title: IRE1aKO-Polysome-heavy-3

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

institute: Charité Universitätsmedizin Berlin

data_processing:
Reads were quantified with Salmon quant --validateMappings to GRCm39 using gene annotation: gencode comprehensive release M33
further analysis steps can be seen in github code
Assembly: GRCm39
Supplementary files format and content: Counts table provides transcript level counts from tximport using option ' countsFromAbundance="scaledTPM" ' across all samples and technical replicates.

source_name: Cortex

growth_protocol: Primary Tissue from Mouse Postnatal Day 0 Cerebral Cortex

extract_protocol:
Tools and work surfaces used for RNA work were thoroughly cleaned with 70% ethanol (Sigma) and rinsed with RNA-Zap (Thermo Fisher) before the procedure. Embryonic brains at E18.5 were dissected in DEPC-PBS and flash-frozen in liquid nitrogen until the purification procedure. RNA was isolated using RNeasy columns (RNeasy Mini Kit, Qiagen).
TruSeq Stranded total RNA libraries were made with Ribo-Zero Gold rRNA depletion and sequenced using Illumina Nextseq 500/550, and in later runs (batch 3) using Novaseq 6000.
Total RNAseq with rRNA depletion

treatment_protocol: Ribosome fractionation and polysome purification from P0 cortex was performed as published protocol (Kraushar et al., 2021 doi: 10.1016/j.molcel.2020.11.037). Seven brains (14 neocortex hemispheres) of each genotype were pooled per biological replicate.

value: Cortex

value: Postnatal Day 0

value: IRE1af/f Emx1Cre

value: Purified Polysome heavy Fraction RNA


title: Brca1/P53-Deficient Mammary Gland Organoids from Age-Matched Nulliparous Mice 5 [A5_Nulip]

status: Public on Jan 10 2024

type: SRA

city: Salamanca

first: Jesús

last: Pérez Losada

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

library_source: transcriptomic

data_processing:
Salmon calculated TPM values
Assembly: GRCm38
Supplementary files format and content: Excel format (XLSX), TPM values

molecule: total RNA

organism: Mus musculus

source_name: Mammary Gland

extract_protocol:
RNA was extracted from the organoids using the Qiagen miRNeasy Mini Kit (Catalog #217004). Manufacturer's protocols were followed for the procedure
rRNA was removed using the Epicentre Ribo-Zero Kit (#20040526, Illumina). Isolated total RNA was then fragmented, reverse transcribed to cDNA, and prepped for sequencing with NEBNext Ultra RNA Library Prep (#E7770, Illumina)

tag: tissue

value: Mammary Gland

tag: cell type

value: Organoids

tag: genotype

tag: treatment

value: untreated

tag: time point

value: Age-Matched with 60 Days Post-Lactational Involution


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 3 [D3_Mult_lact]

value: 60-Day Post-Lactation Involution Period


title: IRE1aKO-Polysome-heavy-1

country: Germany

tag: time


title: IRE1aKO-Polysome-light-2

value: Purified Polysome light Fraction RNA


title: IRE1aKO-Polysome-heavy-2


title: IRE1aKO-Polysome-light-3


title: Cornea2mo

city: Detroit

first: Shunbin

last: Xu

state: MI

address: 540 E Canfield St, Scott Hall 8133/8137

department: Opthalmology, Visual and Anatomical Sciences

country: USA

institute: Wayne State University, School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

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

source_name: eye

growth_protocol: Naïve, young adult (2 and 6mo), female miR-183C KO, miR-183CGT/GT, and their age- and sex-matched WT control mice on a 129S2–C57BL/6-mixed background were used for scRNA sequencing.

extract_protocol:
Adult mouse corneas anterior to the limbus were harvested and dissociated into single cells by enzymatic digestion with collagenase A (MilliporeSigma. Cat No. 10103578001) and DNase I (MilliporeSigma. Cat No. 11284932001) in Hanks' Balanced Salt solution (HBSS) and trituration
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cornea

value: eye

tag: strain background

value: WT

tag: age

tag: Sex

value: female


title: WT-Polysome-light-2


title: WT-Polysome-heavy-3


title: IRE1aKO-Polysome-light-1


title: WT-Polysome-heavy-2


title: WT-Polysome-light-3


title: Cornea2moKO

description: 10x Genomics

value: miR-183C knockout (KO)


title: Cornea6moKO

description: 10x Genomics


title: CRICKO

description: 10x Genomics

value: CRIC


title: EAE, WT, rep 2

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
The barcoded processing and gene counting were made using the Cell Ranger software v7.1.0 [Zheng2017] and post-alignment processing and visualisation was performed using Seurat v4.3.0.1 [Stuart2019]. Data was normalised using Sctransform [Hafemeister2019].
The clustering was performed using SLM; ClustAssess was used for identifying stable clusters; the identification of markers was performed per cluster vs its complement.
The visualisation and community accessible overview were complied using ShinyCell [Ouyang2021]
Assembly: GRCm38 (Ensembl 93 from pre-built Cell Ranger reference 3.1.0)
Supplementary files format and content: count matrix containing raw gene expression (csv)

molecule: polyA RNA

source_name: Spinal cord

extract_protocol:
Mice were perfused with actinomycin D and triptolide in ice cold HBSS, spinal cords were extracted and underwent mechanical dissociation in digestion buffer. After myelin removal, cells were used for library preparation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, the cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Spinal cord

tag: disease state

value: EAE

value: Various


title: EAE, WT, rep 1


title: EAE, KO, rep 2


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 2 [D2_Mult_lact]


title: Post-Lactation Organoids from Brca1/P53-Deficient, Multiparous Mice (60 Days) 1 [D1_Mult_lact]


title: EAE, KO, rep 1


title: No EAE, WT, rep 2

value: Healthy control


title: No EAE, WT, rep 1


title: CRICWT

description: 10x Genomics


title: HC, WT


title: No EAE, KO, rep 1


title: No EAE, KO, rep 2


title: EAE, WT, rep 1


title: Cornea6mo

description: 10x Genomics


title: EAE, ND6, rep 2


title: HC, ND6


title: EAE, ND6, rep 1


title: EAE, WT, rep 2


title: ARKO-1 Mesonephros E14.5

city: Madison

first: Fei

last: Zhao

state: Wisconsin

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin-Madison

data_processing:
Partek flow platform was used for data analysis. Raw data was uploaded to Partek to be analyzed. All analysis followed the default settings on Partek flow.
For our analysis pipeline of ARKO vs CT bulk RNA-seq of E14.5 XY mesonephros we first trim bases, with pre-alignment QA/QC.
Next we mapped our trimmed reads to reference genome mm10 using STAR aligner.
We took our aligned reads and quantified to annotation model to get gene counts and transcript counts.
Finally to get DEG, we filtered our gene counts, performed DESeq2 statistical analysis and compared ARKO vs CT.
Assembly: mm10

source_name: Mesonephros

extract_protocol:
RNA was harvested using PicoPure RNA Isolation Kit from ThermoFisher Scientific cat#KIT0204
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Male

value: Mesonephros


title: Ca75KI3

city: Bronx

first: Robyn

middle: D

last: Moir

state: NY

address: 1300 Morris Park Ave

department: Biochemistry

institute: Albert Einstein College of Medicine

data_processing:
mapping using HISAT2
DESeq2
Assembly: mm10
Supplementary files format and content: txt files contain gene counts for sample
Supplementary files format and content: results csv files contain DESeq2 comparison of specific group

source_name: cerebrum

growth_protocol: ad libitum fed

extract_protocol:
Trizol extraction as per protocol, plus NaOAc precipitation
mRNA library preparation (polyA enrichment) Novogene Co. (Sacramento CA, USA).

treatment_protocol: tamoxifen-induced recombination at P28

value: cerebrum

value: M

value: Polr3a mutant

value: tamoxifen

tag: strain


title: Ca75KI1


title: ARKO-2 Mesonephros E14.5


title: ARKO-3 Mesonephros E14.5


title: Ca42KI1


title: Cb42KI1

source_name: cerebellum

value: cerebellum


title: CbWT1

value: Wildtype


title: Cb42KI3

value: F


title: Ca42WT1


title: Ca75KI4


title: Ca42WT3


title: Ca75WT3


title: Ca42WT2


title: CbWT2


title: Ca75WT2


title: Ca42KI2


title: CbWT4


title: Cb42KI4


title: Cb42KI2


title: Ca42WT4


title: Control (CT3) Mesonephros E14.5


title: Ca42KI4


title: CbWT3


title: Ca42KI3


title: Ca75WT4


title: Ca75WT1


title: Control (CT2) Mesonephros E14.5


title: Control (CT1) Mesonephros E14.5


title: Ca75KI2


title: T4_7d

city: beijing

first: lihong

last: zhang

address: panjiayuan

country: China

institute: , Chinese Academy of Medical Sciences and Comparative Medicine Center

data_processing:
lllumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Reasearch, 2009.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: thymus

extract_protocol:
Tissues were removed, flsah frozen on dry ice, and RNA was harvested using Trizol reagent. Lllumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction
RNA libraries were prepared for sequencing using standard lllumina protocols

value: thymus

value: WT

value: CA6 infection


title: S2_7d

source_name: spleen

value: spleen


title: M3_7d

source_name: muscle

value: muscle


title: T5_7d


title: T2_7d


title: M1_7d


title: S1_7d


title: B1_7d

source_name: blood

value: blood


title: B3_7d


title: N5_7d

source_name: brain

value: brain


title: N1_7d


title: S4_7d


title: N2_7d


title: N3_7d


title: T1_7d


title: M4_7d


title: S5_5d


title: M2_7d


title: B4_7d


title: T3_7d


title: B5_7d


title: S3_5d


title: S2_5d


title: M5_7d


title: B2_7d


title: S4_5d


title: S3_7d


title: S5_7d


title: S1_5d


title: N4_7d


title: T4_5d


title: T5_5d


title: N3_5d


title: N2_5d


title: M5_5d


title: N4_5d


title: T1_5d


title: N5_5d


title: T2_5d


title: N1_5d


title: M2_5d


title: M4_5d


title: S5_3d


title: B2_5d


title: M1_5d


title: S1_3d


title: B3_5d


title: S2_3d


title: B1_5d


title: T5_3d


title: T3_3d


title: B5_5d


title: S3_3d


title: T2_3d


title: N4_3d


title: N5_3d


title: B4_5d


title: S4_3d


title: M3_5d


title: T1_3d


title: T4_3d


title: M5_3d


title: T3_5d


title: N1_3d


title: N3_3d


title: M1_3d


title: B5_3d


title: M4_3d


title: M3_3d


title: M2_3d


title: B3_3d


title: S5_0d

value: Negative control


title: B2_3d


title: B1_3d


title: T5_0d


title: N2_3d


title: S2_0d


title: B4_3d


title: S1_0d


title: T3_0d


title: T2_0d


title: T4_0d


title: S4_0d


title: N4_0d


title: S3_0d


title: N5_0d


title: M4_0d


title: N2_0d


title: M3_0d


title: N1_0d


title: M1_0d


title: N3_0d


title: M5_0d


title: M2_0d


title: B5_0d


title: B2_0d


title: B1_0d


title: T1_0d


title: MLECs HEY1-WT-1

city: Hangzhou

first: Luyang

last: Yu

address: College of Life Sciences, Zijingang Campus, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China

institute: Zhejiang University

data_processing:
Quality control was performed using FastQC v0.19.7.
The SAM files generated from HISAT2 2.1.0 were brought into BAM format using SAMtools v1.9.
We generated read counts with StringTie v1.3.3b.
Assembly: Sequencing reads were aligned using mm10 assembly of the mouse genome.
Supplementary files format and content: MLEC_gene_fpkm.xlsx file includes mRNA expression for each sample.

source_name: MLECs

growth_protocol: MLECs were cultured in EGM-2 supplemented with EGM-2 plus 10% FBS, 1% MEM and 1% L-Glucose.

