title: whole blood, subject 6b1b752d, sample time point T13, library prep Plate_14


title: U2OS_JQ1_B2_t3

status: Public on Dec 06 2022

type: SRA

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

description: U2OS cells JQ1 Chem-map

library_source: genomic

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with qualiti lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome, and only the reads within the whitelist have been retained.
bw files were created using bamCoverage with counts per milion normalisation (CPM)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: Chem-map

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Mycoplasma-free human chronic myelogenous leukemia K562 cells (RRID:CVCL 0004) were purchased from ATCC and cultured in RPMI 1640 (Gibco, 21875034) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco, A3840401). Human bone osteosarcoma epithelial U2OS cells (RRID:CVCL_0042) derived from a moderately differentiated sarcoma were obtained from ATCC and cultured in DMEM (Gibco, 41966029) supplemented with 10% FBS. Both cell lines were grown in accordance with ENCODE cell culture protocols and tested for mycoplasma contamination and identity confirmed by STR typing.

extract_protocol:
For Chem-map experiment, U2OS cells were detached using accutase (Stem Cell Technologies, 07920) and quenched using complete culture media. U2OS and K562 cells were collected by centrifugation and fixed in 0.1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 2 min at room temperature, followed by quenching with glycine (Sigma-Aldrich, 50046) to a final concentration of 75 mM. Fixed cells were collected by centrifugation at 600x g for 4 min, followed by resuspension in cold wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl and 0.5 mM spermidine (Sigma-Aldrich, S0266)) in nuclease-free water supplemented with a Complete Protease Inhibitor, EDTA-free (Sigma-Aldrich, 11873580001). [Note: For Chem-map of G4 ligands, NaCl was replaced by equivalent concentrations of KCl in all buffers to maintain G4 stability]. For 5 samples, 50 μL (for JQ1-btn) or 75 µL (for G4 ligands and biotinylated doxorubicin) concanavalin A beads (Bangs Labs, BP531) were washed twice in 1 mL binding buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2 in nuclease-free water) and resuspended in 75 µL binding buffer. 100 µL of cell suspension were incubated with 10 µL pre-washed concanavalin A beads at 25 °C for 10 min at 600 rpm. Beads-bound cells were gently washed twice with wash buffer, before resuspending in 100 µL probe-1st Ab pre-complex (small molecule concentration is 400 nM with a ratio of 1.2:1 to anti-biotin (D5A7) Rabbit mAb (Cell Signaling Technology, 5597)) in antibody buffer (2 mM EDTA, 0.1% BSA (Sigma-Aldrich, A8577), 0.05% digitonin (EMD Millipore, 300410) in wash buffer) and incubating at 4 °C overnight at 600 rpm. [Note: For Dox-btn1, final Dox-btn1 concentration is diluted to 0.2 µM]. Cells were washed 3x with 500 µL Dig-wash buffer (0.05% digitonin in wash buffer) and resuspended in 100 µL 2nd Ab-Tn5 transposome complex (2nd Ab (Antibodies-Online, ABIN101961, ~ 8 µM) ratio is 1:100; 2nd Ab and pA-Tn5 at a ratio of 2:1) in Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin in nuclease-free water supplemented with Complete Protease Inhibitor, EDTA-free) and incubated at 25 °C for 1 hr at 600 rpm. Cells were then washed 3x in 500 µL Dig-300 buffer before incubation in 300 µL tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) at 37 °C for 1 hr at 600 rpm. After tagmentation, cells were washed twice with 500 µL TAPS wash buffer (10 mM [tris(hydroxymethyl) methylamino] propanesulfonic acid (TAPS, Alfa Aesar, J63268.AE), 0.2 mM EDTA in nuclease-free water). 150 µL of extraction buffer (0.5 mg/mL proteinase K (Thermo Fisher Scientific, EO0491), 0.5% SDS (Sigma-Aldrich, L4509) in 10 mM Tris-HCl, pH8.0) were added, vortexed and incubated at 55 °C for 1 hr at 800 rpm. Next, 150 µL phenol-chloroform-isoamyl alcohol (Invitrogen, 15593049) was added and mixed. The mixture was transferred to MaXtract High Density phase-lock tubes (QIAGEN, 129046) and centrifuged at room temperature for 3 min at 16,000x g. 150 µL chloroform were added to the top aqueous phase, mixed by inverting the phase-lock tubes for 10 times and centrifuged at room temperature for 3 min at 16,000x g. The top aqueous layer was transferred to a 1.5 mL DNA Lo-bind tube (Eppendorf, 022431021). 6 µL 5 M NaCl and 375 µL cold ethanol were added, mixed and incubated at -20 °C overnight. Samples were centrifuged at 4 °C for 30 min at 21,130x g. The supernatant was carefully poured off and the DNA pellet rinsed with 1 mL cold 100% ethanol followed by centrifugation at 4 °C for 2 min at 21,130x g. After pouring off the wash and draining the residual liquid with paper towel, the pellet was left to air-dry. Finally, the pellet was resuspended in 25 µL elution buffer 1 (10 mM Tris-HCl, pH8, 1 mM EDTA, 1/400 RNAse A (Thermo Fisher Scientific, EN0531) in nuclease-free water) by vortexing and incubating at 37 °C for 10 min at 800 rpm.
For BRD4 CUT&Tag experiment, U2OS cells were detached using accutase (Stem Cell Technologies, 07920) and quenched using complete culture media. U2OS and K562 cells were collected by centrifugation and fixed in 0.1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS for 2 min at room temperature, followed by quenching with glycine (Sigma-Aldrich, 50046) to a final concentration of 75 mM. Fixed cells were collected by centrifugation at 600x g for 4 min, followed by resuspension in cold wash buffer (20 mM HEPES, pH 7.5, 150 mM NaCl and 0.5 mM spermidine (Sigma-Aldrich, S0266)) in nuclease-free water supplemented with a Complete Protease Inhibitor, EDTA-free (Sigma-Aldrich, 11873580001). ConA beads (Bangs Labs, BP531) per sample were washed twice in 1 mL binding buffer (20 mM HEPES, pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2 in nuclease-free water) and resuspended in 75 µL binding buffer. 100 µL of cell suspension were incubated with 10 µL pre-washed concanavalin A beads at 25 °C for 10 min at 600 rpm. Beads-bound cells were gently washed twice with wash buffer, before resuspending in 50 µL anti-BRD4 (E2A7X) rabbit antibody (Cell Signalling Technology, 13440) in antibody buffer (2 mM EDTA, 0.1% BSA (Sigma-Aldrich, A8577), 0.05% digitonin (EMD Millipore, 300410) in wash buffer) at a ratio of 1:50 and incubating at 4 °C overnight at 600 rpm. Cells were washed 3x with 500 µL Dig-wash buffer (0.05% digitonin in wash buffer) and resuspended in 50 µL Guinea Pig anti-rabbit antibody (Antibodies-Online, ABIN101961) in Dig-wash buffer at a ratio of 1:100. Diluted pA-Tn5 adapter complex (1:250 ratio) was then added in Dig-300 buffer followed by the tagmentation reaction in tagmentation buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin in nuclease-free water supplemented with Complete Protease Inhibitor, EDTA-free) and incubated at 25 °C for 1 hr at 600 rpm. Cells were then washed 3x in 500 µL Dig-300 buffer before incubation in 300 µL tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) at 37 °C for 1 hr at 600 rpm. After tagmentation, cells were washed twice with 500 µL TAPS wash buffer (10 mM [tris(hydroxymethyl) methylamino] propanesulfonic acid (TAPS, Alfa Aesar, J63268.AE), 0.2 mM EDTA in nuclease-free water). 100 µL of extraction buffer (0.5 mg/mL proteinase K (Thermo Fisher Scientific, EO0491), 0.5% SDS (Sigma-Aldrich, L4509) in 10 mM Tris-HCl, pH8.0) were added, vortexed and incubated at 55 °C for 1 hr at 800 rpm. Next, 100 µL phenol-chloroform-isoamyl alcohol (Invitrogen, 15593049) was added and mixed. The mixture was transferred to MaXtract High Density phase-lock tubes (QIAGEN, 129046) and centrifuged at room temperature for 3 min at 16,000x g. 100 µL chloroform were added to the top aqueous phase, mixed by inverting the phase-lock tubes for 10 times and centrifuged at room temperature for 3 min at 16,000x g. The top aqueous layer was transferred to a 1.5 mL DNA Lo-bind tube (Eppendorf, 022431021). 4 µL 5 M NaCl and 250 µL cold ethanol were added, mixed and incubated at -20 °C overnight. Samples were centrifuged at 4 °C for 30 min at 21,130x g. The supernatant was carefully poured off and the DNA pellet rinsed with 1 mL cold 100% ethanol followed by centrifugation at 4 °C for 2 min at 21,130x g. After pouring off the wash and draining the residual liquid with paper towel, the pellet was left to air-dry. Finally, the pellet was resuspended in 25 µL elution buffer 1 (10 mM Tris-HCl, pH8, 1 mM EDTA, 1/400 RNAse A (Thermo Fisher Scientific, EN0531) in nuclease-free water) by vortexing and incubating at 37 °C for 10 min at 800 rpm.
In a 0.2 mL PCR tube, 25 µL NEBNext® Ultra™ II Q5 2x PCR master mix (NEB, M0544), 2 µL of 10 µM uniquely barcoded v2 Ad1.x primer, 2 µL of 10 µM uniquely barcoded v2 Ad2.x primer and 21 µL tagmented DNA were added and subjected to PCR (72 °C for 5 min, 98 °C for 30 s, followed by 10 cycles of 98 °C for 10 s and 63 °C for 10 s, and one cycle of 72 °C for 1 min). Libraries were purified using 1.3x ratio (65 µL) Ampure XP beads (Beckman Coulter, A63882). After 10 min incubation at room temperature, bead-bound DNA was washed twice with 80% ethanol and libraries were eluted with 25 µL 10 mM Tris-HCl for 5 min at room temperature. [Note: PCR program condition for Dox-btn1 is 72 °C for 5 min, 98 °C for 2 min, followed by 10 cycles of 98 °C for 10 s and 63 °C for 10 s, and one cycle of 72 °C for 1 min, to maximally disrupt doxorubicin-DNA interaction]

tag: cell line

tag: cell type

value: osteosarcoma epithelial

tag: chip antibody


title: whole blood, subject 695f8fdc, sample time point T4, library prep Plate_19

city: New York

first: Ryan

middle: Conrad

last: Thompson

state: NY

address: 1 Gustave L. Levy Place

department: Charles Bronfman Institute for Personalized Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data, RNA-seq QC data, and other data and metadata.

