title: PASMC.18mg_rep7

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: PASMC

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: PASMC and AECII were isolated from C57Bl/6J mice.   After isolation PASMC were kept undisturbed for 5 day, then the iron particle were removed and seeded in a new culture dish. When the cells were confluent, they were seeded in to passage 1. Smooth muscle culture medium containing supplements, 1 % Normocin and 15% fetal bovine serum (FBS).   Isolated AECII were cultured in AECII culture medium (DMEM + 2% L-Glutamin + 1% Pen/strep + 10% FBS) on 24 well plate (300,000 cells/well). 24hr after isolation, AECII were exposed to 15% ECVE for 24hr.  Both cells were cultured at 37oC in a humidified atmosphere with 5% CO2, 21% O2.

extract_protocol: QIAgen Rneasy Mini Kit

treatment_protocol: Cells were treated with 15% ECVE for 24hr. ECVE was prepared from 2 different electronic liquids (e-liquids) [0mg/ml nicotine and 18 mg/ml nicotine].  After 24hr after treatment cells were harvested and RNA was isolated according to the manufacture's protocol.

value: PASMC

value: smoke

tag: concentration


title: PASMC.18mg_rep8

status: Public on May 01 2023

type: RNA

country: Germany

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

tag: treatment


title: PASMC.Ctrl_rep7

value: room air

value: Ctrl


title: 110507_4_S59

type: SRA

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

country: USA

institute: Colorado School of Public Health

library_source: transcriptomic

data_processing:
FASTQ files for the two runs for each sample were concatenated. Reads were trimmed to remove adapters and low-quality base calls with Cutadapt (13). Reads were aligned to the reference human genome (hg19) with use of TopHat2 (14). Individual samples were quantified against the most up-to-date Ensembl reference transcriptome with the RSEM (RNA-Seq by Expectation-Maximization) algorithm (15). The expected counts were used for further processing and normalization. For removal of any technical variation, the data first were quantile normalized with DESeq2 (16) and then normalized with removal of unwanted variation (17). Based on scree plots, we adjusted for one factor, as it explained the most variability in the data. The data were then transformed with the regularized log function (16). The transformed data were used in all subsequent analyses. We filtered out genes if ≥20% of the samples did not have a read mapped to the gene (transcripts per million value of 0) or the average transcripts per million value across all samples was <1. A total of 12,477 genes passed the filtering criteria.
Assembly: hg19/Ensembl.v87
Supplementary files format and content: RSEM.RUVs.k1.rlog.Dec2020.csv  Final normalized and cleaned dataset used in analyses, each row a gene and column a sample.
Supplementary files format and content: RSEM.estCounts.geneLevel.csv Estimated counts per gene from the RSEM output.  Not normalized or cleaned.

organism: Homo sapiens

source_name: blood

extract_protocol:
In DAISY, venous blood samples are collected at 9, 15, and 24 months and yearly thereafter. Beginning in November of 2007, RNA samples were collected from all DAISY participants with Tempus tubes (Applied Biosystems). We selected samples from two visits (termed IA-1 and IA-2) that occurred after the onset of IA for mRNA sequencing. The IA-1 visit was selected as the first available visit after the onset of IA for all groups. In the progressor group, the visit that preceded clinical onset of T1D was selected as the IA-2 visit. In the maintainer and reverter groups, the IA-2 visit was selected as the visit where age was closest to median age in the progressor group at the IA-2 visit.
Total RNA was isolated and purified from frozen (−80°C), peripheral whole blood samples ofn= 138 subjects meeting the inclusion criteria (Supplementary Material). We also included 12 control samples and 12 technical replicates. NuGEN library preparation kits were used to construct the strand-specific total RNA libraries. The Globin AnyDeplete kit was used to remove globin transcripts. RNA integrity number (RIN) scores for all samples were quantitated with use of the TapeStation (Agilent). Paired-end 150-cycle 2 × 150 sequencing was performed with the Illumina NovaSeq 6000 system. Samples were pooled together in a single flow cell and were sequenced twice to obtain the desired read depth, resulting in a median read depth of 90 million paired end reads across the samples (range 54–128 million).

tag: tissue

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: AECII.18mg_rep7

source_name: AECII

value: AECII


title: 110657_2_S11

value: RNA 2

value: Maintainer


title: PASMC.0mg_rep8


title: AECII.Ctrl_rep8


title: AECII.18mg_rep8


title: AECII.Ctrl_rep7


title: AECII.Ctrl_rep6


title: PASMC.Ctrl_rep8


title: AECII.18mg_rep4


title: PASMC.18mg_rep6


title: 110507_1_S66


title: AECII.18mg_rep6


title: PASMC.0mg_rep7


title: AECII.18mg_rep5


title: AECII.0mg_rep7


title: AECII.0mg_rep8


title: 110445_2_S40


title: 110554_2_S32


title: PASMC.0mg_rep6


title: 110509_2_S78


title: 110470_2_S70


title: 110475_1_S32


title: 110430_1_S24


title: 110533_3_S65


title: 110559_3_S73


title: PASMC.Ctrl_rep6


title: PASMC.18mg_rep5


title: PASMC.18mg_rep4


title: AECII.Ctrl_rep5


title: 110713_1_S78

value: Progressor


title: 110442_4_S69


title: 110537_3_S96


title: AECII.0mg_rep5


title: 110431_1_S70


title: 110615_2_S75


title: 110713_2_S55


title: PASMC.0mg_rep5


title: AECII.18mg_rep3


title: AECII.0mg_rep4


title: PASMC.Ctrl_rep5


title: PASMC.18mg_rep3


title: 110620_2_S67


title: AECII.Ctrl_rep3


title: 110505_2_S12


title: AECII.Ctrl_rep4


title: PASMC.0mg_rep4


title: AECII.0mg_rep6


title: AECII.18mg_rep2


title: 110456_2_S4


title: 110537_4_S70


title: 110546_1_S21


title: PASMC.Ctrl_rep3


title: 110498_1_S29


title: 110565_2_S44


title: 110460_1_S40


title: PASMC.Ctrl_rep4


title: PASMC.0mg_rep3


title: AECII.Ctrl_rep2


title: AECII.0mg_rep3


title: 110508_1_S48


title: 110513_2_S36


title: 110512_3_S41


title: 110601_1_S22


title: 110459_3_S33


title: 110526_1_S93


title: 110434_1_S85


title: PASMC.18mg_rep2


title: PASMC.Ctrl_rep2


title: PASMC.18mg_rep1


title: AECII.0mg_rep2


title: 60B

city: Saskatoon

first: Brian

last: Eames

state: Saskatchewan

address: 107 Wiggins Road

department: Anatomy and Cell Biology

country: Canada

institute: University of Saskatchewan

data_processing:
The paired-end Illumina reads were trimmed using Trimmomatic v0.36 (Bolger et al. 2014).
Mapped to the JGI 4.2 Xenopus tropicalis genome fom Ensembl using STAR v 2.5.3a (Dobin et al. 2013).
TMM normalization (Robinson and Oshlack 2010) was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts.
Assembly: JGI 4.2
Supplementary files format and content: comma-delimited text file includes counts for all samples

organism: Xenopus tropicalis

source_name: bone

growth_protocol: Specimens were raised to the stage of interest (NF57) in nursery system tanks with water recirculation

extract_protocol:
RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific; Cat# KIT0204) according to the manufacturer’s instructions and DNase treatment was done using RNase-Free DNase (Qiagen; Cat#79254). RNA was amplified one round using MessageAmp II aRNA Kit (ThermoFisher Scientific; Cat# AM1751). The RNA integrity was evaluated on the observation of a signature electropherogram pattern (Bioanalyzer). A minimum of 5-10 ng of amplified RNA was used per sample for the construction of each library.
RNA-seq libraries were prepared by the National Research Council (NRC, Saskatoon) using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute, Prime, Fragment step using5 µl amplified mRNA (the minimum amount was 5-10 ng mRNA as determined using Quant-iT RiboGreen RNA Assay Kit (Invitrogen)). The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer (Agilent Technologies Inc.).

treatment_protocol: WT animals received no treatment other than daily feedings after stage NF45

value: osteoblasts

value: medial angulosplenial (lower jaw)

tag: genotype

value: wild type


title: 61B-2


title: PASMC.0mg_rep2


title: 57B


title: 110691_2_S71


title: PASMC.0mg_rep1


title: AECII.Ctrl_rep1


title: PASMC.Ctrl_rep1


title: 110582_1_S30


title: WAT_CKD_8

city: VILLEURBANNE

first: Christophe

middle: O

last: Soulage

address: 15 avenue Jean Capelle

department: BioSciences

country: France

institute: INSA-Lyon

description: Surgical biopsy of abdominal subcutaneous adipose tissue

hyb_protocol: 1.65µg of cRNA were hybridized for 17 hr at 65C. GeneChips were washed and scanned.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters .  Data treatment was performed with bioconductor and Limma library. Background substraction was performed using the Normexp correction with offset =50. Quantile normalization was then applied.  Features flagged in Feature Extraction as control, as Feature Non-uniform outliers, saturating or too weak were excluded.