extract_protocol:
Total RNA was extracted using the SteadyPure Total RNA Kit (Accurate Biology) according to the manufacturer's instructions.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

tag: cell line

value: MLECs

value: Endothelial cells

value: HEY1-WT KI


title: MLECs HEY1-3KR-3

value: HEY1-3KR KI


title: MLECs HEY1-WT-3


title: Reactive+RGFP966_A_IgG

city: Cleveland

first: Benjamin

last: Clayton

state: OH

address: 2109 Adelbert Rd BRB739A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

library_source: genomic

data_processing:
Sequencing data was processed and analyzed using CUT&RUNTools2.0
For peak calling, reads were quality and adaptor trimmed using Trimmomatic Version 0.36.
Trimmed reads were aligned to mm10 and the spike in genome with Bowtie2 version 2.3.217.
Duplicate reads (potential artifacts of PCR in library preparation) were removed using Picard MarkDuplicates.
For RelA/p65 samples, deduplicated files were filtered for fragments less than 120bp using SAMtools.
Peaks were called with MACS version 2.1.118 with an FDR threshold of 0.01 for H3K27ac and 0.001 for RelA/p65
Peaks were compared and contrasted using bedtools implemented in the R software environment using the BedtoolsR package (http://phanstiel-lab.med.unc.edu/bedtoolsr.html) and peaks were assigned to the nearest gene using the R packages ChIPSeeker60, ChIPpeakanno61, and GenomicRanges62
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (for RelA/p65), broadPeak (for H3K27ac)
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: astrocyte

extract_protocol:
CUT&RUN was performed on fresh or frozen nuclei isolated using the CUTANA ChIC/CUT&RUN kit (EpiCypher Cat#: 14-1048) according to manufacturer’s instructions. Briefly, 500,000 nuclei per sample were bound to activated ConA Beads followed by overnight incubation with primary antibody (1:100 RelA/p65 Cell Signaling Cat #: 8242, 0.5ug IgG EpiCypher Cat#: 14-1048, and 0.5ug either H3K27ac EpiCypher Cat #: 13-0045 or H3K27ac Abcam Cat #: AB4729). Nuclei were then permeabilized followed by addition of pAG-MNase. The reaction was then terminated and E. coli SpikeIn DNA added.
Libraries were prepared for Illumina Sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB Cat # E7645) according to manufacturer’s instructions, with modifications recommended by Epicypher CUT&RUN Kit Manual Version 2.

value: astrocyte

value: pooled male and female

value: wild-type

tag: condition

value: reactive (treated with TNFa, IL1a, C1q)

value: 5uM RGFP966


title: MLECs HEY1-3KR-2


title: MLECs HEY1-WT-2


title: Reactive_A_IgG

value: DMSO


title: Reactive_A_H3K27ac


title: Reactive+RGFP966_A_H3K27ac


title: Resting_A_IgG

value: resting


title: VEHICLE.CTRL.Retina.Male.C

data_processing:
Final libraries were pooled evenly and sequenced on the Illumina NovaSeq with paired-end 150bp reads with a read-depth of at least 20 million reads per sample.
For gene expression analysis, reads were aligned to the mm10 genome and transcripts were collapsed to gene level data using Kallisto v0.46.1
Normalized gene expression was generated by DESEQ2.
Assembly: mm10
Supplementary files format and content: DESEQ2 Normalized Counts

source_name: Retina

extract_protocol:
Retinas were homogenized in RLT buffer and then total RNA extracted using a Qiagen RNeasy Mini Kit according to manufacturer's instructions.
Libraries were prepared following protocols from NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were enriched for mRNA using oligo(dT) beads, which were fragmented randomly and used for cDNA generation and subsequent second-strand synthesis using a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I. cDNA libraries then went through terminal repair, A-base ligation, adapter ligation, size selection, and PCR enrichment.

value: Male

value: Optic Nerve Uncrushed (CTRL)

tag: drug treatment

value: daily i.p. 10mg/kg vehicle


title: Reactive+JSH23_A_H3K27ac

value: 5uM JSH-23


title: Resting_A_H3K27ac


title: VEHICLE.ONC.Retina.Male.C

value: Optic nerve crushed (ONC)


title: RGFP.ONC.Retina.Male.D

value: daily i.p. 10mg/kg RGFP966


title: VEHICLE.ONC.Retina.Male.B


title: VEHICLE.ONC.Retina.Male.D


title: B3_0d

value: blood

value: WT

value: Negative control


title: Resting_A_RelA/p65


title: B4_0d


title: Reactive_A_RelA/p65


title: Reactive+JSH23_A_RelA/p65


title: VEHICLE.CTRL.Retina.Male.D


title: Reactive+RGFP966_A_RelA/p65


title: VEHICLE.ONC.Retina.Male.A


title: MLECs HEY1-3KR-1

value: MLECs

value: Endothelial cells

value: HEY1-3KR KI


title: RGFP.CTRL.Retina.Male.D


title: Reactive+JSH23_A_IgG

value: astrocyte

value: pooled male and female

value: wild-type


title: RGFP.ONC.Retina.Male.C


title: RGFP.CTRL.Retina.Male.C


title: RGFP.CTRL.Retina.Male.A


title: VEHICLE.CTRL.Retina.Male.B


title: RGFP.ONC.Retina.Male.A


title: VEHICLE.ONC.Retina.Female.C

value: Female


title: VEHICLE.CTRL.Retina.Male.A


title: VEHICLE.ONC.Retina.Female.B


title: VEHICLE.CTRL.Retina.Female.C


title: VEHICLE.CTRL.Retina.Female.B


title: VEHICLE.CTRL.Retina.Female.A


title: VEHICLE.ONC.Retina.Female.A


title: RGFP.CTRL.Retina.Male.B


title: RGFP.ONC.Retina.Female.A


title: RGFP.CTRL.Retina.Female.A

description: Retina from female mice with optic nerve crush and treatment with 10mg/kg RGFP966


title: Reactive+JSH23_E

data_processing:
Final libraries were pooled evenly and sequenced on the Illumina NovaSeq with paired-end 150bp reads with a read-depth of at least 20 million reads per sample.
For gene expression analysis, reads were aligned to the mm10 genome and transcripts were collapsed to gene level data using Kallisto v0.46.1
Normalized gene expression was generated by DESEQ2.
Differential expression analysis was performed using DESEQ2. Significant genes were called based on p-adj and fold change.
Assembly: mm10
Supplementary files format and content: DESEQ2 Normalized Counts and DESEQ2 Differential Expression Results

source_name: primary reactive astrocytes

extract_protocol:
Resting and reactive astrocyte cultures were lysed in TRIzol followed by purification and elution of RNA using phenol-chloroform extraction and the RNeasy Mini Kit.
Libraries were prepared following protocols from NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were enriched for mRNA using oligo(dT) beads, which were fragmented randomly and used for cDNA generation and subsequent second-strand synthesis using a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I. cDNA libraries then went through terminal repair, A-base ligation, adapter ligation, size selection, and PCR enrichment.

value: reactive (treated with TNFa, IL1a, C1q) + 5uM JSH-23


title: RGFP.CTRL.Retina.Female.B


title: Reactive+JSH23_F


title: RGFP.CTRL.Retina.Female.C


title: RGFP.ONC.Retina.Female.B


title: Reactive_E

value: reactive (treated with TNFa, IL1a, C1q)


title: Reactive+JSH23_D


title: DD_Control1

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to GRCm38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: GRCm38
Supplementary files format and content: tab-deliminated data matrix of normalized gene counts

source_name: liver tissue

growth_protocol: Liver tissue

extract_protocol:
Flash frozen tissue was pulverized and homogenized in TRIzol RNA isolation reagent (Invitrogen). RNA was then purified based on manufacturer protocol.
Barcoded, Illumina compatible, strand-specific total RNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

treatment_protocol: Animals were fed high fat choline deficient diet for 3 months, starting at 21 days of age.

value: liver tissue

value: Alb-Cre0, Trp53fl/+

value: 3 months on high fat, choline def diet


title: Reactive_F


title: DD_Control3

value: Alb-Cre0, Trp53wm-R245W/+


title: RGFP.ONC.Retina.Male.B

value: Male

value: Optic nerve crushed (ONC)

value: daily i.p. 10mg/kg RGFP966


title: DD_245_3

value: Alb-CreTG, Trp53wm-R245W/+


title: DD_Control2


title: DD_245_2


title: DD_FL_1

value: Alb-CreTG, Trp53fl/+


title: DD_FL_2


title: EarSkin_MC903_IL26_aIL1b_6

city: Basel

first: Katharina

last: Bier

address: Lichtstrasse

department: Immunology

country: Switzerland

institute: Novartis Institutes for Biomedical Research

data_processing:
Alignment with STAR 2.7.3a
Count generation with exone quantification pipeline
Assembly: ensembl-Mus_musculus.GRCm38.98.cdna.all.fa
Supplementary files format and content: raw count table for all samples

source_name: skin

extract_protocol:
For RNA isolation, half a mouse ear was incubated in 1 mL RNAprotect (Qiagen, #76104) for 24 hours at 4 °C.  Subsequently, skin tissue was homogenized in 500 μL RLT RNA lysis buffer (Qiagen, #79216) containing 40mM dithiothreitol (DTT, Sigma, #3483-12-3) using tissue homogenizing CK14 tubes (bertin technologies, #KT03961-1-203.0.5) and a PrecellysTM Evolution SUPER Homogenizer (bertin technologies) for 2 cycles with 3x20 s at 6400 rpm at 4 °C and RNA was prepared using the RNeasy Mini kit (Qiagen, #74106) according to manufacturer’s instructions. After tissue disintegration RNA was isolated using the RNeasy® Mini Kit (Qiagen, #74106) in combination with on column DNA digestion according to manufacturer’s instructions.
TruSeq libraries were prepared from 200 ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, #20020599), according to the manufacturer’s instructions.
Ribo-Zero

value: skin

value: mixed

value: WT


title: DD_245_1


title: EarSkin_MC903_IL26_aIL1b_3


title: EarSkin_MC903_IL26_aIL1b_4


title: EarSkin_MC903_BSA_aIL1b_6


title: EarSkin_MC903_IL26_aIL1b_2


title: EarSkin_MC903_BSA_aIL1b_7


title: EarSkin_MC903_IL26_aIL1b_1


title: EarSkin_MC903_BSA_aIL1b_5


title: EarSkin_MC903_IL26_aIL1b_5


title: EarSkin_MC903_IL26_IgG_5


title: EarSkin_MC903_BSA_aIL1b_3


title: EarSkin_MC903_IL26_IgG_6


title: RGFP.ONC.Retina.Female.C


title: EarSkin_MC903_IL26_IgG_4


title: EarSkin_MC903_BSA_aIL1b_1


title: EarSkin_MC903_BSA_aIL1b_4


title: EarSkin_MC903_IL26_IgG_3


title: EarSkin_MC903_IL26_IgG_2


title: EarSkin_MC903_BSA_aIL1b_2


title: EarSkin_MC903_IL26_IgG_1


title: EarSkin_MC903_BSA_IgG_6


title: EarSkin_MC903_BSA_IgG_5


title: Reactive_D


title: EarSkin_MC903_IL26_aIL1b_7


title: EarSkin_MC903_BSA_IgG_4


title: EarSkin_MC903_BSA_IgG_2


title: EarSkin_MC903_BSA_IgG_3


title: EarSkin_MC903_BSA_IgG_1


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-5_S18_L001]

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: mm10
Supplementary files format and content: Tab Separated File containing gene level counts per sample

source_name: ear skin biopsy

growth_protocol: Mice were either bred in-house or purchased from Jackson Laboratory: MRL/+(#000486) and MRL/lpr mice (#000485), B6.Sle1yaa mice (021569) and their B6 controls were either bred in-house or  purchased from Jackson Laboratory.

extract_protocol:
Female MRL/+ and MRL/lpr 12-14 weeks old and 6 month old B6 and B6.Sle1yaa male mice were used for RNA sequencing. RNA was extracted from ear skin using an RNEasy Kit (Qiagen, Germantown, MD) and quality confirmed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA)
Libraries were prepared with non-stranded and poly-A selection TruSeq RNA Sample Preparation kits. Sequencing libraries were sequenced by the Genomics Core Facility at Weill Cornell Medicine using a HiSeq 2500 (MRL/lpr, MRL/+ samples) and NovaSeq (B6, B6.Sle1yaa) at a depth of 15-30 million mappable paired-end reads per sample.

