name: DL1_E271A_CD19neg_rep3
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: DL1_wt_CD19neg_rep1

description:
matrix column name: DL1_wt_CD19neg_rep1
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: SAM039_probing_1_igg


title: SAM187_probing_1_igg


title: SAM044_probing_1_igg


title: SAM354_probing_1_igg


title: SAM084_probing_1_igg


title: dox_E271A_ChIP

description:
EBF1E271A ChIP-seq in doxycyline-treated pro-B cells
peaks_scaled_counts.txt
peaks.bed

library_source: genomic

data_processing:
Quality control and read mapping was done using snakePipes (v2.5.3), an automatic pipeline for analysis of deep sequencing data.
Reads were separately mapped to the mouse genome (GRCm38 – mm10) and the human genome (GRCh38 – hg19) using bowtie2 (v2.3.5.1).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Peak calling was performed on mouse and human spike-in EBF1 ChIP signals using MACS2 (v2.2.7.1) and using the input sample as a negative control. Default MACS2 settings were used.
Alignments in significant human and mouse EBF1 peak regions were counted using multicov from bedtools2 (v2.27.0).
For spike-in normalization, scaling factors were calculated from human spike-in EBF1 ChIP peak alignments using multiBamSummary from deeptools (v3.5.0), and alignment counts from mouse EBF1 peaks were scaled using these scaling factors.
Mouse EBF1wt and EBF1E271A peaks were combined and filtered for a scaled alignment count ≥ 100 in at least one of the samples.
Fold change differences of scaled peak coverages of mouse EBF1 peaks were calculated between conditions, and only peaks with a fold change > 2 were considered.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) and scaled using the calculated scaling factors.
Assembly: mm10
Supplementary files format and content: A table depicting the combined and filtered EBF1wt and EBF1E271A peaks and their scaled peak coverage is provided in tab-delimited txt format.
Supplementary files format and content: A bed file with the combined and filtered EBF1wt and EBF1E271A peaks is provided.
Supplementary files format and content: An unscaled bigwig file for the input sample and scaled bigwig files for the ChIP samples are provided.

molecule: genomic DNA

growth_protocol: E16.5 Ebf1-/- mouse embryos were collected and c-kit+ lymphocyte progenitors were sorted from the fetal liver using standard MACS enrichment. Cells were cultured in Opti-MEM medium with 4% FCS, 1% Penicillin-Streptomycin-Glutamine, 0.06 mM β-mercaptoethanol, 5 ng/ml IL7, 10 ng/ml SCF and 10 ng/ml Flt3 ligand during all manipulation and culturing steps. For in vitro differentation, cells were co-cultured with OP9 feeder cells. NICD1 expression was  inducted by adding 1µg/ml doxycyline  to the cell culture media and culturing cells for 6 hours without feeder cells prior to ChIP analysis.

extract_protocol:
EBF1 ChIP was performed as previously described (Boller et al. 2016) with minor changes. For spike-in normalization, murine pro-B cells were mixed with the EBF1-expressing human B cell lymphoma cell line BJAB in a 10/1 ratio to simultaneously immunoprecipitate murine and human EBF1 with the same antibody. Cells were harvested, washed with PBS and resuspended in PBS with 2% FCS (4x10^6 cells per 1 ml). formaldehyde (FA) mix (50 mM HEPES-KOH pH 8.0, 100 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 11% (v/v) formaldehyde) was added to a final concentration of 1% FA. Tubes were incubated on a rotator for 10 min at RT. Quenching was performed by adding 2 M glycine to a final concentration of 0.2 M. The cell pellet was resuspended in lysis buffer (50 mM Tris-HCl pH 8.0, 1% (w/v) SDS, 10 mM EDTA; PIM) (4x10^6 cells per 100 μl). Chromatin was sheared with a Bioruptor (25 cycles, output level "High", 30 sec ON, 30 sec OFF, 4°C) and fragment size and DNA concentration were checked. 20 μg DNA was used per ChIP reaction. Chromatin was mixed with 4 µg a-EBF1 (1C) rabbit antibody (Roessler et al., 2007) or rabbit IgG and incubated on rotator over night at 4°C. Chromatin was incubated with 30 μl Protein G Dynabeads suspension (ThermoFisherScientific) per sample on a rotator for four hours at 4°C. Beads were washed four times with wash buffer A (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2 mM EDTA) and once with final wash buffer A (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% (v/v) Triton X-100, 0.1% (w/v) SDS, 2 mM EDTA) for 5 minutes on a rotator at 4°C. Chromatin was eluted with 100 μl elution buffer (10 mM Tris-HCl, pH 8.0; 0.5% SDS; 300 mM NaCl; 5 mM EDTA pH 8.0) by shaking vigorously at 65 °C for 30 min. Samples were reverse crosslinked, treated with 10 µg RNase A and 10 µg Proteinase K, and purified using the QIAquick PCR Purification Kit.
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) according to the manufacturer’s protocol.

value: pro-B

tag: antibody

value: a-EBF1 (1C) rabbit antibody (Roessler et al. 2007)


title: dox_wt_ChIP

description:
EBF1wt ChIP-seq in doxycyline-treated pro-B cells
peaks_scaled_counts.txt
peaks.bed


title: SAM276_probing_1_igg


title: DL1_E271A_CD19neg_rep2

description:
matrix column name: DL1_E271A_CD19neg_rep2
featureCounts_CD19neg.txt
norm_counts_CD19neg.txt


title: SAM219_probing_1_igg


title: SAM323_probing_1_igg


title: SAM136_probing_1_igg


title: dox_input

description: input control for EBF1 ChIP-seq in doxycyline-treated pro-B cells

value: input


title: SAM179_probing_1_igg


title: EV_1_S82370

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: ATAC-seq in alphaTC1 with Empty Vector

data_processing:
Processing was performed using a Snakemake ATAC-seq pipeline available at https://github.com/sreichl/atacseq_pipeline.
Reads were aligned to the mm10 genome with bowtie2 version 2.4.4. Non-uniquely mapped reads were discarded using samtools 2.8.0.
Genome browser tracks in bigWig format were generated using deepTools bamCoverage (version 3.5.1).
Peak calling was performed by MACS2 version 2.2.7.1.
Consensus region sets were generated and read counts quantified using bedtools 2.27.1 (pybedtools wrapper, version 0.8.2).
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig files include coverage tracks.
Supplementary files format and content: narrowPeak and bed files include peak coordinates.
Supplementary files format and content: csv file includes raw read quantification.

source_name: alphaTC1 cell line

extract_protocol:
Protocol was performed on three individual biological replicates according to previous publications (Buenrostro et al., 1013; Schick et al., 2019).
NGS libraries were prepared with NEBNext® High-Fidelity 2X PCR Master Mix with index primers from Buenrostro et al. 2013.
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 75 bp paired-end chemistry.

treatment_protocol: sh95 samples were transduced with Smndc1 shRNA for 5 days, EV samples were transduced with empty vector for 5 days, Atrx samples were transduced with Atrx shRNA for 5 days.

value: murine pancreatic alpha cell line

value: transduced with empty vector


title: sh95_2_S82367

description: ATAC-seq in alphaTC1 with Smndc1 shRNA

value: transduced with Smndc1 shRNA


title: EV_2_S82371

description: ATAC-seq in alphaTC1 with Empty Vector


title: SAM034_probing_1_igg


title: sh95_3_S82366

description: ATAC-seq in alphaTC1 with Smndc1 shRNA


title: Atrx_3_S82365

description: ATAC-seq in alphaTC1 with Atrx shRNA

value: transduced with Atrx shRNA


title: EV_3_S82372

description: ATAC-seq in alphaTC1 with Empty Vector


title: SAM032_probing_1_igg


title: SAM206_probing_1_igg


title: SAM125_probing_1_igg

value: N


title: SAM023_probing_1_igg


title: Atrx_1_S82369

description: ATAC-seq in alphaTC1 with Atrx shRNA


title: SAM224_probing_1_igg


title: Atrx_2_S82368

description: ATAC-seq in alphaTC1 with Atrx shRNA


title: SAM120_probing_1_igg

value: A/H5N1 HA + MF59


title: Input_aTC1_Smndc1_KD

description:
Input_KD_S96890
Input alphaTC1 with Smndc1 shRNA

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programs (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/).
NGS reads were aligned to the mm10 reference assembly with Bowtie2 (2.4.1) with standard options.
Peak calling was performed with MACS2 (2.2.7.1) with standard options.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Called peaks in BED format.
Supplementary files format and content: chipseq_diff_bind_H3woo_H3K9me3_peak_set_genes_complete.tsv: Consensus peak set quantified for each sample.

extract_protocol:
Cells were fixed and chromatin isolated as previously described (Schick et al., 2019). H3K9me3 (Active Motif 39161) antibody was used.
NGS libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645) with NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (E7335).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000 using 50 bp single-read chemistry.

treatment_protocol: KD samples were transduced with Smndc1 shRNAs for 5 days, and EV samples were transduced with empty vector for 5 days.