source_name: Subcutaneous white adipose tissue

label_protocol: 200ng of total RNA were labelled with cy3 using  Low Input Quick Amp labeling One color : Cy3  kit from Agilent (ref : 5190-2305) following manufacturer's instructions

extract_protocol: Total RNA were extracted using Mirvana isolation Kit (ambion ref 1560) according to the manufacturer's recommendations

treatment_protocol: Surgical biopsies of subcutaneous white adipose tissue were snap frozen in liquid nitrogen and stored at -80°C until analysis

tag: gender

value: male

tag: renal function

value: CKD


title: 61M

source_name: mature cartilage

value: mature chondrocytes

value: humerus


title: 110636_3_S15


title: 62M


title: 110693_3_S7


title: N6

city: Chengdu

first: Xin

last: Huang

address: Chenglongdadao

country: China

institute: West China Second University Hospital

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 v4.0.0 (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

molecule: polyA RNA

source_name: Endometrium

extract_protocol:
Endometrial tissues were washed in phosphate-buffered saline three times and then sheared into tiny pieces. Tissue pieces were digested with 2 mg/mL collagenase IV (Sigma) in Dulbecco's modified Eagle's medium (DMEM)/F12 1:1 (Gibco) at 37 °C for 40 min to generate a single-cell suspension. The suspension was passed through 40-μm cell sieves, and the cell concentration was adjusted to 10^6/ml through dilution or centrifugation.
The cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X  Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s

value: Endometrial cells

value: Endometrium


title: N5

description: 10x Genomics


title: N7

description: 10x Genomics


title: 56M


title: YAS12A_1

city: Minato-ku

first: Mie

last: Koabyashi-Ishihara

state: Tokyo

address: 4-6-1 Shirokanedai

department: UTOPIA

country: Japan

institute: The University of Tokyo

data_processing:
RNA-seq reads were mapped and genes quantified with GEMtools 1.7
Gene annotation: gencode v19
Assembly: GRCh37.p13
Supplementary files format and content: tsv file with raw counts

source_name: isolated from PBMC

growth_protocol: Sorted naive CD4+ T cells were cultured as follows: HSP condition – cell cultured with IL-15 and -7 (10 μg/ml, PeproTech); HSP+TCR condition – cells cultured with IL-15 and -7 and activated by anti-CD3 (5 μg/ml, BD Biosciences) and CD28 (1 μg/ml, BD Biosciences) on day 12; TCR condition – cells activated with anti-CD3/CD28 antibodies on day 0 and cultured with IL-2 (2 ng/ml, PeproTech); TCR+TCR condition – cells activated with anti-CD3/CD28 on day 0, cultured with IL-2 and second time activated with anti-CD3/CD28 at day 12.

extract_protocol:
Total RNA from cultured cells was isolated using Qiagen RNeasy Micro kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated by a Ribo-Zero kit (Illumina). cDNA was synthesized and tagged by addition of barcoded Truseq adapters. Libraries were quantified using the KAPA Library Quantification Kit (KapaBiosystems) prior to amplification with Illumina’s cBot.

value: CD4+ T cells

tag: time

value: Day 13

value: TCR+TCR


title: 110699_1_S74

value: blood


title: WAT_CKD_5


title: 110678_2_S63

value: RNA 1


title: WAT_CKD_7


title: WAT_CKD_6


title: 62I

source_name: immature cartilage

tag: cell type

value: immature chondrocytes


title: 110658_1_S82

value: Maintainer


title: WAT_CKD_4


title: WAT_CKD_3


title: WAT_CKD_2


title: 110698_2_S88

value: RNA 2


title: AECII.0mg_rep1

tag: strain

value: AECII

tag: treatment

value: smoke

tag: concentration


title: YAS11A_1

value: TCR


title: AECII.18mg_rep1


title: 59I

tag: tissue

value: wild type


title: WAT_control_9

value: male

value: Control non CKD


title: 110648_2_S96

tag: ID

tag: tr n

tag: visit


title: YAS9A_1

value: HSP


title: YAS7A_1


title: 110695_1_S11

tag: group

tag: female yn

tag: nhw yn


title: YAS8A_1


title: WAT_CKD_1

value: CKD


title: 110492_1_S3

tag: dr34 yn

tag: fdr yn

tag: age


title: YAS6A_1

value: HSP+TCR

tag: gender


title: 110687_1_S35

tag: age ia


title: 60I

value: humerus

tag: genotype


title: WAT_control_7

tag: renal function


title: 110544_1_S43


title: 110692_2_S77

value: Reverter


title: 110514_2_S69


title: YAS3A_1

tag: cell type

value: CD4+ T cells

tag: time

value: Day 13

value: female


title: 110696_2_S53

value: blood


title: YAS2A_1

tag: treatment


title: WAT_control_5


title: WAT_control_8


title: AKZ692-2

city: La Jolla

first: Michael

last: Bollong

state: California

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description: replicate 2

data_processing: Kallisto (https://pachterlab.github.io/kallisto/) was used to align to the reference transcriptome (ftp://ftp.ensembl.org/pub/current_fasta/mus_musculus/cdna/) and estimate transcript abundance.

source_name: IMR32 cells

growth_protocol: IMR32 cells were purchased from American Type Culture Collection (ATCC) and maintained in DMEM (Corning) supplemented 10% with fetal bovine serum (FBS, Gibco) and 1% penicillin-Streptomycin (Pen Strep, Gibco).

extract_protocol:
Total RNA samples were obtained by trypsinization followed by centrifugation and then preparation by an Rneasy kit (Qiagen).
Total RNA samples were sent to BGI Group, Beijing, China, for library preparation and sequencing. Reads (single-end 50bp at a sequencing depth of 20 million reads per sample) were generated by BGISEQ-500

treatment_protocol: IMR32 cells (1x10e6) were plated in 2 mL of growth medium in 6-well tissue culture dishes. The next day, cells were treated with DMSO or sAKZ692 (20 µM) for 24 hours.

tag: cell line

tag: time point

value: 24 hours


title: WAT_control_6


title: WAT_control_3


title: WAT_control_1


title: AKZ692-3

description: replicate 3


title: WAT_control_2


title: 110660_2_S61

tag: tissue

tag: ID

tag: tr n

value: RNA 1

value: Maintainer


title: WAT_control_4


title: YAS5A_1


title: YAS4A_1

value: TCR+TCR


title: YAS1A_1


title: InVitro_SAS_EGFR-KO_WithSerum

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in SAS/EGFR-KO normal culture

hyb_protocol: 1.75 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Human Gene Expression 4x44K v2 Microarray (G4845A-026652) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: SAS_EGFR-KO, normal culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The OSCC cell lines were incubated in a RPMI 1640 medium supplemented with 5% heat-inactivated fetal bovine serum. Following 24h incubation, the cells were then incubated for 48 hours at 37 ºC in the presence or absence of 5% heat-inactivated fetal bovine serum.

value: OSCC cell line

tag: culture

value: normal

value: EGFR-KO

value: Female


title: 110659_1_S27

tag: visit

value: RNA 2

tag: group

tag: female yn

tag: nhw yn


title: Control group patient 3

city: Beijing

first: Ziliang

last: Hou

state: Beijing

address: NO.82 Xinhuananlu, Tongzhou District

department: PCCM

institute: Beijing Luhe Hospital

description: circRNA expression data from TPE person

hyb_protocol: Fifteen ug of cRNA were subjected to fragmentation using 3' fragmentation buffer hybridized for 16hr at 45℃ on GeneChip Clariom D Assay. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw data were analyzed with Affymetrix Expression Console and Transcriptome Analysis Console software using RMA as a normalization algorithm.

label: biotin

source_name: Cell pellets from TPE

label_protocol: Biotinylated cRNA were prepared using the GeneChip WT Pico Reagent Kit from 100 ng total RNA (GeneChip® WT Pico Reagent Kit User Manual, Affymetrix).

growth_protocol: Cell pellets from LA-MPE and TPE which were collected by a standard thoracocentesis technique within 24 hours after hospitalization.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacture's instructions. The purity and concentration of extracted RNA were determined by OD260/OD280 using a NanoDrop ND-1000 instrument. The integrity of the RNA was assessed by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: Fresh PE samples were centrifuged for the isolation of cell pellets.

tag: sample group

value: TPE

tag: age

tag: gender


title: Control group patient 1

description: circRNA expression data from TPE person


title: InVitro_SAS_HER2_WithSerum

description: Gene expression in SAS/HER2-KO normal culture

source_name: SAS_HER2-KO, normal culture

tag: genotype


title: trophoblast 180uM_MEHP_rep3

city: Seattle

first: Alison

last: Paquette

state: Washington

address: 1900 Ninth Ave.