treatment_protocol: No treatment was applied

value: ear skin biopsy

value: 6 months


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-5_S18_L002]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-4_S17_L002]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-3_S16_L002]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-4_S17_L001]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-3_S16_L001]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-2_S15_L002]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-2_S15_L001]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-1_S14_L002]


title: non-lesional ear skin from B6.Sle1yaa SLE mouse model [Sle1-1_S14_L001]


title: non-lesional ear skin from B6 control mice [B6-5_S13_L002]


title: non-lesional ear skin from B6 control mice [B6-3_S11_L002]


title: non-lesional ear skin from B6 control mice [B6-2_S10_L001]


title: non-lesional ear skin from B6 control mice [B6-5_S13_L001]


title: non-lesional ear skin from B6 control mice [B6-3_S11_L001]


title: non-lesional ear skin from B6 control mice [B6-1_S9_L001]


title: MPC-wholetumor

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Raw sequencing data were processed and aligned to the mouse genome (mm10) using the CellRanger pipeline (10x Genomics version 3.1, SCR_017344). Raw count data for all three samples was obtained as h5Seurat format 3.1.5.9900
Filtered raw-count matrices were further analysed using the Seurat (v4.1.0) R package (3) for data integration and unbiased clustering of single cell transcriptomes
Low-quality single cell libraries with less than 250 and more than 4000 detected genes and more than 20% mitochondrial counts were excluded in whole tumor samples.
In addition, low-quality clusters with low numbers of detected genes and high percentages of mitochondrial genes and / or nearly exclusive ribosomal gene expression that lacked expression of biologically relevant cell type markers were removed after clustering.
Datasets from different localisations were integrated using the IntegrateData function in Seurat. Data was centred and scales using the ScaleData function. Principal component analysis (PCA) was used for dimensionality reduction and the K-nearest neighbor (KNN) graph was constructed using the first 30 principal components (PCs). Cells were clustered using the Louvain algorithm and embedded in two- dimensional space (30 PCs) using Uniform Manifold Approximation and Projection (UMAP).
Differentially expressed genes between clusters were identified using Wilcoxon Rank Sum test and clusters were assigned to cell types according to expressed marker genes and their similarity to known cell types.
Assembly: mm10
Supplementary files format and content: h5Seurat file

source_name: Whole-tumor organoid-derived primary CRC

growth_protocol: APTAK organoids are tumor organoids that are devoid of Apc, Tp53, Tgfbr2 and express constitutively active Kras (KrasG12D) and an activated/myristoilated isoform of Akt1. The organoids are a gift from F. Greten, Frankfurt. APTAK tumor organoids were maintained in basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N343 Acetylcysteine 1mmol/l (Sigma)) supplemented with Hygromycin (200 µg/ml) and puromycin (2 µg/ml). The organoids were subcultured in Matrigel every 5-7 days. The APTAK organoids were isolated from a colon of p53flox/flox::Tgfbr2flox/flox mouse. The established organoids harbor loxP sites flanking exon4 of the TGFBR2 gene and Intron 1 and 10 of the TP53 gene. The APC knock out was introduced using CRISPR/Cas9 transgenesis and confirmed by Western Blotting. The organoids were transfected with Cre-IRES-puroR plasmid (Addgene #30205) that encode Cre recombinase to ablate Tgfbr2 and p53. Kras gain of function was obtained by overexpressing the constitutive active version of the murine KRAS gene KRASG12D (cloned in Addgene plasmid #111164) by retroviral transduction. Myrisilated Akt1 was obtained by overexpression the active form of Akt1 (cloned in Addgene plasmid #) by retroviral transduction. Human tumor organoids were cultured in Wnt3a, R-spondin and Noggin conditioned basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N-Acetylcysteine 1mmol/l (Sigma)) supplemented with EGF.

extract_protocol:
For whole tumor samples, samples from PT, LM and PC were processed for RNA isolation, library preparation, single cell RNA sequencing and count data generation by Singleron Biotechnologies via established protocols (Cologne, Germany). Tissue from 6 mice per location were pooled before.
Single cell capture, reverse transcription, and library preparation were carried out on the Chromium platform (10X Genomics) with the single-cell 3’ reagent v2 protocol according to the manufacturer’s recommendations using 50,000 cells as input per reaction well. The final libraries [PT, LM, PC] were pooled and sequenced on two Illumina NovaSeq SP lanes (paired-end 26 bp + 96 bp).

treatment_protocol: In matrigel grown APTAK organoids were dissociated into a single-cell suspension by mechanical disruption followed by enzymatic digestion for 20 minutes at 37°C using TrypLE (Gibco) and were washed once in ice-cold PBS. Single cells were then resuspended in an ice- cold Type I collagen/5x Collagen neutralization Buffer (4:1 (vol/vol) ratio) with a concentration of 150.000 cells/10 µl. The 5x Collagen neutralization buffer is composed of 2.5 g alpha MEM powder (5x) and 2 % (wt/vol) NAHCO3 in 45 ml Aqua dest. and 5 ml of 1M HEPES and set to pH 7.5. 10 µl domes of collagen were plated in 6 well plates. The domes polymerize for 45 minutes at 37 °C. Afterwards basal medium (Advanced DMEM-F12 supplemented with penicillin/streptomycin, HEPES 10mmol/l (Invitrogen), Glutamax 1x (Invitrogen), N2 1x (Gibco), B27 1x (Gibco), and N-Acetylcysteine 1mmol/l (Sigma)) supplemented with Hygromycin and puromycin were added. The collagen domes were cultured overnight till transplantation. At the day of transplantation the mice were shaved and anesthetized with 2.5% (vol/vol) isoflurane. Analgesia was guaranteed by intraperitoneal injections with buprenorphine. The mouse is placed on its back on a heating pad and legs were fixed with leukoplast. Isoflurane was lowered to 1.8 % (vol/vol). A 10 – 15 mm incision was made along the linea alba to open the abdomen. The cecum was placed on a wet sterile gauze. A 3 – 4 mm incision through the cecal serosa is made at the end of the cecum in an area without vessels. The serosa was seperated from the submucosal layer and a deep pocket of about 1 cm length was performed. The pocket was enlarged to the size that the collagen dome could be deeply embedded in it. The collagen dome was placed under the serosa in the pocket and the serosa was tightly closed above the collagen dome securing the collagen dome to be tightly embedded in its pocket. The incision in the serosa was covered with a 20 x 5 mm piece of Seprafilm (Baxter). The cecum was carefully placed back in the abdomen. The peritoneum and abdominal wall are seperately closed by a continuous suture. The mice were placed on drinking water supplemented with metamizole (5 mg/ml) for 3 days.

tag: crc murine model

value: PC


title: non-lesional ear skin from B6 control mice [B6-4_S12_L002]


title: non-lesional ear skin from B6 control mice [B6-2_S10_L002]


title: MLM-wholetumor

value: Whole-tumor organoid-derived primary CRC

value: LM


title: MPT-wholetumor

value: PT


title: MPC-TIL

source_name: TILs from organoid-derived primary CRC

extract_protocol:
For analyses of infiltrative immune cells, single-cell suspensions (also see Flow cytometry) from APTKA PT, LM and PC samples (cells from 6 mice per location were pooled before) were subjected to single-cell sorting using a MoFlow Astrios machine. After exclusion of CD45- cells, all CD45+ / CD11B- cells were sorted into Eppendorf tubes and directly processed for 10X protocols.
Single cell capture, reverse transcription, and library preparation were carried out on the Chromium platform (10X Genomics) with the single-cell 3’ reagent v2 protocol according to the manufacturer’s recommendations using 50,000 cells as input per reaction well. The final libraries [PT, LM, PC] were pooled and sequenced on two Illumina NovaSeq SP lanes (paired-end 26 bp + 96 bp).

value: TILs from organoid-derived primary CRC


title: TA, ∆Ig3-MuSK, Rep 9

city: Providence

first: Justin

last: Fallon

state: RI

address: 185 Meeting St

department: Neuroscience

institute: Brown University

data_processing:
Sequence reads were trimmed using Trimmomatic (Sliding window 10:25; Minlen: 75) and read quality was assessed using Fastqc.
Trimmed reads were aligned to GRCm38.89 using GSNAP and converted to BAM files using Samtools.
Read count matrices were generated using htseq-count.
Assembly: GRCm38.89
Supplementary files format and content: CSV files containing gene count matrices.

source_name: Whole skeletal muscle

extract_protocol:
Muscle tissue was preserved in RNAlater. Total RNA was isolated using RNeasy Fibrous Tissue Kit (Qiagen) according to manufacturer's protocol. RNA integrity was assessed using Agilent Bioanalyzer.
NEBNext® Ultra™ II RNA Library Prep Kit

value: Whole skeletal muscle

tag: muscle

value: TA muscle

value: 3 months


title: MLM-TIL


title: TA, ∆Ig3-MuSK, Rep 6


title: TA, ∆Ig3-MuSK, Rep 7


title: TA, ∆Ig3-MuSK, Rep 8


title: MPT-TIL


title: TA, ∆Ig3-MuSK, Rep 4


title: TA, ∆Ig3-MuSK, Rep 3


title: non-lesional ear skin from B6 control mice [B6-4_S12_L001]

value: Male


title: TA, ∆Ig3-MuSK, Rep 5


title: TA, WT, Rep 9


title: TA, WT, Rep 4


title: TA, WT, Rep 5


title: TA, WT, Rep 7


title: TA, WT, Rep 2


title: TA, WT, Rep 8


title: TA, WT, Rep 3


title: TA, WT, Rep 1


title: Soleus, ∆Ig3-MuSK, Rep 9

extract_protocol:
Muscle tissue was preserved in RNAlater. Total RNA was isolated using RNeasy Fibrous Tissue Kit (Qiagen) according to manufacturer's protocol. RNA integrity was assessed using Agilent Bioanalyzer.
NEBNext® Ultra™ RNA Library Prep Kit

value: soleus muscle


title: Soleus, ∆Ig3-MuSK, Rep 8


title: Soleus, ∆Ig3-MuSK, Rep 7


title: Soleus, ∆Ig3-MuSK, Rep 6


title: TA, WT, Rep 6


title: Soleus, ∆Ig3-MuSK, Rep 5


title: Soleus, ∆Ig3-MuSK, Rep 3


title: non-lesional ear skin from B6 control mice [B6-1_S9_L002]


title: Soleus, ∆Ig3-MuSK, Rep 2


title: Soleus, ∆Ig3-MuSK, Rep 1


title: Soleus, WT, Rep 5


title: Soleus, WT, Rep 7


title: TA, ∆Ig3-MuSK, Rep 2


title: Soleus, WT, Rep 8


title: Soleus, WT, Rep 9


title: Soleus, WT, Rep 6


title: TA, ∆Ig3-MuSK, Rep 1


title: Soleus, WT, Rep 4


title: Soleus, WT, Rep 3


title: Soleus, WT, Rep 2


title: Soleus, WT, Rep 1


title: skeletal muscle satellite cells RNAseq KO rep3

city: wuhan

first: wei

last: jiang

address: No.1, Shizishan Street, Hongshan District, Wuhan, China

institute: Huazhong Agricultural University

data_processing:
Raw reads were filtered by trim_galory (v0.6.4) to remove low quality and adapters sequences.
Paired-end reads were aligned to mm10 genome with hisat2 (v2.2.1).
Featurecounts (v2.0.1) is used to quantify gene expression to obtain original count estimates
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: skeletal muscle satellite cells

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions
For library construction, we used a protocol as described before.(Zhou et al., 2015) The purified library products were evaluated using a Bioanalyzer (Agilent) and SYBR qPCR and sequenced on an Illumina Hi-seq2000 sequencer

value: skeletal muscle

value: satellite cells

value: lncMREF KO


title: skeletal muscle satellite cells RNAseq KO rep1


title: skeletal muscle satellite cells RNAseq WT rep2


title: Soleus, ∆Ig3-MuSK, Rep 4


title: skeletal muscle satellite cells p300 ChIP-seq KO rep2

data_processing:
Raw reads were pocessed by Trimmomatic (v 0.39) to remove low quality and adapters sequences.
The trimmed reads were aligned to mm10 by Bowtie2-align-s (v2.4.4).
Duplicate reads were marked and removed by Picard MarkDuplicates.
The reads whose mapping quality > 30 were used for further analysis
The Bam files were converted to BigWig profiles using Deeptools (v3.5.1) for visualization in the Integrative Genomics Viewer (v2.9.2).
Peaks were identified using the Macs2 (v2.2.7.1) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Deeptools (v3.5.1).