library_source: transcriptomic

data_processing:
Quality-filtered raw data was converted into FASTQ files using bcl2fastq (Illumina).
RNA-seq reads were aligned to the GRCh38 primary assembly with Gencode gene annotation v30 by STAR (v2.7.3a) using per-sample 2-pass mapping (--twopassMode Basic) and chimeric alignment options (--chimOutType Junctions SeparateSAMold -chimSegmentMin 15 -chimJunctionOverhangMin 15).
RNA-seq QC metrics were calculated by fastqc (v0.11.8) and Picard Tools (v2.22.3).
Quantification was done at the gene-level with antisense specificity using featureCounts (Subread R package v1.6.3 and strandness option -s 2) with gene-level grouping / primary alignments only / count all overlapped features (-t exon -g gene_id -primary -O).
MultiQC was used to compile and summarize per-sample statistics from STAR, Picard Tools and featureCounts (e.g. gene-level counts, mtRNA counts, globinRNA counts, etc.) into an interactive HTML report.
We excluded samples with DV200 below 80% as well as samples with fewer than 10 million mapped reads counted by featureCounts.
To remove the unwanted signal due to globin gene expression in whole blood, counts for all annotated globin genes (gene symbols CYGB, HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, HBZ, and MB) were discarded, and the remaining count matrix was transformed to counts per million (CPM).
Genes with CPM ≥1 in ≥36 samples (half the number of subjects with no positive PCR or antibody test for SARS-CoV-2 during the study period) were included in our analyses (21,194).
Gene expression was normalized for composition bias using the trimmed mean of M-values method, implemented by calcNormFactors in the edgeR package and transformed to normalized log2 CPM with observation weights computed by voomWithDreamWeights from the variancePartition package.
Batch effects were residualized from the data by fitting a linear mixed model to the normalized log2 CPM and weights for each gene with random effects for library prep plate (the batch effect to be residualized out) and blood sample ID (the biological signal to be retained) using dream, and then subtracting the best linear unbiased predictors for library prep plate while retaining the differences between blood samples and the residuals.
The technical replicates for each batch control sample were summarized to a single residualized expression value equal to the weighted mean of the technical replicates with a weight equal to the sum of the individual weights of the technical replicates.
Assembly: GRCh38 primary genome assembly with Gencode v30 gene annotation (corresponds to Ensembl version 96)
Supplementary files format and content: rnaseq_raw_count_matrix.csv: comma-delimited raw RNA-seq read counts
Supplementary files format and content: rnaseq_logCPM_matrix.csv: comma-delimited filtered, normalized, batch-corrected log2 counts per million computed by voomWithDreamWeights with values for technical replicates summarized to a single weighted mean value per blood sample
Supplementary files format and content: rnaseq_voom_weight_matrix.csv: comma-delimited voom weight matrix corresponding to normalized batch-corrected log2 CPM values

molecule: total RNA

source_name: whole blood

extract_protocol:
Frozen blood samples were thawed and total RNA was extracted from the samples using a modification of the MagMax protocol for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher, #4451893).
Samples that yielded sufficient RNA (>50 ng) were barcoded and prepared for pooled whole transcriptome sequencing using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020599), which is designed to remove ribosomal, globin, and mitochondrial RNA. Libraries were amplified with 15 cycles of PCR, pooled, and sequenced on a NovaSeq 6000 (Illumina) using Sprime flow cells with 100 base pair paired-end reads, targeting a mean of 50 million read pairs per sample. For a minority of samples in which the first extraction failed (N=24), RNA was re-extracted from the supernatant saved from the first centrifugation pellet. The extraction protocol was repeated starting with the second wash step after re-pelleting the RNA.

tag: tissue

value: whole blood

tag: subject id

tag: blood sample_id

tag: library prep_plate

tag: Sex

value: Female

tag: sampling time_point_label

tag: days since_first_sample

tag: patient classification_at_first_sample

tag: covid-19 positive

value: Positive


title: whole blood, subject 695f8fdc, sample time point T2, library prep Plate_19


title: whole blood, subject 68b25dd2, sample time point T4, library prep Plate_10

value: Male


title: whole blood, subject 695d5202, sample time point T1, library prep Plate_15


title: whole blood, subject 68b25dd2, sample time point T1, library prep Plate_12


title: whole blood, subject 68b25dd2, sample time point T2, library prep Plate_3


title: whole blood, subject 67dec94d, sample time point T2, library prep Plate_3


title: U2OS_BRD4_B2_t4

description: U2OS cells BRD4 CUT&TAG

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with qualiti lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome, and only the reads within the whitelist have been retained.
bw files were created using bamCoverage with counts per milion normalisation (CPM)
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&TAG

value: anti-BRD4 (E2A7X) rabbit


title: U2OS_JQ1_B1_t3

description: U2OS cells JQ1 Chem-map


title: U2OS_JQ1_B1_t1

description: U2OS cells JQ1 Chem-map


title: U2OS_JQ1_B2_t5

description: U2OS cells JQ1 Chem-map


title: U2OS_JQ1_B1_t2

description: U2OS cells JQ1 Chem-map


title: U2OS_BRD4_B2_t5

description: U2OS cells BRD4 CUT&TAG


title: whole blood, subject 67905ea6, sample time point T12, library prep Plate_14


title: U2OS_JQ1_B1_t4

description: U2OS cells JQ1 Chem-map


title: U2OS_BRD4_B2_t3

description: U2OS cells BRD4 CUT&TAG


title: U2OS_BRD4_B2_t2

description: U2OS cells BRD4 CUT&TAG


title: U2OS_BRD4_B1_t5

description: U2OS cells BRD4 CUT&TAG


title: U2OS_BRD4_B2_t1

description: U2OS cells BRD4 CUT&TAG


title: whole blood, subject 677c538e, sample time point T1, library prep Plate_16


title: U2OS_BRD4_B1_t4

description: U2OS cells BRD4 CUT&TAG


title: whole blood, subject 67905ea6, sample time point T2, library prep Plate_6


title: whole blood, subject 667ae48e, sample time point T1, library prep Plate_3


title: whole blood, subject 67905ea6, sample time point T4, library prep Plate_16


title: whole blood, subject 677c858d, sample time point T2, library prep Plate_6


title: whole blood, subject 67905ea6, sample time point T8, library prep Plate_14


title: whole blood, subject 667ae48e, sample time point T0, library prep Plate_6


title: U2OS_BRD4_B1_t2

description: U2OS cells BRD4 CUT&TAG


title: U2OS_BRD4_B1_t1

description: U2OS cells BRD4 CUT&TAG


title: K562_Tucidino_DOX-btn1_200nM_B3_t5

description: K562 cells treated with Tucidinostat Dox-btn1 Chem-map

value: erythroleukemia type


title: whole blood, subject 67dec94d, sample time point T1, library prep Plate_10


title: K562_Tucidino_DOX-btn1_200nM_B3_t4


title: whole blood, subject 650d88a1, sample time point T2, library prep Plate_8


title: whole blood, subject 66535e14, sample time point T1, library prep Plate_18


title: K562_Tucidino_DOX-btn1_200nM_B3_t1


title: whole blood, subject 66535e14, sample time point T2, library prep Plate_2


title: whole blood, subject 650d88a1, sample time point T1, library prep Plate_15


title: K562_Tucidino_DOX-btn1_200nM_B3_t2


title: whole blood, subject 6579a1ae, sample time point T2, library prep Plate_7


title: whole blood, subject 6579a1ae, sample time point T4, library prep Plate_7


title: whole blood, subject 64eb2619, sample time point T4, library prep Plate_6


title: K562_Tucidino_DOX-btn1_200nM_B2_t3


title: K562_Tucidino_DOX-btn1_200nM_B2_t5


title: U2OS_BRD4_B1_t3

description: U2OS cells BRD4 CUT&TAG


title: whole blood, subject 64eb2619, sample time point T1, library prep Plate_7


title: whole blood, subject 64dd6b5e, sample time point T1, library prep Plate_17


title: whole blood, subject 648cd6e5, sample time point T1, library prep Plate_14

value: Negative


title: whole blood, subject 62deb59c, sample time point T12, library prep Plate_19


title: K562_Tucidino_DOX-btn1_200nM_B3_t3


title: whole blood, subject 6463f11b, sample time point T1, library prep Plate_5


title: K562_Tucidino_DOX-btn1_200nM_B2_t1


title: K562_Tucidino_DOX-btn1_200nM_B1_t3


title: K562_Tucidino_DOX-btn1_200nM_B1_t2


title: K562_Tucidino_DOX-btn1_200nM_B1_t1


title: K562_Tucidino_DOX-btn1_200nM_B2_t4


title: K562_Tucidino_DOX-btn1_200nM_B1_t4


title: K562_Tucidino_DOX-btn1_200nM_B2_t2


title: whole blood, subject 62deb59c, sample time point T8, library prep Plate_19


title: whole blood, subject 62deb59c, sample time point T4, library prep Plate_14


title: whole blood, subject 62deb59c, sample time point T1, library prep Plate_13


title: K562_DMSO_DOX-btn1_200nM_B3_t5


title: whole blood, subject 626935c9, sample time point T4, library prep Plate_7


title: whole blood, subject 626935c9, sample time point T1, library prep Plate_5


title: K562_DMSO_DOX-btn1_200nM_B3_t1

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 60e2038d, sample time point T4, library prep Plate_6


title: K562_DMSO_DOX-btn1_200nM_B3_t2

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 6295c70b, sample time point T2, library prep Plate_3


title: K562_DMSO_DOX-btn1_200nM_B3_t3

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B3_t4

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B2_t4

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B2_t5

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 602c8cc5, sample time point T4, library prep Plate_16


title: K562_Tucidino_DOX-btn1_200nM_B1_t5


title: whole blood, subject 602c8cc5, sample time point T2, library prep Plate_9


title: whole blood, subject 602c8cc5, sample time point T1, library prep Plate_12


title: whole blood, subject 5f81193a, sample time point T12, library prep Plate_15


title: K562_DMSO_DOX-btn1_200nM_B2_t3

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B2_t2

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5f81193a, sample time point T1, library prep Plate_10


title: whole blood, subject 5f81193a, sample time point T2, library prep Plate_10


title: K562_DMSO_DOX-btn1_200nM_B1_t5

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B2_t1

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5ea543fd, sample time point T4, library prep Plate_7


title: K562_DMSO_DOX-btn1_200nM_B1_t4

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B1_t3

description: K562 cells Dox-btn1 Chem-map


title: K562_DMSO_DOX-btn1_200nM_B1_t2

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5ea543fd, sample time point T1, library prep Plate_7


title: whole blood, subject 62deb59c, sample time point T2, library prep Plate_11


title: K562_DMSO_DOX-btn1_200nM_B1_t1

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5e2f7e89, sample time point T4, library prep Plate_5


title: whole blood, subject 5e2f7e89, sample time point T1, library prep Plate_10


title: K562_Dox-btn1_200nM_B2_t4

description: K562 cells Dox-btn1 Chem-map


title: K562_Dox-btn1_200nM_B2_t3

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5d55118b, sample time point T4, library prep Plate_18


title: K562_Dox-btn1_200nM_B2_t5

description: K562 cells Dox-btn1 Chem-map


title: K562_Dox-btn1_200nM_B2_t2

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5d04a912, sample time point T12, library prep Plate_16


