title: 140

city: Copenhagen

first: tik

last: muk

state: copenhagen

address: Dyrlægevej 68,1870 Frederiksberg C, Dyrlægevej 68, 1870 Frederiksberg C

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using HISAT2
The annotated gene information of porcine genome was downloaded from Ensembl (release 99).
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Assembly: Sscrofa11.1
Supplementary files format and content: Raw counts of sequencing reads for each gene (Ensembl gene IDs) generated from htseq-count.

organism: Sus scrofa

source_name: whole blood

extract_protocol:
Total RNA was isolated with RNeasy Lipid Tissue Mini Kit  (Qiagen).
RNA libraries were prepared by Novogene Europe (Cambridge, UK) and sequenced on the Illumina NovaSeq platform with paired-end 150-bp reads production.

value: whole blood

value: CON-Std


title: Ripk3-KO-LSK-1

status: Public on Jun 29 2022

type: SRA

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the mm9 genome assembly using Tophat
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples.

molecule: total RNA

organism: Mus musculus

source_name: Lin- Sca1+ Kit+ Ripk3-/- Bone marrow cells

growth_protocol: Total bone marrow cells were isolate from WT and Ripk3-KO mice, and sorted with Lin-, Sca1+ and Kit+ markers.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LSK and LK cells from transgenic mice without any treatment

tag: strain background

tag: genotype/variation

tag: tissue

value: Bone marrow

tag: cell type


title: 139

tag: treatment

value: CON-High


title: Ripk3-KO-LSK-2

value: Lin- Sca1+ Kit+ Ripk3-/- Bone marrow cells


title: 137

value: SE-Std


title: 138


title: 142


title: 128


title: 130

value: SE-High


title: 126


title: 134


title: 125


title: 129


title: 136


title: 135


title: 133


title: 132


title: 131


title: 127


title: 124


title: 118


title: 122


title: 141


title: 114


title: 111


title: 123


title: 121


title: 116


title: 106


title: 117


title: 112


title: 113


title: 103


title: 108


title: 102


title: 115


title: 101


title: 105


title: 100


title: IAIPSliver38

source_name: Liver

value: Liver


title: 104


title: IAIPSliver39


title: 120


title: 107


title: IAIPSliver35


title: IAIPSliver36


title: IAIPSliver37


title: IAIPSliver32


title: IAIPSliver34


title: 110


title: IAIPSliver29


title: IAIPSliver31


title: IAIPSliver24


title: IAIPSliver26


title: IAIPSliver22


title: IAIPSliver25


title: IAIPSliver23


title: IAIPSliver16


title: 119


title: IAIPSliver12


title: IAIPSliver21


title: IAIPSliver18


title: IAIPSliver14


title: IAIPSliver10


title: IAIPSliver11


title: IAIPSliver3


title: IAIPSliver4


title: IAIPSliver5


title: IAIPSliver17


title: IAIPSliver1


title: IAIPSliver8


title: IAIPSliver13


title: IAIPSliver27


title: IAIPSliver15


title: IAIPSliver30


title: InpigL-DCA

value: DCA


title: InpigH-CON

value: Control


title: InpigH-DCA


title: IAIPSliver6


title: 109


title: InpigL-S2

value: SE


title: IAIPSliver2


title: IAIPSliver20


title: IAIPSliver19


title: InpigB-CON


title: InpigB-S2


title: InpigL-CON


title: InpigH-S2


title: InpigH-S2DCA

value: SE+DCA


title: IAIPSliver9


title: InpigE-S2


title: InpigL-S2DCA


title: InpigE-S2DCA


title: FFL_plus_EV3

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

country: USA

institute: Colorado State University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
Sequence reads were mapped to Sus scrofa reference genome (release Sscrofa11.1) using Bowtie2 (2.2.2)
Mapped reads were used for annotation against both mature and precursor miRNAs of porcine and all other organism listed in the mirBase database (release 22)
Raw expression data were normalized using the trimmed mean of M-values normalization method (TMM normalization)
The differential expression analysis was done using the DESeq2 statistical software package
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: xlsx file include CPM values for each sample

source_name: Follicular fluid extracellular vesicles

extract_protocol:
EVs were isolated from FF groups (3 biological replicates/group; 0.5 mL FF/replicate) using the Exo-spin kit. Total RNA was isolated from EV samples using Trizol and miRNeasy Micro Kit.
Small-RNA libraries were prepared using QIAseq miRNA Library Kit

tag: follicle size

tag: coressponding oocyte quality

value: Low


title: InpigE-DCA


title: InpigE-CON


title: FFL_minus_EV2

value: High


title: FFL_plus_EV2


title: IAIPSliver7


title: FFL_minus_EV3


title: FFL_minus_EV1


title: FFL_plus_EV1


title: InpigB-S2DCA


title: InpigB-DCA


title: WT HEK293

city: Beijing

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

description: RNA Immunoprecipitation and high-throughput sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie v2.2.4 for read alignment.
Cuﬄinks v2.2.1 for read quantification
Genome_build: human: GRCh38/hg38
Genome_build: Human herpesvirus 1 strain 17: NC_001806
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism:
Homo sapiens
Human alphaherpesvirus 1

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HSV-1 infection for 8h

tag: cell line

value: embryonic kidney

tag: antibody

value: Anti-Hnrnpu antibody,Cat# sc-32315, RRID:AB_627741; Santa Cruz


title: HA-DCS 140

type: RNA

city: New York

first: Limary

last: Cancel

state: NY

address: 160 Convent Ave

department: Biomedical Engineering

institute: The City College of New York

description:
HA-DCS
test

data_processing:
Raw Ct values were obtained from the Applied Biosystems 7300 Real Time PCR System as .csv files and data was processed in Excel.
Matrix non-normalized reports the average Ct value of duplicate samples.
Target signal normalized against the average of two housekeeping genes: GAPDH and ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Fold Change worksheet reports test/control ratios. For each experiment, test samples were normalized to the corresponding control (conS) sample.

label: SYBR Green

organism: Homo sapiens

source_name: Human astrocytes from healthy normal brain; Cell Applications, Inc.

label_protocol: Total RNA was reversed transcribed using the High-capacity cDNA Reverse Transcription kit from Thermo Scientific. Real time RT-qPCR was performed on the 7300 Real Time PCR System from Applied Biosystems with 45 cycles at 95 oC for 20 seconds, 60 oC for 30 seconds, and 72 oC for 30 seconds.

growth_protocol: Human Astrocytes were grown according to the manufacturer's instructions and plated at 3x104 cells/cm2 in Transwell filters coated with fibronectin and cultured for 5-6 days before DCS experiments.

extract_protocol: Total RNA was collected either immediately after DCS, or 1 hour after DCS using the RNeasy Mini kit from Qiagen.

treatment_protocol: Each experiment consisted of four groups: conP, DCS P, conS, and DCS S. Direct Current Stimulation was applied with (DCS P) or without (DCS S) a pressure differential that induced convective fluid flow across the cell monolayer. Monolayers exposed only to convective flow (conP) were also examined. A static control (conS) kept in an incubator for the duration of the experiment was used as the calibrator sample for gene expression analysis.

tag: treatment group

value: DCS S

tag: dcs current (ma)

tag: rna collection time


title: HA-DCS 136

description:
HA-DCS
test


title: HA-convective flow and DCS 138

description:
HA-convective flow and DCS
test

value: DCS P


title: HA-no flow (static) control 135

description:
HA-no flow (static) control
control

value: conS


title: HA-convective flow and DCS 134

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 139

description:
HA-no flow (static) control
control


title: HA-convective flow control 137

description:
HA-convective flow control
test

value: conP


title: HA-convective flow control 133

description:
HA-convective flow control
test


title: HA-convective flow and DCS 130

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 127

description:
HA-no flow (static) control
control


title: HA-DCS 128

description:
HA-DCS
test


title: HA-DCS 132

description:
HA-DCS
test


title: HA-convective flow control 129

description:
HA-convective flow control
test


title: M025_BLD_IIV_1D

city: Los Angeles

first: Pia

middle: S

last: Pannaraj

state: California

address: 4650 Sunset Blvd, MS#51

department: Infectious Diseases

institute: Children's Hospital of Los Angeles

description: Whole blood RNA 1 day after IIV vaccination

hyb_protocol: Samples were hybridized to Human Exon 1.0 ST arrays (Thermo Fisher) using reagents from the GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher) and following vendor protocols.  Arrays were hybridized for 20 hours at 45° at 60rpm and washed on the GeneChip Fluidics Station 450 using protocol FS450_0001.

scan_protocol: Arrays were scanned using Thermo Fisher’s GeneChip Scanner 3000 7G driven by the GeneChip Operating Software (v. 1.1.1) and the Command Console Software (AGCC, v. 4.0).

data_processing:
Signal intensities for the probe selection regions (PSR) were quantile normalized by robust multichip averaging using affy R package (v. 3.14).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: Biotin

source_name: whole blood, IIV vaccine, 1D

label_protocol: Amplified cDNA was generated using the Ovation FFPE WTA System (NuGen Technologies).  Chemical and enzymatic fragmentation of amplified cDNA was followed by biotin labelling using the Encore Biotin Module (NuGen Technologies).