extract_protocol:
Lysates were clarified from sonicated nuclei and p300-DNA complexes were isolated with antibody.
The ChIP experiments were performed as described previously.(Rossi et al., 2019) Briefly, lysates were generated from 4 × 106 cells. Each lysate was immunoprecipitated with 5 µg of anti-p300 (ab8580 from Abcam) and the corresponding control IgG, respectively. Antibodies were pre-conjugated to 25 µl of A/G protein-coupled paramagnetic beads (ThermoFisher) in 0.5% PBS/BSA at 4℃. Beads were then added to the lysate and allowed to undergo overnight incubation. Beads were washed six times with modified RIPA buffer (50 mM HEPES [pH 7.6], 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate) and once with TE containing 50 mM NaCl. DNA was eluted in solution TE containing 2% SDS and cross-linking was incubated at 65 °C for 2 h in reverse. DNA was then purified by Qiaquick columns (Qiagen). The DNA was used for library construction or qPCR analysis using specific primers (Supplementary Table S1). Libraries were constructed using the ChIP Elution Kit and the DNA Smart ChIP Seq Kit from a low input DNA template (Illumina) sequencing library preparation with 75nt paired ends.

tag: chip antibody

value: p300 (Abcam)


title: skeletal muscle satellite cells RNAseq KO rep2

tag: tissue


title: skeletal muscle satellite cells RNAseq WT rep3

tag: cell type

value: WT


title: skeletal muscle satellite cells RNAseq WT rep1

tag: genotype


title: skeletal muscle satellite cells p300 ChIP-seq WT rep2


title: skeletal muscle satellite cells H3k27ac ChIP-seq KO rep1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP experiments were performed as described previously.(Rossi et al., 2019) Briefly, lysates were generated from 4 × 106 cells. Each lysate was immunoprecipitated with 5 µg of anti-histone H3 lysine 27 demethylated (H3K27ac, ab4729 from Abcam) and the corresponding control IgG, respectively. Antibodies were pre-conjugated to 25 µl of A/G protein-coupled paramagnetic beads (ThermoFisher) in 0.5% PBS/BSA at 4℃. Beads were then added to the lysate and allowed to undergo overnight incubation. Beads were washed six times with modified RIPA buffer (50 mM HEPES [pH 7.6], 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% sodium deoxycholate) and once with TE containing 50 mM NaCl. DNA was eluted in solution TE containing 2% SDS and cross-linking was incubated at 65 °C for 2 h in reverse. DNA was then purified by Qiaquick columns (Qiagen). The DNA was used for library construction or qPCR analysis using specific primers (Supplementary Table S1). Libraries were constructed using the ChIP Elution Kit and the DNA Smart ChIP Seq Kit from a low input DNA template (Illumina) sequencing library preparation with 75nt paired ends.

value: H3k27ac (Abcam)


title: skeletal muscle satellite cells H3k27ac ChIP-seq KO rep2


title: skeletal muscle satellite cells p300 ChIP-seq WT rep1


title: skeletal muscle satellite cells ATAC-seq KO rep2

data_processing:
Trimomatic (v 0.39) was used for raw reads to remove low quality and adapters sequences.
The resulting trimmed reads were aligned to mm10 by BWA-mem (v0.7.17)
Duplicate reads were marked and removed by Picard MarkDuplicates
The reads whose mapping quality > 20 were used for further analysis.
The reads that were compared with mitochondria were removed by Samtools (v1.3.1) and then were converted to BigWig profiles by Deeptools (v3.5.1) for visualization in the Integrative Genomics Viewer (v2.9.2).
Peaks were identified using the Macs2 (v2.2.7.1) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Deeptools (v3.5.1).

extract_protocol:
Cell pellets were resuspended in lysis buffer, pelleted and tagmented by using the enzyme and buffer provided in the TruePrep DNA Library Prep Kit V2 for Illumina.
ATAC-seq was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (Nanjing Vazyme, China) according to the manufacturer’s instructions. Briefly, cell pellets were resuspended in lysis buffer, pelleted and tagmented using the enzyme and buffer provided in the TruePrep DNA Library Prep Kit V2 for Illumina.


title: skeletal muscle satellite cells H3k27ac ChIP-seq WT rep1


title: skeletal muscle satellite cells H3k27ac ChIP-seq WT rep2


title: skeletal muscle satellite cells ATAC-seq KO rep1


title: skeletal muscle satellite cells ATAC-seq WT rep2


title: skeletal muscle satellite cells ATAC-seq WT rep1


title: skeletal muscle satellite cells p300 ChIP-seq KO rep1


title: TB_9611_Pre-Plasma IgG

type: protein

first: Jacqueline

middle: M.

last: Achkar

description: IgG

hyb_protocol: Slides with 8 arrays on each were blocked with 3% BSA (GEMINi Bio-Products, standard grade) in PBS at 4°C overnight, washed with 0.1 % PBS-T, and then incubated with BALF (1:8) or plasma (1:100), diluted in 0.1% PBST with 3% BSA, for 4 hrs at 37°C. After washing, bound antibodies were detected by Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882. Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The slides were scanned using the GenePix 4000 Microarray scanner system. Scanned images were analyzed with by the image-processing software G\enePix Pro 7.3.0.0 to analyze the images and measure the median pixel intensity (MPI).

data_processing: The median pixel intensity of each feature was background subtracted. A minimum value of pixel intensity (400) was determined by the median pixel intensity of the spots with low quality, which was determined by the software quality control score for each spot depending on signal-to-noise ratio and spot shape. The scanned images were visually inspected. The spots with obvious local artifacts were excluded from analysis. The array features were printed in triplicate. The final data were averaged from the triplicates.

label: Alexa 647 Goat Anti-Human IgG

molecule: protein

organism: Macaca fascicularis

source_name: Pre-Plasma

extract_protocol: Plasma was obtained from peripheral blood samples and the BAL procedure was performed as previously described via direct visualization of the airway and lavage of ~ 40 ml normal saline (0.9%). Animal protocols and procedures were approved by the University of Pittsburgh’s Institutional Animal Care and Use Committee before the collection of samples.

treatment_protocol: BALF dilted (1:8) or plasma diluted (1:100)

tag: infection states

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_9611_Pre-BALF IgG

description: IgG

source_name: Pre-BALF

label_protocol: Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882


title: TB_9711_3mo-BALF IgG

description: IgG


title: TB_9711_Pre-BALF IgG

description: IgG


title: TB_9711_Pre-Plasma IgG

description: IgG


title: Resting_A

data_processing:
Final libraries were pooled evenly and sequenced on the Illumina NovaSeq with paired-end 150bp reads with a read-depth of at least 20 million reads per sample.
For gene expression analysis, reads were aligned to the mm10 genome and transcripts were collapsed to gene level data using Kallisto v0.46.1
Normalized gene expression was generated by DESEQ2.
Differential expression analysis was performed using DESEQ2. Significant genes were called based on p-adj and fold change.
Genome_build: mm10
Supplementary_files_format_and_content: DESEQ2 Normalized Counts
Supplementary_files_format_and_content: DESEQ2 Differentiation Expression Results

source_name: primary cortical astrocytes

extract_protocol:
Resting and reactive astrocyte  cultures were lysed in TRIzol followed by purification and elution of RNA using phenol-chloroform extraction and the RNeasy Mini Kit.
Libraries were prepared following protocols from NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were enriched for mRNA using oligo(dT) beads, which were fragmented randomly and used for cDNA generation and subsequent second-strand synthesis using a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I. cDNA libraries then went through terminal repair, A-base ligation, adapter ligation, size selection, and PCR enrichment.