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Childrens

data_processing:
Transcript abundances were estimated using the pseudo-alignment program kallisto with bias correction (Bray et al. 2016), and condensed to Ensembl Gene IDs using tximport (Soneson et al. 2015). Filtering was performed to remove genes with a mean log CPM<0. Normalization was performed using the Trimmed Mean of M-values (Robinson and Oshlack 2010). Differentially expressed genes between treatment groups compared to DMSO controls were identified using generalized linear models implemented within edgeR (Chen et al. 2016). Dispersion parameters were estimated using the Cox-Reid method, and then differentially expressed genes were identified using the quasi-likelihood F-tests, which is more robust and produces more reliable error rates when the number of replicates is small (Lun et al. 2016). Regression models for primary cells were adjusted for confounders including RNA Integrity Number (RIN) and Sample ID, which minimized interindividual variation and sex differences in our full model (not stratified for sex). Genes were considered differentially expressed at a Benjamini-Hochberg false discovery rate (FDR) <0.05.
Assembly: GRCH38
Supplementary files format and content: Processed data files are kallisto abundance (TPM) per sample in tab separated format (tsv).

source_name: placenta

growth_protocol: The first trimester EVT cell line, HTR-8/SVneo, was obtained from ATCC (#CRL-3271, Batch: 70016636, Obtained: January 2021). HTR-8/SVneo cells were cultured at 37°C in 6-well tissue culture dishes between passages 4-7 using RPMI-1640 with L-glutamate supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (P-S), 1mM sodium pyruvate, and 10mM HEPES. Primary cytotrophoblast cells were cultured in IMDM with 10% FBS and 1% Penicillin/Streptomycin. Cells were plated at ~1.5 x 106 cells per well in 12 well plates and given 24 hr to adhere prior to changing the media to remove non-adherent cells. Syncytialization was confirmed under a light microscope at 48 hr.

extract_protocol:
RNA from HTR-8/SVneo cells was isolated by a phenol:chloroform extraction using TRIzol. Primary Trophoblast RNA isolation was performed with the Zymo Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA) following manufacturer’s instructions after lysing cells in 350µL TRIzol.
Novogene prepared libraries with high quality RNA after measuring the RNA Integrity Number (RIN)>7 with the Agilent High Sensitivity RNA Screentape Assay (Agilent Technologies; Santa Clara, CA). Sample library preparation was performed using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara Bio Inc.; Kusatsu, Japan) for primary syncytiotrophoblast cells followed by paired end sequencing (150BP) using an Illumina HiSeq with a read depth of 30 million read pairs/sample. Library preparation for HTR-8/SVneo cells was performed using an optimized NEBNext Ultra II kit followed by paired end sequencing (150BP) with a NovaSeq 6000 and a read depth of 30 million read pairs/sample.

treatment_protocol: MEHP (Sigma Aldrich; St. Louis, MO) was prepared in 100% DMSO as a 180mM stock solution that was stored at -20°C prior to treatment. HTR-8/SVneo and primary trophoblast cells were each treated with DMSO (0.1%) or one of three final concentrations (1µM, 90µM, and 180µM) of MEHP with three replicates per concentration. For the primary syncytiotrophoblast cells, cells from 3 male and 3 female placentas were used per treatment group with each replicate representing the placenta of a unique individual. There were no statistical differences in maternal BMI, maternal age, or gestational length between male and female samples (Table 1). Cells were incubated with dosed media for 24 hours at 37°C. MEHP was added to cultures at the 48 hr time point and incubation continued for an additional 24 hr at 37°C before removal of media and isolation of RNA from cells.

value: placenta

tag: cell type

value: trophoblast

value: 180uM MEHP


title: AKZ692-1

description: replicate 1


title: trophoblast 180uM_MEHP_rep2


title: Control group patient 2

description: circRNA expression data from TPE person

value: male


title: Test group patient 2

description: circRNA expression data from LA-MPE person

source_name: Cell pellets from LA-MPE

value: LA-MPE


title: DMSO-1

description: replicate 1

value: DMSO


title: 110577_1_S19

value: blood

tag: dr34 yn

tag: fdr yn

tag: age ia


title: Test group patient 3


title: DMSO-2

description: replicate 2

tag: cell line

tag: treatment

tag: time point

value: 24 hours


title: 110539_2_S90

tag: tissue

tag: ID

tag: tr n

value: RNA 1


title: trophoblast 180uM_MEHP_rep1


title: 110539_4_S56

tag: visit

tag: group

value: Maintainer


title: DM11 untreated replicate 2

city: Nijmegen

first: Leontien

last: van der Bent

address: Geert Grooteplein 26-28

department: Cell Biology

country: Netherlands

institute: Radboudumc

data_processing:
Reads were filtered by internal SOAPnuke software (https://github.com/BGI-flexlab/SOAPnuke) to exclude reads that contained adapter sequences, > 5% unknown bases, or > 20% bases with a quality score < 15. Clean reads were mapped to the Hg38 reference genome using HISAT2. StringTie was used to reconstruct transcripts, and novel transcripts were identified using Cuffcompare and CPC.
Novel coding transcripts were merged with reference transcripts, after which clean reads were mapped to this complete reference using Bowtie 2. Gene expression levels were calculated with RSEM. Differential gene expression analysis was performed using a NOIseq algorithm.
Differential splicing events were detected using rMATS.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files are in .xls format and contain NOIseq and rMATS output, comparing the negative control group (DM11_NT, DM11_gapmer_control and DM11_blocking_control) with either of the three specific AONs (DM11_blocking_repeat, DM11_gapmer_repeat or DM11_gapmer_nonrepeat), or DM11_NT with C25_NT.

source_name: cultured myoblasts

growth_protocol: Myoblasts were grown in a 1:1 mix of Skeletal Muscle Cell Growth Medium (PromoCell) with 1x GlutaMAX (Gibco) and Ham's F-10 Nutrient Mix with GlutaMAX (Gibco), supplemented with 20% (v/v) HyClone Bovine Growth Serum Supplemented Calf (GE Healthcare). All tissue culture vessels were coated with 0.1% gelatin (Sigma G2500) in milliQ for at least 30 minutes prior to cell seeding. Cells were incubated at 37°C in humidified incubators with 7.5% CO2.

extract_protocol:
Aurum total RNA Mini Kit (Bio-Rad)
Library preparation was done on poly-(A) enriched samples and libraries were sequenced paired-end (100 bp read length), generating at least 30 Mb clean reads per sample on the BGI-Seq500 platform.

treatment_protocol: Cells were incubated for 24 hours with peptide nanoparticles consisting of the cell-penetrating peptide PepFect14 and antisense oligonucleotides.

value: human immortalized myoblast line

tag: ctg repeat size dmpk gene

tag: aon type


title: trophoblast 1uM_MEHP_rep2

value: 1uM MEHP


title: Test group patient 1

tag: sample group

tag: age

value: female


title: DM11 untreated replicate 1


title: InVitro_SAS_EGFR-WT_WithSerum

description: Gene expression in SAS/EGFR-WT normal culture

source_name: SAS_EGFR-WT, normal culture

value: OSCC cell line

tag: culture

value: normal

tag: genotype

value: EGFR-WT

tag: gender


title: InVitro_SAS_EGFR-WT_NoSerum

description: Gene expression in SAS/EGFR-WT serum starvation

source_name: SAS_EGFR-WT, serum-free culture

tag: cell type

value: serum-free

value: Female


title: trophoblast 1uM_MEHP_rep3

value: placenta

value: trophoblast


title: 110681_2_S21

source_name: blood

value: RNA 2

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: trophoblast 1uM_MEHP_rep1

tag: tissue

tag: cell line

tag: treatment


title: DM11 repeat gapmer replicate 3

value: gapmer


title: DM11 repeat gapmer replicate 2


title: trophoblast 90uM_MEHP_rep3

value: 90uM MEHP


title: InVitro_HSC-3_HER2_WithSerum

description: Gene expression in HSC-3/HER-KO normal culture

source_name: HSC-3_HER2-knockout (KO), normal culture

value: HER2-knockout (KO)

value: Male


title: InVitro_HSC-3_EGFR-KO_WithSerum

description: Gene expression in HSC-3/EGFR-KO normal culture

source_name: HSC-3_EGFR-KO, normal culture

value: EGFR-KO


title: 9_5_3_7_CTATAC_S10_L001

city: Chapel Hill

first: Kyle

last: Roell

address: 135 Dauer Drive

institute: University of North Carolina Chapel Hill

data_processing:
Sequencing counts were processed through our published BCGSC miRNA profiling pipeline (publicly available at: https://github.com/bcgsc/mirna), aligned to the UCSC GRCm38/mm10, and annotated to miRBase 22.1.
Assembly: miRBase 22.1
Supplementary files format and content: Count data are provided as a .csv, aligned to microRNA symbols, and represent count values prior to any normalization or batch effect correction algorithms.

source_name: Extracellular vesicles from HepG2 cell conditioned media

growth_protocol: HepG2 cells were cultured in Minimal Essentials Media supplemented with 10% Fetal Bovine Serum. Cells were plated at 2 million cells per 100 mm dish and incubated at 37°C in 5% CO2 until achieving 70–80% confluence.

extract_protocol:
Conditioned media samples were collected 24 h postexposure  and stored at -80 degrees C until further analysis.  Extracellular vesicles were isolated using the Invitrogen Total Exosome Isolation Reagent from Cell Culture Media (Thermo Fisher Scientific, Waltham, MA) according to manufacturer’s protocol, with an additional centrifugation step at 10,000 x g for 30 minutes. RNA molecules with 18 nucleotides or greater were extracted with Invitrogen’s Total Exosome RNA & Protein Isolation Kit according to manufacturer’s protocol. RNA was purified and concentrated using the RNA Clean and Concentrator kit (Zymo Research, Irvine, CA) and quantified with a Nanodrop 1000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and tested for small RNA yield and quality was measured using the LabChip® Small RNA Assay (PerkinElmer).
Isolated RNA samples were analyzed using next generation sequencing technologies enabled through the Illumina HiSeq 4000 platform. mRNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Ultra-High-Throughput Sequencing System (HiSeq) 4000.

treatment_protocol: HepG2 cells were seeded in a 6-well cell culture plate at 300,000 cells per well and incubated for 24 h prior to treatment. On the day of treatment, individual PFAS stock solutions were diluted in MEM cell culture media supplemented with 10% exosome-depleted FBS to achieve 35uM concentrations of each PFAS in the mixture. Each well was washed with PBS and the media was replaced with either 2 mL of mixture treatment condition or 2 mL of 0.1% methanol control. Cells were treated in biological triplicate and incubated at 37˚C in 5% CO2 for 24 h.