tag: chip antibody


title: H3K9me3_ChIP_aTC1_Smndc1_KD_1

description:
KD1_H3K9me3_S96888
H3K9me3 ChIP in alphaTC1 with Smndc1 shRNA

value: H3K9me3 (Active Motif 39161)


title: Input_aTC1_control

description:
Input_EV_S96884
Input alphaTC1 with Empty Vector


title: SAM343_probing_1_igg

value: A/H5N1 HA + PBS

value: Y


title: SAM063_probing_1_igg

value: A/H5N1 HA + AS03


title: sh95_1_S82373

description: ATAC-seq in alphaTC1 with Smndc1 shRNA


title: Input_bTC3

description:
Input_bTC3_S96899
Input betaTC3

source_name: betaTC3 cell line

value: murine pancreatic beta cell line


title: H3K9me3_ChIP_aTC1_control_2

description:
EV2_H3K9me3_S96881
H3K9me3 ChIP in alphaTC1 with Empty Vector


title: SAM167_probing_1_igg


title: SAM170_probing_1_igg


title: SAM270_probing_1_igg


title: SAM143_probing_1_igg


title: SAM107_probing_1_igg


title: H3K9me3_ChIP_bTC3_2

description:
b2_H3K9me3_S96896
H3K9me3 ChIP in betaTC3


title: H3K9me3_ChIP_aTC1_Smndc1_KD_2

description:
KD2_H3K9me3_S96889
H3K9me3 ChIP in alphaTC1 with Smndc1 shRNA


title: H3K9me3_ChIP_bTC3_1

description:
b1_H3K9me3_S96891
H3K9me3 ChIP in betaTC3


title: H3K9me3_ChIP_aTC1_control_1

description:
EV1_H3K9me3_S96879
H3K9me3 ChIP in alphaTC1 with Empty Vector


title: SAM295_probing_1_igg


title: SAM147_probing_1_igg


title: SAM335_probing_1_igg


title: SAM165_probing_1_igg


title: SAM255_probing_1_igg


title: SAM212_probing_1_igg


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Negative 4

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen), including DNase treatment, following the manufacturer’s instructions.
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 75 bp paired-end protocol.

value: alpha cell

value: transduced with Smndc1 shRNA and RIP-mCherry – sorted for the NEGATIVE mCherry population


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Positive 4

value: transduced with Smndc1 shRNA and RIP-mCherry – sorted for the POSITIVE mCherry population


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Positive 2


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Positive 3


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Negative 3


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Positive 1


title: SAM025_probing_1_igg


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Negative 2


title: SAM184_probing_1_igg


title: SAM150_probing_1_igg


title: SAM092_probing_1_igg


title: AlphaTC1 cells, Empty Vector + RIP-mCherry 3

value: transduced with empty vector and RIP-mCherry


title: SAM314_probing_1_igg


title: AlphaTC1 cells, Empty Vector + RIP-mCherry 2


title: SAM254_probing_1_igg


title: SAM002_probing_1_igg


title: SAM052_probing_1_igg


title: AlphaTC1 cells, Empty Vector + RIP-mCherry 4


title: AlphaTC1 cells, Smndc1 shRNA 3

source_name: AlphaTC1 cells, Smndc1 shRNA


title: AlphaTC1 cells, Empty Vector + RIP-mCherry 1


title: AlphaTC1 cells, Smndc1 shRNA 2


title: SAM273_probing_1_igg


title: SAM296_probing_1_igg


title: AlphaTC1 cells, Smndc1 shRNA 1


title: SAM068_probing_1_igg


title: AlphaTC1 cells, Empty Vector Control 2

source_name: AlphaTC1 cells, Empty Vector Control


title: AlphaTC1 cells, Smndc1 shRNA + RIP-mCherry Negative 1


title: AlphaTC1 cells, Empty Vector Control 3


title: SAM263_probing_1_igg


title: SAM144_probing_1_igg


title: CH25H_LDLR DKO_3_LPS_4_hours

city: New York

first: Alberto

last: Canfran-Duque

state: New York

address: 550 1st Avenue

institute: NYU Langone

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Genome_build: mmu10
Supplementary_files_format_and_content: quantification matrix
Supplementary_files_format_and_content: raw counts

source_name: Thioglycollated elicited periotneal macrophages

growth_protocol: Thioglycollate-elicited peritoneal macrophages were mantain in RPMI with 10%FBS for a total of 14 hours.

extract_protocol:
After the treatment thioglycollate-elicited peritoneal macrophages were harvested and RNA was isolated Total RNA from liver samples treated with ASOs as described above was extracted and purified using a RNA isolation Kit (Qiagen) followed by DNAse treatment to remove genomic contamination using RNA MinElute Cleanup (Qiagen).
rRNA was depleted from RNA samples using Ribo-Zero rRNA Removal Kit (Illumina). RNA libraries were performed using TrueSeq Small RNA Library preparation (Illumina).
Libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 100bp read length).

treatment_protocol: Thioglycollate-elicited peritoneal macrophages were treated with 100 ng/ml of LPS for 4 hours or 12 hours or kept untreated.

value: macrophage

value: 100 ng/ml LPS

tag: time point

value: 4 hours


title: CH25H_LDLR DKO_1_LPS_12_hours

value: 12 hours


title: CH25H_LDLR DKO_2_LPS_12_hours


title: AlphaTC1 cells, Empty Vector Control 1

value: transduced with empty vector


title: SAM325_probing_1_igg


title: SAM229_probing_1_igg


title: SAM035_probing_1_igg


title: CH25H_LDLR DKO_3_LPS_12_hours


title: SAM353_probing_1_igg


title: SAM146_probing_1_igg


title: SAM108_probing_1_igg


title: CH25H_LDLR DKO_2_LPS_4_hours


title: SAM241_probing_1_igg


title: SAM318_probing_1_igg


title: SAM306_probing_1_igg


title: CH25H_LDLR DKO_1_LPS_4_hours


title: CH25H_LDLR DKO_2_Mock

value: Mock treated


title: LDLR KO_2_LPS 12 hours


title: SAM098_probing_1_igg


title: SAM358_probing_1_igg

value: N


title: CH25H_LDLR DKO_1_Mock


title: SAM370_probing_1_igg


title: SAM020_probing_1_igg


title: LDLR KO_2_LPS 4 hours


title: LDLR KO_1_LPS 12 hours


title: SAM193_probing_1_igg


title: SAM383_probing_1_igg


title: LDLR KO_1_Mock


title: CH25H_LDLR DKO_3_Mock


title: SAM209_probing_1_igg


title: LDLR KO_1_LPS 4 hours


title: SAM186_probing_1_igg


title: SAM177_probing_1_igg


title: LDLR KO_3_Mock


title: SAM011_probing_1_igg


title: LDLR KO_2_Mock


title: LDLR KO_3_LPS 4 hours


title: LDLR KO_3_LPS 12 hours


title: SAM252_probing_1_igg


title: SAM175_probing_1_igg


title: SAM062_probing_1_igg


title: SAM009_probing_1_igg


title: SAM368_probing_1_igg


title: AD7_2

city: Jaen

first: Francisco

last: Hernandez-Torres

address: Paraje Las Lagunillas s/n

department: Experimental Biology

country: Spain

institute: University of Jaen

description: 7 days after CTX and antimiR106b inyection. Replicate 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastq reads quality were analized with FastQC (Galaxy Version 0.72+galaxy1) by using defalut parameters
Sequenced reads were trimmed with Trim Galore! (Galaxy Version 0.4.3.1) by using defalut parameters
Sequenced reads were mapped to mm10 whole genome through RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.6.0b-2) by using defalut parameters
Features (genes) were counted by featureCounts () function from R Rsubread package v1.28.1. Counts scaled by the number of fragments sequenced (counts per million or CPM) were calculated  and normalized by cpm() and calcNormFactors(method = "TMM") functions respectively  from R edgeR package v3.20.9. Data are expressed in a log scale
Finally, differential gene expression (DEG) were measured by "limma+voom" aproach trough edgeR package v3.20.9 and limma package v3.34.9 funtions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file (lcpm.txt) include logcpm values for each Sample

source_name: 7 days after CTX and antimiR106b injection. Replicate 2

extract_protocol:
Tibialis anterior  were removed, flash frozen on dry ice, and RNA was harvested using Direct-zol™ RNA MiniPrep-Zymo Research kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by CNAG Services (Spain)

treatment_protocol: Cardiotoxin were injected together with either anti-miR106b or anti-miR-Scrambled control in tibialis anterior muscles. Muscles in regeneration were  collected 3 or 7 days after injection

value: Tibialis anterior muscle

tag: age

value: 4 months old

tag: injected with

value: CTX and antimiR106b

tag: days after injection


title: AD7_3

description: 7 days after CTX and antimiR106b inyection. Replicate 3

source_name: 7 days after CTX and antimiR106b injection. Replicate 3


title: CD7_1

description: 7 days after CTX and antimiR-Scrambled control inyection. Replicate 1

source_name: 7 days after CTX and antimiR-Scrambled control injection. Replicate 1

