title: DKO mice Lung sample  G185.9A

source_name: DKO Lung 3


title: only LPS (4μg/ml) treatment biol rep 3 tech rep 1

status: Public on Oct 22 2021

type: RNA

city: Taipei

first: Chen

middle: Yi

last: Ling

address: 128 Academia Road, Section 2

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1095 control probes, spotted onto glass slides using a proprietary non-contact printing method.

hyb_protocol: HOA v4.3 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 600~630 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: The raw data were adjust by Rosetta Resolver® error model calculation. The statistic values were calculated after the replicated probes queezing and median scaling normalization.

molecule: total RNA

organism: Homo sapiens

source_name: U937 cell line (human histiocytic lymphoma cell)

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The U937 cells were maintained at 2-3 × 106 cells/ml in a RPMI 1640 medium  supplemented with 10% FBS, the incubation time of the culture was 48 hours.

extract_protocol: RNA extraction by column based extraction kit (RiboPure-Blood, Ambion). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN>8).

treatment_protocol: Human macrophage cells were untreatment, LPS (4μg/ml) only, preteated PBD150 inhibitor (10μM) for 2 hrs before the addition LPS (4μg/ml) treatment, the incubation time of the culture was 48 hours.

tag: cell line

tag: treatment

value: only LPS (4μg/ml)


title: NRas-KO+NAC mice lung sample T453.7

city: Salamanca

first: Eugenio

last: Santos

address: Campus Miguel de Unamuno

department: Instituto de Biología Celular y Molecular del Cáncer

country: Spain

institute: Universidad de Salamanca y CBERONC

description: Gene expression data from whole NRAS-deficient lung extracts treated antenatally with N-acetyl cysteine.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package Affy from R/Bioconductor was applied to the raw expression data.

label: biotin

organism: Mus musculus

source_name: NRas-KO Lung +NAC 3

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Ambion)

growth_protocol: Animals were housed in type IIL individually ventilated cages, in a temperature- and humidity-controlled room with a 12h light/dark cycle, with food (Teklad 2014, Harlan Laboratories) and water available ad libitum.  All the lung samples were collected from postnatal day 0 mice.

extract_protocol: Manually selected lungs of Control, HRas-KO, NRas-KO and DKO from postnatal day 0 were used for RNA extraction using the TRIZOL protocol. RNA was further purified using Qiagen Rneasy mini kit. Each RNA sample for each microarray was obtained from one individual animal.

treatment_protocol: Pregnant females were treated throughout the pregnancy with 0.5% N-acetyl cysteine (NAC) pH 7.4 (Only in SAMPLES 15, 16 and 17)

tag: genotype/variation

value: NRas-KO

tag: tissue

value: Lung tissue obtained from postnatal day 0 mice

value: N-acetyl cysteine (NAC)


title: S68 [P15763_134]

type: SRA

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

library_source: transcriptomic

data_processing:
NOT PROVIDED; REQUESTED
Genome_build: MesAur1.0.101
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mesocricetus auratus

source_name: Liver_HFD + MI_D2

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

value: Liver

tag: age

value: 22 weeks

value: HFD + MI_D2


title: K_6 [20183_S6]

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12
then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab)
Remaining reads were aligned to the Mesocricetus auratus genome assembly version 1.0 using Hisat2 (Kim et al., 2015)
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Differential expression analysis was performed using the Bioconductor package DESeq2  (Love et al., 2014)
Genome_build: NC_041754.1 Macaca mulatta :  JF416958.1 Kyasanur forest disease virus strain P9605 :  JF416954.1 Alkhumra hemorrhagic fever virus strain 200300001
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample and matrix table with normalized gene counts.

organism: Macaca nemestrina

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 6

growth_protocol: Twelve female PTMs aged 10 to 16 years of age were housed in a humidity, temperature, and light controlled facility in adjacent cages for social interaction. Virus seed stocks were propagated once on Vero cells, and virus working stocks were aliquoted and frozen in liquid nitrogen tanks.

extract_protocol:
RNA was extracted from 140 ml plasma using the QIAamp Viral RNA Mini Kit (Qiagen). RNA was irradiated (10 megarad) for removal from the BSL4 according to established sample removal protocols (54). Following removal, cDNA was generated using SuperScript VILO cDNA Synthesis Kit (ThermoFisher).
100 ng of RNA was used for initial treatment with the Qiagen FastSelect -H/M/R and -Globin kit to inhibit cDNA synthesis of rRNA and globin transcripts.  The two viral stocks were not rRNA/Globin treated.  The only modification was to reduce the initial fragmentation step to 2 minutes to account for the degradation of the RNA.  After incubation with the probes from the FastSelect kit, the samples proceeded with cDNA synthesis and library preparation following the Illumina Stranded RNA Prep, Ligation kit.

treatment_protocol: Virus inoculations were performed with the indicated virus diluted in sterile PBS. For subcutaneous (sc) infections, 1x105 pfu was delivered in a single injection between the shoulder blades (1 ml volume)

tag: agent

value: Kyasanur forest disease virus

tag: time point

value: day 6


title: K_0 [20184_S7]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 0

value: day 0


title: S69 [P15763_135]


title: K_2 [20182_S5]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 2

value: day 2


title: K_6 [20180_S3]


title: S67 [P15763_133]


title: K_0 [20181_S4]


title: S65 [P15763_131]


title: K_2 [20179_S2]


title: K_0 [20178_S1]


title: S66 [P15763_132]


title: DKO mice Lung sample  G185.2A

description: Gene expression data from whole HRAS and NRAS-deficient lung extracts.

source_name: DKO Lung 1

value: DKO


title: NRas-KO+NAC mice lung sample T195.3

source_name: NRas-KO Lung +NAC 2


title: NRas-KO mice Lung sample  H058.3

description: Gene expression data from whole NRAS-deficient lung extracts.

source_name: NRas-KO Lung 2


title: only LPS (4μg/ml) treatment biol rep 1 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1091 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: only LPS (4μg/ml) treatment biol rep 1 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1090 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: only LPS (4μg/ml) treatment biol rep 2 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1092 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: NRas-KO mice Lung sample  H058.7

source_name: NRas-KO Lung 3


title: S64 [P15763_130]


title: HRas-KO mice lung sample T453.8

description: Gene expression data from whole HRAS-deficient lung extracts treated antenatally with N-acetyl cysteine.

source_name: HRas-KO Lung + NAC 3

value: HRas-KO


title: NRas-KO mice Lung sample  C118.3

source_name: NRas-KO Lung 1


title: KO ILC2-2

city: Shanghai

first: Jingjing

last: Zhang

state: Shanghai

address: No.280 South Chongqing Road

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw reads were aligned to the mouse reference genome (version mm10) by using Hisat2 RNASeq alignment software.
Quantitated relative mRNA expression levels (FPKM) were calculated based on exon regions using Cufflinks and the mm10 reference genome annotations.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values files include readcounts (column J-M) and FPKM values (column N-Q) for each Sample and every gene

source_name: lung ILC2

extract_protocol:
Total RNA from sorted lung ILC2s of R5/+ (WT) and R5/+ Nrp1f/f (KO) mice treated with bleomycin was extracted by Trizol reagent. Each sample was a pool of 3-4 mice. RNA quality was examined with an Agilent Bioanalyzer 2100 (Agilent). The concentration of RNA was from 7ng/ul to 14ng/ul. The SMART-Seq HT Kit (Takara Bio USA, Inc) was used to generate high-quality, full-length cDNA.
Libraries were generated using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) following manufacturer’s protocol.

tag: strain

value: lung

tag: cell type

value: bleomycin treated

tag: genotype


title: S63 [P15763_129]


title: only LPS (4μg/ml) treatment biol rep 2 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1094 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: Untreated biol rep 3 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1088 control probes, spotted onto glass slides using a proprietary non-contact printing method.

value: Untreated


title: only LPS (4μg/ml) treatment biol rep 1 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1089 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: KO ILC2-1


title: HRas-KO mice lung sample T453.6

source_name: HRas-KO Lung + NAC 2


title: only LPS (4μg/ml) treatment biol rep 2 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1093 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: NRas-KO+NAC mice lung sample T317.8

source_name: NRas-KO Lung +NAC 1


title: S62 [P15763_128]

source_name: Liver_HFD + MI_D1

value: HFD + MI_D1


title: WT ILC2-1


title: WT ILC2-2


title: S60 [P15763_126]


title: Untreated biol rep 3 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1086 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: HRas-KO mice lung sample T453.5

source_name: HRas-KO Lung + NAC 1


title: Untreated biol rep 2 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1085 control probes, spotted onto glass slides using a proprietary non-contact printing method.

source_name: U937 cell line (human histiocytic lymphoma cell)


title: S61 [P15763_127]


title: Untreated biol rep 3 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1087 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: ChIP-INPUT-DT40-Ri GFP2

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
For DT40 data, ChIP-seq reads were aligned to Gallus_gallus-4.0 genome with the region spanning pseudoV and IgL locus (chr15:7,921,694–7,955,323) replaced with respective reporter construct sequence; for Ramos data ChIP-seq reads were aligned to the human GRCh38 genome with the lentivirus reporter appended as an extra chromosome.
Alignment done using Bowtie (version 1.1.2) with seed length 50 and 2, 3, and 3 mismatches allowed, respectively
Peaks were called using MACS 1.4.3 (Zhang et al., 2008). Default parameters were used (p value cutoff for peak detection = 1x10e-5;–keep-dup = auto), with corresponding DNA input as a control.
Genome_build: human GRCh37/hg19;GalGal4
Supplementary_files_format_and_content: Aligned-reads bed files were first converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

molecule: genomic DNA

organism: Gallus gallus

source_name: DT40 cell line

growth_protocol: Ramos cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Gibco), 1X GlutaMAX (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 37 °C.  DT40 cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Hyclone), 1 % chicken serum (Biowest), 1X GlutaMAX (Gibco), 50 µM β-mercaptoethanol (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 41 °C.