value: primary cortical astrocytes

tag: treatment

value: DMSO


title: Reactive+RGFP_B

value: TNFa, IL1a, C1q, and RGFP966


title: Reactive_B

value: TNFa, IL1a, Ciq, and DMSO


title: Reactive+RGFP_C


title: Reactive_C


title: TB_9511_Pre-BALF IgG

description: IgG


title: Resting_C


title: Resting_B


title: TB_9711_6mo-Plasma IgG

description: IgG


title: TB_9711_3mo-Plasma IgG

description: IgG


title: Reactive+RGFP_A


title: TB_7009_6mo-BALF IgG

description: IgG


title: TB_9511_Pre-Plasma IgG

description: IgG


title: TB_9711_6mo-BALF IgG

description: IgG


title: TB_7009_6mo-Plasma IgG

description: IgG


title: TB_7009_Pre-BALF IgG

description: IgG


title: Reactive_A


title: TB_9511_6mo-Plasma IgG

description: IgG


title: TB_9611_3mo-BALF IgG

description: IgG


title: TB_7009_2mo-Plasma IgG

description: IgG


title: TB_9611_3mo-Plasma IgG

description: IgG


title: TB_9511_3mo-BALF IgG

description: IgG


title: TB_9511_3mo-Plasma IgG

description: IgG


title: TB_9511_6mo-BALF IgG

description: IgG


title: TB_23110_2mo-Plasma IgG

description: IgG


title: TB_23110_Pre-BALF IgG

description: IgG


title: TB_23210_2mo-BALF IgG

description: IgG


title: TB_23110_2mo-BALF IgG

description: IgG


title: TB_22910_Pre-Plasma IgG

description: IgG


title: TB_7009_Pre-Plasma IgG

description: IgG


title: TB_23110_Pre-Plasma IgG

description: IgG


title: TB_3808_2mo-Plasma IgG

description: IgG


title: TB_4108_2mo-BALF IgG

description: IgG


title: TB_3808_Pre-Plasma IgG

description: IgG


title: TB_3808_Pre-BALF IgG

description: IgG


title: TB_6809_2mo-Plasma IgG

description: IgG


title: TB_6809_2mo-BALF IgG

description: IgG


title: TB_4108_Pre-BALF IgG

description: IgG


title: TB_4508_2mo-Plasma IgG

description: IgG


title: TB_23210_2mo-Plasma IgG

description: IgG


title: TB_23210_Pre-BALF IgG

description: IgG


title: TB_4508_Pre-BALF IgG

description: IgG


title: TB_22910_2mo-Plasma IgG

description: IgG


title: TB_22910_Pre-BALF IgG

description: IgG


title: TB_4508_2mo-BALF IgG

description: IgG


title: TB_22010_Pre-Plasma IgG

description: IgG


title: TB_6809_Pre-BALF IgG

description: IgG


title: TB_6809_Pre-Plasma IgG

description: IgG


title: TB_7009_2mo-BALF IgG

description: IgG


title: TB_22910_2mo-BALF IgG

description: IgG


title: TB_23210_Pre-Plasma IgG

description: IgG


title: TB_22010_Pre-BALF IgG

description: IgG


title: TB_22010_6mo-Plasma IgG

description: IgG


title: TB_4108_2mo-Plasma IgG

description: IgG


title: TB_21410_Pre-Plasma IgG

description: IgG


title: TB_22010_6mo-BALF IgG

description: IgG


title: TB_21310_Pre-BALF IgG

description: IgG


title: TB_21310_Pre-Plasma IgG

description: IgG


title: TB_21410_2mo-Plasma IgG

description: IgG


title: TB_20708_2mo-Plasma IgG

description: IgG


title: TB_3808_2mo-BALF IgG

description: IgG


title: TB_21310_2mo-BALF IgG

description: IgG


title: TB_21310_2mo-Plasma IgG

description: IgG


title: TB_20708_Pre-BALF IgG

description: IgG


title: TB_17406_6mo-BALF IgG

description: IgG


title: TB_20708_5mo-BALF IgG

description: IgG


title: TB_20708_5mo-Plasma IgG

description: IgG


title: TB_17406_6mo-Plasma IgG

description: IgG


title: TB_18106_2mo-BALF IgG

description: IgG


title: TB_21410_Pre-BALF IgG

description: IgG


title: TB_20708_1mo-plasma IgG

description: IgG


title: TB_17406_2mo-Plasma IgG

description: IgG


title: TB_17106_6mo-Plasma IgG

description: IgG


title: TB_18106_2mo-Plasma IgG

description: IgG


title: TB_18106_6mo-Plasma IgG

description: IgG


title: TB_18106_6mo-BALF IgG

description: IgG


title: TB_17106_6mo-BALF IgG

description: IgG


title: TB_17406_1mo-plasma IgG

description: IgG


title: TB_17406_2mo-BALF IgG

description: IgG


title: TB_21410_2mo-BALF IgG

description: IgG


title: TB_17106_2mo-BALF IgG

description: IgG


title: TB_17106_2mo-Plasma IgG

description: IgG


title: TB_20708_Pre-Plasma IgG

description: IgG


title: TB_10908_Pre-Plasma IgG

description: IgG


title: TB_20708_2mo-BALF IgG

description: IgG


title: TB_10908_2mo-BALF IgG

description: IgG


title: TB_10808_6mo-Plasma IgG

description: IgG


title: TB_10808_6mo-BALF IgG

description: IgG


title: TB_10808_2mo-Plasma IgG

description: IgG


title: TB_10808_2mo-BALF IgG

description: IgG


title: TB_10208_Pre-BALF IgG

description: IgG


title: TB_10208_6mo-Plasma IgG

description: IgG


title: LTBI_9911_Pre-BALF IgG

description: IgG

value: Asymptomatic controlled Mtb infection


title: LTBI_9911_Pre-Plasma IgG

description: IgG


title: TB_17106_1mo-plasma IgG

description: IgG


title: TB_10208_Pre-Plasma IgG

description: IgG


title: LTBI_9911_3mo-Plasma IgG

description: IgG


title: LTBI_9811_Pre-BALF IgG

description: IgG


title: TB_10208_6mo-BALF IgG

description: IgG


title: LTBI_9911_3mo-BALF IgG

description: IgG


title: LTBI_9811_6mo-Plasma IgG

description: IgG


title: LTBI_9811_6mo-BALF IgG

description: IgG


title: LTBI_9811_3mo-Plasma IgG

description: IgG


title: LTBI_9911_6mo-Plasma IgG

description: IgG


title: LTBI_9808_6mo-Plasma IgG

description: IgG


title: TB_10908_Pre-BALF IgG

description: IgG


title: TB_10908_2mo-Plasma IgG

description: IgG


title: TB_10908_6mo-Plasma IgG

description: IgG


title: TB_10908_6mo-BALF IgG

description: IgG


title: LTBI_9811_3mo-BALF IgG

description: IgG


title: LTBI_9808_Pre-BALF IgG

description: IgG


title: TB_10208_3mo-BALF IgG

description: IgG


title: LTBI_9811_Pre-Plasma IgG

description: IgG


title: LTBI_9411_Pre-Plasma IgG

description: IgG


title: LTBI_9808_6mo-BALF IgG

description: IgG


title: LTBI_9808_2mo-Plasma IgG

description: IgG


title: LTBI_9411_6mo-BALF IgG

description: IgG


title: LTBI_9411_Pre-BALF IgG

description: IgG


title: LTBI_9808_2mo-BALF IgG

description: IgG


title: LTBI_9411_6mo-Plasma IgG

description: IgG


title: LTBI_9411_2mo-Plasma IgG

description: IgG


title: LTBI_9208_Pre-Plasma IgG

description: IgG


title: LTBI_9311_6mo-BALF IgG

description: IgG


title: LTBI_9311_2mo-Plasma IgG

description: IgG


title: LTBI_9311_6mo-Plasma IgG

description: IgG


title: LTBI_9208_Pre-BALF IgG

description: IgG


title: LTBI_9311_Pre-BALF IgG

description: IgG


title: LTBI_9311_Pre-Plasma IgG

description: IgG


title: LTBI_9208_6mo-BALF IgG

description: IgG


title: LTBI_9208_2mo-Plasma IgG

description: IgG


title: LTBI_6909_Pre-Plasma IgG

description: IgG


title: LTBI_6909_6mo-Plasma IgG

description: IgG


title: LTBI_9208_6mo-Plasma IgG

description: IgG


title: LTBI_6909_Pre-BALF IgG

description: IgG


title: LTBI_6909_6mo-BALF IgG

description: IgG


title: LTBI_6709_6mo-BALF IgG

description: IgG


title: LTBI_9311_2mo-BALF IgG

description: IgG


title: LTBI_6709_6mo-Plasma IgG

description: IgG


title: LTBI_6709_2mo-BALF IgG

description: IgG


title: LTBI_6609_Pre-BALF IgG

description: IgG


title: LTBI_6609_6mo-Plasma IgG

description: IgG


title: LTBI_6609_6mo-BALF IgG

description: IgG


title: LTBI_9911_6mo-BALF IgG

description: IgG


title: LTBI_6609_2mo-Plasma IgG

description: IgG


title: LTBI_9208_2mo-BALF IgG

description: IgG


title: LTBI_6509_Pre-Plasma IgG

description: IgG


title: LTBI_6509_Pre-BALF IgG

description: IgG


title: LTBI_9411_2mo-BALF IgG

description: IgG


title: LTBI_6509_6mo-Plasma IgG

description: IgG


title: LTBI_6609_2mo-BALF IgG

description: IgG


title: LTBI_6509_6mo-BALF IgG

description: IgG


title: TB_10208_3mo-Plasma IgG

description: IgG


title: LTBI_6909_2mo-BALF IgG

description: IgG


title: LTBI_6709_Pre-Plasma IgG

description: IgG


title: LTBI_6909_2mo-Plasma IgG

description: IgG


title: LTBI_6309_Pre-Plasma IgG

description: IgG


title: LTBI_6509_2mo-BALF IgG

description: IgG


title: LTBI_6309_Pre-BALF IgG

description: IgG


title: LTBI_6509_2mo-Plasma IgG

description: IgG


title: LTBI_6309_6mo-BALF IgG

description: IgG


title: LTBI_6309_2mo-Plasma IgG

description: IgG


title: LTBI_6709_2mo-Plasma IgG

description: IgG


title: LTBI_6609_Pre-Plasma IgG

description: IgG


title: LTBI_4808_2mo-Plasma IgG

description: IgG


title: LTBI_4808_Pre-BALF IgG

description: IgG


title: LTBI_6309_2mo-BALF IgG

description: IgG


title: LTBI_23010_Pre-Plasma IgG

description: IgG


title: LTBI_23010_Pre-BALF IgG

description: IgG


title: LTBI_22810_Pre-BALF IgG

description: IgG


title: LTBI_22810_2mo-BALF IgG

description: IgG


title: LTBI_22710_3mo-Plasma IgG

description: IgG


title: LTBI_22810_2mo-Plasma IgG

description: IgG


title: LTBI_23010_2mo-BALF IgG

description: IgG


title: LTBI_23010_2mo-Plasma IgG

description: IgG


title: LTBI_22810_Pre-Plasma IgG

description: IgG


title: LTBI_21910_Pre-Plasma IgG

description: IgG


title: LTBI_21710_Pre-BALF IgG

description: IgG


title: LTBI_21710_2mo-BALF IgG

description: IgG


title: LTBI_22710_3mo-BALF IgG

description: IgG


title: LTBI_21710_2mo-Plasma IgG

description: IgG


title: LTBI_4808_2mo-BALF IgG

description: IgG


title: LTBI_21610_Pre-BALF IgG

description: IgG


title: LTBI_21610_2mo-Plasma IgG

description: IgG


title: LTBI_21810_2mo-Plasma IgG

description: IgG


title: LTBI_21810_Pre-BALF IgG

description: IgG


title: LTBI_21910_Pre-BALF IgG

description: IgG


title: LTBI_21910_2mo-Plasma IgG

description: IgG


title: LTBI_21810_Pre-Plasma IgG

description: IgG


title: LTBI_21510_Pre-BALF IgG

description: IgG


title: LTBI_21910_2mo-BALF IgG

description: IgG


title: LTBI_21510_Pre-Plasma IgG

description: IgG


title: LTBI_21510_2mo-Plasma IgG

description: IgG


title: LTBI_21610_2mo-BALF IgG

description: IgG


title: LTBI_21510_2mo-BALF IgG

description: IgG


title: LTBI_21810_2mo-BALF IgG

description: IgG


title: LTBI_21408_2mo-BALF IgG

description: IgG


title: LTBI_21408_Pre-BALF IgG

description: IgG


title: LTBI_21308_Pre-Plasma IgG

description: IgG


title: LTBI_21308_Pre-BALF IgG

description: IgG


title: LTBI_21408_2mo-Plasma IgG

description: IgG


title: LTBI_21610_Pre-Plasma IgG

description: IgG


title: LTBI_20808_6mo-Plasma IgG

description: IgG


title: LTBI_21308_2mo-BALF IgG

description: IgG


title: LTBI_21308_2mo-Plasma IgG

description: IgG


title: LTBI_21308_5mo-BALF IgG

description: IgG


title: LTBI_21308_5mo-Plasma IgG

description: IgG


title: LTBI_20808_Pre-Plasma IgG

description: IgG


title: LTBI_20808_6mo-BALF IgG

description: IgG


title: LTBI_20808_3mo-Plasma IgG

description: IgG


title: LTBI_20808_3mo-BALF IgG

description: IgG


title: LTBI_19808_Pre-Plasma IgG

description: IgG


title: LTBI_17906_6mo-Plasma IgG

description: IgG


title: LTBI_20808_Pre-BALF IgG

description: IgG


title: LTBI_19808_Pre-BALF IgG

description: IgG


title: LTBI_17906_2mo-BALF IgG

description: IgG


title: LTBI_17806_6mo-BALF IgG

description: IgG


title: LTBI_19808_2mo-Plasma IgG

description: IgG


title: LTBI_17806_6mo-Plasma IgG

description: IgG


title: LTBI_17906_2mo-Plasma IgG

description: IgG


title: LTBI_19808_2mo-BALF IgG

description: IgG


title: LTBI_19808_5mo-BALF IgG

description: IgG


title: LTBI_19808_5mo-Plasma IgG

description: IgG


title: LTBI_17806_2mo-Plasma IgG

description: IgG


title: LTBI_17906_6mo-BALF IgG

description: IgG


title: LTBI_17806_2mo-BALF IgG

description: IgG


title: LTBI_6709_Pre-BALF IgG

description: IgG


title: LTBI_17606_6mo-BALF IgG

description: IgG


title: LTBI_17706_2mo-Plasma IgG

description: IgG


title: LTBI_17706_6mo-Plasma IgG

description: IgG


title: LTBI_17706_2mo-BALF IgG

description: IgG


title: LTBI_17006_6mo-Plasma IgG

description: IgG


title: LTBI_17706_6mo-BALF IgG

description: IgG


title: LTBI_17606_6mo-Plasma IgG

description: IgG


title: LTBI_17006_2mo-Plasma IgG

description: IgG


title: LTBI_17006_6mo-BALF IgG

description: IgG


title: LTBI_11108_Pre-BALF IgG

description: IgG


title: LTBI_11108_6mo-BALF IgG

description: IgG


title: LTBI_21710_Pre-Plasma IgG

description: IgG


title: LTBI_11108_Pre-Plasma IgG

description: IgG


title: LTBI_17606_2mo-BALF IgG

description: IgG


title: LTBI_17606_2mo-Plasma IgG

description: IgG


title: LTBI_17006_2mo-BALF IgG

description: IgG


title: LTBI_10111_3mo-Plasma IgG

description: IgG


title: LTBI_10111_3mo-BALF IgG

description: IgG


title: LTBI_10011_Pre-Plasma IgG

description: IgG


title: LTBI_10011_6mo-Plasma IgG

description: IgG


title: LTBI_10011_Pre-BALF IgG

description: IgG


title: LTBI_10011_6mo-BALF IgG

description: IgG


title: LTBI_10211_Pre-Plasma IgG

description: IgG


title: LTBI_10708_2mo-BALF IgG

description: IgG


title: LTBI_10408_Pre-Plasma IgG

description: IgG


title: LTBI_11008_2mo-BALF IgG

description: IgG


title: LTBI_11008_Pre-BALF IgG

description: IgG


title: LTBI_10708_Pre-Plasma IgG

description: IgG


title: LTBI_10708_2mo-Plasma IgG

description: IgG


title: LTBI_10708_Pre-BALF IgG

description: IgG


title: LTBI_10011_3mo-BALF IgG

description: IgG


title: LTBI_11108_2mo-BALF IgG

description: IgG


title: LTBI_11008_6mo-BALF IgG

description: IgG


title: LTBI_10011_3mo-Plasma IgG

description: IgG


title: LTBI_10408_2mo-Plasma IgG

description: IgG


title: LTBI_10408_2mo-BALF IgG

description: IgG


title: LTBI_10211_3mo-Plasma IgG

description: IgG


title: LTBI_10211_6mo-BALF IgG

description: IgG


title: LTBI_10211_6mo-Plasma IgG

description: IgG


title: LTBI_10211_Pre-BALF IgG

description: IgG


title: LTBI_10111_6mo-Plasma IgG

description: IgG


title: LTBI_10111_6mo-BALF IgG

description: IgG


title: LTBI_10408_Pre-BALF IgG

description: IgG


title: LTBI_10408_6mo-BALF IgG

description: IgG


title: LTBI_10211_3mo-BALF IgG

description: IgG


title: LTBI_10408_6mo-Plasma IgG

description: IgG


title: LTBI_10111_Pre-BALF IgG

description: IgG


title: LTBI_10111_Pre-Plasma IgG

description: IgG


title: TB_9711_Pre-BALF IgA

description: IgA

label: Cy3 Goat Anti-Human Serum IgA

label_protocol: Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB 2337721)