value: CTX and antimiR-Scrambled


title: SAM374_probing_1_igg

value: A/H5N1 HA + PBS

value: Y


title: AD3_2

description: 3 days after CTX and antimiR106b inyection. Replicate 2

source_name: 3 days after CTX and antimiR106b injection. Replicate 2


title: AD7_1

description: 7 days after CTX and antimiR106b inyection. Replicate 1

source_name: 7 days after CTX and antimiR106b injection. Replicate 1


title: CD7_3

description: 7 days after CTX and antimiR-Scrambled control inyection. Replicate 3

source_name: 7 days after CTX and antimiR-Scrambled control injection. Replicate 3


title: SAM203_probing_1_igg

value: A/H5N1 HA + MF59


title: AD3_1

description: 3 days after CTX and antimiR106b inyection. Replicate 1

source_name: 3 days after CTX and antimiR106b injection. Replicate 1


title: SAM232_probing_1_igg


title: SAM195_probing_1_igg


title: SAM227_probing_1_igg


title: CD3_2

description: 3 days after CTX and antimiR-Scrambled control inyection. Replicate 2

source_name: 3 days after CTX and antimiR-Scrambled control injection. Replicate 2


title: SAM333_probing_1_igg

source_name: serum


title: SAM006_probing_1_igg


title: CD3_1

description: 3 days after CTX and antimiR-Scrambled control inyection. Replicate 1

source_name: 3 days after CTX and antimiR-Scrambled control injection. Replicate 1


title: CD3_3

description: 3 days after CTX and antimiR-Scrambled control inyection. Replicate 3

source_name: 3 days after CTX and antimiR-Scrambled control injection. Replicate 3


title: SAM233_probing_1_igg


title: AD3_3

description: 3 days after CTX and antimiR106b inyection. Replicate 3

source_name: 3 days after CTX and antimiR106b injection. Replicate 3


title: SAM301_probing_1_igg


title: SAM059_probing_1_igg


title: CD7_2

description: 7 days after CTX and antimiR-Scrambled control inyection. Replicate 2

source_name: 7 days after CTX and antimiR-Scrambled control injection. Replicate 2


title: SAM222_probing_1_igg


title: SAM361_probing_1_iga


title: SAM272_probing_1_igg


title: SAM087_probing_1_iga


title: SAM102_probing_1_iga


title: SAM379_probing_1_iga


title: SAM221_probing_1_igg


title: SAM344_probing_1_iga


title: SAM077_probing_1_iga


title: SAM331_probing_1_iga


title: SAM140_probing_1_igg


title: SAM290_probing_1_iga


title: SAM311_probing_1_iga


title: SAM004_probing_1_iga


title: SAM121_probing_1_igg


title: SAM176_probing_1_igg


title: SAM256_probing_1_iga

value: A/H5N1 HA + AS03


title: SAM288_probing_1_iga


title: SAM119_probing_1_iga


title: SAM014_probing_1_iga


title: SAM071_probing_1_iga


title: SAM339_probing_1_iga


title: SAM347_probing_1_iga


title: SAM364_probing_1_iga


title: SAM322_probing_1_iga


title: SAM207_probing_1_iga


title: SAM047_probing_1_iga


title: SAM267_probing_1_iga


title: SAM057_probing_1_iga


title: SAM208_probing_1_iga


title: SAM051_probing_1_iga


title: SAM156_probing_1_iga


title: SAM202_probing_1_iga


title: SAM045_probing_1_iga


title: SAM178_probing_1_iga


title: SAM274_probing_1_iga


title: SAM317_probing_1_iga


title: SAM082_probing_1_iga


title: SAM060_probing_1_iga


title: SAM007_probing_1_iga


title: SAM157_probing_1_iga


title: SAM237_probing_1_iga


title: SAM134_probing_1_iga


title: SAM340_probing_1_iga


title: SAM247_probing_1_iga


title: SAM216_probing_1_iga


title: SAM053_probing_1_iga


title: SAM172_probing_1_iga


title: SAM386_probing_1_iga


title: SAM330_probing_1_iga


title: SAM265_probing_1_iga


title: SAM342_probing_1_iga


title: SAM375_probing_1_iga


title: SAM280_probing_1_iga


title: SAM054_probing_1_iga


title: SAM155_probing_1_iga


title: SAM008_probing_1_iga


title: SAM122_probing_1_iga


title: SAM277_probing_1_iga


title: SAM188_probing_1_iga


title: SAM182_probing_1_iga


title: SAM169_probing_1_iga


title: SAM149_probing_1_iga


title: SAM363_probing_1_iga


title: SAM109_probing_1_iga


title: SAM230_probing_1_iga


title: SAM329_probing_1_iga


title: SAM327_probing_1_iga


title: SAM214_probing_1_iga


title: SAM069_probing_1_iga


title: SAM114_probing_1_iga


title: SAM211_probing_1_iga


title: SAM328_probing_1_iga


title: SAM204_probing_1_iga


title: SAM061_probing_1_iga


title: SAM031_probing_1_iga


title: SAM106_probing_1_iga


title: SAM142_probing_1_iga


title: SAM115_probing_1_iga


title: SAM153_probing_1_iga


title: SAM173_probing_1_iga


title: SAM192_probing_1_iga


title: SAM100_probing_1_iga


title: SAM390_probing_1_iga


title: SAM086_probing_1_iga


title: SAM291_probing_1_iga


title: SAM293_probing_1_iga


title: SAM196_probing_1_iga


title: SAM076_probing_1_iga


title: SAM226_probing_1_iga


title: SAM117_probing_1_iga


title: SAM137_probing_1_iga


title: SAM348_probing_1_iga


title: SAM326_probing_1_iga


title: SAM095_probing_1_iga


title: SAM148_probing_1_iga


title: SAM070_probing_1_iga


title: SAM046_probing_1_iga


title: case_547 850k methylation

type: genomic

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: not provided

scan_protocol: not provided

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

label: Cy3, Cy5

source_name: tissue-Explant

label_protocol: not provided

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

value: lung

tag: center

value: UCSF

tag: dx

value: ipf

value: case

tag: methylationid

tag: Sex

value: m

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: SAM089_probing_1_iga

tag: subject id

tag: treatment

tag: day


title: case_545 850k methylation

tag: tissue


title: case_546 850k methylation


title: case_543 850k methylation

value: unknown

value: hispanic


title: control_544 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f


title: case_542 850k methylation


title: SAM183_probing_1_iga

value: N


title: control_541 850k methylation

value: Y


title: control_540 850k methylation


title: SAM309_probing_1_iga

value: A/H5N1 HA + MF59


title: SAM030_probing_1_iga


title: SAM372_probing_1_iga


title: SAM055_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM133_probing_1_iga


title: case_539 850k methylation

value: lung


title: case_537 850k methylation

value: UCSF


title: control_538 850k methylation


title: SAM123_probing_1_iga


title: SAM096_probing_1_iga


title: SAM382_probing_1_iga


title: SAM236_probing_1_iga


title: case_536 850k methylation

value: ipf


title: control_532 850k methylation


title: case_534 850k methylation

value: case


title: case_533 850k methylation

value: m


title: SAM282_probing_1_iga


title: case_530 850k methylation

source_name: tissue-Biopsy

value: white


title: case_531 850k methylation

value: not hispanic or latino


title: SAM234_probing_1_iga


title: control_529 850k methylation

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


title: case_528 850k methylation


title: SAM320_probing_1_iga


title: SAM338_probing_1_iga


title: case_527 850k methylation


title: SAM298_probing_1_iga


title: SAM308_probing_1_iga


title: SAM300_probing_1_iga


title: SAM003_probing_1_iga


title: SAM065_probing_1_iga


title: case_524 850k methylation


title: control_523 850k methylation


title: control_535 850k methylation


title: SAM166_probing_1_iga


title: case_521 850k methylation


title: control_526 850k methylation


title: SAM366_probing_1_iga


title: SAM385_probing_1_iga


title: SAM201_probing_1_iga


title: SAM279_probing_1_iga


title: case_518 850k methylation

source_name: tissue-Unknown

value: National Jewish

value: U


title: case_520 850k methylation

value: Pittsburgh Lung Donor Core


title: control_519 850k methylation

value: LTRC

value: other


title: SAM205_probing_1_iga


title: case_516 850k methylation


title: SAM356_probing_1_iga


title: control_517 850k methylation

value: control


title: control_525 850k methylation

value: normal


title: case_514 850k methylation

value: asian

value: unknown

value: N


title: SAM360_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM243_probing_1_iga