extract_protocol: RNA was extracted from whole blood and milk samples using Maxwell Simply RNA purification kit (Promega). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: fluid

tag: specimen

value: BLD

tag: timepoint

tag: run

tag: vaccine

value: IIV

tag: flu season


title: M026_BLD_LAIV_7D

description: Whole blood RNA 7 days after LAIV vaccination

source_name: whole blood, LAIV vaccine, 7D

value: LAIV


title: M025_BLD_IIV_7D

description: Whole blood RNA 7 days after IIV vaccination

source_name: whole blood, IIV vaccine, 7D


title: M027_BLD_LAIV_7D


title: M019_BLD_IIV_7D


title: M026_BMK_LAIV_7D

description: Breast milk RNA 7 days after LAIV vaccination

source_name: breast milk, LAIV vaccine, 7D

value: BMK


title: HA-no flow (static) control 131

description:
HA-no flow (static) control
control


title: HA-convective flow and DCS 126

description:
HA-convective flow and DCS
test


title: M027_BMK_LAIV_7D


title: M027_BLD_LAIV_1D

description: Whole blood RNA 1 day after LAIV vaccination

source_name: whole blood, LAIV vaccine, 1D


title: M019_BLD_IIV_1D


title: M019_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

source_name: whole blood, IIV vaccine, 0D


title: HA-convective flow control 125

description:
HA-convective flow control
test


title: M025_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: HA-DCS 124

description:
HA-DCS
test


title: M027_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination

source_name: whole blood, LAIV vaccine, 0D


title: M026_BLD_LAIV_1D


title: HA-convective flow and DCS 122

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 123

description:
HA-no flow (static) control
control


title: HA-DCS 120

description:
HA-DCS
test


title: M022_BLD_IIV_7D


title: M026_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M022_BLD_IIV_1D


title: HA-convective flow control 121

description:
HA-convective flow control
test


title: HA-no flow (static) control 119

description:
HA-no flow (static) control
control


title: M022_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: HA-convective flow and DCS 118

description:
HA-convective flow and DCS
test


title: HA-DCS 116

description:
HA-DCS
test


title: M020_BLD_LAIV_7D


title: HA-convective flow and DCS 114

description:
HA-convective flow and DCS
test


title: M020_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: HA-convective flow control 113

description:
HA-convective flow control
test


title: HA-convective flow control 117

description:
HA-convective flow control
test


title: HA-no flow (static) control 111

description:
HA-no flow (static) control
control

value: immediate


title: HA-convective flow and DCS 110

description:
HA-convective flow and DCS
test


title: M015_BLD_IIV_7D


title: HA-convective flow control 109

description:
HA-convective flow control
test


title: M018_BLD_LAIV_1D


title: HA-no flow (static) control 115

description:
HA-no flow (static) control
control


title: M018_BLD_LAIV_7D


title: HA-DCS 112

description:
HA-DCS
test


title: M020_BLD_LAIV_1D


title: M026_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

source_name: breast milk, LAIV vaccine, 0D


title: M015_BLD_IIV_1D


title: M026_BMK_LAIV_1D

description: Breast milk RNA 1 day after LAIV vaccination

source_name: breast milk, LAIV vaccine, 1D


title: HA-DCS 108

description:
HA-DCS
test


title: M018_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: HA-DCS 104

description:
HA-DCS
test


title: M027_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M027_BMK_LAIV_1D


title: HA-no flow (static) control 107

description:
HA-no flow (static) control
control


title: HA-DCS 100

description:
HA-DCS
test


title: M022_BMK_IIV_1D

description: Breast milk RNA 1 day after IIV vaccination

source_name: breast milk, IIV vaccine, 1D


title: M022_BMK_IIV_7D

description: Breast milk RNA 7 days after IIV vaccination

source_name: breast milk, IIV vaccine, 7D


title: M025_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

source_name: breast milk, IIV vaccine, 0D


title: HA-convective flow control 101

description:
HA-convective flow control
test


title: M015_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M025_BMK_IIV_1D


title: M022_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-no flow (static) control 103

description:
HA-no flow (static) control
control


title: M025_BMK_IIV_7D


title: HA-convective flow and DCS 106

description:
HA-convective flow and DCS
test


title: M020_BMK_LAIV_1D


title: M020_BMK_LAIV_7D


title: HA-convective flow and DCS 102

description:
HA-convective flow and DCS
test


title: HA-convective flow control 105

description:
HA-convective flow control
test


title: HA-no flow (static) control 99

description:
HA-no flow (static) control
control


title: HA-convective flow and DCS 94

description:
HA-convective flow and DCS
test


title: HA-convective flow control 93

description:
HA-convective flow control
test


title: HA-convective flow control 97

description:
HA-convective flow control
test


title: M020_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M019_BMK_IIV_7D


title: M018_BMK_LAIV_1D


title: M018_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow and DCS 98

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 95

description:
HA-no flow (static) control
control


title: HA-no flow (static) control 91

description:
HA-no flow (static) control
control


title: M138_BMK_LAIV_1D

tag: usbmk


title: HA-convective flow and DCS 90

description:
HA-convective flow and DCS
test


title: M019_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-DCS 92

description:
HA-DCS
test


title: HA-DCS 96

description:
HA-DCS
test


title: HA-convective flow control 89

description:
HA-convective flow control
test


title: M015_BMK_IIV_1D


title: HA-DCS 88

description:
HA-DCS
test


title: M015_BMK_IIV_7D


title: HA-no flow (static) control 87

description:
HA-no flow (static) control
control


title: HA-convective flow control 85

description:
HA-convective flow control
test


title: M015_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M018_BMK_LAIV_7D


title: M137_BMK_LAIV_1D


title: HA-DCS 84

description:
HA-DCS
test


title: M137_BMK_LAIV_7D


title: HA-convective flow control 81

description:
HA-convective flow control
test


title: M138_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow and DCS 86

description:
HA-convective flow and DCS
test


title: HA-convective flow and DCS 82

description:
HA-convective flow and DCS
test


title: HA-convective flow control 77

description:
HA-convective flow control
test


title: HA-convective flow and DCS 78

description:
HA-convective flow and DCS
test


title: HA-DCS 80

description:
HA-DCS
test


title: M128_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-no flow (static) control 75

description:
HA-no flow (static) control
control


title: HA-DCS 76

description:
HA-DCS
test


title: M128_BMK_LAIV_7D


title: M135_BMK_LAIV_1D


title: M135_BMK_LAIV_7D


title: HA-convective flow control 73

description:
HA-convective flow control
test


title: M126_BMK_IIV_1D


title: HA-convective flow and DCS 74

description:
HA-convective flow and DCS
test


title: M135_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M126_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M137_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M126_BMK_IIV_7D


title: HA-no flow (static) control 71

description:
HA-no flow (static) control
control


title: M138_BMK_LAIV_7D


title: HA-no flow (static) control 79

description:
HA-no flow (static) control
control


title: HA-DCS 72

description:
HA-DCS
test


title: M124_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M128_BMK_LAIV_1D


title: M118_BMK_LAIV_7D


title: M124_BMK_IIV_1D


title: M124_BMK_IIV_7D


title: HA-convective flow and DCS 66

description:
HA-convective flow and DCS
test


title: HA-convective flow and DCS 70

description:
HA-convective flow and DCS
test


title: HA-DCS 64

description:
HA-DCS
test


title: M113_BMK_LAIV_7D


title: HA-DCS 68

description:
HA-DCS
test


title: M102_BMK_LAIV_7D


title: M113_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M102_BMK_LAIV_1D


title: M113_BMK_LAIV_1D


title: HA-convective flow control 69

description:
HA-convective flow control
test


title: HA-no flow (static) control 63

description:
HA-no flow (static) control
control


title: HA-no flow (static) control 67

description:
HA-no flow (static) control
control


title: HA-convective flow control 65

description:
HA-convective flow control
test


title: HA-convective flow control 57

description:
HA-convective flow control
test


title: HA-no flow (static) control 59

description:
HA-no flow (static) control
control


title: M118_BMK_LAIV_1D


title: HA-convective flow control 61

description:
HA-convective flow control
test


title: HA-DCS 60

description:
HA-DCS
test


title: M118_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M089_BMK_LAIV_1D


title: M089_BMK_LAIV_7D


title: M102_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M087_BMK_LAIV_7D


title: M087_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow and DCS 58

description:
HA-convective flow and DCS
test


title: M089_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-DCS 56

description:
HA-DCS
test


title: M087_BMK_LAIV_1D


title: HA-convective flow and DCS 62

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 55

description:
HA-no flow (static) control
control


title: M077_BMK_IIV_7D


title: M077_BMK_IIV_1D


title: HA-DCS 52

description:
HA-DCS
test


title: HA-convective flow control 53

description:
HA-convective flow control
test


title: M077_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M077_BLD_IIV_1D


title: M019_BMK_IIV_1D


title: HA-no flow (static) control 51

description:
HA-no flow (static) control
control


title: HA-convective flow and DCS 54

description:
HA-convective flow and DCS
test


title: HA-convective flow control 49

description:
HA-convective flow control
test


title: HA-convective flow and DCS 50

description:
HA-convective flow and DCS
test


title: M077_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: HA-DCS 48

description:
HA-DCS
test


title: HA-no flow (static) control 83

description:
HA-no flow (static) control
control


title: HA-no flow (static) control 47

description:
HA-no flow (static) control
control


title: HA-DCS 44

description:
HA-DCS
test


title: HA-convective flow control 45

description:
HA-convective flow control
test


title: M073_BMK_IIV_7D


title: M073_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-no flow (static) control 43

description:
HA-no flow (static) control
control


title: M077_BLD_IIV_7D


title: HA-convective flow control 41

description:
HA-convective flow control
test


title: HA-convective flow and DCS 42

description:
HA-convective flow and DCS
test


title: HA-DCS 40

description:
HA-DCS
test


title: HA-convective flow and DCS 46

description:
HA-convective flow and DCS
test


title: M073_BLD_IIV_7D


title: M073_BMK_IIV_1D


title: HA-convective flow control 37

description:
HA-convective flow control
test


title: M098_BMK_IIV_7D


title: HA-convective flow and DCS 38

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 39

description:
HA-no flow (static) control
control


title: HA-no flow (static) control 35

description:
HA-no flow (static) control
control


title: M073_BLD_IIV_1D


title: HA-DCS 36

description:
HA-DCS
test


title: M073_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M098_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-convective flow and DCS 34

description:
HA-convective flow and DCS
test


title: HA-convective flow control 33

description:
HA-convective flow control
test


title: M098_BMK_IIV_1D


title: M094_BMK_LAIV_7D


title: M094_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M094_BMK_LAIV_1D


title: M093_BMK_LAIV_7D


title: M093_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M085_BMK_LAIV_7D


title: M093_BMK_LAIV_1D


title: M085_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-DCS 32

description:
HA-DCS
test


title: HA-no flow (static) control 31

description:
HA-no flow (static) control
control


title: M085_BMK_LAIV_1D


title: HA-convective flow and DCS 30

description:
HA-convective flow and DCS
test


title: HA-convective flow control 29

description:
HA-convective flow control
test


title: HA-DCS 28

description:
HA-DCS
test


title: HA-no flow (static) control 27

description:
HA-no flow (static) control
control


title: HA-convective flow and DCS 26

description:
HA-convective flow and DCS
test


title: M083_BMK_LAIV_1D


title: M080_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M080_BMK_IIV_7D


title: HA-DCS 24

description:
HA-DCS
test


title: M072_BMK_IIV_7D


title: M083_BMK_LAIV_7D


title: HA-convective flow control 21

description:
HA-convective flow control
test


title: HA-no flow (static) control 23

description:
HA-no flow (static) control
control


title: M072_BMK_IIV_1D


title: M070_BMK_LAIV_7D


title: M070_BMK_LAIV_1D


title: M080_BMK_IIV_1D


title: HA-convective flow and DCS 18

description:
HA-convective flow and DCS
test


title: HA-DCS 20

description:
HA-DCS
test


title: HA-no flow (static) control 19

description:
HA-no flow (static) control
control


title: M070_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow control 25

description:
HA-convective flow control
test


title: M068_BMK_LAIV_7D


title: M068_BMK_LAIV_1D


title: HA-convective flow control 17

description:
HA-convective flow control
test


title: HA-no flow (static) control 15

description:
HA-no flow (static) control
control


title: HA-DCS 16

description:
HA-DCS
test


title: M072_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M067_BMK_LAIV_7D