title: TB_9711_Pre-Plasma IgA

description: IgA


title: TB_9611_3mo-Plasma IgA

description: IgA


title: TB_9611_Pre-BALF IgA

description: IgA


title: TB_9611_Pre-Plasma IgA

description: IgA


title: TB_9711_3mo-BALF IgA

description: IgA


title: TB_7009_6mo-BALF IgA

description: IgA


title: TB_7009_2mo-BALF IgA

description: IgA


title: TB_9711_6mo-Plasma IgA

description: IgA


title: TB_7009_2mo-Plasma IgA

description: IgA


title: TB_9711_3mo-Plasma IgA

description: IgA


title: TB_9511_Pre-BALF IgA

description: IgA


title: TB_9611_3mo-BALF IgA

description: IgA


title: TB_9511_6mo-Plasma IgA

description: IgA


title: TB_9511_6mo-BALF IgA

description: IgA


title: TB_9711_6mo-BALF IgA

description: IgA


title: TB_7009_Pre-BALF IgA

description: IgA


title: TB_9511_Pre-Plasma IgA

description: IgA


title: TB_7009_Pre-Plasma IgA

description: IgA


title: TB_7009_6mo-Plasma IgA

description: IgA


title: TB_9511_3mo-Plasma IgA

description: IgA


title: TB_9511_3mo-BALF IgA

description: IgA


title: TB_6809_Pre-BALF IgA

description: IgA


title: TB_6809_2mo-Plasma IgA

description: IgA


title: TB_23110_2mo-Plasma IgA

description: IgA


title: TB_23110_2mo-BALF IgA

description: IgA


title: TB_4108_2mo-BALF IgA

description: IgA


title: TB_22910_Pre-BALF IgA

description: IgA


title: TB_3808_2mo-Plasma IgA

description: IgA


title: TB_4108_2mo-Plasma IgA

description: IgA


title: TB_3808_2mo-BALF IgA

description: IgA


title: TB_22910_Pre-Plasma IgA

description: IgA


title: TB_23210_2mo-BALF IgA

description: IgA


title: TB_23210_2mo-Plasma IgA

description: IgA


title: TB_23110_Pre-BALF IgA

description: IgA


title: TB_23210_Pre-Plasma IgA

description: IgA


title: TB_3808_Pre-Plasma IgA

description: IgA


title: TB_22910_2mo-Plasma IgA

description: IgA


title: TB_3808_Pre-BALF IgA

description: IgA


title: TB_22910_2mo-BALF IgA

description: IgA


title: TB_22010_Pre-BALF IgA

description: IgA


title: TB_4508_2mo-Plasma IgA

description: IgA


title: TB_4508_Pre-BALF IgA

description: IgA


title: TB_6809_2mo-BALF IgA

description: IgA


title: TB_22010_6mo-BALF IgA

description: IgA


title: TB_22010_6mo-Plasma IgA

description: IgA


title: TB_23110_Pre-Plasma IgA

description: IgA


title: TB_22010_Pre-Plasma IgA

description: IgA


title: TB_23210_Pre-BALF IgA

description: IgA


title: TB_4108_Pre-BALF IgA

description: IgA


title: TB_4508_2mo-BALF IgA

description: IgA


title: TB_21410_Pre-Plasma IgA

description: IgA


title: TB_21410_Pre-BALF IgA

description: IgA


title: TB_21410_2mo-BALF IgA

description: IgA


title: TB_20708_Pre-Plasma IgA

description: IgA


title: TB_20708_Pre-BALF IgA

description: IgA


title: TB_21310_2mo-Plasma IgA

description: IgA


title: TB_20708_5mo-Plasma IgA

description: IgA


title: TB_21310_2mo-BALF IgA

description: IgA


title: TB_21310_Pre-Plasma IgA

description: IgA


title: TB_21310_Pre-BALF IgA

description: IgA


title: TB_20708_5mo-BALF IgA

description: IgA


title: TB_6809_Pre-Plasma IgA

description: IgA


title: TB_10908_2mo-Plasma IgA

description: IgA


title: TB_10908_6mo-BALF IgA

description: IgA


title: TB_17406_6mo-BALF IgA

description: IgA


title: TB_20708_2mo-Plasma IgA

description: IgA


title: TB_17406_2mo-Plasma IgA

description: IgA


title: TB_10208_Pre-Plasma IgA

description: IgA


title: TB_10908_2mo-BALF IgA

description: IgA


title: TB_10808_6mo-Plasma IgA

description: IgA


title: TB_10808_6mo-BALF IgA

description: IgA


title: TB_10808_2mo-Plasma IgA

description: IgA


title: TB_10808_2mo-BALF IgA

description: IgA


title: TB_10208_Pre-BALF IgA

description: IgA


title: TB_17406_2mo-BALF IgA

description: IgA


title: TB_17106_6mo-Plasma IgA

description: IgA


title: TB_17406_1mo-plasma IgA

description: IgA


title: TB_10908_Pre-BALF IgA

description: IgA


title: TB_10908_6mo-Plasma IgA

description: IgA


title: TB_17406_6mo-Plasma IgA

description: IgA


title: TB_18106_2mo-Plasma IgA

description: IgA


title: TB_18106_2mo-BALF IgA

description: IgA


title: TB_20708_2mo-BALF IgA

description: IgA


title: TB_18106_6mo-BALF IgA

description: IgA


title: TB_20708_1mo-plasma IgA

description: IgA


title: TB_18106_6mo-Plasma IgA

description: IgA


title: TB_10908_Pre-Plasma IgA

description: IgA


title: TB_21410_2mo-Plasma IgA

description: IgA


title: TB_17106_2mo-BALF IgA

description: IgA


title: TB_17106_1mo-plasma IgA

description: IgA


title: TB_17106_2mo-Plasma IgA

description: IgA


title: TB_10208_3mo-Plasma IgA

description: IgA


title: TB_10208_6mo-Plasma IgA

description: IgA


title: TB_10208_3mo-BALF IgA

description: IgA


title: LTBI_9911_Pre-Plasma IgA

description: IgA


title: LTBI_9911_6mo-Plasma IgA

description: IgA


title: LTBI_9911_6mo-BALF IgA

description: IgA


title: TB_10208_6mo-BALF IgA

description: IgA


title: LTBI_9911_Pre-BALF IgA

description: IgA


title: LTBI_9311_Pre-BALF IgA

description: IgA


title: LTBI_9911_3mo-Plasma IgA

description: IgA


title: LTBI_9311_6mo-BALF IgA

description: IgA


title: LTBI_9811_Pre-BALF IgA

description: IgA


title: LTBI_9311_2mo-Plasma IgA

description: IgA


title: LTBI_9311_2mo-BALF IgA

description: IgA


title: TB_17106_6mo-BALF IgA

description: IgA


title: LTBI_9811_3mo-BALF IgA

description: IgA


title: LTBI_9311_6mo-Plasma IgA

description: IgA


title: LTBI_9411_2mo-BALF IgA

description: IgA


title: LTBI_9208_6mo-BALF IgA

description: IgA


title: LTBI_9311_Pre-Plasma IgA

description: IgA


title: LTBI_9811_Pre-Plasma IgA

description: IgA


title: LTBI_9808_6mo-BALF IgA

description: IgA


title: LTBI_9808_Pre-BALF IgA

description: IgA


title: LTBI_9208_2mo-Plasma IgA

description: IgA


title: LTBI_9808_2mo-Plasma IgA

description: IgA


title: LTBI_9808_6mo-Plasma IgA

description: IgA


title: LTBI_6909_Pre-Plasma IgA

description: IgA


title: LTBI_6909_Pre-BALF IgA

description: IgA


title: LTBI_9208_2mo-BALF IgA

description: IgA


title: LTBI_6909_6mo-Plasma IgA

description: IgA


title: LTBI_6709_2mo-Plasma IgA

description: IgA


title: LTBI_6709_6mo-BALF IgA

description: IgA


title: LTBI_9411_6mo-BALF IgA

description: IgA


title: LTBI_9411_2mo-Plasma IgA

description: IgA


title: LTBI_9411_6mo-Plasma IgA

description: IgA


title: LTBI_9411_Pre-BALF IgA

description: IgA


title: LTBI_6609_2mo-BALF IgA

description: IgA


title: LTBI_6909_2mo-BALF IgA

description: IgA


title: LTBI_6709_Pre-Plasma IgA

description: IgA


title: LTBI_6909_2mo-Plasma IgA

description: IgA


title: LTBI_9411_Pre-Plasma IgA

description: IgA


title: LTBI_9808_2mo-BALF IgA

description: IgA


title: LTBI_6609_2mo-Plasma IgA

description: IgA


title: LTBI_6609_6mo-BALF IgA

description: IgA


title: LTBI_6909_6mo-BALF IgA

description: IgA


title: LTBI_9208_Pre-Plasma IgA

description: IgA


title: LTBI_9208_6mo-Plasma IgA

description: IgA


title: LTBI_9208_Pre-BALF IgA

description: IgA


title: LTBI_6609_6mo-Plasma IgA

description: IgA


title: LTBI_6709_2mo-BALF IgA

description: IgA


title: LTBI_6609_Pre-BALF IgA

description: IgA


title: LTBI_6509_Pre-BALF IgA

description: IgA


title: LTBI_9911_3mo-BALF IgA

description: IgA


title: LTBI_6609_Pre-Plasma IgA

description: IgA


title: LTBI_9811_3mo-Plasma IgA

description: IgA


title: LTBI_9811_6mo-Plasma IgA

description: IgA


title: LTBI_9811_6mo-BALF IgA

description: IgA


title: LTBI_6709_6mo-Plasma IgA

description: IgA


title: LTBI_6709_Pre-BALF IgA

description: IgA


title: LTBI_6509_Pre-Plasma IgA

description: IgA


title: LTBI_6509_2mo-Plasma IgA

description: IgA


title: LTBI_6509_6mo-BALF IgA

description: IgA


title: LTBI_6309_Pre-BALF IgA

description: IgA


title: LTBI_6509_2mo-BALF IgA

description: IgA


title: LTBI_6309_Pre-Plasma IgA

description: IgA


title: LTBI_4808_2mo-BALF IgA

description: IgA


title: LTBI_6309_6mo-BALF IgA

description: IgA


title: LTBI_6309_2mo-Plasma IgA

description: IgA


title: LTBI_23010_Pre-Plasma IgA

description: IgA


title: LTBI_6309_2mo-BALF IgA

description: IgA


title: LTBI_4808_2mo-Plasma IgA

description: IgA


title: LTBI_4808_Pre-BALF IgA

description: IgA


title: LTBI_23010_2mo-Plasma IgA

description: IgA


title: LTBI_23010_Pre-BALF IgA

description: IgA


title: LTBI_22710_3mo-Plasma IgA

description: IgA


title: LTBI_22810_Pre-Plasma IgA

description: IgA


title: LTBI_22810_2mo-Plasma IgA

description: IgA


title: LTBI_21910_Pre-Plasma IgA

description: IgA


title: LTBI_22710_3mo-BALF IgA

description: IgA


title: LTBI_23010_2mo-BALF IgA

description: IgA


title: LTBI_22810_2mo-BALF IgA

description: IgA


title: LTBI_21810_2mo-BALF IgA

description: IgA


title: LTBI_6509_6mo-Plasma IgA

description: IgA


title: LTBI_21710_2mo-BALF IgA

description: IgA


title: LTBI_21710_2mo-Plasma IgA

description: IgA


title: LTBI_21710_Pre-Plasma IgA

description: IgA


title: LTBI_21710_Pre-BALF IgA

description: IgA


title: LTBI_21810_2mo-Plasma IgA

description: IgA


title: LTBI_21810_Pre-Plasma IgA

description: IgA


title: LTBI_21910_Pre-BALF IgA

description: IgA


title: LTBI_21810_Pre-BALF IgA

description: IgA


title: LTBI_21910_2mo-Plasma IgA

description: IgA


title: LTBI_22810_Pre-BALF IgA

description: IgA


title: LTBI_21510_Pre-BALF IgA

description: IgA


title: LTBI_21610_2mo-Plasma IgA

description: IgA


title: LTBI_21610_Pre-BALF IgA