value: Human liver cells

value: Control

tag: treatment duration (hrs)


title: VMO, scRNAseq

city: Irvine

first: Christopher

middle: J

last: Hatch

state: CA

address: 2400 Biological Sciences III

institute: University of California, Irvine

description: 10x Genomics

data_processing:
The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v3.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Endothelial colony-forming cell-derived endothelial cells + normal human lung fibroblasts

extract_protocol:
The thin transparent membrane was carefully removed from the bottom of the PDMS layer of the vascularized micro-organ to expose the tissue chambers. The chambers were washed with HBSS prior to adding TrypLE express enzyme in a drop-wise manner. After incubation at 37°C for 5 minutes, the chambers were flushed with a micropipette to collect ~10,000 cells into a centrifuge tube. Cells were then quenched with EGM-2. Next, cells were centrifuged (340xg for 3 min) and resuspended in an HBSS/collagenase type III solution (1 mg mL-1) to digest the matrix fully. The cells were then washed with EGM-2 and pushed through a 70 μm filter to create a single-cell suspension. Finally, a propidium iodide stain was used to remove dead and dying cells by FACS on a BD Flow assisted cell sorting AriaII
The cellular suspensions were loaded onto a Chromium Single Cell Instrument (10X genomics) and processed to generate cDNA using 10X Genomics v2 chemistry according to the Chromium Single Cell 3' Reagents kits v2 user guide. After undergoing quantification and quality control of cDNA libraries using the Qubit dsDNA HS Assay kit (Life Technologies Q32851), high-sensitivity DNA chips (Agilent 5067-4626), and KAPA qPCR (Kapa Biosystems KK4824), cDNA were sequenced on an Illumina HiSeq4000 at the University of California Irvine's Genomics High Throughput Facility to achieve an average of 50,000 reads per cell.

tag: time

value: Day 8


title: 110466_2_S29

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group

value: Maintainer


title: trophoblast 90uM_MEHP_rep2

tag: genotype


title: 110689_3_S5

tag: age


title: DM11 repeat gapmer replicate 1

tag: cell type

value: human immortalized myoblast line

tag: ctg repeat size dmpk gene

tag: aon type


title: 9_5_3_3_CATTTT_S6_L001


title: InVitro_HSC-3_EGFR-WT_NoSerum

description: Gene expression in HSC-3/EGFR-WT serum starvation

source_name: HSC-3_EGFR-wildtype (WT), serum-free culture

value: OSCC cell line

tag: culture

value: serum-free

value: EGFR-wildtype (WT)

tag: gender


title: 110675_3_S13

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: trophoblast 90uM_MEHP_rep1

tag: tissue

value: placenta

tag: cell line

value: trophoblast

tag: treatment


title: 110684_3_S3

tag: ID

tag: tr n

tag: visit

value: RNA 2


title: trophoblast DMSO_rep6

tag: genotype

value: DMSO


title: DM11 DMPK gapmer replicate 3

tag: cell type

value: gapmer


title: DM11 DMPK gapmer replicate 2

tag: ctg repeat size dmpk gene


title: InVitro_HSC-3_EGFR-WT_WithSerum

description: Gene expression in HSC-3/EGFR-WT normal culture

source_name: HSC-3_EGFR-WT, normal culture

value: normal

value: EGFR-WT

value: Male

tag: age


title: trophoblast DMSO_rep5


title: 9_5_3_12_TATAAT_S4_L001

value: Human liver cells

value: PFAS

tag: treatment duration (hrs)


title: WAT_CKD_9

source_name: Subcutaneous white adipose tissue

tag: gender

value: male

tag: renal function

value: CKD


title: 110571_3_S11

value: blood

value: RNA 1

tag: group

value: Maintainer

tag: female yn

tag: nhw yn


title: 9_5_3_5_CGGAAT_S8_L001


title: YAS10A_1

source_name: isolated from PBMC

value: CD4+ T cells

tag: time

value: Day 13

value: HSP+TCR


title: DM11 DMPK gapmer replicate 1

value: human immortalized myoblast line

tag: aon type


title: DM11 control gapmer replicate 2


title: 110677_3_S20

tag: tissue

value: RNA 2

tag: dr34 yn

tag: fdr yn

tag: age ia


title: DM11 control gapmer replicate 1


title: 110573_1_S91

tag: ID

tag: tr n

tag: visit

value: Progressor


title: trophoblast DMSO_rep4

value: placenta

tag: cell line

tag: cell type

value: trophoblast

tag: genotype

tag: treatment

value: DMSO


title: 110655_3_S12

tag: age


title: 9_5_3_6_CTAGCT_S9_L001

tag: treatment duration (hrs)


title: 9_5_3_2_CATGGC_S5_L001

value: Control


title: trophoblast DMSO_rep3


title: trophoblast DMSO_rep1


title: DM11 repeat blocking replicate 2

tag: ctg repeat size dmpk gene

value: blocking


title: 9_5_3_1_CAGGCG_S1_L001

value: Human liver cells


title: 9_5_3_11_TACAGC_S3_L001

value: PFAS


title: 9_5_3_9_GACGAC_S12_L001


title: 110676_3_S48

tag: group

value: Reverter

tag: female yn

tag: nhw yn


title: DM11 repeat blocking replicate 3

tag: aon type


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep6

tag: tissue

value: Primary Syncytiotrophoblasts

value: Male

value: 180uM MEHP


title: 110493_1_S4

value: blood

value: RNA 1

tag: dr34 yn

tag: fdr yn


title: DM11 repeat blocking replicate 1


title: 110545_3_S56

tag: ID

tag: age ia


title: 9_5_3_10_TAATCG_S2_L001


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep5


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep4


title: 110656_1_S72

tag: tr n

tag: visit

value: Maintainer


title: trophoblast DMSO_rep2

tag: cell line

tag: cell type


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep3

tag: genotype

value: Female

tag: treatment


title: C25 untreated replicate 3

value: human immortalized myoblast line


title: 110674_2_S52

value: RNA 2

tag: age


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep2

value: placenta


title: C25 untreated replicate 2

tag: ctg repeat size dmpk gene


title: C25 untreated replicate 1


title: 110467_2_S60

tag: group


title: 110667_1_S75

tag: female yn


title: Primary Syncytiotrophoblasts 180uM_MEHP_rep1


title: Primary Syncytiotrophoblasts 1uM_MEHP_rep5

value: 1uM MEHP


title: 110521_1_S83

tag: nhw yn


title: 9_5_3_8_CTCAGA_S11_L001

tag: treatment duration (hrs)


title: Primary Syncytiotrophoblasts 1uM_MEHP_rep4

tag: tissue


title: DM11 control blocking replicate 2

tag: aon type


title: DLD1 cells, AHR siRNA treatment rep1

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

growth_protocol: The human DLD-1 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of DLD-1 cells with different treatment was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DLD-1 colorectal cells were transfected with control siRNA or AHR siRNA.

value: human colorectal cancer cells

tag: passage

tag: transfection

value: AHR siRNA


title: DLD1 cells, AHR siRNA treatment rep2


title: DLD1 cells, Control siRNA rep3

value: control


title: DLD1 cells, AHR siRNA treatment rep3


title: SAMPLE 106_prime/boost challengeFluB-att/IGIPd14 dpc

type: protein

city: Athens

first: Daniel

middle: Roberto

last: Perez

state: GA

address: 953 College Station Road

institute: University of Georgia

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

hyb_protocol: Serum and NW samples were diluted 1:100 in a protein array blocking buffer (GVS, Sanford,  ME, USA), supplemented with E. coli lysate (GenScript, Piscataway, NJ, USA) to a final  concentration of 10 mg/mL, and preincubated at room temperature (RT) for 30 min. Concurrently,  arrays were rehydrated in blocking buffer (without lysate) for 30 min. Blocking  buffer was removed, and arrays were probed with preincubated serum samples using  sealed chambers to prevent cross-contamination of samples between the pads. Arrays were  incubated overnight at 4  C with gentle agitation. They were then washed at RT three  times with Tris-buffered saline (TBS) containing 0.05% Tween 20 (T-TBS), biotin-conjugated  goat anti-mouse IgA and Biotin-conjugated anti-mouse IgG (Jackson Immuno Research  Laboratories, Inc., West Grove, PA, USA) were diluted 1:400 in blocking buffer and applied  to separate arrays for 1 h, RT with gentle agitation. Arrays were washed three times  with T-TBS, followed by incubation with streptavidin-conjugated Qdot655 (Thermo Fisher  Scientific, Waltham, MA, USA) diluted 1:200 in blocking buffer for 1 h, RT. Arrays were  washed three times with T-TBS and once with water. Arrays were air dried by centrifugation  at 500 g for 5 min. Images were acquired using the ArrayCAM imaging system from  Grace Bio-Labs (Bend, OR, USA). Spot and background intensities were measured using  an annotated grid (.gal) file. Mean fluorescence across antigens grouped by isotypes were  used for subsequent analysis. The different antigens were acquired from Sino biological  (Wayne, PA, USA).

scan_protocol: Images were acquired using the ArrayCAM imaging system from Grace Bio-Labs (Bend, OR) with gain and exposure times of 50 and 400-1000ms, respectively.