title: M068_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow control 13

description:
HA-convective flow control
test


title: M065_BMK_LAIV_7D


title: HA-DCS 12

description:
HA-DCS
test


title: M067_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M065_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: HA-convective flow and DCS 14

description:
HA-convective flow and DCS
test


title: HA-convective flow and DCS 22

description:
HA-convective flow and DCS
test


title: HA-convective flow and DCS 10

description:
HA-convective flow and DCS
test


title: HA-no flow (static) control 11

description:
HA-no flow (static) control
control


title: M063_BMK_LAIV_7D


title: M065_BMK_LAIV_1D


title: M067_BMK_LAIV_1D


title: HA-convective flow control 9

description:
HA-convective flow control
test


title: HA-DCS 8

description:
HA-DCS
test


title: M063_BMK_LAIV_1D


title: HA-DCS 4

description:
HA-DCS
test


title: HA-no flow (static) control 3

description:
HA-no flow (static) control
control


title: HA-convective flow control 5

description:
HA-convective flow control
test


title: HA-convective flow and DCS 6

description:
HA-convective flow and DCS
test


title: M063_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M061_BMK_IIV_7D


title: M061_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-no flow (static) control 7

description:
HA-no flow (static) control
control


title: HA-convective flow control 1

description:
HA-convective flow control
test


title: M060_BMK_IIV_1D


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 120hpi, 1

city: Nanjing

first: Yujie

last: Wang

state: Jiangsu

address: No. 1, Weigang, Xuanwu District

institute: Nanjing Agricultural University

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 120hpi_1

data_processing:
For RNA-seq analysis, all of the raw reads were filtered by Fastp (version 0.18.0) software to remove adapters and low quality reads (quality score≤20).
Clean reads were aligned to the Fg reference genome using Hisat2 (v1.3.3).
Expression levels for each sample were quantified to FPKM (fragment per kilobase of transcript per million mapped reads) using Stringtie (v1.2.0).
Genes displaying log2 [fold change] ≥ 1.5 and an adjusted (false discovery rate) p value < 0.05 were classified as differentially expressed genes (DEGs) by using DESeq2 package.
Genome build: ASM24013v3 (reference genome of F. graminearum strain PH-1)
FPKMs, counts

organism: Fusarium graminearum PH-1

source_name: Mycelium

extract_protocol:
total RNA extraction using TRIZOL reagent following the manufacturer’s instructions.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT)  beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic  Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short  fragments using fragmentation buffer and reverse transcripted into cDNA with random  primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and  buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,  Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters.

tag: tissue

value: Mycelium

tag: genotype

value: WT

tag: infection

value: YES

value: 120 hour post-inoculation


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi, 3

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 48hpi_3

tag: treatment

value: 48 hour post-inoculation


title: M060_BMK_IIV_7D


title: M061_BMK_IIV_1D


title: M059_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M060_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: HA-convective flow and DCS 2

description:
HA-convective flow and DCS
test


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 120hpi, 2

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 120hpi_2


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi, 3

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 24hpi_3

value: 24 hour post-inoculation


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi, 2

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 24hpi_2


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi, 3

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 0hpi_3

value: NO

value: F. graminearum mycelia used for inoculation were collected to represent the time point of 0 hpi


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 120hpi, 3

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 120hpi_3


title: M131_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi, 2

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 48hpi_2


title: M083_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M059_BMK_LAIV_1D


title: M059_BMK_LAIV_7D


title: RNA-Seq of Fusarium graminearum PH-1:deletion mutant FgPacC, 1

description:
PH-1vsFgPacC.all.gene.FPKM.txt
FgPacC_1

value: deletion mutant FgPacC

value: Day 2 of fresh mycelium


title: RNA-Seq of Fusarium graminearum PH-1:deletion mutant FgPacC, 2

description:
PH-1vsFgPacC.all.gene.FPKM.txt
FgPacC_2


title: M131_BMK_LAIV_7D


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi, 1

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 0hpi_1


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 0hpi, 2

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 0hpi_2


title: RNA-Seq of Fusarium graminearum PH-1:Wild type PH-1, 2

description:
PH-1vsFgPacC.all.gene.FPKM.txt
PH-1_2


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 24hpi, 1

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 24hpi_1


title: RNA-Seq of Fusarium graminearum PH-1:Wild type PH-1, 1

description:
PH-1vsFgPacC.all.gene.FPKM.txt
PH-1_1


title: RNA-Seq of Fusarium graminearum PH-1:PH-1 at 48hpi, 1

description:
PH-1.0vs24vs48vs120hpi.all.genes.FPKM.txt
PH-1 at 48hpi_1


title: ChIP-Seq of Fusarium graminearum PH-1:H3K18ac in the PH-1 infection, ip 2

library_source: genomic

data_processing:
For ChIP-seq analysis, 50 bp single-end reads of ChIP-seq were obtained, and quality was controlled using SOAPnuke(v2.1.7). The parameters were as follows: remove reads containing adapters or more than 1% of unknown nucleotides (N); delete the read if there are more than 40% bases having a quality value lower than 20.
Clean reads were mapped to the Fg reference genome by Bowtie2 (version 2.4.5) with default parameters.
The visualization of the average read coverage over 2 kb upstream and downstream of the TSS was performed by Deeptools.
BigWig files generated by Deeptools were used for visualization in Integrative Genome Viewer (version 2.8.9).
RPKM (Reads Per Kilobase per Million mapped reads) were calculated to normalized reads using bamCompare tool in Deeptools (version 2.4.1) with input DNA as a contorl.
Genome build: ASM24013v3 (reference genome of F. graminearum strain PH-1)
BigWig

molecule: genomic DNA

extract_protocol:
fresh mycelia of each sample were cross-linked with 1% formaldehyde for 10 min. Fixation was stopped with 125 mM glycine for 5 min. Subsequently, fixed culture samples were grounded in liquid nitrogen, and re-suspended in 10 ml of nuclear extraction buffer I (0.4 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 5mM β-mercaptoethanol, 0.1 mM PMSF, 1× protease inhibitor). DNA was sheared into 200~500 bp fragments with 30 s on and 6 min off by using a Covaris E220 DNA Sonicator (Covaris, Woburn, MA). After centrifugation, the pellets were suspended in 4 ml of nuclear extraction buffer II (1.7 M sucrose, 10 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol and 1×protease inhibitor). Re-suspended samples were then centrifuged at 13,000 g for 15 min at 4 °C. The resulting pellets were re-suspended in 300 μL of nuclear lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS and 1× protease inhibitor). Samples were then sonicated by two pulses of 30 s sonication and 1 min rest. After centrifugation at 4000 g for 5 min at 4°C, the supernatant was transformed into a clear tube, and was diluted with 10×ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0 and 167 mM NaCl). Immunoprecipitation was conducted using the monoclonal anti-GFP (ab290, Abcam, Cambridge, UK) antibody, anti-H3K18ac (39755, Active Motif Inc., Carlsbad, USA) antibody, or anti-H2BK11ac (ab240613, Abcam, Cambridge, UK) together with the protein A agarose beads (sc-2003, Santa Cruz, CA, USA). The beads were subsequently washed by low salt wash buffer, high salt wash buffer, LiCl wash buffer, and TE buffer. After washing, eluting, reversing the crosslinking, and removing all proteins, the resulting pellets were re-suspended in 50 μL of distilled water.
End repair and adapter ligation:Fill the ends of IP/Input DNA followed by 5' phosphorylation. A 3' sticky-end with an  overhanging A is formed, which could ligate with an overhanging T at the 3' end of the bubble adapter;  PCR amplification: PCR amplify the ligated products with specific primers;  Single-strand separation and circularization: Separate PCR products into single-strands by thermal denaturation.  Then circularize the single-stranded DNA through a bridge primer to obtain single-stranded circular DNA library;  Sequencing: Amplified products DNA Nanoballs (DNBs) are used for sequencing

tag: chip antibody

value: ChIP experiments using 120 hour post-inoculation of  mycelium


title: ChIP-Seq of Fusarium graminearum PH-1:H3K18ac in the PH-1 infection, ip 1

value: anti-H3K18ac (39755, Active Motif Inc., Carlsbad, USA)


title: M131_BLD_LAIV_7D

description: Whole blood RNA 7 days after LAIV vaccination

value: BLD


title: M125_BLD_IIV_1D

description: Whole blood RNA 1 day after IIV vaccination

value: IIV


title: M125_BMK_IIV_7D


title: M131_BLD_LAIV_1D

description: Whole blood RNA 1 day after LAIV vaccination

value: LAIV


title: M125_BLD_IIV_7D

description: Whole blood RNA 7 days after IIV vaccination


title: M131_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M125_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

value: BMK


title: M131_BMK_LAIV_1D

description: Breast milk RNA 1 day after LAIV vaccination


title: ChIP-Seq of Fusarium graminearum PH-1:H3K18ac in the FgPacC infection, ip 1


title: M125_BMK_IIV_1D

description: Breast milk RNA 1 day after IIV vaccination


title: ChIP-Seq of Fusarium graminearum PH-1:H2BK11ac in the PH-1 infection, ip 2

value: anti-H2BK11ac (ab240613, Abcam, Cambridge, UK)


title: M125_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M123_BMK_IIV_7D

description: Breast milk RNA 7 days after IIV vaccination


title: M123_BLD_IIV_7D


title: M123_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M122_BMK_IIV_7D


title: M123_BMK_IIV_1D


title: M123_BLD_IIV_1D


title: M123_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: ChIP-Seq of Fusarium graminearum PH-1:H2BK11ac in the FgPacC infection, ip 2

value: Mycelium


title: ChIP-Seq of Fusarium graminearum PH-1:H3K18ac in the FgPacC infection, ip 2


title: ChIP-Seq of Fusarium graminearum PH-1:H2BK11ac in the PH-1 infection, ip 1

value: WT


title: ChIP-Seq of Fusarium graminearum PH-1:H2BK11ac in the FgPacC infection, ip 1

value: YES


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC30-GFP, ip 2

value: anti-GFP (ab290, Abcam, Cambridge, UK)

value: ChIP experiments using Day 2 of fresh mycelium


title: M122_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC30-GFP, ip 1


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC30-GFP, input 2


title: M122_BMK_IIV_1D


title: M122_BLD_IIV_7D


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1 infection, Input


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC infection, input 1


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC infection, input 2


title: ChIP-Seq of Fusarium graminearum PH-1:PH-1 infection, Input 2


title: ChIP-Seq of Fusarium graminearum PH-1:FgPacC30-GFP, input 1


title: Sara_Hyx_BPD

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: resident mesenchymal Sca1+ sorted cells by FACS