value: A/H5N1 HA + MF59


title: SAM367_probing_1_iga

value: Y


title: SAM285_probing_1_iga


title: SAM286_probing_1_iga


title: control_513 850k methylation

value: lung


title: SAM105_probing_1_iga


title: SAM110_probing_1_iga


title: case_512 850k methylation

value: UCSF

value: ipf

value: case

value: m


title: SAM048_probing_1_iga


title: SAM104_probing_1_iga


title: case_511 850k methylation

value: white

value: not hispanic or latino


title: case_510 850k methylation

value: Pittsburgh Lung Donor Core

value: U


title: control_509 850k methylation

value: control

value: f


title: SAM281_probing_1_iga


title: case_522 850k methylation


title: SAM264_probing_1_iga


title: control_507 850k methylation

value: normal


title: control_505 850k methylation


title: case_506 850k methylation


title: case_508 850k methylation


title: control_515 850k methylation


title: SAM093_probing_1_iga


title: SAM038_probing_1_iga


title: SAM189_probing_1_iga


title: control_503 850k methylation


title: case_504 850k methylation


title: SAM321_probing_1_iga


title: SAM075_probing_1_iga


title: case_500 850k methylation


title: SAM349_probing_1_iga


title: SAM185_probing_1_iga


title: control_501 850k methylation


title: SAM359_probing_1_iga


title: SAM058_probing_1_iga


title: case_499 850k methylation


title: case_502 850k methylation


title: case_495 850k methylation


title: case_497 850k methylation


title: SAM171_probing_1_iga


title: SAM312_probing_1_iga


title: SAM128_probing_1_iga


title: case_494 850k methylation


title: control_496 850k methylation


title: control_498 850k methylation


title: SAM258_probing_1_iga


title: case_491 850k methylation


title: case_489 850k methylation


title: SAM337_probing_1_iga


title: SAM021_probing_1_iga


title: case_493 850k methylation


title: control_492 850k methylation


title: SAM350_probing_1_iga


title: case_487 850k methylation


title: control_490 850k methylation


title: case_486 850k methylation


title: SAM132_probing_1_iga


title: SAM042_probing_1_iga


title: case_484 850k methylation


title: control_485 850k methylation


title: SAM049_probing_1_iga


title: SAM289_probing_1_iga


title: SAM005_probing_1_iga


title: control_488 850k methylation


title: case_483 850k methylation


title: SAM090_probing_1_iga


title: SAM197_probing_1_iga


title: SAM355_probing_1_iga


title: SAM294_probing_1_iga


title: control_480 850k methylation

value: LTRC

value: other


title: control_482 850k methylation

value: N


title: SAM138_probing_1_iga

value: A/H5N1 HA + MF59


title: case_481 850k methylation


title: SAM012_probing_1_iga


title: SAM081_probing_1_iga

value: Y


title: control_474 850k methylation

value: lung

value: asian


title: SAM287_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM239_probing_1_iga


title: SAM135_probing_1_iga


title: control_472 850k methylation


title: SAM064_probing_1_iga


title: case_477 850k methylation

value: ipf

value: case


title: SAM299_probing_1_iga


title: case_476 850k methylation

value: m

value: white


title: case_475 850k methylation

value: Pittsburgh Lung Donor Core

value: not hispanic or latino


title: SAM200_probing_1_iga


title: control_469 850k methylation

value: control


title: case_479 850k methylation

value: f

value: U


title: case_473 850k methylation


title: SAM225_probing_1_iga


title: control_478 850k methylation

value: LTRC


title: SAM190_probing_1_iga


title: SAM250_probing_1_iga


title: case_467 850k methylation


title: SAM371_probing_1_iga


title: case_468 850k methylation


title: SAM213_probing_1_iga


title: case_470 850k methylation


title: SAM152_probing_1_iga


title: case_466 850k methylation

value: White

value: Not Hispanic or Latino


title: SAM017_probing_1_iga


title: case_465 850k methylation


title: case_471 850k methylation

value: N


title: SAM389_probing_1_iga

value: A/H5N1 HA + MF59


title: case_463 850k methylation

value: lung

value: Y


title: control_464 850k methylation

value: normal


title: SAM130_probing_1_iga

value: A/H5N1 HA + PBS


title: SAM231_probing_1_iga


title: SAM097_probing_1_iga


title: case_462 850k methylation

value: ipf

value: case


title: SAM248_probing_1_iga


title: case_461 850k methylation

value: m


title: case_459 850k methylation


title: control_460 850k methylation

value: Pittsburgh Lung Donor Core

value: white


title: SAM160_probing_1_iga


title: SAM257_probing_1_iga


title: SAM307_probing_1_iga


title: SAM158_probing_1_iga


title: control_457 850k methylation

value: control

value: not hispanic or latino


title: case_458 850k methylation


title: case_456 850k methylation

value: UCSF


title: SAM080_probing_1_iga


title: SAM124_probing_1_iga


title: SAM316_probing_1_iga


title: case_453 850k methylation


title: case_452 850k methylation

value: LTRC


title: control_454 850k methylation

value: f


title: SAM304_probing_1_iga


title: SAM01_m50_probing_4_igg

tag: blocking

value: Mini HA -50ug/ml


title: SAM01_m10_probing_4_igg

value: N

value: Mini HA-10ug/ml


title: SAM01_r10_probing_4_igg


title: control_449 850k methylation

value: lung

value: black

value: unknown


title: SAM01_nop_probing_4_igg

value: A/H5N1 HA + PBS

value: no peptide


title: SAM01_r50_probing_4_igg


title: SAM53_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: case_450 850k methylation

value: ipf

value: case

value: m

value: asian

value: Y


title: control_446 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino


title: case_448 850k methylation

source_name: tissue-Autopsy

value: University of Colorado

value: f

value: N


title: SAM53_r50_probing_4_igg


title: case_447 850k methylation

value: lung

value: UCSF


title: SAM53_r10_probing_4_igg


title: SAM50_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: case_451 850k methylation

value: LTRC


title: case_444 850k methylation

value: ipf


title: case_445 850k methylation

value: case


title: SAM50_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_440 850k methylation

value: m


title: SAM68_nop_probing_4_igg

value: A/H5N1 HA + PBS

value: no peptide


title: case_441 850k methylation

value: unknown

value: Y


title: SAM53_m50_probing_4_igg

value: A/H5N1 HA + MF59

value: Mini HA -50ug/ml


title: case_442 850k methylation


title: SAM68_m50_probing_4_igg


title: control_443 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino


title: case_455 850k methylation

value: lung

value: UCSF


title: SAM68_r50_probing_4_igg

value: N


title: SAM50_nop_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM50_m50_probing_4_igg


title: case_437 850k methylation

value: LTRC

value: ipf

value: case


title: control_433 850k methylation

value: m

value: black


title: SAM50_r50_probing_4_igg


title: SAM53_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_431 850k methylation

value: unknown

value: Y


title: case_432 850k methylation

value: asian


title: case_438 850k methylation

value: f

value: U


title: case_439 850k methylation

value: white


title: control_428 850k methylation

value: normal

value: control


title: SAM61_nop_probing_4_igg

value: A/H5N1 HA + MF59

value: no peptide


title: control_430 850k methylation

value: lung

value: UCSF

value: hispanic

value: N


title: SAM68_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM61_m10_probing_4_igg


title: case_427 850k methylation

value: ipf

value: case

value: m

value: other


title: case_436 850k methylation

value: LTRC

value: not hispanic or latino

value: Y


title: SAM68_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM45_nop_probing_4_igg

value: A/H5N1 HA + AS03


title: case_435 850k methylation

value: f

value: white


title: SAM61_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM32_r10_probing_4_igg


title: case_423 850k methylation

value: lung

value: unknown


title: SAM45_r10_probing_4_igg


title: case_426 850k methylation

value: UCSF

value: hispanic


title: SAM32_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: case_434 850k methylation

value: University of Colorado

value: ipf

value: U


title: SAM61_r50_probing_4_igg

value: N


title: case_429 850k methylation

value: case


title: case_420 850k methylation

value: m


title: SAM45_r50_probing_4_igg

value: Y


title: control_425 850k methylation

value: normal

value: control

value: black


title: SAM45_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: case_419 850k methylation

value: lung

value: white


title: case_424 850k methylation

value: UCSF


title: SAM32_nop_probing_4_igg

value: no peptide


title: SAM45_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM69_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM61_m50_probing_4_igg


title: case_422 850k methylation

value: ipf

value: other

value: unknown


title: SAM69_r50_probing_4_igg

value: N


title: case_416 850k methylation

value: case

value: m


title: case_417 850k methylation

value: Y


title: SAM32_m50_probing_4_igg

value: A/H5N1 HA + PBS


title: control_421 850k methylation

value: normal

value: control

value: f

value: black

value: not hispanic or latino


title: SAM32_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_418 850k methylation

value: lung

value: UCSF


title: SAM44_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM69_nop_probing_4_igg

value: A/H5N1 HA + MF59

value: no peptide


title: control_415 850k methylation


title: case_410 850k methylation

value: ipf

value: white


title: case_411 850k methylation

value: case

value: N


title: SAM44_r10_probing_4_igg

value: Y


title: case_414 850k methylation

value: m

value: unknown


title: case_413 850k methylation

value: LTRC

value: White


title: control_406 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: SAM44_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM44_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_412 850k methylation