data_processing: Spot and background intensities were measured using an annotated grid (.gal) file.  Signal intensities (SI) for each antigen on the array were first background corrected by subtracting sample-specific T-PBS buffer signals from purified protein spot signals. For statistical analysis,   A two-way ANOVA was performed. A P value below 0.05 was considered significan. All data analyses and graphs were performed using GraphPad Prism software version 9 (GraphPad Software Inc., San Diego, CA, USA).

molecule: protein

source_name: Nasal wash

extract_protocol: Blood and nasal wash samples were collected at 14 dpc for serology and to determine antigen-specific IgG and IgA responses

value: Nasal wash

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-att/IGIP

tag: time point

value: d14 dpc

tag: mouse id

tag: extracted molecule

value: IgA


title: DLD1 cells, Control siRNA rep2

tag: cell line

tag: cell type


title: SAMPLE 105_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: DM11 control blocking replicate 1

value: blocking


title: 110479_1_S80

value: blood

tag: ID

tag: tr n

tag: visit

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: 110718_1_S54

tag: tissue

tag: group

value: Progressor

tag: female yn

tag: nhw yn


title: 9_5_3_4_CCAACA_S7_L001

value: Human liver cells

tag: treatment

value: PFAS

tag: treatment duration (hrs)


title: Primary Syncytiotrophoblasts 1uM_MEHP_rep3

value: Primary Syncytiotrophoblasts

tag: genotype

value: Male


title: 110510_1_S62

value: RNA 1


title: SAMPLE 104_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: DLD1 cells, Control siRNA rep1

tag: cell line

tag: cell type

tag: passage

tag: transfection


title: Primary Syncytiotrophoblasts 1uM_MEHP_rep2

value: placenta

value: Female

value: 1uM MEHP


title: 110665_2_S42

tag: ID

tag: tr n

tag: visit

value: RNA 2

value: Maintainer

tag: dr34 yn

tag: fdr yn

tag: age

tag: age ia


title: Primary Syncytiotrophoblasts 1uM_MEHP_rep1

tag: tissue

tag: genotype

tag: treatment


title: 110532_2_S34

tag: group

tag: female yn

tag: nhw yn


title: DLD1 cells, lncSLCC1 siRNA treatment 2

treatment_protocol: The DLD-1 colorectal cells were transfected with control siRNA or lncSLCC1 siRNA.

tag: cell line

value: human colorectal cancer cells

value: lncSLCC1 siRNA


title: DLD1 cells, lncSLCC1 siRNA treatment 3

tag: cell type


title: SAMPLE 103_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-att/IGIP

tag: time point

value: d14 dpc

tag: mouse id

tag: extracted molecule


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep6

value: 90uM MEHP


title: SAMPLE 102_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: IgA


title: 110670_2_S47

value: blood

tag: ID

tag: tr n

tag: visit

tag: dr34 yn


title: DLD1 cells, Control siRNA 3

tag: passage

tag: transfection

value: control


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep5

tag: tissue

value: Primary Syncytiotrophoblasts

tag: genotype

value: Male

tag: treatment


title: DLD1 cells, Control siRNA 2


title: 110490_2_S39

value: RNA 1

tag: group

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age

tag: age ia


title: DLD1 cells, lncSLCC1 siRNA treatment 1

tag: cell line

tag: cell type


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep4

value: placenta


title: SAMPLE 99_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

value: FluB-RANS/IGIP

tag: time point

tag: mouse id

tag: extracted molecule


title: SAMPLE 100_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: 110662_3_S58

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: dr34 yn


title: DMSO-3

description: replicate 3

source_name: IMR32 cells

tag: treatment

value: DMSO

value: 24 hours


title: DLD1 cells, Control siRNA 1

value: human colorectal cancer cells

tag: passage

tag: transfection


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep3

tag: tissue

tag: genotype

value: Female


title: 110542_3_S50

tag: group

value: Maintainer

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age

tag: age ia


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep2

tag: cell line

tag: cell type


title: SAMPLE 98_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: eletrical stimulation, ES3

first: Xiangling

last: Li

address: Fuxing

department: orthopedics

institute: PLA General Hospital

data_processing:
Agilent 2100 Bioanalyze.
Trimmed sequence reads were mapped to mapped to reference Genome
Novel Transcript prediction and Structure analysis
Gene expression quantification( including GSEA Enrichment)
Differential expression analysis and functional analysis.
Assembly: rn7
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: sciatic nerve

growth_protocol: Sprague-Dawley rats was fed in an environment with a 12:12h light/dark cycle at controlled temperature and humidity, with free access to food and water.

extract_protocol:
RNA was isolated using TRIzol reagent, and RNA integrity was evaluated using the Agilent 2100 Bioanalyze.
RNA was isolated using TRIzol reagent and  NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was  used for the construction of sequencing libraries.

treatment_protocol:
After nerve was retracted to form a gap of about 6 mm, the ES group was treated immediately with ES for 1 h, and the control group was not treated with ES,
The ES group was treated immediately with ES for 1 h. The control group was not treated with ES, followed by suturing of the proximal and distal nerve end separately for 2mm into the 10mm silicone tube sutured with the 8-0 nylon sutures.

value: sciatic nerve

value: 8 weeks

tag: Sex

value: female

tag: treatment

value: electrical stimulation treatment

tag: time

value: Day 4


title: SAMPLE 97_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue

value: d14 dpc

value: IgA


title: eletrical stimulation, ES2


title: Primary Syncytiotrophoblasts DMSO_rep6

source_name: placenta

value: placenta

value: Primary Syncytiotrophoblasts

tag: genotype

value: Male


title: SAMPLE 96_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP


title: 110641_4_S65

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: group

tag: female yn

tag: dr34 yn


title: eletrical stimulation, ES1

tag: age


title: SAMPLE 95_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen


title: 110609_3_S62

tag: nhw yn

tag: fdr yn

tag: age ia


title: Primary Syncytiotrophoblasts DMSO_rep5

tag: cell line

tag: cell type

value: DMSO


title: SAMPLE 101_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine

value: FluB-att/IGIP

tag: time point

tag: mouse id

tag: extracted molecule


title: Primary Syncytiotrophoblasts DMSO_rep4

tag: tissue

tag: genotype

tag: treatment


title: 110437_3_S54

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group

value: Maintainer


title: non-eletrical stimulation,Control3

value: sciatic nerve

tag: age

tag: Sex

value: non-treatment

tag: time


title: non-eletrical stimulation,Control2

value: 8 weeks

value: female


title: 110650_2_S28

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: SAMPLE 93_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-RAM/IGIP

tag: time point

value: d14 dpc

tag: mouse id


title: non-eletrical stimulation,Control1

tag: tissue

tag: treatment

value: Day 4


title: Primary Syncytiotrophoblasts DMSO_rep3

value: placenta

tag: cell line

tag: cell type

value: Primary Syncytiotrophoblasts

tag: genotype

value: Female


title: Primary Syncytiotrophoblasts DMSO_rep2

value: DMSO


title: SAMPLE 92_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: extracted molecule

value: IgA


title: 110421_2_S20

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group

tag: age


title: Primary Syncytiotrophoblasts 90uM_MEHP_rep1

value: 90uM MEHP


title: wholelar_as3mtmut_1mMiAs_cl3

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads where first assessed for quality using FastQC v0.11.5. Trimmomatic v0.36 was used for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36)
The resulting transcripts from the raw counts were used for further downstream analysis
Assembly: Danio_rerio.GRCz10.84
Supplementary files format and content: txt containing raw counts

organism: Danio rerio

growth_protocol: Zebrafish larvae were kept in 6-well plate at a density of 2 larvae/ per 1 mL embyro medium in a 10:14 light/dark cycle

extract_protocol:
TRIzol/Choloform Extraction
RNA-seq libraries were prepared with Illumina TruSeq V2 RNA kit for Poly A by the staff in the NYUAD genomics facility and quality controled by Bioanalyzer.

value: whole larvae


title: 110653_3_S82

value: RNA 2

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: Primary Syncytiotrophoblasts DMSO_rep1


title: 110489_4_S66

value: Maintainer

tag: age ia


title: SAMPLE 91_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id


title: SAMPLE 90_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue


title: 110453_3_S90

value: Reverter


title: 110683_2_S56


title: wholelar_as3mtmut_0mMiAs_cl3

tag: genotype

tag: treatment


title: wholelar_as3mtmut_1mMiAs_cl1


title: SAMPLE 89_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: extracted molecule


title: 110680_2_S48

tag: ID

tag: tr n


title: MKN-45 - sh-NOTCH1

city: Fuzhou

first: Liangqing

address: No 20, ChaZhong Road, TaiJiang District, Fuzhou 350000, China.