title: whole blood, subject 5d55118b, sample time point T1, library prep Plate_16


title: K562_Dox-btn1_200nM_B2_t1

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5d04a912, sample time point T4, library prep Plate_13


title: K562_Dox-btn1_200nM_B1_t4

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5d04a912, sample time point T2, library prep Plate_6


title: K562_Dox-btn1_200nM_B1_t5

description: K562 cells Dox-btn1 Chem-map


title: K562_Dox-btn1_200nM_B1_t3

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5bc2c935, sample time point T4, library prep Plate_13


title: whole blood, subject 5d04a912, sample time point T1, library prep Plate_4


title: K562_Dox-btn1_200nM_B1_t2

description: K562 cells Dox-btn1 Chem-map


title: whole blood, subject 5bc2c935, sample time point T2, library prep Plate_3


title: whole blood, subject 5ea543fd, sample time point T2, library prep Plate_8


title: K562_PhenDC3_B2_t5

description: K562 cells PhenDC3-btn Chem-map


title: K562_Dox-btn1_200nM_B1_t1

description: K562 cells Dox-btn1 Chem-map


title: K562_PhenDC3_B2_t4

description: K562 cells PhenDC3-btn Chem-map


title: whole blood, subject 5bc2c935, sample time point T1, library prep Plate_4


title: whole blood, subject 5e152c59, sample time point T2, library prep Plate_4


title: whole blood, subject 5bbbd4c9, sample time point T4, library prep Plate_7


title: K562_PhenDC3_B2_t3

description: K562 cells PhenDC3-btn Chem-map


title: whole blood, subject 5e152c59, sample time point T1, library prep Plate_19


title: K562_PhenDC3_B2_t2

description: K562 cells PhenDC3-btn Chem-map


title: whole blood, subject 5badd4f1, sample time point T12, library prep Plate_9


title: whole blood, subject 5bbbd4c9, sample time point T1, library prep Plate_6


title: whole blood, subject 5badd4f1, sample time point T8, library prep Plate_9


title: whole blood, subject 5badd4f1, sample time point T4, library prep Plate_7


title: K562_PhenDC3_B2_t1

description: K562 cells PhenDC3-btn Chem-map


title: whole blood, subject 5badd4f1, sample time point T1, library prep Plate_4


title: K562_PhenDC3_B1_t5

description: K562 cells PhenDC3-btn Chem-map


title: K562_PhenDC3_B1_t4

description: K562 cells PhenDC3-btn Chem-map


title: K562_PhenDC3_B1_t3

description: K562 cells PhenDC3-btn Chem-map


title: K562_PhenDC3_B1_t2

description: K562 cells PhenDC3-btn Chem-map


title: K562_PDS_B2_t5

description: K562 cells PDS-btn Chem-map

value: PDS-btn


title: whole blood, subject 5b116f76, sample time point T3, library prep Plate_5


title: whole blood, subject 5ae80188, sample time point T2, library prep Plate_13


title: K562_PDS_B2_t4

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5ab88658, sample time point T13, library prep Plate_7


title: K562_PDS_B2_t3

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5ab88658, sample time point T12, library prep Plate_4


title: K562_PDS_B2_t2

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5ab88658, sample time point T8, library prep Plate_18


title: whole blood, subject 5ab88658, sample time point T2, library prep Plate_4


title: K562_PDS_B1_t5

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5aabb512, sample time point T1, library prep Plate_7


title: K562_PDS_B2_t1

description: K562 cells PDS-btn Chem-map


title: K562_PDS_B1_t4

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5a184e56, sample time point T1, library prep Plate_18


title: K562_PDS_B1_t3

description: K562 cells PDS-btn Chem-map


title: whole blood, subject 5a0b46e8, sample time point T12, library prep Plate_11


title: whole blood, subject 5a0b46e8, sample time point T8, library prep Plate_10


title: K562_PDS_B1_t2

description: K562 cells PDS-btn Chem-map


title: K562_PDS_B1_t1

description: K562 cells PDS-btn Chem-map


title: K562_PhenDC3_B1_t1

description: K562 cells PhenDC3-btn Chem-map


title: whole blood, subject 5ae80188, sample time point T4, library prep Plate_12


title: K562_JQ1_B2_t5

description: K562 cells JQ1 Chem-map


title: whole blood, subject 5a0b46e8, sample time point T4, library prep Plate_2


title: K562_JQ1_B2_t3

description: K562 cells JQ1 Chem-map


title: whole blood, subject 59d19b7f, sample time point T12, library prep Plate_14


title: K562_JQ1_B2_t4

description: K562 cells JQ1 Chem-map


title: whole blood, subject 5a0b46e8, sample time point T1, library prep Plate_15


title: whole blood, subject 5ae80188, sample time point T1, library prep Plate_17


title: whole blood, subject 59d19b7f, sample time point T8, library prep Plate_18


title: whole blood, subject 59d19b7f, sample time point T4, library prep Plate_16


title: K562_JQ1_B2_t1

description: K562 cells JQ1 Chem-map


title: K562_JQ1_B1_t5

description: K562 cells JQ1 Chem-map


title: whole blood, subject 59d19b7f, sample time point T1, library prep Plate_16


title: K562_JQ1_B1_t4

description: K562 cells JQ1 Chem-map


title: K562_JQ1_B1_t3

description: K562 cells JQ1 Chem-map


title: whole blood, subject 590c4e5a, sample time point T13, library prep Plate_19


title: whole blood, subject 590c4e5a, sample time point T8, library prep Plate_19


title: K562_JQ1_B1_t2

description: K562 cells JQ1 Chem-map


title: K562_BRD4_B2_t5

description: K562 cells BRD4 CUT&TAG


title: whole blood, subject 590c4e5a, sample time point T4, library prep Plate_6


title: whole blood, subject 590c4e5a, sample time point T12, library prep Plate_15


title: whole blood, subject 590c4e5a, sample time point T2, library prep Plate_13


title: K562_BRD4_B2_t4

description: K562 cells BRD4 CUT&TAG


title: whole blood, subject 590c4e5a, sample time point T1, library prep Plate_5


title: whole blood, subject 5816588a, sample time point T1, library prep Plate_10


title: whole blood, subject 5816588a, sample time point T2, library prep Plate_7


title: K562_BRD4_B2_t3

description: K562 cells BRD4 CUT&TAG


title: K562_BRD4_B2_t2

description: K562 cells BRD4 CUT&TAG


title: K562_BRD4_B2_t1

description: K562 cells BRD4 CUT&TAG


title: whole blood, subject 59d19b7f, sample time point T2, library prep Plate_18


title: whole blood, subject 57e835f4, sample time point T1, library prep Plate_10


title: K562_JQ1_B2_t2

description: K562 cells JQ1 Chem-map


title: K562_BRD4_B1_t5

description: K562 cells BRD4 CUT&TAG


title: K562_BRD4_B1_t4

description: K562 cells BRD4 CUT&TAG


title: K562_BRD4_B1_t3

description: K562 cells BRD4 CUT&TAG


title: whole blood, subject 57e3c4f6, sample time point T12, library prep Plate_19


title: whole blood, subject 57e3c4f6, sample time point T8, library prep Plate_8


title: K562_BRD4_B1_t1

description: K562 cells BRD4 CUT&TAG


title: 12_MT-PMA-3

city: Bethesda

first: Jose

last: Martina

state: Maryland

address: 50 South Dr., Building 50, Room 3533

department: NHLBI, CDBC

institute: NIH

data_processing:
Basecalling was performed using Real Time Analysis version 2 (RTA2) software.
RTA2 software was used for basecalling and STAR algorithm version 2.5.2b with default settings was used to align the data to the human GRCh38/hg38 genome assembly to generate BAM files.
Differential gene expression analysis was performed using DESeq2 software version v1.14.1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for all samples.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Excel file containing DESeq2-normalized gene counts and the results of the performed differential analyses

growth_protocol: THP1 (TFEB-WT or CRISPR knock-in TFEB-S401A) cells  were grown in RPMI supplemented with GlutaMAX (Gibco, 61870036), 10% fetal bovine serum (Invitrogen, 21041-025) and 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, 2114).

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104). For each sample, 0.5 μg of total RNA was then used with Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594) for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were incubated with DMSO or 50 ng/ml PMA for 6h.

value: Monocytic

tag: disease

value: Leukemia

tag: treatment

value: Treated with 50 ng/ml PMA for 6h

tag: crispr

value: CRISPR knock-in TFEB-S401A


title: whole blood, subject 57e3c4f6, sample time point T4, library prep Plate_12


title: 11_MT-PMA-2


title: whole blood, subject 57e3c4f6, sample time point T1, library prep Plate_10


title: K562_JQ1_B1_t1

description: K562 cells JQ1 Chem-map


title: 10_MT-PMA-1


title: whole blood, subject 572a7c65, sample time point T8, library prep Plate_5


title: 09_MT-Untreated-3

value: DMSO


title: whole blood, subject 572a7c65, sample time point T4, library prep Plate_5


title: whole blood, subject 572a7c65, sample time point T1, library prep Plate_8


title: 07_MT-Untreated-1


title: 05_WT-PMA-2

value: TFEB-WT


title: 06_WT-PMA-3


title: whole blood, subject 56dee75f, sample time point T8, library prep Plate_2


title: whole blood, subject 56dee75f, sample time point T4, library prep Plate_5


title: whole blood, subject 56dee75f, sample time point T2, library prep Plate_8


title: whole blood, subject 57e835f4, sample time point T2, library prep Plate_12


title: 03_WT-Untreated-3


title: K562_BRD4_B1_t2

description: K562 cells BRD4 CUT&TAG


title: whole blood, subject 55d94f54, sample time point T12, library prep Plate_5


title: whole blood, subject 55d94f54, sample time point T8, library prep Plate_5


title: 04_WT-PMA-1


title: 01_WT-Untreated-1


title: whole blood, subject 55d94f54, sample time point T4, library prep Plate_10


title: whole blood, subject 57e3c4f6, sample time point T2, library prep Plate_5


title: whole blood, subject 55d94f54, sample time point T1, library prep Plate_11


title: whole blood, subject 55967838, sample time point T2, library prep Plate_9


title: whole blood, subject 55967838, sample time point T4, library prep Plate_10


title: whole blood, subject 56b5971d, sample time point T1, library prep Plate_16


title: whole blood, subject 55967838, sample time point T1, library prep Plate_11


title: 08_MT-Untreated-2


title: whole blood, subject 55d94f54, sample time point T2, library prep Plate_15


title: PiZZ61.MM.3

city: Boston

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

data_processing:
Reads were aligned to the ENSEMBL human reference genome GRCh38 using STAR
We used the Bioconductor package edgeR to import, filter and normalize the count matrix, followed by the limma package and voom, for linear model fitting and differential expression testing, using empirical Bayes moderation for estimating gene-wise variability prior to significance testing based on the moderated t-statistic.
Assembly: GRCh38
Supplementary files format and content: EdgeR normalized, counts per million