value: lung

value: UCSF

value: black


title: SAM44_nop_probing_4_igg

value: no peptide


title: SAM76_r10_probing_4_igg


title: control_409 850k methylation

value: white

value: not hispanic or latino


title: case_405 850k methylation

value: National Jewish

value: ipf

value: case

value: f


title: SAM76_m50_probing_4_igg

value: Y

value: Mini HA -50ug/ml


title: SAM29_m50_probing_4_igg

value: N


title: SAM76_m10_probing_4_igg


title: SAM69_m10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM29_r50_probing_4_igg


title: case_402 850k methylation

value: LTRC

value: m


title: case_407 850k methylation

value: unknown


title: SAM69_m50_probing_4_igg


title: case_401 850k methylation

value: lung


title: SAM29_nop_probing_4_igg

value: A/H5N1 HA + PBS


title: case_399 850k methylation


title: case_408 850k methylation


title: case_403 850k methylation


title: SAM29_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_404 850k methylation


title: SAM76_r50_probing_4_igg


title: SAM76_nop_probing_4_igg

value: no peptide


title: case_397 850k methylation

value: white


title: control_400 850k methylation

value: other

value: control

value: not hispanic or latino


title: SAM87_m50_probing_4_igg

value: A/H5N1 HA + AS03


title: case_395 850k methylation

value: Inova Fairfax

value: ipf

value: case


title: SAM29_r10_probing_4_igg

value: N


title: SAM87_r50_probing_4_igg


title: case_398 850k methylation

value: f


title: SAM87_r10_probing_4_igg


title: control_396 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: Y


title: SAM79_m10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM58_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: case_394 850k methylation

value: lung

value: m


title: control_388 850k methylation

value: UCSF

value: unknown

value: hispanic


title: control_393 850k methylation

value: control

value: white

value: not hispanic or latino


title: SAM79_nop_probing_4_igg

value: no peptide


title: control_385 850k methylation

value: black

value: N


title: case_386 850k methylation

value: LTRC

value: ipf

value: case


title: case_387 850k methylation

value: White

value: Y


title: case_392 850k methylation

value: Inova Fairfax


title: SAM58_m10_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA-10ug/ml


title: SAM79_r50_probing_4_igg

value: A/H5N1 HA + MF59


title: case_391 850k methylation

value: lung

value: m


title: SAM58_r10_probing_4_igg


title: case_389 850k methylation

value: U


title: SAM79_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM87_m10_probing_4_igg

value: A/H5N1 HA + AS03


title: case_383 850k methylation

value: white

value: not hispanic or latino


title: SAM58_r50_probing_4_igg

value: N


title: SAM87_nop_probing_4_igg

value: no peptide


title: SAM79_r10_probing_4_igg


title: control_384 850k methylation

value: LTRC

value: other

value: control

value: f


title: SAM43_r10_probing_4_igg


title: control_381 850k methylation

value: Y


title: SAM43_m10_probing_4_igg


title: case_390 850k methylation

value: ipf

value: case

value: White


title: SAM58_nop_probing_4_igg

value: A/H5N1 HA + PBS


title: control_382 850k methylation

value: lung

value: m


title: SAM43_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM43_r50_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM10_r10_probing_4_igg


title: control_380 850k methylation

value: UCSF

value: normal

value: black

value: unknown


title: case_379 850k methylation

value: LTRC

value: not hispanic or latino


title: SAM43_nop_probing_4_igg

value: N

value: no peptide


title: control_374 850k methylation

value: Pittsburgh Lung Donor Core

value: control

value: white


title: control_377 850k methylation

value: f


title: SAM10_m50_probing_4_igg


title: SAM10_nop_probing_4_igg


title: case_378 850k methylation

value: ipf

value: case

value: White

value: hispanic


title: case_372 850k methylation

value: lung

value: Inova Fairfax


title: SAM10_r50_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM82_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: case_370 850k methylation

value: black

value: Y


title: SAM82_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM82_m50_probing_4_igg

value: N

value: Mini HA -50ug/ml


title: SAM82_r50_probing_4_igg


title: SAM82_nop_probing_4_igg

value: no peptide


title: control_369 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino


title: SAM10_m10_probing_4_igg


title: case_368 850k methylation

value: ipf

value: case

value: m

value: white


title: control_371 850k methylation

value: lung


title: SAM78_nop_probing_4_igg


title: control_367 850k methylation

value: LTRC

value: f


title: case_366 850k methylation

value: National Jewish

value: U


title: case_375 850k methylation

value: White


title: case_376 850k methylation

value: N


title: case_365 850k methylation

value: Y


title: case_373 850k methylation

value: Inova Fairfax


title: SAM78_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: SAM78_r50_probing_4_igg


title: control_364 850k methylation

value: other

value: control


title: control_363 850k methylation

value: not hispanic or latino


title: case_362 850k methylation

value: ipf

value: case


title: SAM78_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM56_nop_probing_4_igg

value: A/H5N1 HA + AS03

value: no peptide


title: SAM56_m50_probing_4_igg


title: case_358 850k methylation

value: lung

value: LTRC

value: m

value: black


title: SAM56_m10_probing_4_igg

value: N


title: control_359 850k methylation

value: f

value: white


title: SAM56_r50_probing_4_igg


title: SAM78_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: case_360 850k methylation

value: U


title: SAM52_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: case_357 850k methylation

value: Y


title: SAM52_m50_probing_4_igg

value: Mini HA -50ug/ml


title: control_355 850k methylation

value: other

value: control

value: not hispanic or latino


title: SAM52_r50_probing_4_igg


title: case_356 850k methylation

value: Pittsburgh Lung Donor Core

value: ipf

value: case


title: SAM52_nop_probing_4_igg

value: no peptide


title: SAM52_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_354 850k methylation

value: lung


title: SAM08_r50_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: control_353 850k methylation

value: LTRC

value: f

value: white


title: case_361 850k methylation

value: m


title: SAM08_r10_probing_4_igg


title: SAM08_nop_probing_4_igg


title: SAM56_r10_probing_4_igg


title: control_351 850k methylation

value: U


title: case_350 850k methylation

value: Y


title: case_352 850k methylation


title: case_349 850k methylation

value: black


title: SAM08_m10_probing_4_igg


title: control_348 850k methylation

value: other

value: control


title: case_347 850k methylation

value: not hispanic or latino


title: SAM22_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM22_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_346 850k methylation

value: ipf

value: case


title: case_344 850k methylation

value: lung

value: Inova Fairfax


title: SAM22_m10_probing_4_igg

value: N

value: Mini HA-10ug/ml


title: control_345 850k methylation

value: LTRC

value: hispanic


title: control_343 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: f

value: white


title: SAM31_m50_probing_4_igg


title: SAM31_r50_probing_4_igg


title: case_342 850k methylation

value: m

value: Y


title: SAM31_r10_probing_4_igg


title: case_341 850k methylation

value: not hispanic or latino


title: SAM31_nop_probing_4_igg

value: A/H5N1 HA + MF59

value: no peptide


title: control_340 850k methylation

value: control


title: SAM31_m10_probing_4_igg


title: case_338 850k methylation

value: ipf

value: case


title: SAM25_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: case_339 850k methylation

value: lung

value: Inova Fairfax


title: SAM08_m50_probing_4_igg

value: A/H5N1 HA + AS03

value: N

value: Mini HA -50ug/ml


title: SAM25_r10_probing_4_igg


title: control_337 850k methylation

value: Pittsburgh Lung Donor Core

value: normal


title: case_336 850k methylation

value: LTRC

value: White


title: SAM25_m50_probing_4_igg


title: SAM22_r50_probing_4_igg


title: SAM22_r10_probing_4_igg


title: case_334 850k methylation

value: m

value: white

value: Y


title: control_335 850k methylation

value: UCSF

value: f

value: black

value: unknown


title: SAM25_nop_probing_4_igg

value: A/H5N1 HA + PBS

value: no peptide


title: control_333 850k methylation

value: lung

value: control


title: SAM23_nop_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: case_332 850k methylation

value: ipf

value: case

value: not hispanic or latino


title: SAM23_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM25_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM23_m10_probing_4_igg


title: case_329 850k methylation

value: LTRC

value: m

value: white


title: SAM23_r50_probing_4_igg


title: case_330 850k methylation

value: f

value: White

value: Not Hispanic or Latino


title: control_328 850k methylation

value: other

value: Y


title: SAM23_r10_probing_4_igg


title: case_326 850k methylation

value: lung

value: black


title: SAM46_r50_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM46_nop_probing_4_igg

value: N

value: no peptide


title: case_325 850k methylation

value: Inova Fairfax

value: ipf

value: case


title: SAM46_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_323 850k methylation

value: LTRC


title: SAM46_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_322 850k methylation

value: not hispanic or latino


title: SAM64_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM64_r50_probing_4_igg


title: SAM64_m10_probing_4_igg


title: control_331 850k methylation

value: UCSF

value: normal

value: control

value: m

value: unknown

value: hispanic


title: SAM64_nop_probing_4_igg


title: SAM64_m50_probing_4_igg


title: control_321 850k methylation

value: lung

value: other

value: white


title: SAM42_r50_probing_4_igg

value: N


title: SAM46_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM42_m10_probing_4_igg