description: IgA


title: LTBI_21610_2mo-BALF IgA

description: IgA


title: LTBI_21910_2mo-BALF IgA

description: IgA


title: LTBI_21308_Pre-Plasma IgA

description: IgA


title: LTBI_21408_2mo-BALF IgA

description: IgA


title: LTBI_21610_Pre-Plasma IgA

description: IgA


title: LTBI_21408_Pre-BALF IgA

description: IgA


title: LTBI_21408_2mo-Plasma IgA

description: IgA


title: LTBI_21510_2mo-BALF IgA

description: IgA


title: LTBI_21510_2mo-Plasma IgA

description: IgA


title: LTBI_21510_Pre-Plasma IgA

description: IgA


title: LTBI_20808_3mo-BALF IgA

description: IgA


title: LTBI_21308_5mo-Plasma IgA

description: IgA


title: LTBI_17806_6mo-Plasma IgA

description: IgA


title: LTBI_17806_2mo-Plasma IgA

description: IgA


title: LTBI_17806_6mo-BALF IgA

description: IgA


title: LTBI_17906_6mo-Plasma IgA

description: IgA


title: LTBI_17906_6mo-BALF IgA

description: IgA


title: LTBI_21308_2mo-BALF IgA

description: IgA


title: LTBI_21308_5mo-BALF IgA

description: IgA


title: LTBI_21308_2mo-Plasma IgA

description: IgA


title: LTBI_19808_Pre-Plasma IgA

description: IgA


title: LTBI_21308_Pre-BALF IgA

description: IgA


title: LTBI_19808_5mo-Plasma IgA

description: IgA


title: LTBI_19808_Pre-BALF IgA

description: IgA


title: LTBI_20808_Pre-BALF IgA

description: IgA


title: LTBI_20808_Pre-Plasma IgA

description: IgA


title: LTBI_17706_6mo-BALF IgA

description: IgA


title: LTBI_17706_6mo-Plasma IgA

description: IgA


title: LTBI_17706_2mo-Plasma IgA

description: IgA


title: LTBI_17706_2mo-BALF IgA

description: IgA


title: LTBI_17606_6mo-Plasma IgA

description: IgA


title: LTBI_19808_5mo-BALF IgA

description: IgA


title: LTBI_19808_2mo-BALF IgA

description: IgA


title: LTBI_19808_2mo-Plasma IgA

description: IgA


title: LTBI_17606_2mo-Plasma IgA

description: IgA


title: LTBI_17606_2mo-BALF IgA

description: IgA


title: LTBI_17906_2mo-BALF IgA

description: IgA


title: LTBI_17906_2mo-Plasma IgA

description: IgA


title: LTBI_17006_6mo-Plasma IgA

description: IgA


title: LTBI_17006_6mo-BALF IgA

description: IgA


title: LTBI_20808_3mo-Plasma IgA

description: IgA


title: LTBI_20808_6mo-BALF IgA

description: IgA


title: LTBI_20808_6mo-Plasma IgA

description: IgA


title: LTBI_17806_2mo-BALF IgA

description: IgA


title: LTBI_11108_Pre-BALF IgA

description: IgA


title: LTBI_11108_Pre-Plasma IgA

description: IgA


title: LTBI_11108_6mo-BALF IgA

description: IgA


title: LTBI_17006_2mo-BALF IgA

description: IgA


title: LTBI_17606_6mo-BALF IgA

description: IgA


title: LTBI_11008_6mo-BALF IgA

description: IgA


title: LTBI_10708_2mo-Plasma IgA

description: IgA


title: LTBI_11008_2mo-BALF IgA

description: IgA


title: LTBI_11008_Pre-BALF IgA

description: IgA


title: LTBI_10708_Pre-Plasma IgA

description: IgA


title: LTBI_11108_2mo-BALF IgA

description: IgA


title: LTBI_17006_2mo-Plasma IgA

description: IgA


title: LTBI_10708_2mo-BALF IgA

description: IgA


title: LTBI_10408_Pre-Plasma IgA

description: IgA


title: LTBI_10408_Pre-BALF IgA

description: IgA


title: LTBI_10408_6mo-Plasma IgA

description: IgA


title: LTBI_10408_2mo-Plasma IgA

description: IgA


title: LTBI_10211_Pre-Plasma IgA

description: IgA


title: LTBI_10211_6mo-Plasma IgA

description: IgA


title: LTBI_10211_Pre-BALF IgA

description: IgA


title: LTBI_10211_3mo-BALF IgA

description: IgA


title: LTBI_10211_3mo-Plasma IgA

description: IgA


title: LTBI_10211_6mo-BALF IgA

description: IgA


title: LTBI_10708_Pre-BALF IgA

description: IgA


title: LTBI_10111_Pre-BALF IgA

description: IgA


title: LTBI_10111_6mo-Plasma IgA

description: IgA


title: LTBI_10111_3mo-BALF IgA

description: IgA


title: LTBI_10111_Pre-Plasma IgA

description: IgA


title: LTBI_10111_6mo-BALF IgA

description: IgA


title: hepatic exosomes, hsp90ab1 KO mice, HFFC diet 3

city: Nanjing

first: Weitao

last: Zhang

address: longmian road

institute: China Pharmaceutical University

data_processing: The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam mapping. The software miRDeep2 was used to predict novel miRNA by exploring the secondary structure, and Piano was used to predict piRNAs. RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference. To annotate gene functions, all target genes were aligned against the Kyoto Encyclopedia of Genes (KEGG) and Gene Ontology (GO) database. GO enrichment analysis and KEGG enrichment analysis of target genes were performed using phyper, a function of R. The P-value was corrected using the Bonferroni method, and a corrected P-value ≤ 0.05 was taken as a threshold. GO terms or KEGG terms fulfilling this condition were defined as significantly enriched terms.

source_name: exosome in liver

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA)
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

value: exosome in liver

value: Hsp90beta KO

value: HFFC diet


title: LTBI_10011_Pre-Plasma IgA

description: IgA


title: hepatic exosomes, hsp90ab1 KO mice, HFFC diet 1


title: LTBI_10011_Pre-BALF IgA

description: IgA


title: LTBI_10011_6mo-BALF IgA

description: IgA


title: hepatic exosomes, hsp90ab1 flox mice, HFFC diet 2

value: Hsp90beta flox


title: LTBI_10011_6mo-Plasma IgA

description: IgA


title: hepatic exosomes, hsp90ab1 KO mice, HFFC diet 2


title: LTBI_10408_2mo-BALF IgA

description: IgA


title: hepatic exosomes, hsp90ab1 flox mice, HFFC diet 3


title: hepatic exosomes, hsp90ab1 flox mice, chow diet 2

value: chow diet


title: LTBI_10408_6mo-BALF IgA

description: IgA


title: hepatic exosomes, hsp90ab1 flox mice, HFFC diet 1


title: hepatic exosomes, hsp90ab1 flox mice, chow diet 1


title: Hepa 1-6, Shh 2

source_name: Hepa 1-6

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Hepa 1-6 were lysed in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: Hepa 1-6

value: mouse hepatocyte

value: Shh


title: Hepa 1-6, Shh 3


title: Hepa 1-6, Shh 1


title: Hepa 1-6, vehicle 3

value: vehicle


title: LTBI_10111_3mo-Plasma IgA

description: IgA


title: LTBI_10011_3mo-BALF IgA

description: IgA


title: LTBI_10011_3mo-Plasma IgA

description: IgA


title: C1K-2

city: Kaohsiung

first: Wei

middle: Shiung

last: Lian

address: No.123, Dapi Rd., Niaosong Dist.,

department: Department of Medic al Research

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

data_processing:
CLC Genomics Workbench v10.1 software used for basecalling and operated  based on Mortazavi et al., 2008.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (limit = 0.01), then mapped to Mus GRCm38 whole genome database.
Mapping statistics parameters : Minimum length fraction (applies to long reads) = 0.5, Minimum similarity fraction (applies to long reads) = 0.8, Maximum number of hits for a read = 10.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008. RPKM＝total exon reads / mapped reads (millions) x exon length (KB)
Comparison for a two-group experiment to interpretation the fold change of gene.
Correlation Analysis and calculation by the Pearson correlation method.
PCA analysis used CLC Genomics Workbench v10.1 (PCA for RNA-Seq) for visualization.
Heatmap analysis is based on transforming the genetic RPKM values between individuals by Z-score, then using TreeView (program) to visualization.
Pathway analysis uses the KEGG Automatic Annotation Server (KAAS) to predict the KEGG Orthology (KO) ID and maps ID to the biosynthesis pathway. Then use the R suite "pathview" to compare the KEGG database with genes with more than twice the expression between individuals and P-value <= 0.05.
Genome_build: Mus GRCm38
Supplementary_files_format_and_content: Wig files were generated and contain

source_name: calvarial

growth_protocol: Mice primary osteoblast isolated from 7 day pup's calvarial and following the previously culture protocol (Bonekey Rep. 2016. 5:818. ).

extract_protocol:
Primary osteoblast were cultured for harvested 1x10^8 cells for RNA extraction and subjected to RNA-sequencing.
Using MGIEasy mRNA Library Prep Kit (MGI Tech Co., Ltd., China) for mRNA enrichment, purification, and reverse transcription for sequence analysis.

tag: cell

value: osteoblast cell

value: postnatal day 7

value: Col1alpha1-UTX KO


title: Hepa 1-6, vehicle 2


title: hepatic exosomes, hsp90ab1 flox mice, chow diet 3


title: WT-2

value: wild type


title: C1K-3


title: HUVECs HEY1-3KR-2

data_processing:
Quality control was performed using FastQC v0.19.7.
The SAM files generated from HISAT2 2.1.0 were brought into BAM format using SAMtools v1.9.
We generated read counts with StringTie v1.3.3b.
Assembly: Sequencing reads were aligned using hg38 assembly of the human genome.
Supplementary files format and content: HUVEC_gene_exp.xlsx file includes mRNA expression for each sample.

organism: Homo sapiens

source_name: umbilical vein

growth_protocol: HUVECs were cultured in EGM-2 medium.

extract_protocol:
Total RNA was extracted using the E.Z.N.A. Total RNA Kit (Omega) according to the manufacturer's instructions.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

treatment_protocol: HUVECs were transduced with HEY1-WT or HEY1-3KR adenoviral vectors at an MOI of 30-50 viral particles per cell in Opti-MEM (Gibco) and incubated for 4-6 hours. The medium was then replaced with EGM-2 medium, and the cells were cultured for an additional 48 hours.