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: gastric adenocarcinoma

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protacal

tag: cell type

value: cancer cell

tag: condition

value: disease

value: NOTCH1 interfered


title: AGS- sh-NOTCH1


title: MGC-803

value: untreated


title: SAMPLE 94_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: prime/boost challenge

value: FluB-RAM/IGIP

value: d14 dpc


title: 110680_1_S63

first: Lauren

institute: Colorado School of Public Health

data_processing:
FASTQ files for the two runs for each sample were concatenated. Reads were trimmed to remove adapters and low-quality base calls with Cutadapt (13). Reads were aligned to the reference human genome (hg19) with use of TopHat2 (14). Individual samples were quantified against the most up-to-date Ensembl reference transcriptome with the RSEM (RNA-Seq by Expectation-Maximization) algorithm (15). The expected counts were used for further processing and normalization. For removal of any technical variation, the data first were quantile normalized with DESeq2 (16) and then normalized with removal of unwanted variation (17). Based on scree plots, we adjusted for one factor, as it explained the most variability in the data. The data were then transformed with the regularized log function (16). The transformed data were used in all subsequent analyses. We filtered out genes if ≥20% of the samples did not have a read mapped to the gene (transcripts per million value of 0) or the average transcripts per million value across all samples was <1. A total of 12,477 genes passed the filtering criteria.
Assembly: hg19/Ensembl.v87
Supplementary files format and content: RSEM.RUVs.k1.rlog.Dec2020.csv  Final normalized and cleaned dataset used in analyses, each row a gene and column a sample.
Supplementary files format and content: RSEM.estCounts.geneLevel.csv Estimated counts per gene from the RSEM output.  Not normalized or cleaned.

extract_protocol:
In DAISY, venous blood samples are collected at 9, 15, and 24 months and yearly thereafter. Beginning in November of 2007, RNA samples were collected from all DAISY participants with Tempus tubes (Applied Biosystems). We selected samples from two visits (termed IA-1 and IA-2) that occurred after the onset of IA for mRNA sequencing. The IA-1 visit was selected as the first available visit after the onset of IA for all groups. In the progressor group, the visit that preceded clinical onset of T1D was selected as the IA-2 visit. In the maintainer and reverter groups, the IA-2 visit was selected as the visit where age was closest to median age in the progressor group at the IA-2 visit.
Total RNA was isolated and purified from frozen (−80°C), peripheral whole blood samples ofn= 138 subjects meeting the inclusion criteria (Supplementary Material). We also included 12 control samples and 12 technical replicates. NuGEN library preparation kits were used to construct the strand-specific total RNA libraries. The Globin AnyDeplete kit was used to remove globin transcripts. RNA integrity number (RIN) scores for all samples were quantitated with use of the TapeStation (Agilent). Paired-end 150-cycle 2 × 150 sequencing was performed with the Illumina NovaSeq 6000 system. Samples were pooled together in a single flow cell and were sequenced twice to obtain the desired read depth, resulting in a median read depth of 90 million paired end reads across the samples (range 54–128 million).

tag: visit

tag: group

tag: female yn

tag: age


title: wholelar_as3mtmut_0mMiAs_cl1


title: 110690_3_S72

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: 110686_4_S57


title: SAMPLE 86_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

value: FluB-att/IGIP

tag: time point

tag: mouse id

value: IgG


title: wholelar_wttab14_1mMiAs_cl3

tag: genotype

tag: treatment

tag: tissue


title: AGS

tag: cell type


title: wholelar_as3mtmut_1mMiAs_cl2


title: 110690_2_S64

value: blood

tag: ID

tag: tr n


title: MKN-45

tag: condition


title: SAMPLE 87_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: extracted molecule


title: SAMPLE 85_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: MGC-803- sh-NOTCH1


title: SAMPLE 84_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: wholelar_wttab14_1mMiAs_cl1


title: wholelar_wttab14_1mMiAs_cl2


title: PTL sample90

city: Los Angeles

first: Amal

last: Katrib

address: 609 Charles E Young Dr E

institute: University of California, Los Angeles

data_processing:
Raw RNA-seq reads were trimmed of adapter sequences and mapped against the Ensembl human genome (hg19; GRCh37.75) using the software STAR v2.4.1c with default parameters.
The percentage of mapped reads is 88.6%±2.9% (mean±s.d).
Abundance measurements were obtained using htseq-count v0.6.1 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

source_name: decidua

extract_protocol:
Human placentae were obtained within one hour of delivery with signed informed consent under the protocols approved by the University of Iowa Institutional Review Board (201411731). Placenta decidual tissue samples were macroscopically isolated from the maternal-facing surface of the placenta. Samples were cut into small pieces and placed in RNAlater® solution (Applied Biosystems, Foster City, CA).  Biopsies were obtained after written informed consent, according to the protocol approved by the University of Iowa and in accordance with the Department of Health and Human Services regulations at 45 CFR 46.
Total RNA was extracted from each tissue using the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instruction and stored at -80˚C until used
RNA-seq libraries were prepared using TruSeq RNA Sample Prep Kit v2 (Illumina) and sequenced on an Illumina HiSeq 2000 to produce 27-49 million 2x100nt pair-end reads per sample.

tag: labortype

value: preterm spontaneous

tag: deliverytype

value: vaginal vertex

tag: gestationalage


title: 110673_3_S64

city: Aurora

last: Vanderlinden

address: 13001 E. 17th Place, Mail Stop B119

tag: visit

value: RNA 1

tag: group

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age


title: SAMPLE 88_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id


title: wholelar_wttab14_0mMiAs_cl3

tag: genotype

tag: treatment

tag: tissue

value: whole larvae


title: PTL sample88

tag: labortype


title: SAMPLE 83_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: extracted molecule


title: 110435_3_S18

tag: ID

tag: tr n

value: Maintainer

tag: age ia


title: PTL sample89

tag: deliverytype

tag: gestationalage


title: 110642_3_S26

tag: visit

value: RNA 2

tag: group

tag: female yn

tag: nhw yn

tag: dr34 yn


title: wholelar_as3mtmut_0mMiAs_cl2


title: wholelar_wttab14_0mMiAs_cl2


title: SAMPLE 82_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

tag: vaccine

value: FluB-RANS/IGIP

tag: time point


title: SAMPLE 81_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: mouse id


title: PTL sample87


title: 110646_3_S51

tag: tissue

tag: fdr yn

tag: age


title: 110469_3_S43

tag: ID


title: PTL sample86

tag: labortype


title: wholelar_wttab14_0mMiAs_cl1

tag: genotype

tag: treatment


title: as3mtmut_1mMiAs_liver_cl5

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_5d_S20

source_name: 5 dpf pooled zebrafish livers

treatment_protocol: 1 mM Sodium Arsenite added to treatment groups at 96 hpf - 120 hpf

value: 1 mM iAs 96-120 hpf

value: 5 dpf 12-15 pooled liver


title: SAMPLE 80_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: extracted molecule


title: PTL sample85

tag: deliverytype

value: CS after labor

tag: gestationalage


title: 110567_2_S72

tag: tr n

tag: visit

tag: group

value: Reverter

tag: female yn

tag: age ia


title: as3mtmut_0mMiAs_liver_cl5

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_5c_S19

value: 0 mM iAs 96-120 hpf


title: 110457_2_S80

tag: nhw yn

tag: dr34 yn


title: SAMPLE 79_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: tissue

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

value: d14 dpc

tag: mouse id


title: PTL sample84

tag: labortype


title: 110627_4_S53

tag: ID

tag: fdr yn

tag: age


title: PTL sample83

tag: deliverytype

value: vaginal breech

tag: gestationalage


title: PTL sample82


title: wt_tab5_0mMiAs_liver_cl5

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_5a_S17

tag: genotype

tag: treatment


title: as3mtmut_1mMiAs_liver_cl4

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_4d_S16


title: 110627_1_S25

value: blood

tag: tr n

tag: visit

tag: group

tag: female yn


title: PTL sample81

value: preterm spontaneous


title: 110500_1_S17

tag: tissue

tag: nhw yn

tag: dr34 yn

tag: age ia


title: SAMPLE 76_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

value: FluB-RAM/IGIP

tag: time point

tag: mouse id

tag: extracted molecule

value: IgG


title: SAMPLE 77_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: as3mtmut_0mMiAs_liver_cl4

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_4c_S15


title: SAMPLE 75_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: PTL sample80

tag: labortype

tag: deliverytype


title: 110645_1_S36

tag: ID

tag: fdr yn

tag: age


title: SAMPLE 74_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: wt_tab5_1mMiAs_liver_cl4

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_4b_S14

tag: genotype

tag: treatment


title: SAMPLE 73_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: wt_tab5_0mMiAs_liver_cl4

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_4a_S13


title: 110633_2_S37

tag: tr n

tag: visit

tag: group

tag: female yn


title: PTL sample78

value: preterm induced

value: vaginal vertex

tag: gestationalage


title: PTL sample79


title: as3mtmut_1mMiAs_liver_cl3

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_3d_S12

tag: tissue


title: 110628_2_S45

value: RNA 1

tag: nhw yn

tag: dr34 yn

tag: age ia


title: 110556_1_S33

value: RNA 3

value: Progressor


title: as3mtmut_0mMiAs_liver_cl3

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_3c_S11


title: SAMPLE 71_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: SAMPLE 78_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP


title: SAMPLE 70_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

source_name: Serum

value: Serum

value: FluB-att/IGIP

value: IgA


title: PTL sample50

tag: labortype

tag: deliverytype


title: wt_tab5_1mMiAs_liver_cl5

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_5b_S18

tag: genotype

tag: treatment

value: 1 mM iAs 96-120 hpf

value: 5 dpf 12-15 pooled liver


title: 110714_2_S73

source_name: blood

tag: ID

tag: tr n

tag: visit

value: RNA 2

tag: fdr yn

tag: age


title: PTL sample49

tag: gestationalage


title: wt_tab5_0mMiAs_liver_cl3

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_3a_S9

value: 0 mM iAs 96-120 hpf

tag: tissue


title: 110454_2_S65

value: blood

tag: group

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: age ia


title: PTL sample48

value: preterm spontaneous


title: wt_tab5_1mMiAs_liver_cl3

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_3b_S10


title: as3mtmut_1mMiAs_liver_cl2

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_2d_S8


title: SAMPLE 69_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

value: d14 dpc

tag: mouse id

tag: extracted molecule


title: SAMPLE 68_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: 110607_1_S13