title: SAM42_r10_probing_4_igg


title: case_320 850k methylation

value: ipf

value: case


title: case_316 850k methylation

value: LTRC


title: control_319 850k methylation

value: U


title: case_318 850k methylation

value: not hispanic or latino

value: Y


title: SAM42_m50_probing_4_igg

value: A/H5N1 HA + MF59

value: Mini HA -50ug/ml


title: control_317 850k methylation

value: control


title: control_314 850k methylation

value: m


title: SAM42_nop_probing_4_igg

value: no peptide


title: SAM59_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: case_313 850k methylation

value: lung


title: control_327 850k methylation

value: other


title: case_324 850k methylation

value: White

value: hispanic


title: SAM59_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM59_r50_probing_4_igg


title: control_311 850k methylation

value: UCSF

value: normal

value: black

value: unknown

value: N


title: case_312 850k methylation

value: LTRC

value: ipf

value: case

value: f

value: white

value: not hispanic or latino


title: control_309 850k methylation

value: control

value: m

value: Y


title: case_310 850k methylation

value: lung

value: White


title: SAM59_nop_probing_4_igg

value: A/H5N1 HA + AS03

value: no peptide


title: SAM59_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_308 850k methylation

value: U


title: SAM63_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: case_306 850k methylation

value: Vanderbilt


title: SAM63_r50_probing_4_igg

value: N


title: SAM63_nop_probing_4_igg


title: control_307 850k methylation

value: UCSF

value: normal

value: black

value: unknown


title: case_315 850k methylation

value: LTRC

value: ipf

value: case

value: white

value: not hispanic or latino


title: SAM63_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_302 850k methylation

value: lung

value: University of Colorado

value: f

value: Y


title: case_305 850k methylation

value: m


title: SAM13_nop_probing_4_igg

value: A/H5N1 HA + AS03

value: no peptide


title: control_301 850k methylation

value: other

value: control


title: SAM63_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: N

value: Mini HA -50ug/ml


title: case_304 850k methylation

value: LTRC

value: ipf


title: SAM13_m10_probing_4_igg


title: control_298 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: white


title: case_303 850k methylation

value: lung

value: case

value: unknown


title: SAM13_r50_probing_4_igg

value: Y


title: SAM13_m50_probing_4_igg


title: case_300 850k methylation

value: m

value: not hispanic or latino


title: case_299 850k methylation

value: hispanic


title: SAM40_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: SAM40_nop_probing_4_igg

value: no peptide


title: SAM40_m50_probing_4_igg


title: case_296 850k methylation

value: f

value: black

value: N


title: control_294 850k methylation

value: control


title: SAM40_r50_probing_4_igg


title: case_297 850k methylation

value: LTRC

value: ipf

value: White


title: case_295 850k methylation

value: lung


title: case_293 850k methylation

value: case

value: white


title: SAM89_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM40_r10_probing_4_igg

value: Y


title: SAM13_r10_probing_4_igg


title: SAM89_m10_probing_4_igg


title: SAM89_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_292 850k methylation

value: m

value: not hispanic or latino


title: control_291 850k methylation

value: other

value: unknown


title: SAM89_r50_probing_4_igg


title: control_289 850k methylation

value: f


title: case_288 850k methylation


title: SAM34_r50_probing_4_igg


title: SAM34_m50_probing_4_igg


title: SAM34_r10_probing_4_igg


title: case_285 850k methylation

value: National Jewish

value: U


title: case_286 850k methylation


title: SAM34_nop_probing_4_igg

value: N

value: no peptide


title: SAM34_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_284 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: control_282 850k methylation

value: lung

value: white


title: SAM05_r10_probing_4_igg

value: A/H5N1 HA + AS03

value: Y


title: SAM05_r50_probing_4_igg


title: SAM05_nop_probing_4_igg


title: control_279 850k methylation

value: LTRC


title: SAM05_m10_probing_4_igg


title: case_283 850k methylation

value: ipf

value: case

value: m

value: not hispanic or latino


title: case_281 850k methylation

value: National Jewish


title: case_290 850k methylation

value: hispanic


title: case_278 850k methylation

value: N


title: case_277 850k methylation


title: case_280 850k methylation

value: U


title: SAM19_nop_probing_4_igg

value: no peptide


title: SAM89_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM05_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM19_m50_probing_4_igg


title: case_275 850k methylation


title: SAM19_r50_probing_4_igg


title: control_287 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: SAM19_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: control_273 850k methylation

value: lung

value: LTRC

value: other

value: f

value: black


title: case_274 850k methylation

value: ipf

value: case

value: m

value: white

value: not hispanic or latino

value: Y


title: SAM14_m50_probing_4_igg

value: Mini HA -50ug/ml


title: control_271 850k methylation

value: Pittsburgh Lung Donor Core

value: N


title: case_272 850k methylation

value: White


title: SAM14_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM21_r50_probing_4_igg

value: A/H5N1 HA + MF59


title: control_269 850k methylation

value: lung

value: normal

value: control


title: SAM14_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_266 850k methylation

value: LTRC

value: f


title: case_270 850k methylation

value: ipf

value: case


title: SAM21_nop_probing_4_igg

value: no peptide


title: case_268 850k methylation

value: black

value: not hispanic or latino


title: SAM14_nop_probing_4_igg

value: Y


title: control_276 850k methylation

value: other

value: white


title: case_265 850k methylation

value: m


title: control_264 850k methylation

value: U


title: SAM21_r10_probing_4_igg

value: A/H5N1 HA + MF59

value: N


title: SAM21_m50_probing_4_igg

value: Mini HA -50ug/ml


title: control_267 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: SAM21_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM19_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM75_r10_probing_4_igg


title: case_263 850k methylation

value: LTRC

value: ipf

value: case


title: SAM14_r50_probing_4_igg

value: Y


title: SAM75_m50_probing_4_igg


title: control_262 850k methylation

value: other

value: not hispanic or latino


title: SAM75_nop_probing_4_igg

value: no peptide


title: case_259 850k methylation

value: f

value: white


title: control_260 850k methylation


title: SAM75_r50_probing_4_igg

value: A/H5N1 HA + MF59

value: N


title: SAM75_m10_probing_4_igg


title: SAM20_r10_probing_4_igg


title: SAM20_nop_probing_4_igg


title: SAM20_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_258 850k methylation

value: lung


title: control_257 850k methylation

value: m


title: case_255 850k methylation


title: control_253 850k methylation

value: control

value: black


title: SAM20_r50_probing_4_igg


title: SAM20_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_254 850k methylation

value: LTRC


title: case_261 850k methylation

value: ipf


title: SAM39_m10_probing_4_igg


title: SAM39_m50_probing_4_igg


title: SAM39_r50_probing_4_igg


title: control_251 850k methylation


title: SAM39_r10_probing_4_igg


title: case_249 850k methylation

value: case

value: U


title: case_252 850k methylation

value: Y


title: SAM39_nop_probing_4_igg


title: SAM66_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: case_256 850k methylation

value: not hispanic or latino


title: control_250 850k methylation

value: other

value: f


title: SAM66_r50_probing_4_igg


title: case_248 850k methylation

value: white


title: case_247 850k methylation

value: White

value: N


title: SAM66_nop_probing_4_igg

value: no peptide


title: control_245 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal


title: case_244 850k methylation

value: m


title: SAM66_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM12_m50_probing_4_igg


title: case_242 850k methylation

value: LTRC

value: ipf

value: hispanic


title: control_243 850k methylation

value: control

value: Y


title: SAM12_nop_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM12_m10_probing_4_igg

value: Mini HA-10ug/ml


title: control_241 850k methylation

value: not hispanic or latino


title: control_239 850k methylation

value: f

value: white


title: SAM12_r50_probing_4_igg

value: N


title: SAM73_nop_probing_4_igg

value: no peptide


title: case_237 850k methylation

value: lung

value: case

value: black

value: Not Hispanic or Latino

value: U


title: SAM73_m10_probing_4_igg


title: SAM66_m10_probing_4_igg


title: case_246 850k methylation

value: LTRC

value: m


title: control_236 850k methylation

value: Pittsburgh Lung Donor Core

value: normal


title: case_232 850k methylation

value: ipf

value: White

value: Y


title: control_231 850k methylation

value: control

value: not hispanic or latino


title: case_234 850k methylation


title: case_230 850k methylation

value: f


title: SAM28_nop_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM73_r50_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: control_235 850k methylation

value: lung

value: white


title: SAM73_r10_probing_4_igg


title: SAM28_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_229 850k methylation

value: case


title: case_238 850k methylation

value: LTRC

value: Not Hispanic or Latino


title: control_228 850k methylation

value: Pittsburgh Lung Donor Core

value: m


title: SAM88_nop_probing_4_igg

value: A/H5N1 HA + MF59

value: no peptide


title: SAM28_r10_probing_4_igg

value: Y


title: case_227 850k methylation

value: ipf


title: SAM73_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM12_r10_probing_4_igg


title: case_240 850k methylation

value: White

value: not hispanic or latino

value: U


title: control_226 850k methylation

value: other

value: control


title: case_233 850k methylation

value: lung


title: SAM28_m50_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM88_r50_probing_4_igg