value: umbilical vein

value: HUVECs

value: Endothelial cells

value: overexpressing HEY1-3KR

value: Adenovirus


title: WT-1


title: HUVECs HEY1-3KR-3


title: WT-3


title: Hepa 1-6, vehicle 1


title: HUVECs HEY1-3KR-2-input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.2.5. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to Fragments Per Kilobase Million, fpkmm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.01
Assembly: Sequencing reads were aligned using hg38 assembly of the human genome.
Supplementary files format and content: Diff_peaks.xlsx file includes peaks for each sample.

extract_protocol:
The ChIP assay was constructed  using the EZ ChIP Chromatin Immunoprecipitation Kit (Millipore) according to the manufacturer's instructions.
The library construction was done by BGI.


title: HUVECs HEY1-3KR-2-chip


title: HUVECs HEY1-WT-1-input

value: overexpressing HEY1-WT


title: HUVECs HEY1-3KR-1


title: HUVECs HEY1-WT-2


title: HUVECs HEY1-WT-2-input


title: HUVECs HEY1-3KR-1-input


title: HUVECs HEY1-WT-2-chip


title: HUVECs HEY1-WT-1-chip


title: HUVECs HEY1-WT-3


title: HUVECs LacZ-1

value: overexpressing LacZ


title: HUVECs LacZ-3


title: HUVECs LacZ-2


title: HUVECs HEY1-3KR-1-chip


title: HUVECs HEY1-WT-1


title: C1K-1


title: TB_9711_Pre-BALF IgG

description: IgG

hyb_protocol: Slides with 16 arrays on each were blocked SuperBlock (Thermo Fisher Scientific), then incubated with BALF (1:35) or plasma (1:100) diluted in phosphate buffered saline with 5% skim milk and 0.2% tween 20 (PBST) for 16 hrs at 4°C. After washing with 5% skim milk and 0.2% tween 20 (PBST) (3 x 5 min), slides were incubated with Cy3 Goat Anti-Human Serum IgA (Jackson ImmunoResearch Labs Cat# 109-165-011, RRID:AB_2337721) and Alexa 647 Goat Anti-Human IgG (Jackson ImmunoResearch Labs Cat# 109-605-008, RRID:AB_2337882; diluted at 1:200 in 5% skim milk and 0.2% tween 20 (PBST)) for 2 hrs at 4°C

scan_protocol: Slides were scanned at 635 nm and 535 nm with a Tecan PowerScanner, and images were quantified with the ArrayPro Analyzer Software (Media Cybernetics, Inc.).

data_processing: Spots were considered reactive if the ratio of the median fluorescent intensity (MFI) of the gene was greater than 1.4 x the median of negative control genes

value: Symptomatic uncontrolled Mtb infection/TB disease


title: TB_9711_Pre-Plasma IgG

description: IgG


title: TB_9611_Pre-BALF IgG

description: IgG


title: TB_9511_6mo-Plasma IgG

description: IgG


title: TB_9511_6mo-BALF IgG

description: IgG


title: TB_9711_6mo-BALF IgG

description: IgG


title: TB_9611_3mo-BALF IgG

description: IgG


title: TB_9711_3mo-BALF IgG

description: IgG


title: TB_9611_3mo-Plasma IgG

description: IgG


title: TB_9611_Pre-Plasma IgG

description: IgG


title: TB_9711_6mo-Plasma IgG

description: IgG


title: TB_9711_3mo-Plasma IgG

description: IgG


title: TB_9511_Pre-Plasma IgG

description: IgG


title: TB_9511_Pre-BALF IgG

description: IgG


title: TB_9511_3mo-BALF IgG

description: IgG


title: TB_9511_3mo-Plasma IgG

description: IgG


title: TB_4508_2mo-Plasma IgG

description: IgG


title: TB_4508_Pre-BALF IgG

description: IgG


title: TB_7009_6mo-BALF IgG

description: IgG


title: TB_7009_2mo-Plasma IgG

description: IgG


title: TB_7009_Pre-BALF IgG

description: IgG


title: TB_6809_Pre-Plasma IgG

description: IgG


title: TB_6809_2mo-Plasma IgG

description: IgG


title: TB_7009_6mo-Plasma IgG

description: IgG


title: TB_7009_Pre-Plasma IgG

description: IgG


title: TB_7009_2mo-BALF IgG

description: IgG


title: TB_4108_Pre-BALF IgG

description: IgG


title: TB_4108_2mo-Plasma IgG

description: IgG


title: TB_6809_Pre-BALF IgG

description: IgG


title: TB_4108_2mo-BALF IgG

description: IgG


title: TB_4508_2mo-BALF IgG

description: IgG


title: TB_23110_Pre-BALF IgG

description: IgG


title: TB_3808_2mo-Plasma IgG

description: IgG


title: TB_3808_Pre-BALF IgG

description: IgG


title: TB_22010_6mo-BALF IgG

description: IgG


title: TB_22910_Pre-Plasma IgG

description: IgG


title: TB_23110_Pre-Plasma IgG

description: IgG


title: TB_3808_Pre-Plasma IgG

description: IgG


title: TB_23210_Pre-Plasma IgG

description: IgG


title: TB_22910_2mo-Plasma IgG

description: IgG


title: TB_23110_2mo-BALF IgG

description: IgG


title: TB_21310_Pre-Plasma IgG

description: IgG


title: TB_23210_2mo-BALF IgG

description: IgG


title: TB_3808_2mo-BALF IgG

description: IgG


title: TB_23210_2mo-Plasma IgG

description: IgG


title: TB_23210_Pre-BALF IgG

description: IgG


title: TB_22010_Pre-Plasma IgG

description: IgG


title: TB_22910_Pre-BALF IgG

description: IgG


title: TB_21410_2mo-BALF IgG

description: IgG


title: TB_21310_Pre-BALF IgG

description: IgG


title: TB_23110_2mo-Plasma IgG

description: IgG


title: TB_22010_Pre-BALF IgG

description: IgG


title: TB_21410_2mo-Plasma IgG

description: IgG


title: TB_22910_2mo-BALF IgG

description: IgG


title: TB_21410_Pre-BALF IgG

description: IgG


title: TB_21410_Pre-Plasma IgG

description: IgG


title: TB_22010_6mo-Plasma IgG

description: IgG


title: TB_21310_2mo-Plasma IgG

description: IgG


title: TB_21310_2mo-BALF IgG

description: IgG


title: TB_20708_Pre-Plasma IgG

description: IgG


title: TB_20708_Pre-BALF IgG

description: IgG


title: TB_20708_5mo-Plasma IgG

description: IgG


title: TB_6809_2mo-BALF IgG

description: IgG


title: TB_17406_6mo-Plasma IgG

description: IgG


title: TB_18106_6mo-Plasma IgG

description: IgG


title: TB_17406_2mo-Plasma IgG

description: IgG


title: TB_20708_2mo-BALF IgG

description: IgG


title: TB_18106_2mo-Plasma IgG

description: IgG


title: TB_18106_6mo-BALF IgG

description: IgG


title: TB_17406_6mo-BALF IgG

description: IgG


title: TB_9711_early-plasma IgM

description: IgM

label: Anti-human  IgM  DyLight™ 649

source_name: early-plasma

label_protocol: Anti-human IgM (mu chain) (GOAT) Antibody DyLight™ 649 Conjugated - 609-143-007 (Rockland)

value: Symtomatic uncontrolled Mtb infection/TB disease


title: TB_9711_early-BALF IgM

description: IgM

source_name: early-BALF


title: TB_20708_5mo-BALF IgG

description: IgG


title: TB_9611_pre-BALF IgM

description: IgM

source_name: pre-BALF


title: TB_9611_early-plasma IgM

description: IgM


title: TB_9611_pre-plasma IgM

description: IgM

source_name: pre-plasma


title: TB_18106_2mo-BALF IgG

description: IgG


title: TB_17106_2mo-Plasma IgG

description: IgG


title: TB_17106_2mo-BALF IgG

description: IgG


title: TB_10908_Pre-Plasma IgG

description: IgG


title: TB_17106_6mo-Plasma IgG

description: IgG


title: TB_17106_6mo-BALF IgG

description: IgG


title: TB_20708_2mo-Plasma IgG

description: IgG


title: TB_10908_6mo-Plasma IgG

description: IgG


title: TB_17406_2mo-BALF IgG

description: IgG


title: TB_9611_early-BALF IgM

description: IgM


title: TB_9711_pre-plasma IgM

description: IgM

label: Anti-human  IgM  DyLight™ 650


title: TB_9711_pre-BALF IgM

description: IgM


title: TB_10908_Pre-BALF IgG

description: IgG


title: TB_9511_early-plasma IgM

description: IgM


title: TB_9511_early-BALF IgM

description: IgM


title: TB_10908_2mo-Plasma IgG

description: IgG


title: TB_10908_6mo-BALF IgG

description: IgG


title: TB_7009_pre-plasma IgM

description: IgM


title: TB_9511_pre-plasma IgM

description: IgM


title: TB_9511_pre-BALF IgM

description: IgM


title: TB_10908_2mo-BALF IgG

description: IgG


title: TB_7009_early-BALF IgM

description: IgM


title: TB_10808_6mo-Plasma IgG

description: IgG


title: TB_7009_early-plasma IgM

description: IgM


title: TB_6809_pre-plasma IgM

description: IgM


title: TB_6809_pre-BALF IgM

description: IgM


title: TB_10808_6mo-BALF IgG

description: IgG


title: TB_6809_early-BALF IgM

description: IgM


title: TB_10808_2mo-Plasma IgG

description: IgG


title: TB_4508_pre-BALF IgM

description: IgM


title: TB_4508_early-plasma IgM

description: IgM


title: TB_7009_pre-BALF IgM

description: IgM


title: MCSF, Polysome-associated PolyA RNA

city: Syracuse

first: Gary

last: Chan

address: 750 East Adams Street

institute: SUNY Upstate Medical University

data_processing:
Partek Flow Genomics Analysis Software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow(parameter- Phred >20)
Trimmed sequence reads were mapped to hg38 using Partek Flow (parameters- mismatch match ratio 0.3:  mismatch read ratio 1: Extra alignment score 2: insertion penalty -2: Deletion penalty -2)
Read count extraction and quantile normalization were performed using the Partek Flow analysis suite
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Peripheral Blood Monocyte

extract_protocol:
RNA was harvested using TRIzol Reagent (Sigma-Aldrich). Equal quantities of total RNA were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina's stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Peripheral Blood Monocyte

value: WT

value: MCSF (100ng/mL)

tag: time


title: TB_4508_early-BALF IgM

description: IgM


title: TB_4108_pre-BALF IgM

description: IgM


title: MCSF, Bulk PolyA RNA


title: TB_10808_2mo-BALF IgG

description: IgG


title: TB_6809_early-plasma IgM

description: IgM


title: TB_4108_early-plasma IgM

description: IgM


title: GMCSF, Polysome-associated PolyA RNA

value: GMCSF (100ng/mL)


title: TB_4108_early-BALF IgM

description: IgM


title: TB_3808_pre-plasma IgM

description: IgM


title: TB_3808_pre-BALF IgM

description: IgM


title: GMCSF, Bulk PolyA RNA


title: TB_10208_Pre-BALF IgG

description: IgG


title: TB_3808_early-plasma IgM

description: IgM


title: TB_10208_6mo-Plasma IgG

description: IgG


title: TB_3808_early-BALF IgM

description: IgM


title: HCMV, Polysome-associated PolyA RNA

value: HCMV (TB40E)


title: TB_10208_Pre-Plasma IgG

description: IgG


title: TB_23210_pre-BALF IgM

description: IgM


title: TB_23210_pre-plasma IgM

description: IgM


title: HCMV, Bulk PolyA RNA


title: TB_23210_early-plasma IgM

description: IgM


title: Mock, Polysome-associated PolyA RNA

value: Mock


title: TB_23210_early-BALF IgM

description: IgM


title: TB_23110_pre-plasma IgM

description: IgM


title: Mock, Bulk PolyA RNA


title: TB_23110_pre-BALF IgM

description: IgM


title: TB_23110_early-plasma IgM

description: IgM


title: TB_23110_early-BALF IgM

description: IgM


title: TB_22910_early-plasma IgM

description: IgM


title: TB_22910_pre-BALF IgM

description: IgM


title: TB_22910_pre-plasma IgM

description: IgM


title: TB_22910_early-BALF IgM

description: IgM