molecule: polyA RNA

source_name: PiZZ61 MM 3

growth_protocol: iPSC directed differentiation to the hepatic lineage was performed using our previously published protocol (Kaserman et al., 2020; Wilson et al., 2015)

extract_protocol:
RNeasy Mini Kit (Qiagen)
poly(A) selection & reverse transcription


title: PiZZ61.MM.2

source_name: PiZZ61 MM 2


title: PiZZ61.MM.1

source_name: PiZZ61 MM 1


title: whole blood, subject 558be967, sample time point T12, library prep Plate_2


title: whole blood, subject 558be967, sample time point T8, library prep Plate_12


title: PiZZ61.MZ.3

source_name: PiZZ61 MZ 3


title: PiZZ61.MZ.2

source_name: PiZZ61 MZ 2


title: whole blood, subject 558be967, sample time point T4, library prep Plate_18


title: whole blood, subject 558be967, sample time point T1, library prep Plate_10


title: 02_WT-Untreated-2


title: PiZZ61.ZZ.3

source_name: PiZZ61 ZZ 3


title: whole blood, subject 5386f49e, sample time point T1, library prep Plate_11


title: whole blood, subject 5386f49e, sample time point T2, library prep Plate_13


title: PiZZ61.ZZ.2

source_name: PiZZ61 ZZ 2


title: whole blood, subject 535274a5, sample time point T4, library prep Plate_9


title: whole blood, subject 535274a5, sample time point T2, library prep Plate_8


title: whole blood, subject 535274a5, sample time point T1, library prep Plate_13


title: whole blood, subject 535274a5, sample time point T13, library prep Plate_15


title: PiZZ61.ZZ.1

source_name: PiZZ61 ZZ 1


title: whole blood, subject 52c9ea6b, sample time point T2, library prep Plate_2


title: P2_C_NOR_S7_R1

city: Milan

first: Edoardo

last: Pedrini

state: Lombardy

address: Via Olgettina 60

department: Division of Neuroscience

country: Italy

institute: Hospital San Raffaele

description: Cells treated at 21% oxygen for 24h

data_processing:
Sequenced were mapped to GRCh38 whole genome using STAR 2.7.0d with parameters --readFilesCommand zcat --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate
feature counted with htseq-count version 0.11.2
Genome_build: GRCh38 release 96
Supplementary_files_format_and_content: raw table of counts for each sample

source_name: Endothelial Progenitor Cells

growth_protocol: Cells were grown in EGM2 media (Lonza) with addition of 10% FCS. The media was changed every three days.

extract_protocol:
Total RNA was isolated from cells using a Maxwell RSC instrument (Promega) following manufacturer’s instructions
KAPA RNA HyperPrep Kit with RiboErase

treatment_protocol: Cells were grown at either 1% or 21% oxygen concentration for 24h before RNA extraction

value: Normoxia

value: Endothelial Progenitor Cells

tag: passage

value: P6 to P14


title: P1_C_NOR_S1_R1

description: Cells treated at 21% oxygen for 24h


title: P3_C_NOR_S13_R1

description: Cells treated at 21% oxygen for 24h


title: whole blood, subject 52c9ea6b, sample time point T1, library prep Plate_5

value: whole blood


title: P2_C_HYP_S10_R1

description: Cells treated at 1% oxygen for 24h

value: Hypoxia


title: whole blood, subject 511a0966, sample time point T1, library prep Plate_5

value: Female


title: whole blood, subject 4fb7a031, sample time point T8, library prep Plate_15

value: Positive


title: P1_C_HYP_S4_R1

description: Cells treated at 1% oxygen for 24h


title: whole blood, subject 4fb7a031, sample time point T4, library prep Plate_3


title: LGN, axon-TRAP, P14 [PT321]

city: Seoul

first: Jane

last: Jung

state: Yonsei-ro, Seodaemun-gu

department: Department of Anatomy

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
The sequence reads were processed in Salmon on mm10 (GENCODE M24).
Read counts were merged at the gene-level by tximport.
Assembly: mm10
Supplementary files format and content: comna-separated text files include TPM and count values for each Sample

organism: Mus musculus

source_name: LGN (lateral geniculate nucleus)

extract_protocol:
Following vitreal EU injections, we dissected out superior colliculi from three animals and isolated total RNA using TRIzol reagent (Invitrogen 15596029). Twenty µg of total RNA was reacted with biotin-azide using Click-iT™ Nascent mRNA capture kit (Invitrogen C10365) to label EU-containing RNAs with a biotin tag. The tagged RNAs were affinity-purified using MyOne™ streptavidin T1-dynabeads resuspended in 50 µl nuclease-free water.
Purified RNAs were converted to double-stranded (ds) DNA using the previously described method (Shigeoka et al., 2016) with slight modification.
Amplified cDNAs were converted to sequencing libraries using Nextera XT DNA library preparation kit (Illumina FC-131-1024) and sequenced in Novaseq 6000.

value: LGN (lateral geniculate nucleus)

tag: genotype

value: wild type

tag: axotomy

value: naïve

tag: technique

value: axon-TRAP

tag: age


title: whole blood, subject 51b22678, sample time point T1, library prep Plate_8

tag: tissue

value: Male

value: Negative


title: SC, axon-TRAP, P14 [PT311]

source_name: SC (superior colliculus)

value: SC (superior colliculus)


title: LGN, axon-TRAP, P14 [PT221]


title: whole blood, subject 4f7c6b2f, sample time point T1, library prep Plate_12

tag: subject id


title: whole blood, subject 4f6fb5f1, sample time point T12, library prep Plate_18

tag: blood sample_id


title: LGN, EU labeled, P14 [EU221]

value: EU labeled


title: whole blood, subject 4f6fb5f1, sample time point T8, library prep Plate_2

tag: library prep_plate


title: LGN, axon-TRAP, P14 [PT121]


title: PiZZ61.MZ.1

source_name: PiZZ61 MZ 1

tag: cell line


title: P3_C_HYP_S16_R1

description: Cells treated at 1% oxygen for 24h


title: SC, EU labeled, P14 [EU211]


title: whole blood, subject 4f6fb5f1, sample time point T4, library prep Plate_7

tag: Sex

tag: sampling time_point_label


title: LGN, EU labeled, P14 [EU121]


title: whole blood, subject 4f2957ee, sample time point T4, library prep Plate_10

tag: days since_first_sample

tag: patient classification_at_first_sample


title: whole blood, subject 4ee897a3, sample time point T2, library prep Plate_5

tag: covid-19 positive


title: SC, EU labeled, P14 [EU111]


title: whole blood, subject 4f2957ee, sample time point T2, library prep Plate_5


title: whole blood, subject 4ee897a3, sample time point T1, library prep Plate_4


title: whole blood, subject 4f2957ee, sample time point T1, library prep Plate_7


title: whole blood, subject 4ecf7ee5, sample time point T1, library prep Plate_12


title: whole blood, subject 4e59b73d, sample time point T12, library prep Plate_12


title: whole blood, subject 4d1159dd, sample time point T2, library prep Plate_5


title: whole blood, subject 4ba22d3c, sample time point T1, library prep Plate_3


title: whole blood, subject 4d1159dd, sample time point T1, library prep Plate_12


title: whole blood, subject 4b09fa79, sample time point T4, library prep Plate_2


title: SC, axon-TRAP, P14 [PT211]


title: whole blood, subject 4a4e5a82, sample time point T12, library prep Plate_15


title: whole blood, subject 4a4e5a82, sample time point T2, library prep Plate_5


title: whole blood, subject 4a1d25b3, sample time point T1, library prep Plate_13


title: whole blood, subject 4a298280, sample time point T1, library prep Plate_11


title: whole blood, subject 4a4e5a82, sample time point T4, library prep Plate_11


title: whole blood, subject 492ef74f, sample time point T4, library prep Plate_10


title: whole blood, subject 4850aa1a, sample time point T12, library prep Plate_6


title: whole blood, subject 4850aa1a, sample time point T1, library prep Plate_11


title: whole blood, subject 484011ee, sample time point T1, library prep Plate_11


title: whole blood, subject 476283f6, sample time point T4, library prep Plate_18


title: whole blood, subject 4e59b73d, sample time point T1, library prep Plate_3


title: whole blood, subject 476283f6, sample time point T2, library prep Plate_12


title: Bastle3_F_S24_L003

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Raw sequencing reads from mice were mapped to mm10 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing counts

source_name: Brain (TMN)

extract_protocol:
TMN tissue punches were homogenized in Trizol (Thermo Fisher), and RNA was isolated on RNeasy Microcolumns (Qiagen) following manufacturer’s instructions. RNA concentrations were assessed using a Qubit spectrophotometer and quality was confirmed using a bioanalyzer.
RNA-seq libraries were prepared according to manufacturer’s protocols using the Illumina TruSeq RNA Library Preparation Kit v2 (Illumina cat# RS-122-2001).

value: Brain (TMN)

tag: viral genotype

tag: time point

value: 21 d post viral delivery


title: Bastle3_E_S23_L003

value: WT


title: Bastle3_C_S21_L003


title: Bastle3_D_S22_L003

value: GFP


title: Bastle3_I_S27_L003


title: Bastle3_H_S26_L003


title: whole blood, subject 476283f6, sample time point T1, library prep Plate_3


title: Bastle3_G_S25_L003


title: whole blood, subject 47090582, sample time point T2, library prep Plate_3


title: whole blood, subject 4ba22d3c, sample time point T2, library prep Plate_10


title: Bastle3_B_S20_L003


title: Bastle3_A_S19_L003


title: whole blood, subject 47090582, sample time point T1, library prep Plate_11


title: whole blood, subject 49d8bfa6, sample time point T1, library prep Plate_10


title: Bastle2_I_S18_L002


title: whole blood, subject 4a298280, sample time point T8, library prep Plate_16


title: whole blood, subject 464a28c7, sample time point T13, library prep Plate_17


title: whole blood, subject 492ef74f, sample time point T2, library prep Plate_5


title: Bastle2_G_S16_L002


title: Bastle2_F_S15_L002


title: whole blood, subject 464a28c7, sample time point T8, library prep Plate_4


title: whole blood, subject 464a28c7, sample time point T4, library prep Plate_7


title: Bastle2_E_S14_L002


title: Bastle2_D_S13_L002


title: whole blood, subject 46021e50, sample time point T8, library prep Plate_16


title: whole blood, subject 44fc8c3b, sample time point T12, library prep Plate_16


title: whole blood, subject 46021e50, sample time point T2, library prep Plate_8


title: Bastle2_A_S10_L002


title: whole blood, subject 46021e50, sample time point T4, library prep Plate_10