extract_protocol:
Chromatin Immunoprecipitation was performed using the following protocol. 4 x 107 formaldehyde-fixed cells were lysed in SDS lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, supplemented with Complete, EDTA free protease inhibitor cocktail (Roche)) and diluted 4-fold with dilution buffer (16.4 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 0.01% SDS, 1.1% Triton X-100, supplemented with inhibitors). The lysate was sonicated in aliquots using a water bath sonicator (Diagenode Bioruptor Pico) for 11 cycles (30s on/30s off) and cleared by centrifugation. The combined sonicated material was further diluted 1.5-fold in dilution buffer and 1.7 x 107 cell equivalents were subjected to immunoprecipitation with 5 μg (α-H3K27Ac, α-H3.3, α-RPB1, α-S5P CTD and α-S2P CTD), 7 μg (α-Spt5) or 1:50 dilution (α-H3K36me3) of antibodies at 4°C overnight. The next day, immune complexes were incubated with 30 µl magnetic beads (Protein G Dynabeads, Thermo Fisher Scientific) or (Protein A/G magnetic beads, Pierce). The magnetic beads were washed twice with low salt wash buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with ChIP wash buffer (50 mM HEPS, pH 7.6, 500 mM LiCl, 1 mM EDTA, 0.7% sodium deoxycholate and 1 % Igepal CA-630) and twice with TE buffer with 50 mM NaCl.     Chromatin Immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (#9003) according to the manufacturer’s protocol with minor modifications. In brief, 40 x 10e6 Ramos cells were spun down at 90xg for 10 min before the pellet was reconstituted in 9 ml of RPMI with 2% FBS in a 15 ml conical tube. Then, 0.6 ml of 16% Formaldehyde (Pierce/ThermoFisher #28906) was added and the cells were placed on a rocker for 10 min at RT. One ml of 10x glycine solution was added to quench the reaction, and the cells were then returned to the rocker for 5 min at RT before being spun down at 300xg and washed 2x with PBS. All following steps were performed on ice or at 4°C unless otherwise noted. Cells were reconstituted in 10 ml of Buffer A with protease inhibitors and allowed to rest for 10 minutes and the lysed cells were spun down at 2000xg for 5 min to pellet nuclei. Pelleted nuclei were washed with 10 ml of Buffer B, pelleted at 2000xg for 5 min, and then resuspended in 1 ml of Buffer B. 1.7 µl of micrococcal nuclease (CST #10011) was added to the nuclei and the tube incubated in a 37°C water bath for 20 min. The reaction was stopped with 100 µl of 0.5 ml of EDTA, and the nuclei pelleted at 16,000xg for 1 min. The pellet was then resuspended in 1 ml of 1x ChIP Buffer with protease inhibitors and sonicated in 200 µl aliquots in a Qsonica sonicator for 2 cycles of 15 s on, 45 s off at 20% power. The lysate was then clarified at 10,000xg for 10 min before the supernatant was removed and diluted five-fold in 1x ChIP Buffer with protease inhibitors. For each ChIP, 500 µl of chromatin was incubated with 1-2 µg of antibody in a 1.5 ml Eppendorf tube at 4°C overnight on a rotator. The next day, 30 µl of Protein G Magnetic beads (CST #70024) was added to each tube and the mixture incubated at 4°C for 2 hours on a rotator. The beads were pelleted using a magnetic separation rack and the supernatant discarded.  The beads were then washed 3x with a low-salt wash and 1x with a high-salt wash using 5 min incubations on a rotator. Chromatin was eluted from beads with the addition of 150 µl of 1x Elution Buffer and incubation at 1200 rpm on a thermal mixer for 2 hours at 65°C. The beads were pelleted and the supernatant was moved to a new 1.5 ml Eppendorf tube and 2 µl of Proteinase K (CST #10012) added. The mixture was incubated for 2 hr at 65°C and then DNA was purified using SimpleChIP DNA Purification Buffers and Columns (CST #14209) and eluted in a volume of 50 µl.
ChIP-seq libraries were prepared for each ChIP from three independent ChIP experiments using TruSeq ChIP Sample Preparation kit (Illumina) or NEBNext Ultra II DNA Library Prep kit (New England Biolabs) according to manufacturer’s instructions.

value: B lymphocyte

value: IgL(-) AIDR1 Ri GFP2

value: bursal lymphoma

value: Unknown

tag: Sex

value: female

tag: chip antibody

value: INPUT

tag: chip antibody cat. #


title: ChIP-INPUT-DT40-Ri GFP2 2-3

value: IgL(-) AIDR1 Ri GFP2 2-3


title: ChIP-H3K36me3-DT40-Ri GFP2

description: input used:ChIP-INPUT-DT40-Ri GFP2

tag: chip antibody vendor

value: Cell Signaling Technology


title: S57 [P15763_123]

value: Liver

value: 22 weeks


title: S56 [P15763_122]


title: ChIP-H3K36me3-DT40-Ri GFP2 2-3

description: input used:ChIP-INPUT-DT40-Ri GFP2 2-3


title: Untreated biol rep 2 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1084 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: S59 [P15763_125]


title: ChIP-S2P-DT40-Ri GFP2

description: input used:ChIP-INPUT-DT40-Ri GFP2

value: Abcam


title: Jurkat Cas9 PRMT7 KO5_3

city: Tampere

first: Laura

last: Oksa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: Jurkat Cas9 PRMT7 KO5 repl. 3

data_processing:
Base calling was mabe using CASAVA base recognition software and SecureCRT was used to data demultiplexin. These steps were performed by Novogene Europe (Cambridge, UK).
The quality of the raw reads was ensured with FastaQC (v0.11.08)
STAR software (version 2.5.3a) was used to map the reads to the human reference genome (hg19).
Tag directories were made from the alingment files and raw read counts were calculated using Homer tool kit ( v.4.11)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw read counts of the samples and replicates.

source_name: Jurkat Cas9 cell line

growth_protocol: Cells were cultured in RPMI (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 2 mM L-glut, 100 U penicillin, 100 ug/ml streptomycin and 10% FBS (Gibco).

extract_protocol:
Total RNA extraction was performed with PureLink™ RNA Mini Kit and On-Column PureLink® DNase Treatment Protocol was used to avoid contamination by genomic DNA (Ambion® by Life Technologies and Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols (Hiseq-PE150)

treatment_protocol: Cells were transfected with 2µg of px321-GFP plasmid, containing PRMT7 KO gRNA (PRMT7 KO3 or PRMT7 KO5), targeting exon3 (PRMT7 KO3) and exon4 (PRMT7 KO55), containing the AdoMet MTase I binding site. After 24h, GFP positive cells were single cell sorted. Single cell clones were Sanger sequenced to confirm the mutations. Western blot and Immunohistoshemistry were used to confirm the decreased level of PRMT7 protein. PRMT7 KO3 clone has 10 nucleotides deletion (chr16:68349960_68349969delCCACCAGGAG) and the amino adid changes Y26* resulting an early stop codon. PRMT7 KO5 clone consists of cells having insertion of 5 or 1 nucleotides (chr16:68358662_68358663insCGGTC or chr16:68358661_68358662insA) and amino acid changes I71Gfs*12 or D70Efs*32 respectilevly, resulting the early stop codons.

value: Jurkat-Cas9 T-ALL

value: PRMT7 KO5

tag: replicate


title: HRas-KO mice Lung sample  H058.2

description: Gene expression data from whole HRAS-deficient lung extracts.

source_name: HRas-KO Lung 3

value: HRas-KO

value: Lung tissue obtained from postnatal day 0 mice


title: S54 [P15763_120]


title: Jurkat Cas9 PRMT7 KO5_2

description: Jurkat Cas9 PRMT7 KO5 repl. 2


title: HRas-KO mice Lung sample  C118.5

source_name: HRas-KO Lung 2


title: Untreated biol rep 1 tech rep 3

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1082 control probes, spotted onto glass slides using a proprietary non-contact printing method.

value: Untreated


title: ChIP-S2P-DT40-Ri GFP2 2-3

description: input used:ChIP-INPUT-DT40-Ri GFP2 2-3


title: ChIP-S5P-DT40-Ri GFP2

description: input used:ChIP-INPUT-DT40-Ri GFP2


title: Untreated biol rep 2 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1083 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: Jurkat Cas9 PRMT7 KO5_1

description: Jurkat Cas9 PRMT7 KO5 repl. 1


title: HRas-KO mice Lung sample C117.4

source_name: HRas-KO Lung 1


title: Control+NAC mice Lung sample T445.5

description: Gene expression data from whole Control lung extracts treated antenatally with N-acetyl cysteine.

source_name: Control Lung + NAC 3

value: Control

value: N-acetyl cysteine (NAC)


title: Untreated biol rep 1 tech rep 1

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1080 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: Jurkat Cas9 PRMT7 KO3_3

description: Jurkat Cas9 PRMT7 KO3 repl. 3

value: PRMT7 KO3


title: Control+NAC mice Lung sample T453.2

source_name: Control Lung + NAC 4


title: S58 [P15763_124]

value: HFD + MI_D1


title: Control+NAC mice Lung sample T445.2

source_name: Control Lung + NAC 1


title: Control+NAC mice Lung sample T445.3

source_name: Control Lung + NAC 2


title: Untreated biol rep 1 tech rep 2

description: Phalanx Biotech Group's Human OneArray contains 32,048 features, 30968 detection probes and 1081 control probes, spotted onto glass slides using a proprietary non-contact printing method.


title: HEK293T RNA 3

city: San Francisco

first: Manuel

middle: D

last: Leonetti

state: CA

address: 499 Illinois St 4th floor

institute: Chan Zuckerberg Biohub

description: biological replicate 3

data_processing:
Transcript abundance was obtained using kallisto: https://pachterlab.github.io/kallisto/about
Genome_build: hg38
Supplementary_files_format_and_content: Processed data includes transcript abundance for each replicate expressed in transcript per million (tpm)

source_name: HEK293T cell line

growth_protocol: High-glucose DMEM media with 10% FBS (normal conditions). Cells were 70% confluent upon harvest.

extract_protocol:
Trizol
Oligo-dT capture followed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (part # E7760S)
Directional RNA library prep


title: S52 [P15763_118]

value: HFD


title: K_2 [20185_S8]

source_name: Macaca nemestrina infected with Kyasanur forest disease virus at day 2

value: Kyasanur forest disease virus

value: day 2


title: Control mice Lung sample  H058.1

description: Gene expression data from whole Control lung extracts.