value: N


title: SAM88_m10_probing_4_igg

value: Mini HA-10ug/ml


title: case_225 850k methylation

value: LTRC

value: case

value: f

value: white


title: SAM28_r50_probing_4_igg


title: control_224 850k methylation

value: m


title: SAM88_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM09_nop_probing_4_igg

value: Y

value: no peptide


title: SAM09_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM88_m50_probing_4_igg


title: case_221 850k methylation

value: ipf

value: not hispanic or latino


title: control_222 850k methylation

value: other


title: SAM09_m10_probing_4_igg


title: SAM09_r10_probing_4_igg


title: SAM07_r10_probing_4_igg

value: A/H5N1 HA + AS03


title: SAM09_r50_probing_4_igg


title: case_223 850k methylation

value: lung


title: case_219 850k methylation


title: control_217 850k methylation

value: control

value: U


title: control_220 850k methylation


title: control_215 850k methylation


title: case_218 850k methylation


title: SAM07_m50_probing_4_igg

value: N


title: case_214 850k methylation

value: LTRC

value: asian


title: SAM07_r50_probing_4_igg


title: SAM07_m10_probing_4_igg

value: Mini HA-10ug/ml


title: SAM74_m50_probing_4_igg


title: SAM74_r10_probing_4_igg


title: SAM74_nop_probing_4_igg


title: case_211 850k methylation

value: case

value: white


title: case_212 850k methylation

value: m

value: unknown


title: SAM07_nop_probing_4_igg

value: no peptide


title: SAM74_r50_probing_4_igg


title: case_210 850k methylation

value: f


title: SAM41_r10_probing_4_igg

value: A/H5N1 HA + MF59

value: Y


title: case_205 850k methylation

value: ipf

value: White

value: Not Hispanic or Latino


title: control_206 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino


title: case_216 850k methylation

value: LTRC


title: control_203 850k methylation

value: other


title: SAM41_r50_probing_4_igg


title: case_207 850k methylation

value: case

value: multiple-unspecified

value: N


title: control_204 850k methylation

value: white


title: control_213 850k methylation

value: f


title: case_209 850k methylation

value: m


title: SAM80_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: Mini HA -50ug/ml


title: SAM41_m50_probing_4_igg

value: A/H5N1 HA + MF59

value: Y


title: control_208 850k methylation

value: lung


title: control_200 850k methylation


title: SAM80_r50_probing_4_igg


title: SAM41_nop_probing_4_igg

value: no peptide


title: SAM74_m10_probing_4_igg

value: A/H5N1 HA + AS03

value: Mini HA-10ug/ml


title: SAM80_r10_probing_4_igg


title: case_199 850k methylation

value: ipf

value: not hispanic or latino


title: case_202 850k methylation

value: LTRC


title: SAM27_nop_probing_4_igg


title: SAM41_m10_probing_4_igg


title: SAM27_r10_probing_4_igg


title: SAM80_nop_probing_4_igg


title: SAM27_m10_probing_4_igg


title: control_198 850k methylation

value: other

value: control


title: SAM80_m10_probing_4_igg

value: N


title: control_195 850k methylation

value: Pittsburgh Lung Donor Core

value: normal

value: white


title: control_196 850k methylation

value: m


title: SAM17_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM17_nop_probing_4_igg

value: A/H5N1 HA + MF59


title: case_201 850k methylation

value: case

value: Y


title: control_192 850k methylation

value: lung

value: f


title: case_190 850k methylation

value: U


title: Granta519-mock ChIP-seq rep 1

city: Stockholm

first: Dan

last: Huang

address: Neo, Department of Biosciences and Nutrition, Huddinge, Stockholm.

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: wild type

data_processing:
After using FastQC v0.11.9 to check the QC of ChIPseq fastq.gz files, trim_galore v0.6.6 was used to remove adapters and low quality reads. ChIP-Seq reads were mapped to the human reference genome assembly hg38(GRCh38) using bowtie2 v2.3.4.3. Sequencing tags were read and imported using HOMER v4.11 followed by calling peaks with default settings and normalized to the input. Only peaks with FDR < 0.001 and fold enrichment over input tag count >4 (default settings) were kept. De novo motif analysis was performed by HOMER within +/- 100 bp from the peak center.
Genome_build: hg38(GRCh38)
Supplementary_files_format_and_content: bigwig was created using HOMER makeBigWig.pl.

source_name: Mantle cell lymphoma

growth_protocol: Stable Granta-519 cell lines with or without transduced full-length ESR2 expression (Granta519-ESR2 or Granta519-mock) were cultured in phenol red free RPMI 1640 with 10% charcoal stripped FBS, 100 IU penicillin/mL and 100ug/mL streptomycin in 5% CO2 at 37 °C

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and nuclear chormatin fractions were separated and sonicated,  followed by immunoprecipitated with ESR2 anitboides (PPZ0506, R&D systems). Magnetic beads were used to pull down the immunoprecipitated DNA and separated by elution buffer containing proteinase K. Then ChIP DNA was purified with QIAquick PCR Purification kit (Qiagen).
The libraries of ChIP DNA were prepared by using the kit NEB Next Ultra II DNA Library Prep Kit for Illumina following user instrcutions

treatment_protocol: All Cells were treated with 100 nM diarylpropionitrile(DPN) dissolved in DMSO for 2h before ChIP experiment.

tag: cell type

value: Mantle cell lymphoma

tag: cell line

value: chip antibody:PPZ0506, R&D systems, lot no:A2, mouse monoclonal

tag: genotype/variation

value: without ESR2 over-expression


title: case_191 850k methylation

value: LTRC

value: ipf

tag: age

value: not hispanic or latino


title: SAM71_m50_probing_4_igg

value: A/H5N1 HA + PBS

value: N


title: case_194 850k methylation

value: white


title: case_187 850k methylation

value: m


title: case_197 850k methylation


title: SAM27_m50_probing_4_igg

value: Mini HA -50ug/ml


title: SAM71_r10_probing_4_igg


title: SAM27_r50_probing_4_igg

value: A/H5N1 HA + MF59


title: SAM17_r10_probing_4_igg


title: Granta519-mock input DNA

description: wild type

tag: chip antibody

value: All Cells were treated with 100 nM diarylpropionitrile(DPN) dissolved in DMSO for 2h before ChIP experiment.


title: SAM17_r50_probing_4_igg


title: SAM17_m10_probing_4_igg

value: Mini HA-10ug/ml


title: Granta519-mock ChIP-seq rep 2

description: wild type


title: ΔnagZ rep3

city: Chenggu

first: Xianggui

state: 四川省

address: 278 Baoguang Road, Xindu

country: China

institute: Clinical Medical College

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Enterobacter cloacae complex

source_name: Blood

growth_protocol: Wild type Enterobacter cloacae (WT) and nagZ knock out Enterobacter cloacae（NagZ) were cultured in LB media

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: Blood

tag: genotype

value: nagZ knock out


title: ΔnagZ rep1


title: control_188 850k methylation

value: lung

tag: center

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f


title: WT REP3

value: wild type


title: Granta519-ESR2 ChIP-seq rep 1

description: ESR2 over expression

value: Mantle cell lymphoma

value: chip antibody:PPZ0506, R&D systems, lot no:A2, mouse monoclonal

value: ESR2 over-expression


title: Granta519-ESR2 ChIP-seq rep 2

description: ESR2 over expression


title: Granta519-ESR2 input DNA

description: ESR2 over expression


title: SAM71_r50_probing_4_igg

value: A/H5N1 HA + PBS

value: N


title: case_183 850k methylation

value: LTRC

tag: dx

value: ipf

value: case

value: m

value: white

value: not hispanic or latino


title: Dual-Seq_BatchC_EMB

city: Ithaca

first: Monique

last: Theriault

state: NY

address: 930 Campus Rd C5-105 VMC, Cornell University

department: Microbiology and Immunology

institute: Cornell University

data_processing:
Flexbar (v. 3.4) has been used to remove low quality reads and trim Illumina adapters.
rRNA reads have been removed using Bowtie2 (--sensitive mode)
rRNA filtered fastq files were split using Bowtie2 (--very-sensitive mode) into species-specific files using the two reference genomes, GRCh38.98 for Homo sapiens and NCBI assembly GCA_00668235.1 for Mtb Erdman
Hisat2 (v. 2.1.0) was used to align reads to the respective transcriptomes
Raw read counts for each sample were obtained using HTSeq (v. 0.11.0)
Genome_build: Genome_build: GRCh38.98 for Homo sapiens and NCBI assembly GCA_00668235.1 for Mtb Erdman

organism:
Mycobacterium tuberculosis
Homo sapiens

source_name: Mtb infected human macrophages

growth_protocol: Dual RNA-seq: Human monocyte derived macrophages (HMDMs) were infected with Erdman smyc’::mCherry reporter Mtb strain at MOI 2:1. Cholesterol RNA-Seq: Wildtype Erdman Mtb was grown in 7H9 OADC for 2 days in a roller bottle.