title: Bastle2_C_S12_L002


title: Bastle2_B_S11_L002


title: whole blood, subject 46021e50, sample time point T1, library prep Plate_3


title: whole blood, subject 44fc8c3b, sample time point T2, library prep Plate_8


title: Bastle1_E_S5_L001


title: whole blood, subject 45c43e5a, sample time point T1, library prep Plate_2


title: Bastle2_H_S17_L002


title: whole blood, subject 44fc8c3b, sample time point T4, library prep Plate_15


title: Bastle1_I_S9_L001


title: Bastle1_D_S4_L001


title: whole blood, subject 464a28c7, sample time point T12, library prep Plate_13


title: whole blood, subject 44fc8c3b, sample time point T1, library prep Plate_12


title: Bastle1_H_S8_L001


title: whole blood, subject 44ddfe84, sample time point T8, library prep Plate_18


title: Bastle1_F_S6_L001


title: Bastle1_G_S7_L001


title: whole blood, subject 44ddfe84, sample time point T4, library prep Plate_16


title: Bastle1_B_S2_L001


title: whole blood, subject 46021e50, sample time point T12, library prep Plate_19


title: whole blood, subject 44da5870, sample time point T4, library prep Plate_12


title: whole blood, subject 44ddfe84, sample time point T2, library prep Plate_13


title: Bastle1_C_S3_L001


title: Bastle1_A_S1_L001


title: whole blood, subject 44da5870, sample time point T1, library prep Plate_9


title: whole blood, subject 449c6103, sample time point T12, library prep Plate_10


title: whole blood, subject 449c6103, sample time point T8, library prep Plate_2


title: whole blood, subject 449c6103, sample time point T4, library prep Plate_16


title: whole blood, subject 449c6103, sample time point T3, library prep Plate_12


title: whole blood, subject 449c6103, sample time point T1, library prep Plate_13


title: whole blood, subject 43a53f1f, sample time point T4, library prep Plate_8


title: whole blood, subject 43a53f1f, sample time point T2, library prep Plate_11


title: whole blood, subject 43a53f1f, sample time point T1, library prep Plate_5


title: whole blood, subject 43a02363, sample time point T12, library prep Plate_6


title: P2y WT rep1

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
Reads were aligned using STAR
Quantification was accomplished using Salmon
Differential expression was determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts matrix generated using DESeq2

source_name: Excised liver

extract_protocol:
Liver was excised and total RNA was isolated using the Qiagen miRNeasy kit.
Libraries were constructed using Illumina TruSeq.

tag: strain

value: liver


title: P60 p53+/−; miR−29TG rep2


title: P60 p53+/−; miR−29TG rep1


title: P60 miR−29TG rep2


title: P60 WT rep1


title: P2y WT rep2


title: P60 WT rep2


title: whole blood, subject 42cde147, sample time point T1, library prep Plate_16

value: whole blood


title: whole blood, subject 43a02363, sample time point T4, library prep Plate_5


title: whole blood, subject 41663b51, sample time point T4, library prep Plate_15


title: pstB_adh1_ADH1_Ca_rep1

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above =  NO,  filter length below = NO
Alingment to Pseudomonas aeruginosa strain PA14  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Reporting - CLC Workbench export raw counts, TPM, CPM and RPKM
Genome_build: UCBPP-PA14 (www.pseudomonas.com)
Supplementary_files_format_and_content: csv including read counts and TPM

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa colony biofilm on C. albicans

growth_protocol:
pstB::TnM P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown ethanol-producing C. albicans (adh1∆/ADH1) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit with on-column Dnase treatment.
RNA was treated with Dnase using the Rneasy MinElute protocol and ribo-depletion using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.

treatment_protocol: P. aerguinosa was grown on MOPS (0.2% glucose, 7 mM phosphate) with and without 1% ethanol and on YPD with adh1∆/ADH1  adh1∆/∆ C. albicans.

tag: genotype

value: pstB

tag: growth protocol

value: co-culture with ethanol-producing C. albicans

value: colony biofilm on C. albicans


title: phoB_adh1_ADH1_Ca_rep2

growth_protocol:
∆phoB P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown ethanol-producing C. albicans (adh1∆/ADH1) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.

value: phoB


title: WT_adh1_ADH1_Ca_rep2

growth_protocol:
WT P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown ethanol-producing C. albicans (adh1∆/ADH1) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: pstB_adh1_ADH1_Ca_rep2

growth_protocol:
pstB::TnM  P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown ethanol-producing C. albicans (adh1∆/ADH1) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: phoB_adh1_ADH1_Ca_rep1


title: WT_adh1_ADH1_Ca_rep1


title: P60 miR−29TG rep1


title: phoB_adh1_Ca_rep2

growth_protocol:
∆phoB P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown non-ethanol-producing C. albicans (adh1∆/∆) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.

value: co-culture with non-ethanol-producing C. albicans


title: phoB_adh1_Ca_rep1


title: whole blood, subject 449c6103, sample time point T2, library prep Plate_15

value: Positive


title: pstB_adh1_Ca_rep1

growth_protocol:
pstB::TnM  P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown non-ethanol-producing C. albicans (adh1∆/∆) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: whole blood, subject 41663b51, sample time point T1, library prep Plate_4


title: whole blood, subject 41663b51, sample time point T0, library prep Plate_12


title: whole blood, subject 406b17b7, sample time point T13, library prep Plate_19

value: Female


title: whole blood, subject 406b17b7, sample time point T12, library prep Plate_14


title: WT_adh1_Ca_rep2

growth_protocol:
WT P. aeruginosa PA14 colony biofilm grown on a filter (0.1µm pores) atop a lawn of pre-grown non-ethanol-producing C. albicans (adh1∆/∆) on YPD for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: WT_adh1_Ca_rep1


title: whole blood, subject 416ded86, sample time point T1, library prep Plate_13

value: Male


title: whole blood, subject 406b17b7, sample time point T8, library prep Plate_6


title: phoB_mops_etoh_rep2

source_name: P. aeruginosa colony biofilm

growth_protocol:
∆phoB P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃ treated with 1% ethanol
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.

value: minimal medium,  1% ethanol

value: colony biofilm


title: phoB_mops_etoh_rep1


title: pstB_mops_etoh_rep2

growth_protocol:
pstB::TnM  P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃ treated with 1% ethanol
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: whole blood, subject 406b17b7, sample time point T1, library prep Plate_19

source_name: whole blood


title: whole blood, subject 406b17b7, sample time point T4, library prep Plate_7


title: WT_mops_etoh_rep2

growth_protocol:
WT P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃ treated with 1% ethanol
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: pstB_mops_etoh_rep1


title: whole blood, subject 40604ef2, sample time point T1, library prep Plate_4


title: whole blood, subject 406b17b7, sample time point T2, library prep Plate_2


title: whole blood, subject 3fb3ab81, sample time point T8, library prep Plate_15


title: pstB_adh1_Ca_rep2


title: phoB_mops_rep2

growth_protocol:
∆phoB P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.

value: minimal medium


title: WT_mops_etoh_rep1


title: phoB_mops_rep1


title: whole blood, subject 3fb3ab81, sample time point T12, library prep Plate_14


title: whole blood, subject 3fb3ab81, sample time point T2, library prep Plate_8


title: pstB_mops_rep2

growth_protocol:
pstB::TnM  P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: whole blood, subject 3eafb97f, sample time point T8, library prep Plate_11


title: whole blood, subject 41663b51, sample time point T2, library prep Plate_11


title: whole blood, subject 3fb3ab81, sample time point T4, library prep Plate_13


title: WT_mops_rep2

growth_protocol:
WT P. aeruginosa PA14 colony biofilm grown on MOPS minimal medium with 0.2% glucose and 7 mM phosphate for 16 h at 37℃
For mono-culture, P. aeruginosa was grown overnight in 5 mL LB on. a roller. from at 37℃ for 16 then 5 µl of culture was spotted onto a 1.5% agaer plate with MOPS minimal. medium with 0.2% glucose and 0.7 mM. phosphate. Plates were inclubaed for 16 h at 37℃ then cells were scraped from the plates. For co-culture, C. albicans was grown as a lawn on YPD agar plates for 16 hours at 30℃ then 32 hours at room temperature before 5 µl of P. aeruginosa overnight culture from LB was spotted onto a folter with 0.22 micron pores placed on top of the lawn. Co-culture colony biofilms were incubated at 30℃ for 16 hours before P. aeruginosa cells were collected from atop the filter.


title: whole blood, subject 3fb3ab81, sample time point T1, library prep Plate_10


title: pstB_mops_rep1


title: WT_mops_rep1


title: whole blood, subject 3eafb97f, sample time point T4, library prep Plate_9


title: whole blood, subject 3eafb97f, sample time point T1, library prep Plate_17


title: whole blood, subject 3d6e228f, sample time point T1, library prep Plate_17


title: whole blood, subject 3d426f83, sample time point T2, library prep Plate_11


title: whole blood, subject 3d6e228f, sample time point T2, library prep Plate_15


title: whole blood, subject 3e99c9ad, sample time point T1, library prep Plate_6


title: whole blood, subject 3d426f83, sample time point T1, library prep Plate_15


title: dvh4_S10

city: Tampa

first: chengqi

last: wang

address: 4202 E Fowler Ave

institute: University of South Florida

data_processing:
Quality control was performed on fastq files by using FastQC. Sequencing reads with Phred quality score higher than 30 were further processed for genomic mapping using STAR with parameter chimsegmentMin=20, minimum overhang for spliced alignments =1, and missing values = 0.04. Feature Counts (Subread) were used to count raw reads on each transcript.
Assembly: GRCH38
Supplementary files format and content: Comma delimited text file for raw read counts

source_name: HMC3 (ATCC CRL-3304)

growth_protocol: The microglial cell line HMC3 (ATCC CRL-3304, Manassas, Virginia) was used for in vitro experimentation following successful cell line authentication and My- coplasma testing (Genetica, Burlington, NC). HMC3 cells (passage eight) were seeded in T-25 flasks with 2 x 105 viable cells and incubated at 37àC and 5% CO2.

extract_protocol:
One cell pellet per flask was placed in -80C storage for future DNA extraction; the remaining cell pellet underwent RNA extraction using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) protocol adapted for the QIAcube automated system (QIAGEN). On the final day of the washout period (D6), cells from each flask were imaged, collected in suspension and then quantified on the Countess II. Cell suspensions were split equally into two aliquots and then prepped for nucleic acid extraction as described for D3.
RNA samples from D3 and D6 were DNase treated (Dnase I kit; Sigma), quan- tified on the Qubit (RNA BR Assay Kit; Invitrogen) and scored for RNA integrity on the TapeStation (High Sensitivity RNA ScreenTape; Agilent, Santa Clara, CA). Library preparation was performed following the Illumina TruSeq Stranded Total RNA Library Prep Kit protocol (Illumina, San Diego, CA) with TruSeq RNA Sin- gle Indexes (Set A and B; Illumina). Library quantity and quality were assessed using the Qubit 1X dsDNA HS Assay (Invitrogen), TapeStation High Sensitiv- ity D1000 ScreenTape (Agilent) and the KAPA Library Quantification Kit (Roche Basel, Switzerland) for the LightCycler 96 (Roche). RNA sequencing was conducted on the NextSeq 550using the High Output Kit with 76 paired-end cycles (Illumina).