source_name: Control Lung 2


title: Control mice Lung sample  C118.4

source_name: Control Lung 1


title: S55 [P15763_121]


title: ChIP-S5P-DT40-Ri GFP2 2-3

description: input used:ChIP-INPUT-DT40-Ri GFP2 2-3

value: B lymphocyte

value: IgL(-) AIDR1 Ri GFP2 2-3

value: bursal lymphoma

value: Unknown

value: female


title: S48 [P15763_114]

value: Liver

value: 22 weeks


title: 36-hour replicate 2

city: Missoula

first: J. Stephen

last: Lodmell

address: 32 Campus Drive

department: Division of Biological Sciences

institute: University of Montana

data_processing:
Cutadapt (Galaxy ver. 3.4)
RNA STAR (Galaxy ver. 2.7.8a)
Samtools
PEAKachu (Galaxy ver. 0.1.0.2)
UROPA
Genome_build: hg38
Supplementary_files_format_and_content: tab deliminated text COMMENT: The 12h_PEAKachu_finalhits.txt file contains only one hit. We hypothesize that the lack of hits in this file is primarily linked to the relatively low amount of total immuno-precipitable viral N protein in the samples 12-hours post-RVFV infection. Despite the presence of sequenced reads after the CLIP procedure, their low statistical values led to only one PEAKachu final hit.

source_name: HEK293 cell

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% fetal bovine serum, penicillin, and streptmicin

extract_protocol:
Cells were lysed, and the nucleocapsid-RNA complexes were immunoprecipitated. The experimental sequencing libraries were constructed from the immunoprecipitated RNAs, and the control libraries were prepared from pre-immunoprecipitation samples.
NEB Ultra II directional RNA library prep kit was used

treatment_protocol: Cells were infected with Rift Valley fever virus (strain MP-12) and UV irradiated

value: 36 hour


title: ChIP-POL2-DT40-Ri GFP2

description: input used:ChIP-INPUT-DT40-Ri GFP2

value: IgL(-) AIDR1 Ri GFP2

value: Santa Cruz Biotechnology


title: ChIP-POL2-DT40-Ri GFP2 2-3

description: input used:ChIP-INPUT-DT40-Ri GFP2 2-3


title: 36-hour replicate 1

value: infected with Rift Valley fever virus (strain MP-12)


title: S53 [P15763_119]


title: S46 [P15763_112]


title: RSV_1967_sample_1

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Raw reads were quality checked, trimmed and mapped to the reference genome (GRCh37/hg19) using STAR with NCBI RefSeq annotated genes as transcriptome index data.
Raw read counts were normalized across all samples and then used for differential expression analysis using DESeq, EdgeR and Cuffdiff (Slug Genomics, UV Santa Cruz) (Available as Data Files S2, S3 and S4, respectively). Using log2 normalized FPKM values heatmaps were generated in R.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: EdgeR_output

extract_protocol:
H&E stained slides were soaked overnight in fresh xylene. Cover slips were removed and sections were scraped into a microcentrifuge tube using a sterile razor blade. Tissue was rehydrated in ethanol /RNAse free water dilutions (100%, 95%, 75%) for 15 minutes per wash. Slides were washed in RNAse free water for 10 minutes (2x). Tissues were then incubated in proteinase K solution PKD buffer with the addition of proteinase K (Qiagen) at 56oC for 3 hrs. 1ml Trizol (Thermo-Fisher) was added and RNA was extracted according to the Trizol protocol. RNA concentration was determined with the Qubit 3.0 Fluorometer (ThermoFisher Scientific). Quality RNA integrity number scores, and fragment sizes (DV200 metrics) 15 were obtained utilizing either the Agilent 2100 Bioanalyzer or the Agilent 4200 TapeStation.
Sequencing library preparation was performed as previously described using a minimum of 25 ng RNA according to Illumina’s TruSeq RNA Access Library Preparation protocol. Indexed, pooled libraries were then sequenced on the Illumina NextSeq 550 platform with high-output flow cell–producing stranded, single end reads (1× 75 bp). A target count of 50 million reads per sample was used to plan indexing and sequencing runs.

tag: subject status

value: deceased participants from the 1867 RSV vaccine trial

tag: subject age

value: 16 months

tag: tissue type

value: FFPE lung sample


title: RSV_1967_Sample_2

value: 14 months


title: ChIP-SPT5-DT40-Ri GFP2

description: input used:ChIP-INPUT-DT40-Ri GFP2


title: HEK293T RNA 2

description: biological replicate 2

tag: cell line


title: Jurkat Cas9 PRMT7 KO3_2

description: Jurkat Cas9 PRMT7 KO3 repl. 2

value: Jurkat-Cas9 T-ALL

value: PRMT7 KO3


title: HEK293T RNA 1

description: biological replicate 1


title: 24-hour replicate 2

value: 24 hour

tag: treatment


title: S51 [P15763_117]

tag: tissue

value: HFD


title: S45 [P15763_111]

tag: age


title: S47 [P15763_113]


title: ChIP-SPT5-DT40-Ri GFP2 2-3

description: input used:ChIP-INPUT-DT40-Ri GFP2 2-3

value: B lymphocyte

value: IgL(-) AIDR1 Ri GFP2 2-3

value: bursal lymphoma


title: LG3

city: Tai an

first: Rong

last: Xuan

state: Shan Dong

address: 61 Daizong Street

department: College of Animal Science and Veterinary Medicine

institute: Shandong Agricultural University

data_processing:
Sequencing was performed on a HiSeq 2500 platform (Illumina).
Sequencing quality was assessed using FastQC software. The high-throughput sequencing reads were processed using Trimmomatic software to remove adapter sequences, primers, poly-A tails and other unwanted sequences (Bolger et al., 2014).
HISAT2 software (Kim et al., 2015) was used to construct indices of the goat genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/704/415/GCF_001704415.1_ARS1), and sequence alignment was performed.
The numbers and percentages of sequence alignment were quantified using SAMtools (Li et al., 2009).
The expression level of each gene was quantified using HTSeq (Anders et al., 2015).
Genome_build: Capra hircus (Bio Sample:SAMN03863711)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Capra hircus

source_name: mammary gland

extract_protocol:
Cryopreservation of the mammary gland tissue in liquid nitrogen and total RNA was harvested using Trizol reagent (Code No 9108Q, Takara). TruSeq RNA Library Prep Kit v2 (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: late gestation

value: mammary gland


title: S44 [P15763_110]

value: Liver

value: 22 weeks


title: S50 [P15763_116]


title: Jurkat Cas9 PRMT7 KO3_1

description: Jurkat Cas9 PRMT7 KO3 repl. 1


title: Control mice Lung sample  H058.5

source_name: Control Lung 3

tag: genotype/variation

value: Control

value: Lung tissue obtained from postnatal day 0 mice


title: 12-hour replicate 2

tag: time point

value: 12 hour

value: infected with Rift Valley fever virus (strain MP-12)


title: 12-hour size-matched control

value: control


title: DP3

value: dry period


title: S49 [P15763_115]


title: 36-hour size-matched control

value: 36 hour


title: 24-hour size-matched control


title: 12-hour replicate 1


title: Ctrl_2_RSV_D168

value: controls from LungMAP

value: 15 months

value: FFPE lung sample


title: Ctrl_1_RSV_D060

value: 24 months


title: DP2


title: GRO-DT40-Ri_GFP2_2-3

data_processing:
Library strategy: GRO-seq
The reads from libraries were aligned with Bowtie2 (Langmead and Salzberg, 2012) to the customized Gallus_gallus-4.0 genome with the reporter construct appended as an extra chromosome. The alignment was done as previously described (Meng et al., 2014).
Genome_build: GalGal4
Supplementary_files_format_and_content: Aligned-reads bed files were seperated by strand and then converted to bedgraph files using bedtools genomecov (Quinlan and Hall, 2010) following by bedGraphToBigWig to make a bigwig file (Kent et al., 2010).

growth_protocol: DT40 cells were propagated in RPMI 1640 medium (Sigma), supplemented with 10 % fetal bovine serum (Hyclone), 1 % chicken serum (Biowest), 1X GlutaMAX (Gibco), 50 µM β-mercaptoethanol (Gibco) and 1 % antibiotic mixture (Sigma) in a 5 % CO2 atmosphere at 41 °C.

extract_protocol: Nucleus were prepared from about 20 millions cells of each line. The GRO-seq was done as previously described (Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (80-. ). 322, 1845–1848.)

tag: cell type

value: B lymphocyte

value: IgL(-) AIDR1 Ri GFP2

value: Bursal lymphooma

value: Unknown


title: LG2

value: late gestation

value: mammary gland


title: S43 [P15763_109]

source_name: Liver_Chow diet

value: Liver

value: 22 weeks

value: Chow diet


title: Patient 83 NPH 0083

city: Obu

first: Yuya

last: Asanomi

state: Aichi

address: 7-430 Morioka-cho

country: Japan

institute: National Center for Geriatrics and Gerontology

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.)

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

source_name: serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

tag: diagnosis

value: NPH

value: male


title: Patient 84 NPH 0084

tag: Sex

value: female


title: LL3

value: late lactation


title: GRO-DT40-Ri_GFP2

source_name: DT40 cell line

treatment_protocol: The GRO-seq was done as previously described (Core, L.J., Waterfall, J.J., and Lis, J.T. (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (80-. ). 322, 1845–1848.)

tag: genotype

value: IgL(-) AIDR1 Ri GFP2 2-3


title: RNAseq_4

city: Bethesda

first: Dinah

middle: S.

last: Singer

state: MD

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

data_processing:
RNA-seq reads were aligned to human reference genome (hg19) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

source_name: HeLa TAF7 (WT) cells

growth_protocol: HeLa TAF7 (WT) cells were cultured in F12K medium supplemented with 10% fetal bovine serum.

extract_protocol:
Cytoplasmic total RNA was extracted from HeLa TAF7 (WT) cytoplasmic extracts using RNeasy Plus Mini Kit, followed by treatment with RNase free-DNase.
Libraries were prepared using the SMARTer Ultra Low RNA Kit for Illumina Sequencing and Illumina® Nextera XT DNA Library Preparation Kit according to manufacturers' instructions.

value: HeLa

value: WT

tag: expressing

tag: rna population

value: Cytoplasmic RNA


title: S42 [P15763_108]


title: S39 [P15763_105]


title: LG1


title: S38 [P15763_104]


title: FLAG_RIP_5

data_processing:
RIP-seq reads were aligned to human reference genome (hg19) with STAR aligner. Raw read counts were obtained using htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts of sequencing reads for each sample

extract_protocol:
TAF7-RNA complexes in HeLa TAF7 (WT) cytoplasmic extracts were immunoprecipitated using anti-FLAG® M2 affinity gel. RNA was released from the TAF7-RNA complexes by proteinase K treatment followed by an acid phenol: chloroform (pH 4.5) extraction.
Libraries were prepared using the SMARTer Ultra Low RNA Kit for Illumina Sequencing and Illumina® Nextera XT DNA Library Preparation Kit according to manufacturers' instructions.