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 323 cells in total that did not express between 300 and 10000 genes or had an mitochondrial content less than 20%. Further, we filtered genes if they were detected in less than 30 cells (<0.3%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Genome_build: mm10
Supplementary_files_format_and_content: starsolo output files

source_name: Lung resident mesenchymal Sca1+ cells

extract_protocol:
Digestion of the P45 lungs with collagenase and FACS using CD31, CD45, Epcam and Sca1
The cell suspensions were counted with Biorad cell counter and diluted according to manufacturer’s protocol to obtain 9000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol.

tag: cell type

value: resident mesenchymal Sca1+ cells

tag: Stage


title: M122_BLD_IIV_1D


title: PrSC 3, TGFB  (T3)

first: Hao

last: Ping

state: China

address: Department of Urology, Beijing Tongren Hospital, Capital Medical University, No1. Dongjiaomingxiang street, Dongcheng District, Beijing, 100730, China.

data_processing:
Illumina HiSeq 2000 (Beijing Annoroad Co. Ltd).
Profiling of transcriptome analysis was performed with 2μg high quality total RNA per sample by RNA-seq at Annoroad Gene Technology Corporation (Beijing, China) according to procedures described previously
Briefly, Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific). RNA samples were rRNA depleted, and RNA libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced as 150 bp paired-end reads by Illumina HiSeq 2000 (Beijing Annoroad Co. Ltd).
We filtered RNA-seq next-generation sequencing (NGS) reads to obtain clean reads for further evaluation and analysis, including quality inspection of reads according to Phred Score, comparison to the human genome reference assembly (hg19) using HiSAT2 and merger of transcripts in StringTie. We used fragments per kilobase of transcript per million mapped reads (FPKM) to assess mRNA expression. Finally, the heatmap was generated using R software with differentially expressed genes (|logFC|>1, q-value<0.05).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary PrSC 3

growth_protocol: Primary PrSCs were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB）following manufacturer's protocols.

treatment_protocol: PrSCs were treated with TGF-β1 (10 ng/mL, R&D Systems, MN, USA) or solvent for 72 h.

tag: cell line

value: Primary PrSC 3

value: mesenchymal cells

value: TGFB

tag: time

value: Day 3


title: PrSC 2, TGFB  (T2)

institute: Beijing Tongren Hospital, Capital Medical University

source_name: Primary PrSC 2

value: Primary PrSC 2


title: PrSC 4, TGFB  (T4)

source_name: Primary PrSC 4

value: Primary PrSC 4


title: PrSC 5, TGFB  (T5)

source_name: Primary PrSC 5

value: Primary PrSC 5


title: PrSC 1, TGFB  (T1)

source_name: Primary PrSC 1

value: Primary PrSC 1


title: M121_BMK_LAIV_1D

value: LAIV


title: M122_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

value: BLD

value: IIV


title: M121_BMK_LAIV_7D

description: Breast milk RNA 7 days after LAIV vaccination

value: BMK


title: M121_BLD_LAIV_7D

source_name: whole blood, LAIV vaccine, 7D


title: M121_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M121_BLD_LAIV_1D


title: Sara_Nox_BPD


title: M053_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M051_BMK_LAIV_1D


title: M051_BMK_LAIV_7D

source_name: breast milk, LAIV vaccine, 7D


title: M053_BMK_IIV_7D


title: M053_BMK_IIV_1D


title: PrSC 2, Control (C2)


title: M121_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: PrSC 1, Control (C1)


title: M045_BMK_LAIV_1D


title: Fresh_1

first: Ligong

last: Chen

address: No.1, Qinghuayuan, Haidian District

department: School of Pharmaceutical Sciences

institute: Tsinghua University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v2.0.4 with parameters -t -p 8 --no-unal --dta-cufflinks
Fragments per Kilobase Million (FPKM) were calculated. 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.
Differential expression analysis of two conditions/groups was performed using the DESeq R package(1.18.0)
Genome_build: GRCh38
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

source_name: Cord blood CD34+ cells

extract_protocol:
Total RNA from 1 x 10^6 CB CD34+ cells was extracted using the RNeasy Plus Mini Kit (Qiagen). Briefly, CB CD34+ cells pellet were first lysed and homogenized. The lysate was passed through a gDNA Eliminator spin column, 70% ethanol was added to the flow-through, and the sample was applied to an RNeasy MinElute spin column. High quality RNA was eluted in 30 µl RNAase free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the isolated cord blood CD34+ cells were cultured in StemSpan SFEM II supplemtented with rhSCF (100 ng/ml), rhTPO (50 ng/ml), rhFL (100 ng/ml) for 24 h. DMSO (0.01%) and JNK-IN-8 (15μM) were added to the culture medium, respectively.

value: Cord blood

value: Cord blood CD34+ cells

value: Uncultured


title: PrSC 5, Control (C5)


title: M047_BMK_IIV_7D


title: PrSC 4, Control (C4)


title: M044_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M047_BMK_IIV_1D


title: A375-Bottom20-5-R2

city: Knoxville

first: Rosela

last: Golloshi

state: TN

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

description:
Bottom20-5
Normalized_counts_file_on_Bottom20-5_vs_Control.tabular.txt

data_processing:
Quality trimming of the reads was performed using BBTools and any reads with a lower than 28 quality score were discarded
Reads were then aligned using STAR alignment with default parameters with an average alignment rate of 89%.
The aligned reads were then sorted by genomic position and feature counts was performed using htseq 0.11.1.  Differential expression of genes was determined by using DESeq through Galaxy
Genome_build: hg19

source_name: Skin Epithelium

growth_protocol: Melanoma (A375) cells were grown to confluency under normal conditions. For the transwell experiments, 100000 cells suspended in media with no supplements were pippetted into the transwell and incubated for a 24 hr period. After incubation, migration efficiency was measured and highly migratory (Bottom) and non-migratory (Top) were isolated and grown until confluency. This experiment was repeated in tranwells with 5 and 12μm pore sizes for 10 rounds (Top5, Bottom5, Top12, Bottom12) and 20 rounds (Top20-5, Bottom20-5).

extract_protocol:
For Control, Top-5 and Bottom-5, RNA was extracted using Qiagen RNAeasy plus mini kit. RNA libraries were prepared using NebNext Ultra II RNA library prep Kit. For Top20-5, Bottom20-5, Top-12 and Bottom-12, RNA was extracted using the Qiagen RNAeasy plus mini kit as described above. Total RNA was then sent for library preparation and sequencing at GeneWiz.
RNA libraries were prepared using NebNext Ultra II RNA library prep Kit (Cat. No. E7770G). After rRNA depletion, RNA was fragmented (~200 nt) and primed following first and second strand cDNA synthesis. The double stranded cDNA was then purified using AmpureXP beads at a 1.8X concentration. After purification, cDNA libraries were end prepped, ligated adapter and PCR amplified for 7 cycles to enrichment for adaptor ligated DNA using NebNext Multiplex Oligos for illumine (Cat. No. E7335G). cDNA librariers were then purified using AmpureXP beads at a 0.9X concentration and their quality was checked using Agilent Bioanalyzer high sensitivity DNA kit. cDNA samples were then sent to Oklahoma Medical Research Facility (OMRF) for high throughput sequencing.

value: Skin Epithelium


title: M044_BMK_LAIV_1D


title: M116_BMK_IIV_7D


title: M116_BMK_IIV_1D


title: J8_1

value: Cultured with JNK-IN-8 for 24 h


title: Fresh_2


title: M116_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

source_name: whole blood, IIV vaccine, 0D


title: M047_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: A375-12-Top12-R2

description:
Top-12
Normalized_counts_file_on_Top12_vs_Control.tabular.txt


title: A375-12-Bottom12-R2

description:
Bottom-12
Normalized_counts_file_on_Bottom12_vs_Control.tabular.txt


title: A375-Control-R2

description: Control


title: A375-12-Bottom12-R1


title: M116_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: DMSO_2

value: Cultured with DMSO for 24 h


title: M045_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

source_name: breast milk, LAIV vaccine, 0D


title: M116_BLD_IIV_7D

source_name: whole blood, IIV vaccine, 7D


title: DMSO_1


title: J8_2


title: PrSC 3, Control (C3)

value: Primary PrSC 3

value: mesenchymal cells


title: M045_BMK_LAIV_7D


title: M116_BLD_IIV_1D

source_name: whole blood, IIV vaccine, 1D


title: A375-12-Top12-R1


title: A375-Top20-5-R1

description:
Top20-5
Normalized_counts_file_on_Top20-5_vs_Control.tabular.txt


title: M044_BMK_LAIV_7D


title: A375-Top20-5-R2


title: A375-Bottom20-5-R1


title: M110_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M110_BMK_LAIV_7D


title: M110_BMK_LAIV_1D

source_name: breast milk, LAIV vaccine, 1D


title: M108_BMK_LAIV_7D


title: M108_BMK_LAIV_1D


title: M110_BLD_LAIV_1D

source_name: whole blood, LAIV vaccine, 1D


title: M110_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination

source_name: whole blood, LAIV vaccine, 0D


title: M110_BLD_LAIV_7D


title: M108_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M105_BMK_LAIV_1D


title: M108_BLD_LAIV_1D


title: M108_BLD_LAIV_7D


title: hApoF_11

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

hyb_protocol: according to manufacturer's protocol

scan_protocol: according to manufacturer's protocol

data_processing: raw data were analyzed in R with Bioconductor tools using the oligo package with RMA normaliztion.