treatment_protocol: After 24 hours, the growth medium in each T-25 was replaced with media supplemented with one of the following treatments: dexamethasone (1 or 0.01 μM), hydrocortisone (10 or 0.01 μM), vehicle (ethanol alcohol) or control (untreated me- dia). Cells were incubated in treatment media for three days at 37àC and 5% CO2 and imaged daily using the Axio Vert.A1 inverted microscope (Zeiss Oberkochen, Germany). At three days post-exposure (D3), cells were collected from each flask individually, quantified on the Countess II cell counter (Invitrogen Waltham, MA), seeded at 2 x 105 viable cells/flask in new T-25 flasks with normal growth medium, and incubated for three additional days (i.e., washout period). The remaining D3 cell suspension for each flask was divided equally between two microcentrifuge tubes, pelleted and washed with PBS.

value: HMC3 (ATCC CRL-3304)

tag: cell type

value: microglial cell

tag: treatment

value: dex vehicle high3

tag: time (days)


title: dvl1_S3

value: dex vehicle low3


title: dvhwo4_S9

value: dex vehicle high6


title: dvlwo3_S17

value: dex vehicle low6


title: dvl2_S6


title: dvl3_S2


title: whole blood, subject 3d426f83, sample time point T4, library prep Plate_15

tag: tissue

value: whole blood

tag: subject id


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_19

tag: blood sample_id

tag: library prep_plate


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_15

tag: Sex


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_11

tag: sampling time_point_label


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_13

tag: days since_first_sample


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_9

tag: patient classification_at_first_sample


title: dvh1_S4

tag: cell line


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_7

tag: covid-19 positive


title: dexl3_S9

value: dex low3


title: dexhwo4_S5

value: dex high6


title: dexlwo2_S3

value: dex low6


title: dexl1_S16


title: dexlwo1_S22


title: dexl2_S15


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_5


title: dvh2_S8


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_2


title: dexhwo3_S17


title: dexhwo2_S12


title: whole blood, subject 3d2f9980, sample time point T2, library prep Plate_17


title: dexh4_S7

value: dex high3


title: whole blood, subject 3b625ef6, sample time point T8, library prep Plate_9

value: Positive


title: whole blood, subject 3b625ef6, sample time point T4, library prep Plate_8

value: Female


title: whole blood, subject 3c08d358, sample time point T2, library prep Plate_18


title: cvl2_S11

value: cort vehicle low3


title: cvl4_S7


title: dexh3_S20


title: whole blood, subject 3c08d358, sample time point T1, library prep Plate_17


title: whole blood, subject 3d2f9980, sample time point T1, library prep Plate_12

value: Male


title: whole blood, subject 399596aa, sample time point T4, library prep Plate_2


title: dexlwo3_S21


title: cvl1_S18


title: dexh2_S15


title: whole blood, subject 3b625ef6, sample time point T1, library prep Plate_12


title: whole blood, subject 38a81b25, sample time point T13, library prep Plate_18


title: cvhwo1_S1

value: cort vehicle high6


title: whole blood, subject 399596aa, sample time point T1, library prep Plate_17


title: cvh3_S14

value: cort vehicle high3


title: whole blood, subject 38a81b25, sample time point T12, library prep Plate_18


title: ctl4_S5

value: HMC3 (ATCC CRL-3304)


title: cvh1_S21

value: microglial cell


title: cvh2_S16


title: cvlwo2_S1

value: cort vehicle low6


title: whole blood, subject 38a81b25, sample time point T2, library prep Plate_12


title: ctl3_S10


title: whole blood, subject 388ec55e, sample time point T1, library prep Plate_6


title: whole blood, subject 38a81b25, sample time point T1, library prep Plate_12


title: cortlwo4_S2

value: cort low6


title: whole blood, subject 399596aa, sample time point T2, library prep Plate_13


title: cortlwo3_S6


title: Ctl1_S8


title: whole blood, subject 338e187c, sample time point T8, library prep Plate_19


title: whole blood, subject 36b52008, sample time point T1, library prep Plate_11


title: whole blood, subject 338e187c, sample time point T4, library prep Plate_13


title: whole blood, subject 3380e771, sample time point T1, library prep Plate_10


title: whole blood, subject 338e187c, sample time point T1, library prep Plate_13


title: whole blood, subject 38a81b25, sample time point T8, library prep Plate_11


title: whole blood, subject 334d7085, sample time point T4, library prep Plate_18


title: whole blood, subject 334d7085, sample time point T1, library prep Plate_10


title: whole blood, subject 334d7085, sample time point T2, library prep Plate_7


title: corth3_S12

value: cort high3


title: corth2_S20


title: whole blood, subject 32cc1628, sample time point T4, library prep Plate_18

value: Negative


title: whole blood, subject 32cc1628, sample time point T12, library prep Plate_18

value: whole blood


title: whole blood, subject 32cc1628, sample time point T8, library prep Plate_17


title: whole blood, subject 338e187c, sample time point T2, library prep Plate_14


title: corthwo2_S11

value: cort high6


title: corthwo3_S13


title: cortl2_S14

value: cort low3


title: cortl3_S19


title: Sample_22

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
We aligned the sequences to the cattle reference genome (Bos_taurus.ARS-UCD1.2.105) in the Ensembl database with hisat2 using the -very-sensitive parameter. Then, we used Samtools to filter sequences to remove secondary alignments, duplicates, and unmapped reads. Next, we used biobambam2 to mark and remove duplicates.
Assembly: ARS-UCD1.2.105
Supplementary files format and content: tab-delimited text file include raw counts for each Sample

organism: Bos taurus

source_name: white blood cells

extract_protocol:
Total RNA was extracted using the Zymo Research Direct-zol DNA/RNA Miniprep kit, according to the manufacturer's instructions
Libraries were prepared using the Illumina Stranded mRNA prep kit. 900 ng of total RNA was used for preparation.

value: white blood cells

tag: breed

value: Angus

tag: phenotype

value: fertile


title: Sample_21


title: cortlwo2_S18


title: whole blood, subject 32cc1628, sample time point T1, library prep Plate_17


title: corth4_S19


title: cortl4_S13


title: whole blood, subject 31e42f3b, sample time point T2, library prep Plate_11


title: corthwo4_S4


title: Sample_19


title: Sample_20


title: whole blood, subject 31e42f3b, sample time point T1, library prep Plate_19


title: whole blood, subject 318dda84, sample time point T1, library prep Plate_7

value: Positive


title: Sample_17

value: sub-fertile


title: whole blood, subject 310c5346, sample time point T1, library prep Plate_9

value: Female


title: whole blood, subject 30f3e5be, sample time point T12, library prep Plate_3

value: Male


title: Sample_15


title: Sample_16


title: Sample_13


title: Sample_12


title: whole blood, subject 30f3e5be, sample time point T2, library prep Plate_11


title: whole blood, subject 30f3e5be, sample time point T8, library prep Plate_5


title: whole blood, subject 30f3e5be, sample time point T4, library prep Plate_5


title: Sample_14


title: whole blood, subject 318dda84, sample time point T8, library prep Plate_7


title: whole blood, subject 30f3e5be, sample time point T1, library prep Plate_6


title: Sample_18


title: whole blood, subject 302cac50, sample time point T1, library prep Plate_18


title: Sample_9

value: Holstein


title: whole blood, subject 30f3e5be, sample time point T0, library prep Plate_6


title: whole blood, subject 302cac50, sample time point T4, library prep Plate_16


title: Sample_7


title: Sample_8


title: whole blood, subject 2e801d88, sample time point T2, library prep Plate_4


title: Sample_6


title: whole blood, subject 2e801d88, sample time point T4, library prep Plate_11


title: whole blood, subject 2e801d88, sample time point T8, library prep Plate_16


title: Sample_3


title: Sample_10


title: Sample_11


title: whole blood, subject 2e7e0b48, sample time point T2, library prep Plate_14


title: Sample_5


title: whole blood, subject 2db62a52, sample time point T2, library prep Plate_7


title: Sample_4


title: whole blood, subject 2db62a52, sample time point T4, library prep Plate_18


title: whole blood, subject 2bdfdc7c, sample time point T8, library prep Plate_17


title: Sample_1


title: whole blood, subject 2e801d88, sample time point T1, library prep Plate_3


title: Sample_2


title: Female_body_adult_70dWT_Hongjie_S6_S18

city: Houston

first: Hongjie

last: Li

state: TX

address: One Baylor Plaza

department: Huffington Center on Aging

institute: Baylor College of Medicine

data_processing:
Removing index-hopping reads
Removing ambient RNA by decountX
Removing doublets by scrublet
Using scanpy for the general analysis of single-cell data
Assembly: Flybase version r6.31
Supplementary files format and content: h5ad files contatining cell barcodes, sex, age, cell-type information

organism: Drosophila melanogaster

source_name: body

extract_protocol:
Neclei extraction were performed following the Fly Cell Atlas procedure.
10x Genomics libraries were prepared following the standard protocol from 10x Genomics 3’ v3.1 kit.

value: body

tag: strain

tag: age

tag: batch


title: Female_body_adult_70dWT_Hongjie_S4_S16


title: whole blood, subject 30efa05e, sample time point T4, library prep Plate_3


title: whole blood, subject 2db62a52, sample time point T1, library prep Plate_16


title: Female_body_adult_70dWT_Hongjie_S5_S17


title: whole blood, subject 2bdfdc7c, sample time point T4, library prep Plate_11


title: whole blood, subject 2bdfdc7c, sample time point T2, library prep Plate_12


title: whole blood, subject 2bdfdc7c, sample time point T1, library prep Plate_7


title: Female_head_adult_70dWT_Hongjie_S6_S12

source_name: head

value: head


title: Female_head_adult_70dWT_Hongjie_S5_S11


title: Female_body_adult_70dWT_Hongjie_S1_S13


title: Female_head_adult_70dWT_Hongjie_S4_S10


title: Female_body_adult_70dWT_Hongjie_S2_S14


title: Female_body_adult_70dWT_Hongjie_S3_S15


title: whole blood, subject 2b5aef5b, sample time point T8, library prep Plate_16


title: whole blood, subject 2b5aef5b, sample time point T12, library prep Plate_16


title: Female_head_adult_70dWT_Hongjie_S3_S9


title: Female_head_adult_70dWT_Hongjie_S1_S7


title: whole blood, subject 2ba3e340, sample time point T1, library prep Plate_17


title: whole blood, subject 2b5aef5b, sample time point T4, library prep Plate_9


title: whole blood, subject 2b5aef5b, sample time point T2, library prep Plate_19