tag: rip antibody

value: Anti-FLAG (MilliporeSigma, A2220)


title: RNAseq_5


title: 24-hour replicate 1

value: 24 hour

value: infected with Rift Valley fever virus (strain MP-12)


title: S37 [P15763_103]


title: S41 [P15763_107]


title: Patient 82 NPH 0082


title: Patient 81 NPH 0081


title: DP1

value: dry period


title: Patient 77 NPH 0077


title: Patient 80 NPH 0080


title: Patient 78 NPH 0078


title: FLAG_RIP_6


title: FLAG_RIP_4


title: LL1

value: mammary gland


title: LL2


title: S40 [P15763_106]

value: Liver


title: S36 [P15763_102]

value: 22 weeks


title: S35 [P15763_101]

value: Chow diet


title: NusA- merged [dA_merged]

city: University Park

first: Oshadhi

last: Jayasinghe

state: PA

address: 203 Althouse Laboratory

department: Biochemistry and Molecular Biology

institute: Penn State University

description: NusA depletion RNETseq merged data

data_processing:
Library strategy: RNET-seq
Base calling and quality scoring conducted via BaseSpace
Adaptor trimming from the 5'end of the reads via cutadapt v. 1.18 and retaining only reads between 14 to 30 bases
Duplicate reads within each sample were removed using clumpify routine from BBmap (V38.34.0)
Removal of 6bp barcode from 5' end via cutadapt v. 1.18
RNET-seq .fastq files were aligned to the B. subtilis genome using bowtie v1.2.2 rejecting multi-mapped reads via parameters-best-strata -v 1 -m 1
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
A custom python script built on samools/htslib was used to identify 3' ends from RNET-seq .fastq derived .bam files using parameters -r 10 -c 431 -w 100 and generate .bed and .bw graphs
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: .bw files, containing the called 3' ends.

organism: Bacillus subtilis

source_name: bacterial cell culture

growth_protocol: Strains were grown at 37°C in Gln-minimal medium (1x Spizizen salts, 0.1% glutamine, 0.5% glucose, 10 µM CaCl2, and 10 µM FeSO4 in tap water) in the presence of 0.2 mM IPTG and appropriate antibiotics. One ml of a shaking overnight culture was transferred to 25 ml of fresh Gln-minimal medium and growth was continued overnight at 37°C. The next day the cells were pelleted, washed in 0.5 ml of prewarmed medium at 37°C, again pelleted and re-suspended in 1 ml of pre-warmed medium at 37°C. 5 OD600 units was used to inoculate a 250 ml culture supplemented with 20 µg/ml chloramphenicol to an OD600 value of 0.02. Cells were grown at 37°C ± IPTG and then harvested during mid-exponential phase growth. Frozen Slurry buffer was added to stop transcription, cells were pelleted at frozen at -80°C.

extract_protocol:
Cell suspension was digested with lysozyme and RnaseI, lysate was layered on a sucrose cushion, nucleoid with RNAP and nascent RNA pelleted by centrifugation, digested with DNases, native transcription elongation complexes purified by immobilization with Ni-NTA agarose, nucleic acids were isolated and purified, RNA extracted.
Purified nascent RNA was ligated to a 5′-adenylated barcode DNA linker, recovered by phenol extraction/ isopropanol precipitation, reverse-transcribed, and digested with RNase H. The resulting cDNA was fractionated through a urea-polyacrylamide gel, followed by staining with SyBR Gold. Bands of the correct length were excised from the gel, DNA was extracted with water and precipitated with isopropanol. The resulting single-stranded cDNA was circularized with CircLigase and used as a template for PCR amplification with a pair of adapters that contained Illumina i5 and i7 barcodes. The resulting sequencing libraries were purified by electrophoresis in native polyacrylamide gels. SYBR gold-stained gels were imaged under ultraviolet light, and slices containing PCR products of interest were excised. DNA was extracted with water and precipitated with isopropanol. Library recovery was estimated by electrophoresis of DNA samples followed by SYBR gold staining and quantification using reference DNA samples and ImageQuant software. The quality and concentration of DNA libraries was also determined using a Bioanalyzer DNA high-sensitivity chip and qPCR.

value: rpoC-10His amyE::Physpank-nusA lacIq nusA::Spr


title: Patient 76 NPH 0076

value: serum

value: NPH


title: NusA-NusG- merged [dAdG_merged]

description: NusA depletion nusG deletion RNETseq merged data

value: rpoC-10His nusG::kan amyE::Physpank-nusA lacIq nusA::Spr


title: Patient 74 NPH 0074

value: male


title: NusA-NusG- sample 2 [dAdG-2]

description: NusA depletion nusG deletion RNETseq


title: Patient 79 NPH 0079

value: female


title: WGBS_KO_Bet3

city: shenzhen

first: xin

last: dai

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
The library was sequenced on Illumina Novaseq platform. Image analysis and base calling were  performed with Illumina CASAVA pipeline, and finally generated 150bp paired-end reads.
First of all, we used FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads.  Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed  through fastp (fastp 0.20.0). The remaining reads that passed all the filtering steps was counted as clean  reads and all subsequent analyses were based on this. Finally, we used FastQC to perform basic  statistics on the quality of the clean data reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated  reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into  bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead  B, 2012). Clean reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-  A converted) before being aligned to the similarly converted versions of the genome in a directional  manner. Sequence reads that produce a unique best alignment from the two alignment processes  (original top and bottom strand) were then compared to the normal genomic sequence and the  methylation state of all cytosine positions was inferred. The same reads that aligned to the same regions  of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized  using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor, -- no_overlap) were transformed  into bigWig format for visualization using IGV browser. The sodium bisulfite non-conversion rate was  calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda  genome.
Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts  (mC+umC) and the non-conversion rate (r). Sites with FDR-corrected p-value<0.05 were considered  as a methylated site. To calculate the methylation level of the sequence, we divided the sequence into  multiple bins, with bin size is 10 kb. The sum of methylated and unmethylated read counts in each  window were calculated. Methylation level (ML) for each window or C site shows the fraction of  methylated Cs, and is defined as: ML(C) = reads(mC)/ (reads(mC) + reads(C)).
Genome_build: mm10

source_name: Vascular tissue

extract_protocol:
Genomic DNA degradation and contamination was validated by agarose gels. DNA purity was checked  using NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured  using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 100 ng genomic DNA spiked with 0.5 ng lambda DNA were fragmented by  sonication to 200-300 bp with Covaris S220. These DNA fragments were treated with bisulfite using  EZ DNA Methylation-GoldTM Kit (Zymo Research), and the library was constructed by Novogene  Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina  platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

value: vascular

value: ApoE-/-/SAHH+/- +Betaine


title: NusA- sample 2 [dA-2]

description: NusA depletion RNETseq


title: Non diabetic adipocyte Exosomes (ND) 3

city: Boston

first: Naser

last: Jafari

state: MA

address: 72 East Concord

department: Hem Onc

institute: Boston University

description: Test

data_processing: Ct values were generated by ABI 7500 Fast System Software

label: SYBR Green

source_name: MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM including 10% FBS and 1% antibiotics for an over night

extract_protocol: RNA isolated using Qiagen RNA purification protocol and reagents

treatment_protocol: MCF7 Cancer cells were treated with ND or T2D adipocytes exosomes for 5 days

value: breast cancer

value: Non diabetic adipocyte Exosomes (ND) 3


title: Patient 73 NPH 0073


title: NusA-NusG- sample 1 [dAdG-1]

description: NusA depletion nusG deletion RNETseq


title: Type-2 diabetic adipocyte Exosomes (T2D) 3

description: Test


title: Patient 72 NPH 0072


title: Patient 75 NPH 0075


title: Type-2 diabetic adipocyte Exosomes (T2D) 2

description: Test


title: Type-2 diabetic adipocyte Exosomes (T2D) 1

description: Test


title: WGBS_KO_Bet1


title: NusA- sample 3 [dA-3]

description: NusA depletion RNETseq


title: Patient 71 NPH 0071


title: NusA-NusG- sample 3 [dAdG-3]

description: NusA depletion nusG deletion RNETseq


title: Non diabetic adipocyte Exosomes (ND) 2

description: Test

value: Non diabetic adipocyte Exosomes (ND) 2


title: WGBS_KO3

value: ApoE-/-/SAHH+/-


title: WGBS_KO_Bet2


title: NusA- sample1 [dA-1]

description: NusA depletion RNETseq


title: WGBS_KO2


title: Patient 70 NPH 0070


title: Patient 69 NPH 0069


title: Patient 67 NPH 0067


title: Patient 68 NPH 0068


title: RNAseq_3

value: HeLa

value: WT

value: Cytoplasmic RNA


title: Non diabetic adipocyte Exosomes (ND) 1

description: Test

value: Non diabetic adipocyte Exosomes (ND) 1


title: WGBS_WT2

value: ApoE-/-/SAHHWT


title: Control for exosomes replicate 3

description: Control

value: Control


title: Patient 66 NPH 0066

value: serum


title: Patient 65 NPH 0065

value: NPH


title: WGBS_WT1


title: RNAseq_2


title: WGBS_WT3


title: FLAG_RIP_3

value: Anti-FLAG (MilliporeSigma, A2220)


title: WGBS_KO1


title: KO_Bet3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
vascular tissue of mice were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vascular tissue


title: FLAG_RIP_2


title: RNAseq_1


title: tsp5 OverExpress Exosome 2

description: Test

treatment_protocol: MCF-7 cells, upon treatment with exosomes released from TSP5-overexpressing human primary adipocytes (ND; ABM-007), compared to exosomes released from matched control adipocytes transduced with control lentiviral vector.

value: tsp5 OverExpress Exosome 2


title: Patient 64 NPH 0064

value: male


title: genomic DNA from H1299 cells siRNA TET1 kd

type: genomic

city: Albuquerque

first: Steven

middle: A

last: Belinsky

state: NM

address: 2425 Ridgecrest Dr SE

department: Lung Cancer Program

institute: Lovelace Respiratory Research Institute

description:
H1299 TET1 kd cell line
H1299_Tkd

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner settings

data_processing: Data were normalized and background substracted using Bioconductor methylumi package noob procedure in R

label: Cy5 and Cy3

source_name: lung cancer cell line

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was treated with proteinase K, digested with Rnase and phenol chloroform extracted

tag: sirna

value: siRNA TET1 kd


title: Control for exosomes replicate 1

description: Control

value: breast cancer


title: KO_Bet1

value: ApoE-/-/SAHH+/- +Betaine


title: genomic DNA from A549 cells siRNA TET1 kd

description:
A549 TET1 kd cell line
A549_Tkd


title: genomic DNA from H1299 cells

description:
parent H1299 cell line
H1299

value: parent


title: Tram-/- High dose LPS monocyte

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

data_processing:
Cellranger
Genome_build: mm10
Supplementary_files_format_and_content: gz file with matrix can be read by Seurat

molecule: polyA RNA

source_name: monocyte

growth_protocol: BM cells isolated from WT C57BL/6 mice and Tram-/- mice were cultured in complete RPMI 1640 medium supplemented with M-CSF (10 ng/mL).