label: biotin

source_name: liver

label_protocol: RNA was prepared according to manufacturers instructions

growth_protocol: C57BL6/J male mice, age 8-10wks old, housed in 12h/12h day/night cycle at 22°C

extract_protocol: total RNA was extracted by Qiagen column purification (RNEasy)

treatment_protocol: Mice were injected by tail vain with Ad5 adenovirus constructs and mice were sacrificed 4 days after injection at 3 pm following a 6 hour fast

tag: virus

value: Ad-hApoF

tag: strain

tag: gender

value: male

tag: age

value: 8-10 weeks-old

value: liver


title: M105_BMK_LAIV_7D

tag: fluid

tag: specimen

tag: timepoint

tag: run


title: hApoF_9

tag: tissue


title: M051_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

tag: usbmk

tag: vaccine

tag: flu season


title: hApoF_12


title: M108_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M105_BLD_LAIV_1D


title: M105_BLD_LAIV_7D


title: GFP_6

value: Ad-GFP


title: M105_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

value: LAIV


title: hApoF_10


title: GFP_2


title: GFP_5


title: GFP_4


title: GFP_3


title: hApoF_8


title: hApoF_7


title: M104_BMK_IIV_7D

source_name: breast milk, IIV vaccine, 7D


title: M105_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination

value: BLD


title: M104_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

value: IIV


title: M099_BMK_IIV_1D

source_name: breast milk, IIV vaccine, 1D

value: BMK


title: Type-17, biological rep2

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix scanner

data_processing: R/Bioconductor: oligo package was used for importing CEL files and performing RMA normalization

source_name: Peripheral lymph node

label_protocol: standard Affymetrix protocol

growth_protocol: Gut content was flushed out with PBS. For the small intestine (SI) Peyer’ Patches were removed. Colon and SI were opened and cut in pieces of 0.5 cm and incubated 20 minutes at 37°C under agitation in a Hank’s Balanced Salt Solution (HBSS; Life Technologies) containing 1 mM Dithiothreitol (DTT), 5mM EDTA, 10 mM HEPES, and 5% Fetal Bovine Serum (Life technologies) (FBS). After incubation, supernatants were filtered through nylon mesh, pelleted, and resuspended in 40% Percoll (GE Healthcare). This cell suspension was overlaid with 70% Percoll and centrifuged at 1300g for 20 min without interruption. iIELs were recovered from the interphase. Peripheral lymph nodes (PLN) (axillary, brachial and inguinal LNs), spleen, and Peyer’ Patches were mashed and filtered to obtain a single-cell suspension.

extract_protocol: RNA from purified cell suspensions was isolated with RNeasy mini kit (Qiagen)

treatment_protocol: Cells were stained with the following antibodies: CD45 (BD Pharmingen, clone  30-F11), CD3 (BD Pharmingen, clone  RM4-5), CD4 (BD Horizon, clone RM-4-5), CD8 (eBiosciences, clone 53-6,7), CD5 ( BD, 53-7.3), CD39 (ebioscience, 24DMS1), CD73 (ebioscience, eBioTY/11.8), CXCR3 (ebioscience, CXCR3-173), CCR6 (Biolegend, 29-2L17), CTLA4 (BD, UC10-4F10-11), PD1 (ebioscience, RMP1-30) LAP (ebioscience, TW7-16B4), TIGIT NK1.1 (BD Pharmingen, clone PK136), TCR b (BD, H57-597) TCR γδ (BD Pharmingen, clone GL3), in PBS 1X, FCS 1% azide. For intracellular staining, cells were fixed and permeabilized with the Foxp3 fixation buffer (eBioscience) and stained with the following antibodies: Helios (Biolegend, 22F6), Foxp3 (eBioscience, FJK-16s), T‐bet (eBiosciences, clone ebio4B10), ROR (BD Pharmingen, clone Q31-378), GATA3 (BD Pharmingen, L50-823), Granzyme A (eBioscience, GzA-3G8.5), Granzyme B (Life Technologies,GB11). Stained cells were analyzed on FORTESSA LSRII and data interpreted with FlowJo sofware. Fixable Yellow Dead Cell Stain kit (Life Technologies) was used in order to eliminate dead cells.

tag: strain background

value: Peripheral lymph node

value: gamma delta T cells

tag: cell subtype


title: Type-1, biological rep3

tag: cell type


title: Naive-like, biological rep2

value: Naive-like


title: Type-1, biological rep2


title: M104_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

source_name: breast milk, IIV vaccine, 0D


title: M099_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: Naive-like, biological rep1


title: Type-17, biological rep3


title: M104_BMK_IIV_1D


title: M097_BMK_IIV_7D


title: Type-17, biological rep1


title: M104_BLD_IIV_1D


title: M104_BLD_IIV_7D


title: M099_BMK_IIV_7D


title: GFP_1


title: Type-1, biological rep1


title: M099_BLD_IIV_7D


title: Naive-like, biological rep3


title: IELs, biological rep3

source_name: Intestinal intraepithelial

value: Intestinal intraepithelial

value: IELs


title: M097_BMK_IIV_1D


title: Total RNA WT mouse 2

city: Rehovot

first: Ariel

last: Ogran

address: 234 Herzl Street

department: Bimolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description: Total RNA

data_processing:
Preprocessing pipeline of CAGE raw reads included quality check (QC) using FSTQC, removal of Phix reads (Escherichia virus PhiX174, NC_001422.1) and rRNA CAGE tags using Bowtie2 (2.3.5.1), demultiplexing and linkers trimming using FASTX-toolKit (0.0.13). Clean CAGE tags were aligned to the mouse reference genome (mm10) using Bowtie2 with the --very-sensitive preset (set as -D 20 -R 3 -N 0 -L 20 -i S,1,0.50), and the resulting SAM files were converted to sorted BAM files using SAMTools (1.9)
BAM files of Light and Heavy polysome fractions were merged to form one BAM file representing all translated fractions, marked as Polysomes.
BAM files were then loaded into the CAGEr package (v1.32 in the Bioconductor environment, v3.12) and uniquely-mapped tags were used for calling CAGE-defined TSSs (CTSSs) setting parameters as follows: sequencingQualityThreshold = 20 and mappingQualityThreshold = 20.
As part of CTSS mapping, CAGEr  performed corrections for the CAGE-specific G-bias caused by template-free guanine incorporation upstream to the true transcription start site by the reverse transcriptase used for cDNA synthesis
Genome_build: mm10
Supplementary_files_format_and_content: BIGWIG (BW)

source_name: B cells

extract_protocol:
Healthy and CLL splenic B cells were isolated from one-year-old WT and Eμ–TCL1 mice by   positive B-cell selection with CD19 magnetic beads (CD19 MicroBeads, Miltenyi Biotec, cat. 130-121-301). Briefly, spleens were squashed, treated with red blood lysis buffer (homemade)  and filtered in PBS using 40-mm cell strainers. The cells were then counted and the B cells were purified according to the manufacturer’s protocol. Splenocytes subjected for polysome profiling were isolated using buffers (above) supplied with 100 ug/ml Cycloheximide (Sigma-Aldrich) to form 80S-mRNA complex.
Five ug of RNA extracted from WT and Eµ-Tcl1 purified B cells together with RNA extracted from the three main polysomal fractions (Free, Light and Heavy) were subjected to library preparation of Cap Analysis Gene Expression CAGE using CAGE-seq protocol adapted for Illumina sequencing (Takahashi, Hazuki, et al. "5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing." Nature protocols 7.3 (2012): 542-561.)

value: Spleen

tag: isolation

tag: genotype

value: 12 months

value: B cells


title: Polysomes fraction Eu-Tc mouse 1

description: Heavy + Light polysome fractions of total RNA


title: 125

city: Madison

first: Alan

last: Attie

state: Wisconsin

address: 433 Babcock Drive

department: Biochemistry

institute: University of Wisconsin-Madison

description:
For generation of the mice, see Keller et al. JCI 2019.
Islet RNA sequencing

data_processing:
Mouse islet RNA-sequencing reads were mapped via bowtie against the RefSeq mm10 mouse reference genome.
Gene expression values were estimated via RSEM.
Expected transcripts per million were normalized using median-by-ratio normalization.
Normalized gene abundance was analyzed for differential expression by EBSeq (Leng, N., Dawson, JA., Stewart, RM., Ruotti, V., Rissman, AI., Smits, BMG., Haag, JD., Gould, MN., Thomson, JA., and Kendziorski, C. (2013). EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29.8 1035-1043). Significantly different genes were determined as having posterior probability of differential expression > 0.95 (equivalent to FDR < 0.05). For coding genes, PPDE was determine for three tests: Zfp148floxed/floxed vs beta-ZFP148KO males, Zfp148floxed/floxed vs beta-ZFP148KO females, Zfp148floxed/floxed vs beta-ZFP148KO with both sexes included. Only genes intersecting all of these tests with PPDE > 0.95 were included for further analysis. This was repeated for ncRNAs, and the resulting genes meeting PPDE threshold for coding and non-coding genes were pooled into the final list for GO and subsequent analyses.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Emfinger_et_al_RNA_seq_PPDE_0.95.xlsx: This is an Excel (.xlsx) file containing tabs for the PPDE results for the three independent tests for coding and non-coding sequences, and the final intersected list. Transcript abundance is indicated for each sample in transcript reads per million (TPM).

source_name: pancreatic islet

growth_protocol: β-Zfp148KO and control littermate mice of both sexes were used.

extract_protocol:
Mouse islets were isolated as described (Rabaglia et al. American Journal of Physiology-Endocrinology and Metabolism 289, E218-E224 (2005). PMID: 15741243). After isolation, islets were placed in 350 uL of QIAzol Lysis Reagent (Qiagen) and stored at -80˚C before purifying RNA using Mini RNeasy purification kit. Purified RNA was reverse-transcribed and sequenced by the UW Madison Biotechnology Center.
RNA libraries were prepared for sequencing at the UW Madison Biotechnology Center. RNA integrity was determined using assayed on Agilent 2100 BioAnalyzer. Libraries were prepared using Illumina® TruSeq® Stranded Total RNA Sample Prep Gold kit (Illumina Inc., San Diego, California, USA). Complementary DNA (cDNA) was purified using Agencourt AMPure XP bead purification (Beckman-Coulter) following rRNA reduction. Libraries were quantified using Qubit DNA HS kit (ThermoFisher) and assayed on Agilent HS DNA Chips. Sequencing was done on Illumina HiSeq 2500 units.

treatment_protocol: Mice were kept on a high-fat/high-sucrose Western-style diet (Envigo Teklad TD.08811, IACUC protocol A005821-R01) for 20 weeks.