tag: ID

value: Maintainer


title: 110447_1_S28

tag: tr n

value: RNA 1

value: Reverter


title: NSVD sample76

tag: labortype

value: term spontaneous

tag: deliverytype

value: vaginal vertex


title: as3mtmut_0mMiAs_liver_cl2

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_2c_S7

tag: genotype

tag: treatment


title: NSVD sample75

tag: gestationalage


title: 110569_1_S5

tag: tissue

tag: visit

tag: group

tag: fdr yn

tag: age


title: SAMPLE 72_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Nasal wash

tag: vaccine regimen

value: FluB-RAM/IGIP

value: IgG


title: SAMPLE 67_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine

value: FluB-att/IGIP

value: IgA


title: SAMPLE 66_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: time point


title: SAMPLE 65_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: mouse id


title: 110631_3_S25

value: RNA 2

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: age ia


title: wt_tab5_0mMiAs_liver_cl2

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_2a_S5

value: 0 mM iAs 96-120 hpf

value: 5 dpf 12-15 pooled liver


title: 110520_3_S17

value: blood

tag: ID

tag: tr n


title: NSVD sample73

tag: labortype

value: term induced

tag: deliverytype


title: 110630_3_S95

tag: tissue

value: Progressor


title: NSVD sample77

tag: gestationalage


title: SAMPLE 63_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: prime/boost challenge

value: d14 dpc

tag: extracted molecule


title: SAMPLE 64_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: as3mtmut_0mMiAs_liver_cl1

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_1c_S3

tag: genotype

tag: treatment


title: 110550_3_S87

tag: visit

value: RNA 1

tag: group

tag: fdr yn

tag: age


title: NSVD sample71

value: term spontaneous


title: wt_tab5_1mMiAs_liver_cl1

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_1b_S2

value: 1 mM iAs 96-120 hpf


title: NSVD sample72

value: vaginal vertex


title: 110625_1_S69

value: Maintainer

tag: female yn


title: wt_tab5_1mMiAs_liver_cl2

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_2b_S6


title: NSVD sample69


title: SAMPLE 61_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

value: FluB-RANS/IGIP

tag: time point

tag: mouse id


title: NSVD sample74


title: 110461_1_S77

tag: ID

tag: tr n

tag: nhw yn

tag: dr34 yn

tag: age ia


title: wt_tab5_0mMiAs_liver_cl1

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_1a_S1

tag: tissue


title: 110561_1_S7


title: SAMPLE 62_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: extracted molecule


title: SAMPLE 59_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: amiRCWC15 Rep1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome with miRNA annotation using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with  htseq-count
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: 16 hour light; 8 hour dark;  at 22 oC

extract_protocol:
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol

value: inflorescence

tag: genotype

tag: molecule subtype

value: small RNA


title: 110455_1_S15

tag: visit

tag: group


title: as3mtmut_1mMiAs_liver_cl1

description:
polyAAA RNA, stored at -80 until use
pmd3_L20230214-1_1d_S4

tag: treatment


title: amiRCWC15 Rep2


title: NSVD sample67

tag: labortype

tag: deliverytype

tag: gestationalage


title: SAMPLE 60_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine

tag: time point

value: IgA


title: SAMPLE 58_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: mouse id


title: Col WT Rep2

value: WT Col


title: NSVD sample65


title: SAMPLE 57_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: Col WT Rep1


title: NSVD sample53


title: 110517_1_S79

tag: ID

tag: tr n

value: Reverter

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age


title: 110612_3_S63

tag: tissue

value: blood

value: RNA 2

tag: dr34 yn

tag: age ia


title: NSVD sample70


title: SAMPLE 56_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: extracted molecule


title: SAMPLE 55_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: NSVD sample34

tag: labortype

value: term induced


title: NSVD sample68

tag: deliverytype


title: ATAC-Nono_KO1

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

library_source: genomic

data_processing:
All reads for each sample were combined and aligned to Rn6 with bowtie2. Peaks were called for each sample using MACS2. The peak annotation was assessed using the  ‘ChIPseeker’ library from R/Bioconductor. Motif analysis on peak regions was performed by HOMER function. Heatmaps and profile plots were generated using  DeepTools. Visualization of genome-wide read coverage was performed by converting raw bam files to bigwig files using IGV tools.
Assembly: Rn6
Supplementary files format and content: bigwig files

molecule: genomic DNA

source_name: cardiac muscle

growth_protocol: Rat cardiomyocytes H9c2 were purchased from American Type Culture Collection (ATCC, cat. no. CRL-1446), cultured in DMEM (Gibco, cat. no. C11995500BT) supplemented with 10% fetal bovine serum (Hyclone, cat. no. SV30208.02) and maintained in a humidified incubator (Thermo Scientific, cat. no. 3131) with 5% CO2 atmosphere at 37℃. The medium was changed every 2-3 days.

extract_protocol:
Nuclei were isolated from cells for each replicate, followed by the transposition reaction in the presence of Tn5 transposase (Vazyme) for 45 minutes at 37°C.
ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). Nuclei were isolated, permeabilized, and tagmented using Tn5 transposase (Vazyme), reverse-crosslinked, and amplified using NEBNext High-Fidelity 2 x PCR Master Mix (NEB). Library preparation and sequencing were performed by HiSeq X Ten (paired-end 150bp reads) .

treatment_protocol: The day before transfection, cells (1.0×106 cells/well) were seeded in six-well plates and cultured overnight until almost 70–80% cell confluence. The pSpCas9(BB)-2A-Puro(PX459) plasmid vector (available from our lab) was constructed in the sgRNA (5’- caccgATTTCCTCGGCCTGTGACTG), and the pEGFP-N1 plasmid vector (available from our lab) was used as control plasmid. 2 µg plasmid was diluted in 80 µL Opti-MEM (Sigma, cat. no. 408727), 6 µL PEI (Polysciences, cat. no. 23966-1) was diluted in 80 µL Opti-MEM, the two were mixed and incubated at room temperature for 10 minutes. PEI/plasmid mixture was then added to single well of 6-well plate. After 12 h, green fluorescence was examined under a fluorescence microscope (Nikon Eclipse TSZR). Then, Puromycin (Yeasen Biotechnology, cat. no. 60210ES60) was used to screen and achieve the stable cell lines.

tag: genotype

value: Nono gene knockout

tag: cell line


title: SAMPLE 54_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

value: FluB-RAM/IGIP

value: d14 dpc


title: NSVD sample31

tag: gestationalage


title: 110613_2_S49

tag: ID

tag: visit

tag: group

value: Progressor


title: ATAC-WT2

value: wild type


title: SAMPLE 53_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: time point

tag: mouse id


title: 110428_3_S55

tag: tr n

value: RNA 1

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age


title: ATAC-WT1


title: 110593_1_S71

tag: tissue

tag: dr34 yn

tag: age ia


title: 110450_2_S57


title: KO3

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads  containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the mRatBN7.2 refSeq refFlat GTF file.
Genes with P-value < 0.05 and foldChange >1.2 were defined as differentially expressed genes (DEGs).
Assembly: mRatBN7.2
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
The total RNA was extracted from H9c2 cell lines using the TRIzol Reagent (Invitrogen) according to the manufacturer's instructions and stored at -80℃. The concentration and purity of RNA were determined using a NanoPhotometer (ThermoFisher Scientific Intertek, Cat. 3100668).
RNA purification, cDNA synthesis and RNA-Seq of each group (n = 3) were performed by Oebiotech company (Shang hai, China). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 were subjected to the following analysis. The cDNA libraries were constructed through TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).

tag: genotype

tag: cell line


title: CS sample98

tag: labortype

value: no labor

tag: deliverytype

value: CS without labor


title: CS sample99

tag: gestationalage


title: 110610_3_S46

tag: ID

tag: visit

value: Maintainer


title: 110541_3_S38

tag: group


title: KO2


title: CS sample97


title: ATAC-Nono_KO2


title: SAMPLE 51_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

tag: vaccine

tag: time point

tag: mouse id

tag: extracted molecule


title: SAMPLE 50_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: IgA


title: CS sample96


title: 110572_2_S68

tag: tr n

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age


title: KO1

tag: genotype

tag: cell line


title: 110484_2_S76

tag: tissue

tag: dr34 yn

tag: age ia


title: SAMPLE 48_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: CS sample95

tag: labortype

tag: deliverytype

tag: gestationalage


title: NSVD sample109

value: term spontaneous

value: vaginal vertex


title: WT2


title: SAMPLE 52_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: vaccine


title: 110518_4_S72

value: blood

tag: ID

tag: visit

tag: group


title: CS sample94


title: SAMPLE 47_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: time point

tag: mouse id

tag: extracted molecule


title: WT1


title: CS sample93


title: 110515_4_S71

tag: tr n

tag: female yn

tag: nhw yn

tag: fdr yn

tag: age


title: CS sample92


title: 110547_1_S6

tag: tissue

value: RNA 2

value: Reverter

tag: dr34 yn

tag: age ia


title: 110451_1_S14


title: RT, replicate 2, scRNAseq

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. File format is compatible with the R package Seurat. Requires the corresponding features (genes) and barcodes (cell names) files.