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.

treatment_protocol: Cultured monocytes were treated with PBS or 100 ng/ml LPS on day 0, 2, and 4 of the 5 day culture period.

value: BM derived

value: High dose LPS

value: Tram -/-


title: genomic DNA from A549 cells

description:
parent A549 cell line
A549


title: KO_Bet2


title: FLAG_RIP_1

value: HeLa

value: WT

value: Cytoplasmic RNA


title: Patient 63 NPH 0063

value: female


title: KO3

value: ApoE-/-/SAHH+/-


title: tsp5 OverExpress Exosome 1

description: Test

value: tsp5 OverExpress Exosome 1


title: Patient 60 NPH 0060

value: serum

value: NPH


title: KO1

value: Vascular tissue


title: Control Vector Exosome 1

description: Control

value: Control Vector Exosome 1


title: WT High dose LPS monocyte


title: WT2

value: ApoE-/-/SAHHWT


title: Insulin resistant (IR) 3

description: Test

treatment_protocol: Cells were co cultured either innsulin sensitye or insulin resistant adipocytes for 5 days. Then RNA of the cells were isolated and cDNA synthesized

value: breast cancer

value: Co-cultured with insulin resistant adipocytes


title: Patient 57 NPH 0057

value: male


title: Patient 62 NPH 0062


title: Insulin sensitive (IS) 1

description: Test

value: Co-cultured with insulin sensitive adipocytes


title: Control Vector Exosome 2

description: Control

value: Control Vector Exosome 2


title: Control replicate 3

description: Control

value: Control


title: Lin28_SP_cK_N

city: San Diego

first: Oscar

middle: E

last: Echeagaray

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

data_processing:
The raw data was processed with the Cell Ranger pipeline (10X Genomics; version 3.0.1). Reads were aligned to the 10x mouse genome mm10.
Preparations derived from Lin28 cell surface sorting yielded 7086 barcoded cells for analysis, from which 4334 corresponded to Lin28S-, and 2752 corresponded to Lin28S+(874 Lin28S+/cKit-, 1878 Lin28S+/cKit+). Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.2)
Sequenced reads were aligned to the human reference genome mm-10
Genome_build: mm-10
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

extract_protocol:
Briefly, heart samples were mechanically minced into 1-mm3 pieces and digested in collagenase II (150 U mg/mL, Worthington, LS004174) followed by brief low-speed (850 rpm for 2 minutes) centrifugation to remove cardiomyocytes and tissue debris.Lin28S+/- cardiac interstitial cells were obtained by FACS sorting  with Lin28 antibody and concurrent cell surface expression of Lin28/cKit
The Chromium Single Cell 3' Library & Gel Bead Kit v3.1 (PN- 1000268), Chromium Single Cell 3' Chip G kit v2 (PN-1000120) and Dual Index Kit TT Set A, (PN-1000215) were used according to the manufacturers instructions in the Chromium Single Cell 3' Reagents Kits V3.1 User Guide.


title: Patient 58 NPH 0058


title: Control replicate 2

description: Control


title: Patient 59 NPH 0059


title: Patient 53 NPH 0053


title: Patient 54 NPH 0054


title: Patient 61 NPH 0061


title: WT3


title: KO2


title: Patient 56 NPH 0056


title: Insulin sensitive (IS) 3

description: Test


title: Insulin resistant (IR) 2

description: Test


title: Patient 50 NPH 0050


title: WT1


title: Insulin resistant (IR) 1

description: Test


title: Insulin sensitive (IS) 2

description: Test


title: TAFs Co-culture 3

city: Stanford

first: Gina

last: Bouchard

address: 318 Campus Drive, Clark Center, W-250

institute: STANFORD UNIVERSITY

data_processing:
Expression levels of RNA sequencing data were quantified using a quasi-mapping two-phase inference algorithm implemented in Salmon (version 091).
Genome_build: Transcript sequences GRCh38 from Gencode were used for reference transcriptome indexing.
Supplementary_files_format_and_content: Transcript-per-million (TPM) value was used as normalized expression level unit.

source_name: Lung adenocarcinoma

growth_protocol: Immediately following surgery, fresh lung adenocarcinoma matched specimens were collected from different tumor regions, namely Normal Fibroblasts (NFs, >5 cm away from the tumor), Tumor-Adjacent Fibroblasts (TAFs, leading edge) and Tumor Core Fibroblasts (TCFs, tumor core). Samples were immersed and transferred from Stanford Hospital to the laboratory in MACS Tissue Storage Solution (Miltenyi Biotec). Then, tumors were cut into small pieces with dissecting scissors. The dissociation was performed utilizing the MACS Tumor Tissue Dissociation Kit (Miltenyi Biotec) for the tumor core samples or the Lung Dissociation Kit (Miltenyi) for the normal and adjacent tissues as per the manufacturer’s protocol. The single-cell suspensions were centrifuged at 500 × g for 5 minutes to pellet tumor cells, which were subsequently resuspended in RPMI-1640 and applied on a MACS SmartStrainer (70 µm, Miltenyi Biotec) for filtration Following centrifugation (500 × g, 5 minute), and red blood cells were removed using the Red Blood Cell Lysis Solution according to the manufacturer’s instructions (Miltenyi Biotec). Cells were then washed, resuspended in RPMI-1640 and plated in a 35 mm dish for fibroblast expansion. At confluency, all cells were trypsinized and transferred to a 25 cm2 flask until confluency, then all cells were split in two 75 cm2 flasks for further expansion. At confluency of the 75 cm2 flasks, primary fibroblasts were divided equally and frozen in 10 vials, designated here as “passage 1”.

extract_protocol:
Cell cultures were rinsed with PBS 1X and detached using TrypLE. Cocultured cells were then separated with the optimized amount of Anti-Fibroblast MicroBeads (Miltenyi Biotec) according to the manufacturer’s protocol to reach minimal contamination in each compartment. For each cell sample, RNA was extracted from 1x105 cells using a Macherey-Nagel Nucleospin analyzer (Fisher Scientific) according to the manufacturer’s protocol and stored in RNA later stabilization solution (Invitrogen).
the RNA was extracted using a Macherey-Nagel Nucleospin analyzer (Fisher Scientific) in accordance with the manufacturer’s protocol. Sample and library quality control were performed with Qubit (ThermoFisher) and Tapesation (Agilent) bioanalyzers. The library was prepared using Illumina TruSeq stranded mRNA and the NovaSeq PE100 sequencing run type.

treatment_protocol: HCC827 lung adenocarcinoma cells were cocultured at 1:1 ratio (8x105 cells each cell type) with primary fibroblasts for 24 hours. In parallel, monocultures (1.6x106 cells) were plated and, after 24 hours, conditioned media were collected and spun down at 500 x g for 5 minutes. The cells were rinsed PBS 1X and treated with conditioned media from the opposite cell type for 24 hours. Then, cocultures and monoculture controls or cultures induced with supernatant for 24 hours.

value: Tumor adjacent-derived primary fibroblasts


title: WT PBS monocyte

value: BM derived

value: PBS

value: WT


title: Tibialis anterior 6month_1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: 6 months old replicate 1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 30 samples

source_name: tibialis anterior muscles from male C57BL/6J mice

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from UBR4 mKO tibialis anterior muscle at 6 and 24 months of age.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: tibialis anterior muscles