value: Pancreatic islets

tag: Sex

tag: diet

value: Western diet

tag: age (wks)


title: M099_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: IELs, biological rep1


title: Polysomes fraction Eu-Tcl mouse 2

tag: strain

tag: age


title: Free fraction Eu-Tc mouse 1

description: Polysome-Free fraction of total RNA


title: Free fraction Eu-Tcl mouse 2

description: Polysome-Free fraction of total RNA


title: M041_BMK_LAIV_7D

source_name: breast milk, LAIV vaccine, 7D

tag: fluid

tag: specimen


title: M041_BMK_LAIV_1D

tag: timepoint

tag: run


title: M099_BLD_IIV_1D

tag: usbmk


title: IELs, biological rep2

tag: tissue


title: M097_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

tag: vaccine

tag: flu season


title: 114

value: male

tag: strain background


title: M097_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M097_BLD_IIV_7D


title: Total RNA Eu-Tcl1 mouse 2

description: Total RNA

tag: cell type


title: 119


title: 121

description:
For generation of the mice, see Keller et al. JCI 2019.
Islet RNA sequencing
β-Zpf148KO


title: Total RNA WT mouse 1

description: Total RNA

tag: isolation


title: M097_BLD_IIV_1D


title: 115

tag: genotype


title: 109

tag: Sex


title: 108

value: female

tag: diet


title: 107

tag: age (wks)


title: 103


title: M120_BMK_IIV_7D


title: Total RNA Eu-Tcl1 mouse 1

description: Total RNA

tag: strain


title: M096_BMK_LAIV_7D


title: M041_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M120_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M120_BMK_IIV_1D


title: 104


title: M120_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M120_BLD_IIV_1D


title: 105


title: 99


title: M096_BLD_LAIV_1D


title: M092_BMK_IIV_7D


title: M120_BLD_IIV_7D


title: 93


title: 98


title: 102


title: M096_BMK_LAIV_1D


title: M096_BLD_LAIV_7D

source_name: whole blood, LAIV vaccine, 7D


title: 100


title: 91


title: 83


title: 92


title: M096_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: Case 7

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

country: Japan

institute: Yamaguchi university

data_processing:
To produce the raq bcl, or base call files, quality assessment and image analyses were performed using Next-seq packaging software Real Time Analysis
bcl2fastaq Conversion Software v2.19 was used for de-multiplexing of the samples
Reads with more than two ambiguous nucleotides and reads with quality scores less than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.8.01, Qiagen)
Gene expression values were calculated as “transcripts per million” (TPM).
Assembly: hg19
Supplementary files format and content: abundance measurements

source_name: human granulosa cells

extract_protocol:
Total RNA was isolated from the granulosa cells with an RNeasy® Mini Kit (QIAGEN).
Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.

treatment_protocol: Patients who failed to become pregnant in the previous ART cycle due to poor fertilization rate, poor embryo development rate (EDR) (low formation rate of the good quality embryo or low formation rate of blastocyst), or repeated ART failure were administered melatonin orally in the next cycle as reported previously.  They were given a 3 mg tablet of melatonin orally at 22:00 hr from the fifth day of the previous menstrual cycle until the day of oocyte retrieval.  For patients who were treated with a short GnRH agonist protocol, melatonin was simultaneously started on day1 of COH.

value: human granulosa cells

value: ovary

tag: age

tag: melatonin treatment

value: no

tag: art outcomes

value: good


title: M096_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

source_name: breast milk, LAIV vaccine, 0D

tag: fluid

tag: specimen

value: BMK

tag: timepoint

value: LAIV


title: M092_BLD_IIV_7D

source_name: whole blood, IIV vaccine, 7D

tag: usbmk

value: BLD

tag: run

value: IIV


title: M092_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

tag: vaccine

tag: flu season


title: Case 5

tag: cell type

tag: tissue


title: Case 6


title: M092_BLD_IIV_1D

source_name: whole blood, IIV vaccine, 1D


title: 82

tag: strain background

tag: genotype


title: M092_BMK_IIV_1D


title: Case 4


title: Case 2 under melatonin treatment

value: yes


title: Case 2 before melatonin treatment

value: poor


title: M091_BMK_IIV_1D


title: M092_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

source_name: whole blood, IIV vaccine, 0D


title: M091_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: Case 3 under melatonin treatment


title: Case 1 before melatonin treatment


title: M091_BLD_IIV_7D


title: M091_BMK_IIV_7D


title: M091_BLD_IIV_1D


title: Case 1 under melatonin treatment


title: M091_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: 19cl105006tyIPcdFXS0tp42

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description: Single Cell 5’ Gene Expression

data_processing:
scRNA-seq bcl to fastq conversion using CellRanger (v2.1.1; 10x Genomics) cellranger mkfastq
scRNA-seq mapping using CellRanger (v2.1.1; 10x Genomics) cellranger count. The 98-bp-long read 2 containing the cDNA sequence  was mapped using STAR against the human GRCh38 reference genome using CellRanger (v2.1.1; 10x Genomics). refdata-cellranger-GRCh38-1.2.0 was used as a gene model for the alignment and was provided as part of the CellRanger pipeline as a compatible transcriptome reference.
scRNA-seq mapping using CellRanger (v2.1.1; 10x Genomics) cellranger count. The 26-bp-long read 1 was processed to extract cell bar codes and Unique molecular identifiers (UMI). UMIs quantification, GemCode, and cell barcodes filtering based on error detection by Hamming distance were performed as described by Zheng et al
Loupe™ Cell Browser (v2.0.0) was used to view the entire dataset and interactively find significant genes, cell types, and substructure within cell clusters.
Assembly: GRCh38
Supplementary files format and content: .cloupe  10x genomics Loupe™ Cell Browser (v2.0.0) files for interactive exploratory tertiary analysis
Supplementary files format and content: .tar archive containing outputs of cellranger_reanalyse secondary analyis step (clustering, diffexp, pca, tsne)

molecule: polyA RNA

source_name: GABAergic differentiation culture day 42-48

growth_protocol: hPSCs were dissociated with Accutase (Life Technologies) and plated on Geltrex-coated 12-well plates at 2.1 × 105 cell/cm2 in E6 (STEMCELL Technologies) medium, supplemented with 10µM rock inhibitor Y-27632 (REPROCELL). The next day, Y-27632 was withdrawn, and neural induction was initiated in E6 medium in the presence of 10µM SB421542 (TGF-β receptor kinase inhibitor; Tocris), 100nM LDN193189 (BMP signaling inhibitor; Tocris) and 2µM XAV939 (WNT pathway inhibitor; REPROCELL), referred to as “neural induction medium”. On day 10 of differentiation, neural progenitors were passaged as aggregates by dispase with a 1:3 ratio, and were replated on poly-d-lysine- and laminin-coated plates in a progenitor expansion medium supplemented with Y-27632. The progenitor expansion medium is a 1-to-1 ratio of DMEM/F12 and Neurobasal medium, with 1× N2 supplement and 1 × B27 supplement without vitamin A, 0.5mg/ml BSA, 1× Pen-Strep, and 100µM beta-mercaptoethanol (referred to as “progenitor medium”, all from Life Technologies). Progenitor expansion was allowed from day 10-25, during which cells were replated as aggregates weekly. On day 25 of differentiation, cells were dissociated with Accutase, and seeded at 1.3 × 105 cell/cm2 in neuronal maturation medium supplemented with 10µM Y-27632. Maturation medium is composed of Neurobasal Plus, 1× B27 plus, 1× N2 (all from Life Technologies), 100µM cAMP (Sigma), 20ng/ml BDNF (Peprotech), 20ng/ml GDNF (Peprotech), and 200nM ascorbic acid (Sigma).

extract_protocol:
Single-cell suspension was prepared following 10X Genomics Single cell protocols: Cell preparation guide (CG00053, Rev C).
Single Cell Labelling with the BD™ Single-Cell Multiplexing Kits was performed following protocol Doc ID: 210970 Rev. 2.0 23-21340-00
Droplet-based single-cell partitioning and single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) as per the manufacturer’s protocol based on the 10X GemCode proprietary technology

value: hPSC-derived GABAergic inhibitory neurons

tag: disease status

value: FXS

tag: differentiation day


title: M090_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: Case 3 before melatonin treatment


title: M084_BMK_LAIV_1D

source_name: breast milk, LAIV vaccine, 1D


title: 15clAb1000tyEMcdCTRLtp42

description: Single Cell 5’ Gene Expression

value: Unaffected


title: M090_BLD_IIV_7D


title: vipsc_control

description: Single Cell 5’ Gene Expression


title: M090_BLD_IIV_1D


title: M090_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: 105_6FXS

description: Single Cell 5’ Gene Expression


title: M084_BMK_LAIV_7D


title: M084_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M084_BLD_LAIV_7D


title: M090_BMK_IIV_7D


title: 08cl215001tyIPcdFXS0tp22

description: Single Cell 5’ Gene Expression

source_name: GABAergic differentiation culture day 22

value: day 22


title: 18cl215001tyIPcdFXS0tp42

description: Single Cell 5’ Gene Expression


title: 12clH10000tyEMcdFXS0tp42

description: Single Cell 5’ Gene Expression


title: M090_BMK_IIV_1D


title: 14cl714517tyIPcdCTRLtp42

description: Single Cell 5’ Gene Expression


title: 05clAb1000tyEMcdCTRLtp22

description: Single Cell 5’ Gene Expression


title: 11clH10000tyEMcdCTRLtp42

description: Single Cell 5’ Gene Expression


title: M079_BLD_IIV_7D


title: M084_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination

source_name: whole blood, LAIV vaccine, 0D


title: 04cl714517tyIPcdCTRLtp22

description: Single Cell 5’ Gene Expression


title: M079_BLD_IIV_1D


title: 01clH10000tyEMcdCTRLtp22

description: Single Cell 5’ Gene Expression


title: genome

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

data_processing:
The fastq fieles were generated using bcl2fastq software.
Sequenced reads were mapped to hg38 using HISAT2 (v2.1.0) with default parameter.
Reads Per Kilobase of exon per Megabase of library size (RPKM)  and Transcripts per Million (TPM) were calcurated by StringTie (v1.3.4d) with default parameter.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
Total RNA of the peripheral blood mononuclear cells and human iPSCs were extracted with TRIzol reagent (Thermo Fisher Scientific) according to manufacturer instructions.
The libraries were constructed using  SMART-Seq HT kit according to manufacturer instructions.