title: whole blood, subject 2b5aef5b, sample time point T1, library prep Plate_9


title: Male_body_adult_70dWT_Hongjie_S6_S6


title: Female_head_adult_70dWT_Hongjie_S2_S8


title: Male_body_adult_70dWT_Hongjie_S5_S5


title: whole blood, subject 2b440626, sample time point T2, library prep Plate_6


title: whole blood, subject 2ba3e340, sample time point T2, library prep Plate_2


title: Male_body_adult_70dWT_Hongjie_S4_S4


title: whole blood, subject 2b440626, sample time point T4, library prep Plate_16


title: whole blood, subject 2b440626, sample time point T1, library prep Plate_9


title: whole blood, subject 2a548e63, sample time point T2, library prep Plate_17


title: Male_body_adult_70dWT_Hongjie_S2_S2


title: Male_body_adult_70dWT_Hongjie_S3_S3


title: Male_body_adult_70dWT_Hongjie_S1_S1


title: whole blood, subject 2a548e63, sample time point T1, library prep Plate_13


title: whole blood, subject 2a142bf4, sample time point T13, library prep Plate_17


title: Male_head_adult_70dWT_Hongjie_S5_S17


title: Male_head_adult_70dWT_Hongjie_S4_S16


title: Male_head_adult_70dWT_Hongjie_S3_S15


title: whole blood, subject 2a142bf4, sample time point T12, library prep Plate_17


title: whole blood, subject 2a142bf4, sample time point T8, library prep Plate_14


title: whole blood, subject 2a142bf4, sample time point T2, library prep Plate_19


title: whole blood, subject 2a142bf4, sample time point T4, library prep Plate_11


title: Male_head_adult_70dWT_Hongjie_S6_S18


title: whole blood, subject 293f835a, sample time point T8, library prep Plate_13


title: whole blood, subject 2a142bf4, sample time point T1, library prep Plate_13


title: Female_body_adult_50dWT_Hongjie_S6_S12


title: Male_head_adult_70dWT_Hongjie_S2_S14


title: Male_head_adult_70dWT_Hongjie_S1_S13


title: Female_body_adult_50dWT_Hongjie_S5_S11


title: Female_body_adult_50dWT_Hongjie_S4_S10


title: whole blood, subject 293f835a, sample time point T4, library prep Plate_9


title: whole blood, subject 293f835a, sample time point T1, library prep Plate_10


title: whole blood, subject 293f835a, sample time point T2, library prep Plate_11


title: whole blood, subject 273dc7ae, sample time point T2, library prep Plate_16


title: Female_body_adult_50dWT_Hongjie_S2_S8


title: whole blood, subject 26ced899, sample time point T2, library prep Plate_2


title: Female_head_adult_50dWT_Hongjie_S5_S5


title: whole blood, subject 266e2348, sample time point T13, library prep Plate_15


title: Female_head_adult_50dWT_Hongjie_S4_S4


title: whole blood, subject 266e2348, sample time point T12, library prep Plate_8


title: whole blood, subject 266e2348, sample time point T4, library prep Plate_2


title: whole blood, subject 266e2348, sample time point T8, library prep Plate_2


title: whole blood, subject 293f835a, sample time point T12, library prep Plate_13


title: Female_head_adult_50dWT_Hongjie_S3_S3


title: Female_head_adult_50dWT_Hongjie_S2_S2


title: Female_head_adult_50dWT_Hongjie_S1_S1


title: Male_body_adult_50dWT_Hongjie_S6_S18


title: whole blood, subject 262cc412, sample time point T2, library prep Plate_15


title: whole blood, subject 262cc412, sample time point T1, library prep Plate_16


title: Female_body_adult_50dWT_Hongjie_S3_S9


title: whole blood, subject 26221f93, sample time point T1, library prep Plate_2


title: Male_body_adult_50dWT_Hongjie_S2_S14


title: Male_body_adult_50dWT_Hongjie_S3_S15


title: whole blood, subject 245ec65e, sample time point T8, library prep Plate_9


title: whole blood, subject 26221f93, sample time point T2, library prep Plate_13


title: Female_body_adult_50dWT_Hongjie_S1_S7


title: Male_body_adult_50dWT_Hongjie_S5_S17


title: Male_body_adult_50dWT_Hongjie_S4_S16


title: whole blood, subject 245ec65e, sample time point T12, library prep Plate_13


title: Male_body_adult_50dWT_Hongjie_S1_S13


title: whole blood, subject 245ec65e, sample time point T4, library prep Plate_13


title: whole blood, subject 245ec65e, sample time point T2, library prep Plate_15


title: Female_head_adult_50dWT_Hongjie_S6_S6


title: Male_head_adult_50dWT_Hongjie_S5_S11


title: Male_head_adult_50dWT_Hongjie_S6_S12


title: Male_head_adult_50dWT_Hongjie_S4_S10


title: whole blood, subject 266e2348, sample time point T1, library prep Plate_15


title: whole blood, subject 24064c86, sample time point T2, library prep Plate_4


title: Male_head_adult_50dWT_Hongjie_S2_S8


title: Male_head_adult_50dWT_Hongjie_S1_S7


title: Female_body_adult_30dWT_Hongjie_S6_S6


title: whole blood, subject 23dd0be0, sample time point T13, library prep Plate_17


title: whole blood, subject 24064c86, sample time point T1, library prep Plate_3


title: Female_body_adult_30dWT_Hongjie_S5_S5


title: whole blood, subject 23dd0be0, sample time point T12, library prep Plate_16


title: Female_body_adult_30dWT_Hongjie_S4_S4


title: whole blood, subject 2424324f, sample time point T2, library prep Plate_4


title: Male_head_adult_50dWT_Hongjie_S3_S9


title: whole blood, subject 23dd0be0, sample time point T1, library prep Plate_10


title: Female_body_adult_30dWT_Hongjie_S2_S2


title: whole blood, subject 23dd0be0, sample time point T4, library prep Plate_9


title: whole blood, subject 23d77493, sample time point T1, library prep Plate_18


title: whole blood, subject 237edd62, sample time point T1, library prep Plate_11


title: whole blood, subject 245ec65e, sample time point T1, library prep Plate_16


title: Female_body_adult_30dWT_Hongjie_S1_S1


title: Female_head_adult_30dWT_Hongjie_S4_S16


title: Female_body_adult_30dWT_Hongjie_S3_S3


title: Female_head_adult_30dWT_Hongjie_S5_S17


title: whole blood, subject 23d77493, sample time point T2, library prep Plate_11


title: Female_head_adult_30dWT_Hongjie_S6_S18


title: Female_head_adult_30dWT_Hongjie_S3_S15


title: whole blood, subject 230ded0f, sample time point T1, library prep Plate_13


title: whole blood, subject 22854cea, sample time point T8, library prep Plate_13


title: Female_head_adult_30dWT_Hongjie_S2_S14


title: whole blood, subject 2424324f, sample time point T1, library prep Plate_5


title: whole blood, subject 22854cea, sample time point T4, library prep Plate_3


title: Female_head_adult_30dWT_Hongjie_S1_S13


title: whole blood, subject 23dd0be0, sample time point T8, library prep Plate_18


title: whole blood, subject 22854cea, sample time point T1, library prep Plate_3


title: Male_body_adult_30dWT_Hongjie_S6_S12


title: whole blood, subject 21b7ab7c, sample time point T1, library prep Plate_4


title: whole blood, subject 224dc393, sample time point T2, library prep Plate_17


title: whole blood, subject 21438992, sample time point T2, library prep Plate_10


title: Male_body_adult_30dWT_Hongjie_S4_S10


title: Male_body_adult_30dWT_Hongjie_S3_S9


title: whole blood, subject 21438992, sample time point T1, library prep Plate_11


title: Male_body_adult_30dWT_Hongjie_S1_S7


title: whole blood, subject 209e82df, sample time point T13, library prep Plate_18


title: Male_head_adult_30dWT_Hongjie_S5_S5


title: whole blood, subject 209e82df, sample time point T8, library prep Plate_11


title: Male_head_adult_30dWT_Hongjie_S6_S6


title: Male_body_adult_30dWT_Hongjie_S2_S8


title: whole blood, subject 209e82df, sample time point T2, library prep Plate_8


title: whole blood, subject 209e82df, sample time point T4, library prep Plate_3


title: whole blood, subject 209e82df, sample time point T1, library prep Plate_3


title: Male_head_adult_30dWT_Hongjie_S4_S4


title: intestine, quercetin, rep4

city: Chengdu

first: Yan

last: La

address: 37 Guoxue Lane, Wuhou District, Chengdu City, Sichuan Province

country: China

institute: Sichuan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
The de-duplicated consensus sequences were mapped to Drosophila_Melanogaster ISO1 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}
Assembly: ISO1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: intestine

growth_protocol: Drosophila were maintained on standard cornmeal-agar food and kept at standard conditions (25℃, 60% relative humidity, 12 h light/dark cycle).

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

treatment_protocol: DMSO or Quercetin(10µM, Aladdin)

value: intestine

value: female

tag: genotype

value: WT

tag: treatment

value: Quercetin


title: Male_head_adult_30dWT_Hongjie_S1_S1

tag: tissue


title: whole blood, subject 1f485cb6, sample time point T13, library prep Plate_17

value: whole blood

tag: subject id


title: intestine, quercetin, rep3


title: Male_head_adult_30dWT_Hongjie_S2_S2


title: whole blood, subject 1f485cb6, sample time point T8, library prep Plate_2

tag: blood sample_id


title: whole blood, subject 1f485cb6, sample time point T1, library prep Plate_17

tag: library prep_plate


title: whole blood, subject 1f485cb6, sample time point T12, library prep Plate_12

tag: Sex


title: intestine, quercetin, rep2


title: Male_body_adult_30dWT_Hongjie_S5_S11


title: whole blood, subject 1e96bcf2, sample time point T2, library prep Plate_4

tag: sampling time_point_label

value: Negative


title: whole blood, subject 1e96bcf2, sample time point T1, library prep Plate_6

tag: days since_first_sample


title: whole blood, subject 1e0265de, sample time point T4, library prep Plate_16

tag: patient classification_at_first_sample


title: whole blood, subject 209e82df, sample time point T12, library prep Plate_9


title: intestine, DMSO, rep4

value: DMSO


title: intestine, DMSO, rep3


title: Male_head_adult_30dWT_Hongjie_S3_S3


title: whole blood, subject 1e0265de, sample time point T2, library prep Plate_15


title: intestine, DMSO, rep2


title: whole blood, subject 1e0265de, sample time point T1, library prep Plate_11


title: whole blood, subject 1df07b1d, sample time point T1, library prep Plate_11


title: whole blood, subject 1d5983f7, sample time point T2, library prep Plate_8


title: whole blood, subject 1d5983f7, sample time point T1, library prep Plate_19


title: QCM, replicate 2, snRNAseq

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Low quality cells were removed using scater/scran followed by normalization and clustering via scran.chan
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small intestine, jejunum

growth_protocol: Mouse intestinal organoids were cultured in quiescent or senescent conditioned media.