value: 6 months old


title: Patient 55 NPH 0055

value: serum


title: Lin28_SP_cK_P


title: NFs Co-culture 3

value: Normal lung-derived primary fibroblasts


title: TAFs CTL 3


title: Patient 52 NPH 0052

value: NPH


title: Tibialis anterior 24month_3

description: 24 months old replicate 3

value: 24 months old


title: TAFs Co-culture 1


title: TAFs Co-culture 2


title: NFs Co-culture 1


title: Patient 51 NPH 0051


title: Control replicate 1

description: Control


title: Tibialis anterior 6month_3

description: 6 months old replicate 3


title: Lin28_SN_cK_N


title: NFs CTL 3


title: TAFs CTL 2


title: NFs CTL 2


title: Tibialis anterior 6month_2

description: 6 months old replicate 2


title: TAFs CTL 1


title: Patient 41 NPH 0041


title: Patient 49 NPH 0049

value: female


title: Patient 48 NPH 0048


title: Patient 47 NPH 0047


title: Tibialis anterior dexamethasone_1

description: dexamethasone treatment replicate 1

value: dexamethasone treatment


title: NFs Co-culture 2


title: Patient 46 NPH 0046


title: Tibialis anterior 24month_2

description: 24 months old replicate 2


title: Patient 38 NPH 0038


title: Tibialis anterior Control_dexamethasone_3

description: Control for dexamethasone treatment replicate 3


title: Patient 43 NPH 0043


title: Patient 44 NPH 0044


title: Patient 45 NPH 0045


title: Tibialis anterior 24month_1

description: 24 months old replicate 1


title: Tibialis anterior Control_dexamethasone_2

description: Control for dexamethasone treatment replicate 2


title: HCC827 Co-culture (NFs) 2

value: Human lung adenocarcimoa cell line


title: Patient 36 NPH 0036

value: male


title: Patient 42 NPH 0042


title: Patient 34 NPH 0034


title: Patient 35 NPH 0035


title: HCC827 Co-culture (TCFs) 2


title: Tibialis anterior dexamethasone_4

description: dexamethasone treatment replicate 4


title: Tibialis anterior dexamethasone_3

description: dexamethasone treatment replicate 3


title: HCC827 Co-culture (TCFs) 1


title: Patient 40 NPH 0040


title: Patient 32 NPH 0032


title: Tibialis anterior SICYR61_1

description: Cyr61 siRNAs replicate 1

value: Cyr61 siRNAs


title: Tibialis anterior dexamethasone_2

description: dexamethasone treatment replicate 2


title: HCC827 Co-culture (TAFs) 2


title: Patient 39 NPH 0039


title: HCC827 Co-culture (TAFs) 3


title: Tibialis anterior Control_dexamethasone_4

description: Control for dexamethasone treatment replicate 4


title: NFs CTL 1


title: HCC827 CTL (TAFs) 2


title: HCC827 Co-culture (TAFs) 1


title: Tibialis anterior SINT_3

description: NT siRNAs replicate 3

value: NT siRNAs


title: Tibialis anterior SINT_2

description: NT siRNAs replicate 2


title: HCC827 CTL (TAFs) 3


title: Tibialis anterior Control_dexamethasone_1

description: Control for dexamethasone treatment replicate 1

value: Control


title: Patient 37 NPH 0037


title: Tibialis anterior LLC_4

description: LLC cancer replicate 4

value: LLC cancer


title: HCC827 Co-culture (NFs) 1


title: Tibialis anterior SICYR61_4

description: Cyr61 siRNAs replicate 4


title: Tibialis anterior LLC_3

description: LLC cancer replicate 3


title: HCC827 Co-culture (TCFs) 3


title: HCC827 CTL (TAFs) 1


title: Tibialis anterior LLC_2

description: LLC cancer replicate 2


title: HCC827 Co-culture (NFs) 3


title: Tibialis anterior SICYR61_2

description: Cyr61 siRNAs replicate 2


title: HCC827 CTL (TCFs) 2


title: Patient 25 NPH 0025


title: Patient 33 NPH 0033


title: Patient 24 NPH 0024


title: Tibialis anterior SINT_4

description: NT siRNAs replicate 4


title: Tibialis anterior SICYR61_3

description: Cyr61 siRNAs replicate 3


title: TCFs Co-culture 3

value: Tumor core-derived primary fibroblasts


title: Tibialis anterior Control_LLC_4

description: Control for LLC cancer replicate 4


title: HCC827 CTL (TCFs) 1


title: TCFs Co-culture 2


title: Patient 30 NPH 0030


title: Patient 31 NPH 0031


title: Patient 29 NPH 0029


title: Patient 28 NPH 0028


title: Patient 21 NPH 0021


title: Tibialis anterior Control_LLC_2

description: Control for LLC cancer replicate 2


title: TCFs CTL 3


title: AR2923_18_ScaleSig

city: Handayama, Higashiku, Hamamatsu city

first: Yasuko

last: Fujisawa

state: Shizuoka

department: Pediatrics

institute: Hamamatsu University School of Medicine

description: gene expression of testis from 6 week C offspring

hyb_protocol: The Cy3-labeled cRNA was fragmented and hybridized to the microarray

scan_protocol: The microarrays were scanned on an Agilent SureScan Microarray Scanner (G2600D) using the one-color scan setting for 8 × 60 K

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using the default parameters.

source_name: mouse testis 6w C offspring

label_protocol: The RNA was labeled with Cyanine 3 (Cy3) using a Low Input Quick Amp Labeling Kit (Agilent Technologies), and purified using RNeasy columns (Qiagen)

extract_protocol: RNA was isolated from snap-frozen testes of C- and R- offspring at 6 weeks stored at – 80℃ in RNA later, using an RNeasy Micro Kit (Qiagen) or an RNeasy Mini Kit (Qiagen).  pooled testes from litter mice were utilized in male C- and R-fetuses, whereas single testes were utilized in male C- and R-offspring. The concentration and integrity of RNA samples were assayed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 4200 TapeStation (Agilent, Santa Clara, CA, USA).

treatment_protocol: We used two groups of female mice with vaginal plugs. One group of mice were fed a powdered regular chow diet ad libitum throughout the pregnant course (control females) (C-females), and the other group of mice were fed 50% of the mean daily intake of the C-females from 6.5 days post coitum (dpc) (calorie-restricted females) (R-females). Pregnant C- and R-females gave birth to control offspring (C-offspring) and calorie-restricted offspring (R-offspring), respectively. After determining genetic sex, male mice only were utilized for the subsequent examinations. Male C-offspring were raised by their mothers, whereas male R-offspring were cross-fostered and raised by unrelated C-females. After weaning, male C- and R-offspring were fed a regular chow diet ad libitum until 6 weeks.

value: testis

value: 6 weeks

tag: group

value: C offspring


title: Tibialis anterior SINT_1

description: NT siRNAs replicate 1

value: tibialis anterior muscles


title: AR2923_17_ScaleSig

description: gene expression of testis from 6 week R offspring

source_name: mouse testis 6w R offspring

value: R offspring


title: Patient 19 NPH 0019

value: serum


title: Patient 27 NPH 0027

value: NPH


title: TCFs CTL 2


title: HCC827 CTL (NFs) 2

tag: cell line


title: HCC827 CTL (TCFs) 3


title: Patient 17 NPH 0017


title: BMDM_WT_DMSO_2hr_R2 mRNA-seq

city: Oxford

first: Irina

last: Udalova

state: Oxfordshire

address: The Kennedy Institute of Rheumatology, Roosevelt Drive, Headington

department: NDORMS

country: United Kingdom

institute: Kennedy Institute

description: featureCounts.txt

data_processing:
Reads were mapped to the mm10 genome using STAR with the options "--runMode alignReads --outFilterMismatchNmax 2"
Uniquely mapped reads were counted over annotated genes using featureCounts with the options "-T 18 -s2 -Q 255"
Differential expression testing was conducted with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene level counts for all samples from featureCounts is in tsv format.

source_name: BMDM

growth_protocol: Murine bone marrow derived macrophages cultered with recombinant GM-CSF over 8 days

extract_protocol:
RNA was isolated using Qiagen RNeasy Mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Macrophages pretreated with vehicle DMSO or defactinib inhibitor (3.5uM) for 1h, followed by LPS (100ng/ml) for a further 2hrs

value: WT

tag: treatment

value: DMSO

tag: lps stimulation


title: AR2923_16_ScaleSig

tag: tissue

tag: age


title: HCC827 CTL (NFs) 3


title: AR2923_15_ScaleSig


title: Tibialis anterior LLC_1

description: LLC cancer replicate 1


title: HCC827 CTL (NFs) 1


title: Patient 23 NPH 0023

value: female


title: BMDM_WT_DMSO_0hr_R3 mRNA-seq

description: featureCounts.txt


title: Tibialis anterior Control_LLC_3

description: Control for LLC cancer replicate 3


title: Patient 22 NPH 0022


title: [UNIQUE BARCODE]-2

city: Salt Lake City

first: Gabor

middle: T

last: Marth

state: UT

department: Human Genetics

institute: University of Utah

data_processing:
Raw reads were processed using the 10X cellranger pipepline (v3.0.2)
Seurat (v3.0) was used to remove low quality cells and to normalize expression
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sequenced cell

source_name: Chronic Lymphocytic Leukemia

extract_protocol:
peripheral blood cells
10X scRNAseq (5’ expression)

value: blood

value: B-cell

tag: disease state

value: cancer


title: Patient 14 NPH 0014


title: Patient 20 NPH 0020


title: BMDM_WT_DMSO_0hr_R1 mRNA-seq

description: featureCounts.txt


title: AR2923_14_ScaleSig

value: male


title: TCFs Co-culture 1


title: BMDM_WT_Def_2hr_R3 mRNA-seq

description: featureCounts.txt

value: Def


title: Tibialis anterior Control_LLC_1

description: Control for LLC cancer replicate 1

value: Control


title: BMDM_WT_Def_2hr_R2 mRNA-seq

description: featureCounts.txt


title: AR2923_08_ScaleSig


title: Patient 11 NPH 0011


title: Patient 10 NPH 0010


title: BMDM_WT_DMSO_2hr_R3 mRNA-seq

description: featureCounts.txt


title: TCFs CTL 1

value: Tumor core-derived primary fibroblasts


title: Patient 18 NPH 0018


title: BMDM_IRF5ko_DMSO_2hr_R3 mRNA-seq

description: featureCounts.txt


title: Patient 16 NPH 0016


title: Patient 8 NPH 0008


title: BMDM_WT_DMSO_2hr_R1 mRNA-seq

description: featureCounts.txt


title: [UNIQUE BARCODE]-3


title: BMDM_WT_DMSO_0hr_R2 mRNA-seq

description: featureCounts.txt


title: BMDM_IRF5ko_DMSO_2hr_R1 mRNA-seq

description: featureCounts.txt


title: Patient 15 NPH 0015


title: [UNIQUE BARCODE]-1


title: Patient 13 NPH 0013


title: Patient 6 NPH 0006


title: Patient 12 NPH 0012


title: BMDM_WT_Def_2hr_R1 mRNA-seq

description: featureCounts.txt


title: MeT-5A FedEV High, rep 2

city: Baltimore

first: Fumiya

last: Ito

state: MARYLAND

address: 725 N. Wolfe Street, 119 Hunterian

department: Cell Biology

institute: Johns Hopkins University

description: Cells from FACS sorting

data_processing:
Illumina bcl2fastq.gz2 v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p13 Ensembl release 103 whole genome using Salmon (v1.3.0).
Transcript-level count data was aggregated at the gene-level using tximport (version 1.20.0). Differentially gene expression analysis between FedEVs-high and -low was performed using the DESeq2 package (version 1.32.0) on protein-coding genes.
Genome_build: GRCh38.p13

source_name: mesothelial cell

growth_protocol: 1×10^6 MeT-5A cells were cultured in a 6-well plate with media containing 1% EV-depleted FBS prior to FedEVs loading.

extract_protocol:
MeT-5A cells that have taken up FedEVs [CD63-GFP(+)] were isolated by FACS Melody (~7×105 cells).  Total RNA was isolated, using AurumTM Total RNA Mini Kit (BioRad) according to the manufacture`s protocol.
RNA of 100 ng was used for the preparation of sequencing libraries with NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB) according to the manufacturer’s instructions.

treatment_protocol: After overnight incubation, FedEVs from THP1 cells of 10 cm2 dish were loaded in a total volume of 100 μl in PBS and incubated at 24 h.

value: mesothelium

tag: immortalization

value: SV40 virus transformed

value: treated FedEVs at 24h


title: MeT-5A NT, rep3

value: untreated


title: Patient 9 NPH 0009


title: MeT-5A FedEV Low, rep 3

description: Cells from FACS sorting


title: MeT-5A NT, rep2


title: BMDM_IRF5ko_DMSO_2hr_R2 mRNA-seq

description: featureCounts.txt


title: HBEC-Patient3-Cannabis-Exposed

city: Waterloo

first: Jennifer

middle: A.

last: Aguiar

state: ON

address: 200 University Avenue East

country: Canada

institute: University of Waterloo

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Clariom_S_Human arrays according to ThermoFisher Scientific instructions.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software.