value: PBMC

tag: library type

value: SMARTer


title: M079_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: hiPSC TRIzol DNaseI

source_name: hiPSC

value: hiPSC


title: M040_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

source_name: breast milk, IIV vaccine, 0D


title: 09cl105006tyIPcdFXS0tp22

description: Single Cell 5’ Gene Expression


title: 02clH10000tyEMcdFXS0tp22

description: Single Cell 5’ Gene Expression


title: M040_BMK_IIV_1D

source_name: breast milk, IIV vaccine, 1D


title: M040_BMK_IIV_7D

source_name: breast milk, IIV vaccine, 7D


title: M084_BLD_LAIV_1D

source_name: whole blood, LAIV vaccine, 1D


title: M133_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: AS2_R4

city: Bandung

first: Miftahul

last: Faridl

state: Jawa barat

address: Jalan Ganeca No. 12, Dago, Coblong, Bandung, Jawa Barat, Indonesia

department: School of Life Sciences and Technology

country: Indonesia

institute: Bandung Institute of Technology

data_processing:
Raw fastq file underwent quality processing using BBDuk+ plugin in Geneious (v.2020.2) with the following parameters: Truseq adapter right-end cutting, exclusion of reads below Q30, and exclusion of reads below 30 bp
Quality controlled reads were mapped to the human genome reference (hg19) with Geneious RNA Mapper using the default setting to produce raw gene reads count
Raw fastq file underwent quality processing using BBDuk+ plugin in Geneious (v.2020.2) with the following parameters : exclusion of reads below 70bp
Quality controlled reads were mapped to the MiniKraken_2019 for Kraken 2
Kraken 2 output processed with Kraken-biom package with R with following parameters : filtered for Kingdom of Bacteria
Genome_build: hg19
Supplementary_files_format_and_content: datacount.txt was generated using the Geneious RNA mapper; the first column represents gene symbol; the other column names represent the sample and their replicates (R1-R4)
Supplementary_files_format_and_content: Abundance_rawdata.csv was generated using the Kraken-biom package; the first column represents the sample and their replicates (R1-R4); the second column represents the abundance as reads mapped to a certain taxa; the other columns represent the taxological description of that certain taxa

source_name: Nasopharyngeal swab

extract_protocol:
Total RNA was extracted using the QIAamp Viral RNA Mini Kit (QIAGEN) Spin Protocol with 2x40 uL of elution buffer
cDNA library was constructed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero (Illumina) according to the manufacturer's instructions.

tag: disease severity

value: Mildly Symptomatic

tag: patient's sex assigned at birth

value: Male

tag: patients age


title: M079_BMK_IIV_7D

tag: fluid


title: M079_BMK_IIV_1D

tag: specimen


title: OligodT


title: hiPSC TRIzol


title: M079_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

tag: timepoint


title: FRA013119-008

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Cell line expressing doxycycline inducible constitutively active IKKβ constuct

data_processing:
bulk RNA-seq: Raw reads were mapped to the reference using STAR. Ensembl gene expression was quantified using featureCounts.
scRNA-seq: Raw R2 reads were mapped to the reference transcriptome (hg38  Ensembl gene sequences, exonic only) using BWA MEM. Cell barcodes and UMIs were extracted from R1 using a custom pipeline following OneCellBio adapter design for inDrop. Unique UMI counts were summed for each gene and each unique cell barcode. Only cell barcodes with >500 counts included in the final counts table.
Genome_build: bulk RNA_seq: hg38 (full genome)
Genome_build: scRNA-seq: hg38 Ensembl gene sequences (exonic only)
Supplementary_files_format_and_content: Counts table: Tab-delimited text of counts per gene. Genes down the rows, samples or cells across the columns.
Supplementary_files_format_and_content: Cell list: Tab-delimited text of cell name (matches columns in scRNA-seq counts tables), barcode, number of genes expressed, and UMI counts. All cell barcodes are listed in this file, including those below the 500 count minimum.

source_name: MCF-7 cell line

growth_protocol: Before treatments, cells were cultured for 3 days in Charcoal depleted RPMI 1640 containing charcoal depleted 5% fetal bovine serum, 1% penicillin–  streptomycin, 1% nonessential amino acids and 2 mmol/L L-glutamine.

extract_protocol:
Single cell encapsulation was performed using inDrop system from 1CellBio, followed by transfer to 1CellBio UV Cleavage Device to release oligo linkers from the hydrogel beads and RT reaction.
Sequencing libraries were constructed according to the inDrop Library Preparation Protocol v2.3.

treatment_protocol: Cell treated for 3 days with E2+Doxycycline, then seeded for invasion. Invaded cells were collected and submitted for scRNA sequencing.

value: single-cell (OneCellBio/InDrop)

value: Breast

tag: cell line

tag: treatment

value: E2 + Doxycycline


title: SY2_R4

value: Female


title: M119_BMK_IIV_1D

tag: usbmk

value: BMK

tag: run

tag: vaccine


title: M133_BMK_LAIV_7D

source_name: breast milk, LAIV vaccine, 7D

value: LAIV

tag: flu season


title: AS2_R3


title: M119_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination

value: IIV


title: FRA013119-007

tag: tissue


title: M119_BMK_IIV_7D


title: M133_BLD_LAIV_7D

description: Whole blood RNA 7 days after LAIV vaccination

source_name: whole blood, LAIV vaccine, 7D

value: BLD


title: SY2_R3


title: SY1_R4

value: Asymptomatic


title: M133_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: SY1_R1


title: AS2_R1


title: M071_BMK_LAIV_7D


title: M119_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M133_BLD_LAIV_1D


title: M119_BLD_IIV_7D

source_name: whole blood, IIV vaccine, 7D


title: SY2_R1


title: SY2_R2


title: M071_BMK_LAIV_1D


title: M119_BLD_IIV_1D

description: Whole blood RNA 1 day after IIV vaccination

source_name: whole blood, IIV vaccine, 1D


title: M071_BLD_LAIV_1D

description: Whole blood RNA 1 day after LAIV vaccination


title: AS1_R2


title: AS2_R2


title: M071_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: SY1_R2


title: H661_TVB

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

data_processing:
Reads were aligned to the human hg38 reference genome using STAR (v2.7.3a)
Gencode annotation for human (version v37) was used as reference alignment annotation and downstream quantification
Gene level expression was calculated using featureCounts (v2.0.1) with intersection-strict mode by exon. Counts were calculated based on protein-coding genes from the annotation file.
Low expressed genes were filtered using a per time-point approach with Reads Per Kilobase of exon per Megabase of library size (RPKM) >= 0.5 in all samples in one or the other group.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung cancer

growth_protocol: Cell lines were maintained in RPMI (GE, SH30027) supplemented with 5% heat-inactivated FBS (SIGMA ALDRICH, F6178)

extract_protocol:
Total RNA was extracted with TRIzol Residual genomic DNA was removed with the Turbo DNA-free kit (AM1907, ThermoFisher).
NEBNext Ultra II Directional RNA Library Prep kit

treatment_protocol: Cell lines were treated with  0.2 μM TVB-3664 or 0.2% DMSO, in RPMI (GE, SH30027) supplemented with 5% dialyzed FBS (SIGMA-ALDRICH, F0394) for 4 days

tag: kras status

value: wild-type KRAS

value: 0.2 microM TVB-3664 in 0.2percent DMSO, for 4 days


title: M069_BMK_LAIV_7D

data_processing:
Signal intensities for the probe selection regions (PSR) were quantile normalized by robust multichip averaging using affy R package (v. 3.14).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

extract_protocol: RNA was extracted from whole blood and milk samples using Maxwell Simply RNA purification kit (Promega). RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).


title: AS1_R4


title: H522_vehicle

value: 0.2percent DMSO, for 4 days


title: AS1_R3


title: SY1_R3


title: M069_BLD_LAIV_1D


title: A549_vehicle

value: mutant KRAS


title: H460_TVB


title: AS1_R1


title: A549_TVB


title: H661_vehicle


title: H522_TVB


title: SPF_Cohort1_Mouse9

city: Nashville

first: Ryan

middle: M

last: Allen

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description: Demultiplexed, adapter and degenerate base-trimmed fastq files

data_processing:
After de-multiplexing, FastQC software was used for QC. www.bioinformatics.babraham.ac.uk/projects/fastqc
Cutadapt was used to trim 3' adapters and degenerate bases. Data provided is after this step.
Bowtie was used to map reads, as described here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095027/
Assembly: mm9
Supplementary files format and content: algae_group5_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: bacteria_group1_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: bacteria_group2_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: fungus_group4_pm_RA_97_93.category.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.miRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.other.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.rRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.snoRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.snRNA.count.RPM.txt
Supplementary files format and content: smallRNA_1mm_RA_97_93.tRNA.count.RPM.txt
Supplementary files format and content: RA_97_93.All.TaskReads.csv
Supplementary files format and content: RA_97_93.NonParallel.TaskReads.csv

source_name: Lipoprotein (HDL)

extract_protocol:
https://pubmed.ncbi.nlm.nih.gov/30128086/
NextFlex V3 Small RNA Seq (Perkin Elmer)

treatment_protocol: Age- and facility-matched mice

value: Lipoprotein (HDL)

tag: genotype

value: SPF


title: H460_vehicle


title: SPF_Cohort2_Mouse22


title: SPF_Cohort2_Mouse20


title: M069_BMK_LAIV_1D

first: Pia

last: Pannaraj

address: 4650 Sunset Blvd, MS#51

institute: Children's Hospital of Los Angeles

description: Breast milk RNA 1 day after LAIV vaccination

source_name: breast milk, LAIV vaccine, 1D


title: M071_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination

source_name: breast milk, LAIV vaccine, 0D


title: M071_BLD_LAIV_7D


title: M064_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: SPF_Cohort1_Mouse8


title: M066_BLD_LAIV_7D


title: GF_Cohort2_Mouse19

value: GF


title: M066_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination

source_name: whole blood, LAIV vaccine, 0D


title: M066_BMK_LAIV_7D


title: SPF_Cohort1_Mouse10


title: M069_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M069_BLD_LAIV_7D


title: M066_BLD_LAIV_1D


title: M064_BMK_LAIV_7D


title: M064_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M064_BMK_LAIV_1D


title: M069_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: GF_Cohort2_Mouse18


title: SPF_Cohort2_Mouse21


title: M064_BLD_LAIV_1D


title: M066_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M052_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: GF_Cohort2_Mouse13