extract_protocol:
Nuclei were isolated from frozen samples that were resuspended in TST buffer (146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween20, and BSA) and pelleted by centrifugation. The nuclei pellets were resuspended in ST buffer (146 mM NaCl, 10 mM Tris, 1 mM CaCl2, 21 mM MgCl2)
Generation of gel Beads-in-emulsion, cDNA amplification, and library preparation were performed with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) following the manufacturer’s instructions. 8,000-10,000 nuclei were loaded per channel of a 10x Genomics chip.

tag: cell type

value: Intestinal organoids

value: Small intestine, jejunum

value: quiescent conditioned media

value: 8-12 weeks old


title: intestine, quercetin, rep1


title: SCM, replicate 3, snRNAseq

description: 10x Genomics

value: senescent conditioned media


title: SCM, replicate 2, snRNAseq

description: 10x Genomics


title: SCM, replicate 1, snRNAseq

description: 10x Genomics


title: QCM, replicate 3, snRNAseq

description: 10x Genomics


title: QCM, replicate 1, snRNAseq

description: 10x Genomics


title: whole blood, subject 1cca9f81, sample time point T13, library prep Plate_19

value: Female

tag: covid-19 positive

value: Positive


title: whole blood, subject 1cca9f81, sample time point T1, library prep Plate_6


title: whole blood, subject 1cb60f79, sample time point T8, library prep Plate_4

value: Male


title: whole blood, subject 1cca9f81, sample time point T2, library prep Plate_8


title: Ly6Clow macrophages, KID, IRI, 3

city: Tokyo

first: Taisuke

last: Ishii

address: 7-3-1 Hongo, Bunkyo-ku

department: Division of Nephrology and Endocrinology

country: Japan

institute: The University of Tokyo

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using Hisat2 version 2.1.084 with a “--dta” option.
A statistical differential expression test was used The Differential Expression in Two Groups tool in CLC genomics workbench.
Differentially expressed genes (DEGs) were filtered by FDR < 0.05 among kidney cancer samples. Among kidney cortex samples, DEGs were filtered by FDR < 0.001 and log fold change more than 2.
Low expression genes were filtered by 0 in all samples for downstream analysis and data visalizations.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of statistical tests and expression data

source_name: Ly6Clow macrophages sorted from uIRI kidney cortex

growth_protocol: Standard protocol.

extract_protocol:
RNA were extracted from Ly6Clow macrophages, using the RNeasy Micro Kit (74004, Qiagen)
Llibrary was constracted using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext rRNA Depletion Kit v2 (Cat# E7770S and E7400L; New England Biolabs).

treatment_protocol: Mice received uIRI or sham operation. RenCa cells were inoculated into kidney subcapsule 14 days after operation.

value: BALB/c

value: kidney cortex

value: unilateral ischemia reperfusion injury

value: Ly6Clow macrophage


title: whole blood, subject 1cca9f81, sample time point T8, library prep Plate_16


title: Ly6Clow macrophages, KID, IRI, 2


title: Ly6Clow macrophages, KID, SHAM, 1

source_name: Ly6Clow macrophages sorted from sham kidney cortex

value: sham operation


title: Ly6Clow macrophages, KID, SHAM, 2


title: Ly6Clow macrophages, KID, SHAM, 3


title: Ly6Clow macrophages, KID, IRI, 1


title: whole blood, subject 1c55de37, sample time point T2, library prep Plate_4


title: intestine, DMSO, rep1

value: intestine

value: female

value: WT


title: Ly6Clow macrophages, REN, SHAM, 4

source_name: Ly6Clow macrophages sorted from kidney cancer inoculated into sham kidney

value: kidney cancer


title: whole blood, subject 1c55de37, sample time point T1, library prep Plate_12

value: whole blood


title: whole blood, subject 1b1361b3, sample time point T1, library prep Plate_19


title: whole blood, subject 1d5983f7, sample time point T4, library prep Plate_19


title: whole blood, subject 1a5ad058, sample time point T4, library prep Plate_8


title: whole blood, subject 1a5ad058, sample time point T1, library prep Plate_3


title: whole blood, subject 1cca9f81, sample time point T12, library prep Plate_7


title: Ly6Clow macrophages, REN, SHAM, 2


title: Ly6Clow macrophages, REN, IRI, 4

source_name: Ly6Clow macrophages sorted from kidney cancer inoculated into uIRI kidney


title: Ly6Clow macrophages, REN, SHAM, 1


title: whole blood, subject 188edafa, sample time point T2, library prep Plate_19


title: whole blood, subject 188edafa, sample time point T4, library prep Plate_10


title: Ly6Clow macrophages, REN, IRI, 3


title: whole blood, subject 188edafa, sample time point T1, library prep Plate_6


title: Ly6Clow macrophages, REN, IRI, 2


title: whole blood, subject 1874c2cf, sample time point T2, library prep Plate_4


title: whole blood, subject 1874c2cf, sample time point T1, library prep Plate_4


title: whole blood, subject 17abecb0, sample time point T13, library prep Plate_17


title: Ly6Clow macrophages, REN, IRI, 1


title: Ly6Clow macrophages, REN, SHAM, 3


title: whole blood, subject 17abecb0, sample time point T8, library prep Plate_6


title: whole blood, subject 17abecb0, sample time point T12, library prep Plate_8


title: PN120 Cell 734

city: Stanford

first: Christin

middle: S

last: Kuo

address: 240 Pasteur Dr.

institute: Stanford University

data_processing:
Raw sequence reads were demultiplexed using bcl2fastq (v1.8.4, Illumina)
sequences aligned to the mouse reference genome (GRCm38-mm10, UCSC, supplemented with Zsgreen1 sequence) with STAR
number of reads that mapped to each annotated gene (gene counts) determined with HTSEQ (v0.6.1p1, default parameters except Stranded set to false and Mode set to intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: postnatal 21 days

value: wild type

tag: group


title: PN120 Cell 733


title: whole blood, subject 17abecb0, sample time point T1, library prep Plate_15


title: whole blood, subject 1758a4b0, sample time point T2, library prep Plate_4


title: PN120 Cell 736


title: PN120 Cell 732


title: PN120 Cell 735


title: whole blood, subject 1758a4b0, sample time point T1, library prep Plate_9


title: PN120 Cell 730


title: PN120 Cell 731


title: whole blood, subject 175135fe, sample time point T12, library prep Plate_3


title: whole blood, subject 17abecb0, sample time point T2, library prep Plate_16


title: PN120 Cell 728


title: PN120 Cell 729


title: PN120 Cell 726


title: whole blood, subject 175135fe, sample time point T4, library prep Plate_3


title: PN120 Cell 727


title: whole blood, subject 16ae238f, sample time point T6, library prep Plate_15


title: whole blood, subject 16ae238f, sample time point T0, library prep Plate_2


title: whole blood, subject 17abecb0, sample time point T4, library prep Plate_15


title: PN120 Cell 724


title: PN120 Cell 725


title: PN120 Cell 723


title: whole blood, subject 15dd9db5, sample time point T1, library prep Plate_4


title: PN120 Cell 722


title: whole blood, subject 15a8b3ac, sample time point T1, library prep Plate_7


title: whole blood, subject 1562a93c, sample time point T12, library prep Plate_9


title: PN120 Cell 721


title: whole blood, subject 1562a93c, sample time point T8, library prep Plate_7


title: PN120 Cell 720


title: whole blood, subject 1562a93c, sample time point T2, library prep Plate_14


title: whole blood, subject 175135fe, sample time point T8, library prep Plate_18


title: PN120 Cell 719


title: PN120 Cell 718


title: whole blood, subject 15170ae3, sample time point T2, library prep Plate_16

value: Negative


title: PN120 Cell 716


title: whole blood, subject 15170ae3, sample time point T1, library prep Plate_11

value: Female


title: PN120 Cell 717


title: whole blood, subject 1516340b, sample time point T8, library prep Plate_14

value: Positive


title: PN120 Cell 715


title: whole blood, subject 1516340b, sample time point T4, library prep Plate_16

value: Male


title: PN120 Cell 714


title: whole blood, subject 14eb8045, sample time point T4, library prep Plate_15


title: whole blood, subject 14eb8045, sample time point T2, library prep Plate_17


title: PN120 Cell 713


title: PN120 Cell 712


title: whole blood, subject 148ddee7, sample time point T1, library prep Plate_13


title: whole blood, subject 130b19cd, sample time point T1, library prep Plate_8


title: PN120 Cell 709


title: whole blood, subject 12eac067, sample time point T2, library prep Plate_7


title: PN120 Cell 710


title: whole blood, subject 1562a93c, sample time point T1, library prep Plate_9


title: PN120 Cell 711


title: whole blood, subject 12eac067, sample time point T1, library prep Plate_4


title: PN120 Cell 707


title: PN120 Cell 706


title: PN120 Cell 708


title: whole blood, subject 12c04870, sample time point T1, library prep Plate_11


title: whole blood, subject 128d09dc, sample time point T4, library prep Plate_9


title: whole blood, subject 128d09dc, sample time point T2, library prep Plate_2


title: whole blood, subject 128d09dc, sample time point T1, library prep Plate_18


title: PN120 Cell 702


title: PN120 Cell 705


title: whole blood, subject 14eb8045, sample time point T1, library prep Plate_10


title: PN120 Cell 704


title: PN120 Cell 703


title: PN120 Cell 701


title: whole blood, subject 128639af, sample time point T1, library prep Plate_19


title: whole blood, subject 128443e7, sample time point T13, library prep Plate_6


title: whole blood, subject 128443e7, sample time point T12, library prep Plate_17


title: PN120 Cell 698


title: PN120 Cell 699


title: PN120 Cell 697


title: whole blood, subject 128443e7, sample time point T1, library prep Plate_4


title: whole blood, subject 1228d709, sample time point T8, library prep Plate_6


title: whole blood, subject 1228d709, sample time point T4, library prep Plate_13


title: whole blood, subject 1228d709, sample time point T0, library prep Plate_2


title: whole blood, subject 1228d709, sample time point T1, library prep Plate_6


title: PN120 Cell 694


title: PN120 Cell 696


title: PN120 Cell 695


title: whole blood, subject 128639af, sample time point T2, library prep Plate_2


title: PN120 Cell 692


title: whole blood, subject 112e879c, sample time point T4, library prep Plate_12


title: PN120 Cell 693


title: PN120 Cell 691


title: whole blood, subject 112e879c, sample time point T1, library prep Plate_2


title: whole blood, subject 1147dbe5, sample time point T1, library prep Plate_7


title: PN120 Cell 700


title: PN120 Cell 690


title: PN120 Cell 688


title: PN120 Cell 689


title: PN120 Cell 687


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_18


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_16


title: PN120 Cell 686


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_12


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_10


title: PN120 Cell 685


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_8


title: PN120 Cell 684


title: whole blood, subject 11dc6956, sample time point T1, library prep Plate_9


title: PN120 Cell 682


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_4


title: PN120 Cell 681


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_6


title: PN120 Cell 680


title: PN120 Cell 679


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_2