data_processing: Raw intensity values from the Clariom S microarray experiment were imported into the R statistical language environment (version 3.6.1; R Core Team, 2019). Probe definition files were obtained from the Brainarray database (version 24) (Dai et al., 2005). The Single Channel Array Normalization (SCAN) method was used to obtain log2- transformed normalized expression values with the SCAN.UPC R package (version 2.26.0) (Piccolo et al., 2012), with annotation data from the Bioconductor project (version 3.9) (Huber et al., 2015). All statistical tests were performed on Graphpad® Prism 8 version 8.3.0 (Graphpad Headquarters, San Diego, CA). A paired t-test was performed to assess significance between the differences in epithelial barrier function between the control group and experimental group. An ANOVA followed by a Tukey’s post-hoc test was performed to assess differences in cell cytotoxicity following smoke exposure. Differences in cytokine expression were assessed using paired t-tests. P values less than 0.05 were considered statistically significant.

label: Biotin

source_name: Primary human broncial epithelial cell (HBEC) culture exposed to cannabis smoke

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions.

growth_protocol: All studies using human cells were approved by the Hamilton Integrated Research Ethics Board (HiREB Approval: 5305T). Primary HBECs were isolated from a bronchial brushing from consented subjects undergoing routine clinical procedures, and plated into T25 flasks containing Pneumacult™ Ex-Plus Basal Media (StemCell Technologies; Catalog Number 05040) with PneumaCult™ Ex-Plus 50x Supplement, 0.01% hydrocortisone stock solution (StemCell Technologies; Catalog Number 7925) and 1% antibiotic-antimycotic (Thermofisher; Catalog Number 15240062). Once cultures achieved ~80% confluence, cells were passaged at a density of 50,000 - 100,000 cells/insert into polyester Transwell® inserts for exposure experiments. Cells were fed with 200μl and 750μl of Pneumacult™ Ex-Plus Basal Media in the apical and basal compartments, respectively. Once cultures reached 100% confluency, apical media was removed and culture inserts were fed from the basal side to bring cultures to ALI (Day 0 of ALI). Following 24h, culture inserts were fed from the basal compartment with 750μl of PneumaCult™ ALI Basal Medium (StemCell Technologies; Catalog Number 05001) with PneumaCult™-ALI 10x Supplement, PneumaCult™-ALI Maintenance 100x Supplement, 1% antibiotic-antimycotic, 0.5% hydrocortisone stock solution and 0.2% heparin solution (StemCell Technologies; Catalog Number 7980) to support development and differentiation of a pseudostratified epithelial culture (Day 1 of ALI). Transwell® cultures were fed from the basal compartment and a phosphate buffered saline (PBS) wash was performed on the apical compartment every other day.

extract_protocol: Twenty-four hours post-exposure, basal and apical media was collected, spun down at 7500 x g/4oC for 15 minutes. Total RNA was extracted and isolated using an RNeasy Kit (Qiagen, Toronto, Ontario, Canada). Cells in each Transwell® were lysed in 100ul of RLT Isolation Buffer with 1% beta-mercaptoethanol (2Me) (v/v) and stored at -80oC. Subsequently, RNA was purified using the manufacturer’s protocol and quantified via Nanodrop200. cDNA was prepared and underwent transcriptomic analysis using Clariom S Microarray chips (ThermoFisher, Mississauga, Ontario, Canada).

treatment_protocol: Exposure experiments were performed between Day 14 - Day 15 of ALI culture. Tobacco smoke was derived from a Kentucky Research Grade Cigarette (Lot:3R4f) containing ~0.7g of dried tobacco leaves and has been used extensively in in vitro studies. Using research grade tobacco cigarettes as a reference, cannabis cigarettes with ~0.7g of dried cannabis flower (~10% THC, 0% CBD; Purple Sun God, Lot: 00117 (b161)) were manufactured with RAW rolling papers and cardboard filters. Cannabis was purchased from the Ontario Cannabis Store with a Health Canada approved research license. In a biosafety cabinet, 800ul of PneumaCult™ ALI media was added into each individual chamber of the IVES unit. Transwell® inserts were transferred into the IVES and left in the a 37oC, 5% CO2 humidified incubator to equilibrate for 10 minutes prior to exposures. In a fume-hood, exposures were performed with a 50ml syringe connected to the fresh air inlet of the IVES through a PVC Tygon tube (length: 32 cm, lumen diameter: 2 mm) and a 3-way valve. Another 50ml syringe was connected to the smoke exposure inlet on the IVES through PVC Tygon tube (length: 32 cm, lumen diameter: 2 mm) and a 3-way valve. For the experiments with cannabis, a cigarette was placed into another PVC Tygon tube (length: 32 cm, lumen diameter: 8 mm), with the opening sealed with parafilm and connected to the 3-way valve. The dose was administered according to a modified version of the Foltin Puff Procedure (Abdallah et al., 2018; Chait et al., 1988; Foltin et al., 1987; Ramesh et al., 2013; Wilsey et al., 2013, 2016). This procedure, optimized for our model, consisted of 1 puff of smoke separated by 3 puffs of fresh room air to mimic the behavior of human smoking patterns. Each puff of smoke or room air was 35ml in volume and was perfused over the Transwell® insert at a rate of 7 ml/second. Between each puff, the cells were undisturbed for 10 seconds. Each experimental group received one cigarette smoked to completion using this regimen. Control conditions received as many puffs of room air as the corresponding experimental condition received smoke under the same regimen. Following exposure, inserts were immediately transferred to a new plate with 600ul of PneumaCult™-ALI media in the basal compartment. Plates were then transferred to a 37oC, 5% CO2 humidified incubator.

tag: individual

tag: cell type

value: Primary human bronchial epithelial cells (HBECs)

value: cannabis-exposed


title: MeT-5A NT, rep1


title: MeT-5A FedEV High, rep 3

description: Cells from FACS sorting


title: AR2923_13_ScaleSig

value: testis

tag: Sex

value: 6 weeks

value: C offspring


title: BMDM_IRF5ko_DMSO_0hr_R3 mRNA-seq

description: featureCounts.txt

tag: genotype

value: DMSO


title: AR2923_10_ScaleSig

value: R offspring


title: AR2923_07_ScaleSig


title: AR2923_03_ScaleSig


title: HBEC-Patient8-Cannabis-Exposed


title: Patient 5 NPH 0005

data_processing: Mean and standard deviation (SD) were calculated using a set of pre-selected negative control signals (background signals) that the top and bottom 5% of which were removed. Signal values greater than mean + 2SD of the background signals were replaced using log2(signal – mean) and labeled effective signals. The remaining signal values were replaced by the minimum of the effective signals – 0.1. Undetected signal values were replaced by the average signal of each miRNA signals. To normalize the signals across different microarrays, a set of pre-selected internal control miRNAs (miR-149-3p, miR-2861 and miR-4463), which had been stably detected in more than 500 serum samples, was used. Each miRNA signal value was standardized with the ratio of the average signal of the three internal control miRNA signals30.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: serum

tag: diagnosis

value: NPH

value: female


title: HBEC-Patient21-Cannabis-Exposed


title: Patient 7 NPH 0007


title: HBEC-Patient8-Air-Exposed

source_name: Primary human broncial epithelial cell (HBEC) culture exposed to air

value: air-exposed


title: BMDM_IRF5ko_DMSO_0hr_R2 mRNA-seq

description: featureCounts.txt


title: HBEC-Patient21-Air-Exposed


title: HBEC-Patient3-Air-Exposed


title: Patient 4 NPH 0004

source_name: serum


title: BMDM_IRF5ko_DMSO_0hr_R1 mRNA-seq

description: featureCounts.txt


title: MeT-5A FedEV High, rep 1

description: Cells from FACS sorting


title: MeT-5A FedEV Low, rep 2

description: Cells from FACS sorting


title: Patient 2 NPH 0002

value: male


title: BMDM_IRF5ko_Def_2hr_R3 mRNA-seq

description: featureCounts.txt

value: Def


title: Patient 3 NPH 0003


title: BS168-Q150W-3

status: Public on Oct 21 2021

city: Wuhan

first: Zhuoran

last: Jiang

state: Hubei

address: Bayi Road

department: College of Chemistry and Molecular Sciences

institute: Wuhan University

data_processing:
Quality Control:   In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or   fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by   Cutadapt[1]（version 1.9.1）
Mapping:   Firstly, reference genome sequences and gene model annotation files of relative species were downloaded   from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Bowtie2 (v2.2.6) was used to index   reference genome sequence. Finally, clean data were aligned to reference genome via software Bowtie2   (v2.2.6).
Expression analysis   In the beginning transcripts in fasta format are converted from known gff annotation file and indexed   properly. Then, with the file as a reference gene file, HTSeq (v0.6.1p1) estimated gene expression levels   from the pair-end clean data.
Differential expression analysis   Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative   binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false   discovery rate, Padj of genes were setted <0.05 to detect differential expressed ones.
GO enrichment analysis   GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes   with a significant p-value less than 0.05. And topGO was used to plot DAG.          Novel transcripts prediction   Rockhopper uses a Bayesian approach to create a transcriptome map including transcription start/stop   sites for protein coding genes and novel transcripts identified by Rockhopper.          SNV analysis   Samtools v0.1.19 with command mpileup and Bcftools v0.1.19+ were used to do SNV calling.          Gene structure analysis   Rockhopper(2.0.3) was employed for predict operon, transcription start sites(TSS) and transcription stop   sites(TTS).          SD sequence prediction   RBSfinder(v1.0) was used to SD sequence prediction.          Rho-independent terminator prediction   TransTermHP(v2.09) can accurately detect Rho-independent transcription terminators.          sRNA analysis   Blast intergenic novel transcripts to NR database, non-annotated transcripts are consider as potential   trans-encoded sRNAs. Novel antisense transcript was treat as cis-encoded sRNA. The secondary   structures of the sRNA were predicted using RNAfold(2.3.2)
Genome_build: NC_000964.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: Triplicate samples of single clone of modified B. subtilis 168 and unmodified B. subtilis 168 were grown at 37 °C in antibiotic-free LB medium. Then the cell cultures were diluted to OD600 ~ 0.02 in a total volume of 15 mL with fresh LB medium, and harvested by centrifugation until the OD600 reach ~0.8 (early exponential stage, EES).