title: M066_BMK_LAIV_1D


title: M052_BLD_IIV_7D

description: Whole blood RNA 7 days after IIV vaccination


title: GF_Cohort2_Mouse11


title: GF_Cohort2_Mouse15


title: GF_Cohort1_Mouse6


title: M052_BMK_IIV_1D

description: Breast milk RNA 1 day after IIV vaccination


title: M052_BMK_IIV_7D

description: Breast milk RNA 7 days after IIV vaccination


title: GF_Cohort1_Mouse5


title: M064_BLD_LAIV_7D


title: GF_Cohort1_Mouse2


title: GF_Cohort2_Mouse16


title: GF_Cohort1_Mouse7


title: M055_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M055_BLD_LAIV_1D


title: M052_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination

source_name: whole blood, IIV vaccine, 0D


title: M052_BLD_IIV_1D


title: GF_Cohort2_Mouse14


title: GF_Cohort2_Mouse12


title: GF_Cohort1_Mouse3


title: M050_BMK_IIV_1D


title: GF_Cohort1_Mouse4


title: M032_BMK_LAIV_1D


title: GF_Cohort1_Mouse1


title: M050_BMK_IIV_0D

description: Breast milk RNA prior IIV vaccination


title: M055_BMK_LAIV_7D

description: Breast milk RNA 7 days after LAIV vaccination


title: M032_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M050_BLD_IIV_7D


title: M055_BLD_LAIV_7D


title: M050_BLD_IIV_1D


title: M049_BLD_LAIV_7D


title: M055_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M050_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: M048_BMK_LAIV_1D


title: M049_BMK_LAIV_7D


title: M048_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M043_BMK_LAIV_1D


title: M049_BLD_LAIV_1D


title: M055_BMK_LAIV_1D


title: M043_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M048_BLD_LAIV_1D


title: M048_BLD_LAIV_7D


title: M043_BLD_LAIV_7D


title: M039_BMK_IIV_7D


title: M049_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M035_BLD_LAIV_1D


title: M035_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M048_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M030_BMK_LAIV_7D


title: M043_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M039_BLD_IIV_1D


title: 114_Peach

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

description: pooled RNA from leaves of different individuals

data_processing:
The quality check of the sequenced small RNA libraries was done by FastQC program, embedded in CLC
Trimming of raw reads was performed using the CLC
Removing redundant reads using CLC
Supplementary_files_format_and_content: trimmed redundant list, each read with its number of repeats

organism: Prunus persica

source_name: leaf samples

extract_protocol:
CTAB method (Gambino, 2008: https://doi.org/10.1002/pca.1078 )
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

tag: cultivar/variety

value: Peach varieties

tag: source

value: Samples derived from isolator house

value: leaf


title: M039_BLD_IIV_7D


title: M039_BMK_IIV_1D


title: M030_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: M035_BMK_LAIV_1D


title: M030_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M049_BLD_LAIV_0D

description: Whole blood RNA prior LAIV vaccination


title: 57_Cresthaven_I_h

value: Cresthaven variety


title: M035_BMK_LAIV_0D

description: Breast milk RNA prior LAIV vaccination


title: M035_BMK_LAIV_7D


title: 55_Springcrest_I_h

value: Springcrest variety


title: M039_BLD_IIV_0D

description: Whole blood RNA prior IIV vaccination


title: VSV_H3K27Ac_replicate1

city: Beijing

first: Shengde

last: Liu

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

data_processing:
Reads from ChIP-seq experiments were aligned to the mm9 revision of the mouse reference genome using only annotated chromosomes 1-19, chrX, chrY, and chrM or to the hg19 revision of the human genome using only annotated chromosomes 1-22, chrX, chrY,  and chrM. Alignment was performed using bowtie (Langmead et al., 2009) with parameters –best –k 1 –m 1 –sam and –l set to read  length.
Regions with an exceptionally high coverage of ChIP-Seq reads (i.e., peaks) were identified using MACS with parameters –keepdup = auto –p1e-9 and with corresponding input control.
Genome_build: mm9
Supplementary_files_format_and_content: text files include ChIP-Seq reads for each Sample

source_name: ChIP with anti-H3K27ac antibody and iBMDM cells with VSV treatment for 8h, replicate 1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27AC antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (VAHTS UniversalDNA Library Prep Kit for Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: iBMDM cells were infected with VSV or HSV-1 for 8 hours

tag: cell type

value: iBMDM

tag: strain

value: VSV infection

tag: antibody

value: anti-H3K27ac antibody


title: HSV_H3K27Ac_replicate1

source_name: ChIP with anti-H3K27ac antibody and iBMDM cells with HSV-1 treatment for 8h, replicate 1

value: HSV-1 infection


title: 58_Cresthaven_S_n

description: pooled RNA from leaves of different varieties

value: Samples derived from stock nursery


title: VSV_H3K27Ac_replicate2

source_name: ChIP with anti-H3K27ac antibody and iBMDM cells with VSV treatment for 8h, replicate 2


title: H3K27AC_replicate1

source_name: ChIP with anti-H3K27ac antibody, replicate 1

value: no treatment


title: M030_BLD_LAIV_1D

city: Los Angeles

source_name: whole blood, LAIV vaccine, 1D

tag: fluid

value: BLD

value: LAIV


title: sc_myc_cbf1_nexus_2

city: Stanford

first: Amr

middle: Mohamed

last: Alexandari

address: 240 Pasteur Dr

institute: Stanford University

data_processing:
ChIP-nexus libraries were sequenced in single-end mode (1 X 75 cycles) on a NextSeq 500 instrument. The adapters were trimmed using cutadapt (v 1.8.1) and reads were aligned to the Saccharomyces cerevisiae (sacCer3) genome using bowtie (v1.1.2). Reads were filtered using SAMtools (v1.3.1) to remove unmapped reads and PCR duplicates. Reads aligned to the same position with the same barcode, CIGAR string and the SAM flag were deduplicated using nimnexus dedup (v.0.1.1).
The final filtered BAM file was converted to tagAlign format (BED 3 + 3) using bedtools ‘bamtobed‘ (v.2.26). Cross-correlation scores were obtained for each file using phantompeakqualtools (v.1.2). BigWig tracks containing the strand-specific number of aligned 5′ read ends (pooled across all replicates) were generated using bedtools genomecov -5 -bg –strand <+/−>, followed by bedGraph to BigWig conversion using UCSC bedGraphToBigWig v.4.
Peaks were called using MACS2 (v.2.1.1) by extending the 5’  ends of reads on each strand using a 150-bp window and then computing coverage of extended reads across both strands (shift = -75, extsize = 150). For each TF, peak calling was performed on filtered, aligned reads from each replicate using a relaxed threshold P=0.1.
Assembly: sacCer3
Supplementary files format and content: bigWig (positive and negative strands), narrowPeak
Library strategy: ChIP-nexus

organism: Saccharomyces cerevisiae

growth_protocol: The Myc-tagged Pho4 and Cbf1 Saccharomyces cerevisiae strains were cultured in 50 ml of yeast peptone dextrose (YPD) media at 25oC to OD600 ~ 0.8.

extract_protocol:
The yeast chromatin preparation was performed as previously described with minor modifications (Rossi, Lai, & Pugh, 2018). For each experiment, 50 ml of cells were cross-linked with 1% formaldehyde (Fisher Scientific) for 15 min at 25oC. The reaction was quenched by incubating with 125 mM glycine for 5 min. Cells were washed three times with cold wash buffer (10 mM Tris-HCl, pH 7.5, 100 mM NaCl) at 4oC. The pellet was snap frozen in liquid nitrogen after the last wash. The pellet was then resuspended in 700µl of FA lysis buffer (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% triton-X-100, 0.1% Sodium deoxycholate, supplemented with protease inhibitor) and transferred to 1.5 ml of Sarstedt micro tube. 1 ml of 0.5 mm zirconia/silica beads was added to the tube and cells were lysed in a Mini-BeadBeater 24 (BioSpec products) for three cycles (3 min ON/5 min OFF).Samples were kept on ice during the OFF cycles. Cell lysates were separated from silica beads and collected in a new 1.5 ml tube using a 23G 1” needle (BD Microlance) and centrifuged at maximum speed for 4 min at 4oC to pellet the chromatin. The supernatant was discarded and the pellet was resuspended in 750 µl of FA lysis buffer supplemented with 0.1% SDS. Samples were sonicated with a Bioruptor Pico (Diagenode) for 18 cycles of 30 s ON and 30 s OFF intervals. Chromatin extracts were centrifuged at 16,000 g for 10 min at 4oC and the supernatant was used for the ChIP reaction.
The ChIP-nexus was performed as previously described (He, Johnston, & Zeitlinger, 2015), with some modifications. Briefly, the chromatin was washed with Nexus wash buffers A to D (wash buffer A: 10 mM Tris-EDTA, 0.1% Triton X-100; wash buffer B: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS; wash buffer C: 250 mM NaCl, 5 mM Tris-HCl, pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA; wash buffer D: 250 mM LiCl, 0.5% IGEPAL CA-630, 10 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA) and 10 mM Tris, pH 7.5. End-repair and dA-tailing enzymatic reactions were performed using the NEBNext End Repair and NEBNext dA-tailing module. ChIP-nexus adapter mix containing four fixed barcodes (ACTG, CTGA, GACT and TGAC) were ligated with quick T4 DNA ligase. Following barcode extension, samples were treated with lambda exonuclease to generate high-resolution transcription factor binding footprints. Reverse crosslinking was performed at 65C for overnight, followed by ethanol precipitation of DNA. Purified DNA fragments were circularized, and directly subjected to PCR amplification. The libraries were gel purified before sequencing. For each factor, at least two biological replicates were prepared side-by-side from independent colonies.

treatment_protocol: Pho4 was induced by incubating cells for 2h at 25oCin phosphate-free media from Fisher Scientific (MP114027812), supplemented with 2% glucose and 0.1g/L sodium chloride.

tag: chip antibody

value: ab9E10 (abcam)


title: M035_BLD_LAIV_7D

tag: specimen

tag: timepoint


title: M030_BLD_LAIV_7D


title: sc_myc_cbf1_nexus_1


title: 56_Springcrest_S_n


title: M043_BMK_LAIV_7D

value: BMK


title: M043_BLD_LAIV_1D


title: HSV_H3K27Ac_replicate2

source_name: ChIP with anti-H3K27ac antibody and iBMDM cells with HSV-1 treatment for 8h, replicate 2

tag: cell line

tag: treatment


title: input_replicate1

source_name: input replicate 1

value: input


title: sc_myc_pho4_nexus_1