extract_protocol:
Dual RNA-Seq: To remove host RNA, Trizol samples were centrifuged and approximately 75% (~500 µL) of Trizol supernatant was transferred to a new tube. An additional 400 µL of Trizol and 150 µL of zirconia beads were added to the tubes containing the bacterial pellet and 25% of the remaining Trizol. These tubes were placed on a beat beater for two cycles of one minute each, with 2 minutes of rest on ice in between. After the bead beating, approximately 75% of host RNA in Trizol was added to be bacterial lysate tubes. Chloroform was added to Trizol tubes (200 µL of chloroform for 1 mL of Trizol) and tubes were mixed via shaking vigorously. Trizol:chloroform tubes were centrifuged for 15 minutes and the aqueous phase (~1 mL) was transferred to a fresh tube. 2 µL of glycoblue and 500uL of isopropanol were added to precipitate host and bacterial RNA. RNA was washed in 75% cold ethanol and RNA was eluted in 12 µL of NCFW. Cholesterol RNA-seq: Bacterial pellets in GTC buffer were washed with PBS + 0.05% Tween-80. Bacterial cells were lysed via 5mg/mL lysozyme treatment for 15 minutes at room temperature followed by hot Trizol bead beating for one cycle of 2 minutes. After bead beating, chloroform was added and the tubes were centrifuged to separate phases. The aqueous phase was then added to equal volume of pure ethanol. RNA was then purified using a Qiagen Rneasy Kit.
Sequencing libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced on a HiSeq 4000 (Illumina) in multiple rounds until the desired sequencing depth for bacterial reads was reached.

treatment_protocol: Dual RNA-seq: At 2 dpi, experimental compounds were administered at 10 µM, INH at 67.5 ng/mL, and EMB at 5 µg/mL. Infected HMDMs were treated for 48 hours prior to sorting. Cholesterol RNA seq: After 2 days of growth, drugs were administed at 10x EC50.

tag: bacterial strain

value: Erdman M. tuberculosis, pCherry3

value: 5 5 µg/mL ethambutol


title: control_186 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

tag: methylationid

tag: Sex


title: SAM71_nop_probing_4_igg

value: no peptide


title: control_182 850k methylation

value: control

value: f

tag: race

tag: ethnicity


title: case_185 850k methylation

value: Y


title: case_189 850k methylation


title: case_193 850k methylation


title: ΔnagZ rep2

value: Blood

value: nagZ knock out


title: A549+TGFβ+curcumin

type: RNA

city: shimoga

first: Shivananda

last: Kandagalla

state: Karnataka

address: Jnana sahyadri shankaraghatta

department: Biotechnology

country: India

institute: Kuvempu University

hyb_protocol: First, the exact RNA concentration was performed using Invitrogen Qubit RNA HS assay kit and diluted to 14ng/ul, 5 ul of these diluted RNA samples were taken for NanoString nCounter™ analysis (using PanCancer Progression Panel, NanoString Technologies, Seattle, WA). Total RNA was hybridized with the ‘PanCancer Progression’ code, and hybridization was carried out in ProFlex™ thermocycler at 65°C for 18 hrs. Complete information was found in the NanoString website (https://www.nanostring.com/products/ncounter-assays-panels/oncology/pancancer-progression/).

scan_protocol: Hybridized samples were purified in nuclease free water and they were conjugated to the optical cartridge using the nCounter™ Prep Station. The cartridge was scanned on the nCounter™ Digital Analyzer. Complete information was found in the NanoString website (https://www.nanostring.com/products/ncounter-assays-panels/oncology/pancancer-progression/).

data_processing: The generated RCC files were imported to nSolver™ 4.0 software (NanoString Technologies) and checked for data quality using default QC settings. All the samples passed data quality QC. Further, raw counts were normalized using the geometric mean of the housekeeper genes and differentially expressed genes (DEGs) were identified using DE call (Differential Expression call). Complete information was found in the NanoString website (https://www.nanostring.com/products/ncounter-assays-panels/oncology/pancancer-progression/).

label: Reporter and Capture probes

source_name: Human alveolar basal epithelial cells

label_protocol: As described in the manual (https://www.nanostring.com/products/ncounter-assays-panels/oncology/pancancer-progression/).

growth_protocol: Lung adenocarcinoma cells (A549) were cultured in DMEM culture media supplemented with 10% FBS, 0.37% sodium bicarbonate, penicillin (100 U/ml) and streptomycin (100 μg/ml) in a 5% carbon dioxide, and 95% air at 37°C. At about 90% confluence, the cells were trypsinized with the trypsin-EDTA solution and seeded in 6-well plates, grown to confluence, and rested in a medium without FBS overnight.

extract_protocol: Total RNA extraction was carried out using Qiagen miRNeasy mini kit (Cat No/ID: 217004) as per the manufacturers’ protocol.

treatment_protocol: A549 cells were seeded in 100 mm dishes and treated with 10 ng/mL recombinant human TGF-β1 along with different concentrations of curcumin (10µM) for 24 h.

value: Lung adenocarcinoma cell line

tag: treatment

value: TGF-beta1 + curcumin


title: SAM37_m10_probing_4_igg

tag: subject id

value: A/H5N1 HA + PBS

tag: day

value: Mini HA-10ug/ml


title: case_184 850k methylation

tag: tissue

value: LTRC

value: ipf

value: case

value: m

value: white

value: N


title: A549+TGF-β

treatment_protocol: A549 cells were seeded in 100 mm dishes and treated with 10 ng/mL recombinant human TGF-β1 along with different concentrations of curcumin (10µM and 20µM) for 24 h.

tag: cell type


title: SAM71_m10_probing_4_igg

tag: blocking


title: Dual-Seq_BatchB_INH

value: Erdman M. tuberculosis, pCherry3

value: 67.5 ng/mL isoniazid


title: WT REP2

value: wild type


title: WT REP1


title: SAM37_nop_probing_4_igg

value: no peptide


title: Dual-Seq_BatchA_EMB

value: 5 5 µg/mL ethambutol


title: control_180 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: not hispanic or latino


title: Dual-Seq_BatchC_INH


title: Dual-Seq_BatchB_EMB


title: Dual-Seq_BatchB_DMSO

value: DMSO (untreated)


title: case_181 850k methylation

value: LTRC

value: White

value: Y


title: SAM37_r10_probing_4_igg

value: A/H5N1 HA + PBS


title: SAM37_m50_probing_4_igg

value: Mini HA -50ug/ml


title: Dual-Seq_BatchC_DMSO


title: Dual-Seq_BatchA_DMSO


title: Dual-Seq_BatchC_mCLB073

value: 10 µM mCLB073


title: case_178 850k methylation

value: ipf

value: case

value: m

value: Not Hispanic or Latino


title: Dual-Seq_BatchA_INH

value: Erdman M. tuberculosis, pCherry3

value: 67.5 ng/mL isoniazid


title: Dual-Seq_BatchB_mCLB073


title: Dual-Seq_BatchA_mCLB073


title: control_177 850k methylation

value: lung

value: Pittsburgh Lung Donor Core

value: white

value: N


title: Dual-Seq_BatchA_sAEL057

value: 10 µM sAEL057


title: SAM30_nop_probing_4_igg

value: A/H5N1 HA + AS03

value: no peptide


title: SAM37_r50_probing_4_igg

value: Y


title: SAM30_r50_probing_4_igg


title: Dual-Seq_BatchC_sAEL057


title: case_176 850k methylation

value: LTRC

value: black

value: not hispanic or latino


title: Dual-Seq_BatchB_sAEL057


title: control_179 850k methylation

value: normal

value: control

value: f


title: SAM30_m10_probing_4_igg

value: Mini HA-10ug/ml


title: rhLJ23-BRUSH-Post

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
FASTQ data were generated by Illumina Basespace.
FASTQ data quality assessment and trimming, read mapping, and expression analyses were done by Banana Slug Analytics Platform.
Assembly: hg19
Supplementary files format and content: EdgeR

organism: Macaca mulatta

source_name: BRUSH

extract_protocol: Library was prepared using Illumina Truseq Stranded Total RiboZero Gold

value: bronchial brushing

tag: animal id

value: vaping exposed


title: rhLC91-BAL-Post

source_name: BAL

value: bronchoalveolar lavage


title: case_174 850k methylation

value: lung

value: ipf

value: case

tag: age

value: m


title: case_175 850k methylation

value: White


title: SAM30_r10_probing_4_igg

value: A/H5N1 HA + AS03

value: N


title: SAM30_m50_probing_4_igg

value: Mini HA -50ug/ml


title: case_173 850k methylation

value: LTRC

value: white

value: Y


title: rhLC91-BAL-Pre

value: no exposure


title: control_172 850k methylation

value: other

value: control

value: f

value: not hispanic or latino


title: SAM81_r10_probing_4_igg

value: A/H5N1 HA + MF59


title: rhLC91-BRUSH-Post

value: bronchial brushing

value: vaping exposed


title: case_171 850k methylation

value: lung

value: ipf

value: case


title: SAM81_r50_probing_4_igg


title: SAM81_nop_probing_4_igg

value: no peptide