extract_protocol:
The cell pellets were resuspended by 1 mL RNAlater (ThermoFisher Scientific, USA, LOT. AM7020) and flash frozen by liquid nitrogen, and stored at −80 °C until use.
Upon RNA extraction, the RNAlater were removed by centrifugation and the cell pellet were dissolved in 0.2 mL buffer lysis (30 mM Tris pH 6.2, 10 mM EDTA, 0.1 mg/mL lysozyme, DEPC-treated water), then incubation at 37 °C for 30 min. Subsequently, 1 mL TRIzol reagent (ThermoFisher Scientiﬁc Inc., USA) was added and mixed well, following mixed with 0.2 mL chloroform. The mixture was centrifuged at 15000 ×g for 15 min at 4 °C, and the aqueous phase was transferred to a different RNase-free tube. Then 0.3 mL of saline solution (0.6 M NaCl, 0.4 M sodium citrate), and 1 mL of isopropyl ethanol were added, and the mixture was stored at −20 °C for 2 h. After the mixture was centrifuged at 15000 × g for 20 min at 4 °C, the pellet containing the total-RNA was washed twice with 1 mL of 70% (v/v) ice-cold ethanol. Finally, the RNA pellet was air dried and dissolved with 200 µL of RNase-free water. The concentration and quality of RNA was analysed by NanoDrop 2000 ONEc (thermofisher scientific, USA).

treatment_protocol: The cell pellets were resuspended by 1 mL RNAlater (ThermoFisher Scientific, USA, LOT. AM7020) and flash frozen by liquid nitrogen.

tag: genotype/variation

tag: growth medium

value: LB


title: BMDM_IRF5ko_Def_2hr_R2 mRNA-seq

description: featureCounts.txt


title: BS168-Q150W-2

tag: strain


title: HBEC-Patient4-Cannabis-Exposed


title: BS168-Q150W-1


title: BS168-F91L-3


title: BS168-yerA-KO-3


title: BMDM_IRF5ko_Def_2hr_R1 mRNA-seq

description: featureCounts.txt


title: BS168-F91L-1


title: BS168-WT-2

value: wild type


title: BS168-yerA-KO-2


title: Patient 1 NPH 0001


title: HBEC-Patient16-Cannabis-Exposed


title: HBEC-Patient4-Air-Exposed


title: BS168-yerA-KO-1


title: HBEC-Patient16-Air-Exposed


title: BS168-F91L-2


title: MeT-5A FedEV Low, rep 1

description: Cells from FACS sorting

value: mesothelium

value: SV40 virus transformed

value: treated FedEVs at 24h


title: BS168-WT-3


title: BS168-WT-1


title: Lung_Influenza virus infection_DW_5 day post inoculation__rep03

city: Yoshiwara, Amimachi, Inachiki-gun

first: Akinori

last: Nishi

state: Ibaraki

department: Tsumura Kampo Research Laboratories

institute: Tsumura & Co.

hyb_protocol: The cRNA was hybridized to the microarray. Agilent’s standard protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v. 6.9, December 2015) was referenced for sample preparation and array processing.

scan_protocol: The cRNA hybridized to the microarray were scanned with a DNA microarray Scanner (Agilent). Agilent’s standard protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v. 6.9, December 2015) was referenced for sample preparation and array processing.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Agilent’s standard protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v. 6.9, December 2015) was referenced for sample preparation and array processing. I normalized the data by percentile shift algorithm using GeneSpringGX.

label_protocol: Using the cDNA as template, cRNA labeled by Cy3 was synthesized. Agilent’s standard protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, v. 6.9, December 2015) was referenced for sample preparation and array processing.

extract_protocol: Ten mice from each of the three mouse groups were used to collect lung tissue  at 5 day post inoculation (dpi). In the result, the number of surviving mice in each group was 10/10(NI), 4/10 (IVI) and 9/10 (IVI+MT) at 5 dpi, and the lung tissue sample from these mice were used for transcriptome analysis.

treatment_protocol: Influenza virus (1x10^5　PFU/0.05 mL/mouse) was administered by intranasal inoculation. Maoto (2 g/10mL/kg) was orally administered for 5 days starting 1 hour after inoculation. Mice with no inoculation were used as control mice against the infection, and infected mice that were treated distilled water were used as infected control mice. In total, there were three groups of mice: 1) no-inoculation (NI) group; 2) influenza virus inoculation (IVI) control group;  3) IVI with MT 2 g/10mL/kg treatment (IVI+MT) group.

value: lung

tag: agent

value: Influenza virus + distilled water

value: BALB/c Cr Slc


title: Lung_Influenza virus infection_DW_5 day post inoculation__rep02


title: Lung_No infection_5 day post inoculation__rep06


title: Lung_No infection_5 day post inoculation__rep09


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep01

value: Influenza virus + Maoto


title: Lung_No infection_5 day post inoculation__rep02


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep07


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep02


title: Lung_Influenza virus infection_DW_5 day post inoculation__rep04


title: Lung_No infection_5 day post inoculation__rep03


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep06


title: Rumen_AD_3

city: Hangzhou

first: Jiajin

last: Wu

state: Zhejiang

address: Yuhangtang road

institute: Zhejiang University

data_processing:
Sequences from NovaSeq 6000 system were  de-multiplexed and aligned using CellRanger version 3.1.0, available from 10x Genomics with default parameters.
Genome_build: Bos_taurus ensemblV99
Supplementary_files_format_and_content: Tab-delimited text files include barcodes, gene and count matrix for each Sample

organism: Bos taurus

source_name: Rumen

extract_protocol:
The rumen tissues isolated from dairy cows were stripped of the outer muscle layers, and then minced into 10×0.5mm2 pieces on ice with scissors. The tissues were incubated in a 37℃ water bath with 20 mM EDTA for 30 min, and then were rinsed with DPBS and chopped into 1 mm pieces. Tissue pieces were transferred to a 15 mL centrifuge tube, and re-suspended with 0.25% Trypsin-EDTA (Gibco). After incubated in a 37℃ water bath for 5 min, the centrifuge tube containing tissues was inserted into ice for 2min, and pre-chilled HBSS was added to stop the digestion. After centrifuged at 300 × g for 2 min at 4℃, the supernatant was discarded, and samples were washed twice with cold HBSS and then re-suspended with dissociation enzymes(1.5mg/ml collagenase I, 1.5ml/ml collagenase IV,1.5mg/ml dispase, 100U/ml hyaluronidase, and 50U/ml DNase I) for 30 min at 37℃.
The single-cell RNA-seq library preparation was performed using the Chromium Single Cell 3' Reagent Kits v3.

tag: breed

value: Holstein dairy cows

value: rumen

tag: developmental stage

value: adult


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep09


title: Lung_No infection_5 day post inoculation__rep10


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep03


title: Lung_No infection_5 day post inoculation__rep08


title: Lung_No infection_5 day post inoculation__rep01


title: Lung_No infection_5 day post inoculation__rep07


title: Oxy_rep2

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

data_processing:
The FASTQ file quality was assessed with FastQC v0.11.9 (Babraham Bioinformatics, Cambridge, United Kingdom). After adapter trimming with cutadapt v2.10 (Martin, 2011) reads were mapped on the reference human genome (GENCODE GRCh38.p13) with STAR v2.7.5b (Dobin et al., 2013). The count matrix was generated with GENCODE genome annotation (release 34) (Frankish et al., 2019).
Genome_build: GENCODE GRCh38.p13
Supplementary_files_format_and_content: Read counts matrix

growth_protocol: Caco-2 cells were received from the Russian Vertebrate Cell Culture Collection (Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia). The cells were incubated in Gibco minimal essential medium with L-glutamine, 20% Gibco FBS One Shot, and 1% Gibco Pen Strep (Thermo Fisher Scientific, USA). The cells were seeded in the 6-well culture plates (TPP Techno Plastic Products AG, Germany) at a seeding density of 0.3 x 106 cells per well.

extract_protocol:
Cells were lysed in 700 μL of QIAzol Lysis Reagent (Qiagen, Hilden, Germany) with subsequent RNA extraction with miRNeasy Mini Kit (Qiagen) according to the manufacturer protocol, including on-column treatment with RNase-Free DNase Set (Qiagen). RNA was extracted in 30 μL of RNase-free water. RNA concentration was measured with NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific). A260/A280 and A260/A230 ratios were more than 2.0, and RNA Integrity Number (RIN) according to 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA) was not less than 9.7 for all RNA samples.
Libraries for mRNA sequencing were prepared with TruSeq Stranded mRNA Library Prep (Illumina, San Diego, CA, United States). Library quality check was provided with Agilent High Sensitivity DNA Kit (Agilent Technologies). Sequencing with NextSeq 550 (Illumina) generated single-end 75-nucleotide reads.

treatment_protocol: The cell culture medium of undifferentiated Caco-2 was replaced with either medium with 300 μM CoCl2, medium with 5 μM oxyquinoline derivative (OD) 4896-3212 (ChemDiv Research Institute, Khimki, Russia), or fresh medium. OD stock solution was diluted in DMSO at 10 mM, so 0.5% DMSO was also added to CoCl2 and control medium, and cells were incubated 24 h before lysis for RNA and protein extraction.

tag: cell line

tag: treatment

value: oxyquinoline


title: Lung_Influenza virus infection_DW_5 day post inoculation__rep01

tag: tissue

value: female


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep04


title: Lung_No infection_5 day post inoculation__rep04


title: Lung_No infection_5 day post inoculation__rep05


title: CoCl2_rep2

value: Cobalt (II) chloride


title: Rumen_AD_1


title: Oxy_rep3


title: Control_rep3

value: control


title: Control_rep2


title: Control_rep1


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep05


title: Lung_Influenza virus infection_Maoto_5 day post inoculation__rep08


title: PBMC_ASAP_Phage_compare_B_ATAC

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
Fastqs were generated using CellRanger-ATAC mkfastq v1.1.0
Sequencing reads were aligned using CellRanger-ATAC count for the hg38 reference genome
For Phage libraries, phage tag abundances were quantified per barcode using a custom unix script.
For ASAP libraries, tag abundances were quantified per barcode using a custom unix script
Genome_build: hg38
Supplementary_files_format_and_content: Per-barcode count abundance for phage library including the ATAC singlecell QC metrics; accessible chromatin fragments per atac library

source_name: Peripherial Blood Mononucler Cells

growth_protocol: Cryopreserved cells were thawed in DMEM with 10% FBS and washed in media

extract_protocol:
NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq

value: Peripherial Blood Mononucler Cells

tag: antigen capture


title: PBMC_ASAP_Phage_compare_A_ADT

value: TBNK - Biolegend TotalSeqA


title: CoCl2_rep3


title: CoCl2_rep1