source_name: iWAT

extract_protocol:
The fourth inguinal white adipose tissue (iWAT) depot mgWAT from mice exposed to cold stress (4°C) or room temperature for 24 hr was dissected and placed on a sterile 6-well tissue culture plate with ice-cold 1X DPBS. Excess liquid was removed from fat pads by blotting. Each tissue was cut and minced with scissors and then placed in 15 ml conical tubes containing digestion buffer (2 ml DPBS and Collagenase II at 3 mg/ml; Worthington Biochemical, Lakewood, NJ, USA) for 40 min of incubation at 37°C with gentle shaking at 100 rpm. Following tissue digestion, enzyme activity was stopped with 8 ml of resuspension media (DMEM/F12 with glutamax supplemented with 15%FBS and 1% pen/strep; Thermo Scientific, CA). The digestion mixture was passed through 100 μm cell strainer and centrifuged at 150 x g for 8 min at room temperature. To remove red blood cells, the pellet was resuspended and incubated in RBC lysis buffer (Thermo Scientific, CA) for 3 min at room temperature, followed by centrifugation at 150 x g for 8 min. The pellet was then resuspended in resuspension media and again spun down at 150 x g for 8 min. The cell pellet was resuspended in 1 ml of 0.01% BSA (in DPBS) and passed through a 40 μm cell strainer (Fisher Scientific, Hampton, NH, USA) to discard debris. Cell number was counted for 10X Genomics single cell application.
To yield an expected recovery of 4000-7000 single cells, an estimated 10,000 single cells per channel were loaded onto Single Cell 3’ Chip (10X Genomics, CA). The Single Cell 3’ Chip was placed on a 10X Genomics instrument to generate single cell gel beads in emulsion (GEMs). Chromium Single Cell 3’ v3 Library and Cell Bead Kits were used according to the manufacturer’s instructions to prepare single cell RNA-Seq libraries.

tag: cell type

value: SVF

value: iWAT

tag: strain

value: 8 weeks old

tag: treatment

value: 24hrs at RT


title: SAMPLE 45_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine regimen

value: prime/boost

tag: vaccine

value: FluB-att/IGIP

value: d19 dpb


title: CS sample91

tag: labortype

value: no labor

tag: deliverytype

tag: gestationalage


title: 110483_1_S38

tag: ID

tag: visit

tag: group


title: SAMPLE 44_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: time point

tag: mouse id

tag: extracted molecule


title: RT, replicate 1, scRNAseq

description: 10x Genomics

tag: tissue

tag: age


title: SAMPLE 46_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array


title: SAMPLE 49_prime/boost challengeFluB-RAM/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: prime/boost challenge

value: FluB-RAM/IGIP

value: d14 dpc


title: WT3

tag: genotype

value: wild type

tag: cell line


title: CS sample112

value: CS without labor


title: 4DEG, replicate 2, scRNAseq

description: 10x Genomics

tag: cell type

tag: strain

value: 24hrs at 4 C


title: SAMPLE 43_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

value: IgA


title: CS sample110


title: 4DEG, replicate 1, scRNAseq

description: 10x Genomics

tag: treatment


title: 110624_2_S59

value: blood

tag: tr n

value: RNA 2

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: SAMPLE 42_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine

tag: time point


title: CS sample106

tag: labortype

tag: deliverytype

tag: gestationalage


title: 110599_2_S51

tag: tissue

tag: ID

tag: visit

value: RNA 1

tag: group

tag: age


title: SAMPLE 41_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: mouse id

tag: extracted molecule


title: KO (SRC2fl/fl/CD4-Cre CD4+ cells) Rep 4

city: Duarte

first: ZUOMING

last: SUN

address: 1500 E Duarte Rd, Duarte, CA 91010

institute: City of Hope Medical Center

data_processing: The sequence reads were aligned to the mouse whole genome (GRCm38) with validation of quality through pre-alignment and post-alignment QA/QC. Aligned reads were further subjected to quantification using the Parteck E/M algorithm and normalization to counts per million (CPM) with 0.001 added to each

source_name: CD4 t cells

extract_protocol:
RNA WAS extracted with an RNA extraction kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: SRC2fl/fl/CD4-Cre mice

tag: treatment

value: weeks post adoptive transferred to Rag1-/-


title: KO (SRC2fl/fl/CD4-Cre CD4+ cells) Rep 3


title: SAMPLE 40_prime/boostFluB-att/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: prime/boost

value: FluB-att/IGIP


title: CS sample105

value: no labor


title: CS sample104


title: SAMPLE 39_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP

value: d19 dpb


title: 110549_2_S94

tag: tr n

value: Maintainer

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: KO (SRC2fl/fl/CD4-Cre CD4+ cells) Rep 2


title: 110502_2_S86

tag: age ia


title: SAMPLE 38_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine

tag: time point


title: 110590_1_S87

tag: tissue

tag: ID

value: Progressor


title: CS sample103

tag: labortype

tag: deliverytype

value: CS without labor

tag: gestationalage


title: 110446_1_S46

tag: visit

tag: group

tag: age


title: KO (SRC2fl/fl/CD4-Cre CD4+ cells) Rep 1

tag: genotype

tag: treatment


title: WT (SRC2fl/fl) Rep 4

value: SRC2fl/fl mice


title: CS sample102


title: SAMPLE 37_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

tag: mouse id

tag: extracted molecule


title: WT (SRC2fl/fl) Rep 3


title: 110586_1_S39

tag: tr n

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: 110511_1_S95

tag: tissue

tag: ID

tag: age ia


title: SAMPLE 36_prime/boostFluB-RANS/IGIPd19 dpb

description:
Fig. 3 and 5
UGA#3 IBV-IGIP array

tag: vaccine

tag: time point

value: IgA


title: CS sample101

tag: labortype

tag: deliverytype

tag: gestationalage


title: CS sample100


title: WT (SRC2fl/fl) Rep 2

tag: genotype

tag: treatment


title: SAMPLE 35_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

value: prime/boost challenge

value: d14 dpc

tag: mouse id

value: IgG


title: 110578_1_S47

value: blood

tag: tr n

tag: visit

value: RNA 1

tag: group

value: Reverter

tag: age


title: WT (SRC2fl/fl) Rep 1

value: weeks post adoptive transferred to Rag1-/-


title: 110534_2_S43

value: RNA 2

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: CSR_PQRXLF-3

city: New York

first: Yimeng

last: Zhu

state: NY

address: 1130 ST NICHOLAS AVE.

department: Institute for Cancer Genetics

institute: Columbia University

description: Class Switch Recombination junctions

data_processing:
Basecalls performed using Illumina RTA version 1.18.54.
Miseq reads were first de-multiplexed by fastq-multx tool from ea-util, then adaptor sequence was further trimmed with SeqPrep utility.
Pre-processed reads were then mapped to customized mm9 (for CSR) or mm10 (for chromosomal V(D)J recombination) genome using Bowtie2. The best-path searching algorithm (related to YAHA; G. G. Faust, et al. Bioinformatics 28, 2417-2424 (2012)) was used to identify optimal sequence alignments from Bowtie2-reported top alignments (alignment score > 50).
The reads were then filtered to exclude mis-priming events, germline (unmodified) sequence, sequential joints, and duplicated reads. A “duplicate read” is defined by bait and prey alignment coordinates within 2 nt of another read’s bait and prey alignments. Since signal joint reads number was very low after applying deduplication filter, this filter was not used for SJ analysis. For SJ and CJ deletion analyses, the deletion size was capped at 1,000 bp. Since some switch region sequences are very repetitive, the alignments in those regions were filtered out by the mappability filter. But they do unequivocally map to an individual switch region, so to plot all the switch region junctions, we added the ones filtered out by the mappability filter back after deduplication (J. Dong, et al. Nature 525, 134-139 (2015)). MHs are defined as regions of 100% homology between the bait and prey-break site. Insertions are defined as regions containing nucleotides that map to neither the bait nor prey-break site. Blunt junctions are considered to have no MHs or insertions.
The IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816; C57/BL6) of customized mm9 genome (mm9sr) was replaced by the corresponding region of 129 strain in NCBI gene accession sequence AJ851868.3.
Supplementary files format and content: .xlsx files generated from tab-delimited text files after analysis for reads distribution.

source_name: Spleen

growth_protocol: Purified splenic B (CD43-) cells from mice were cultured in RPMI medium with cytokines (anti-CD40 (1 µg/mL; BD Pharmingen) and IL-4 (20 ng/mL; R&D)).

extract_protocol:
Genomic DNA was extracted from treated B cells on day 4.
Libraries were prepared according to the protocol in (Hu J, et al. Nat Protoc 11:853–871 (2016)). Linear amplifications were performed using Sμ-specific biotin primer (/5Bios/CAGACCTGGGAATGTATGGT) and followed by nesting PCR with (5′-CACACAAAGACTCTGGACCTC-3′). AflII was used to remove germline sequence.
High-throughput genome translocation sequencing (HTGTS). Sequenced with MiSeq 500v.

treatment_protocol: Cells were cultured for 4 days and analyzed via flow cytometry before DNA extraction.

tag: tissue

value: Spleen

tag: cell line

value: anti-CD40 and IL-4 activated B cell

tag: cell type

value: B cells

value: DNA-PKcsPQR/PQRXlf-/-

value: anti-CD40 and IL-4 for 4 days


title: SAMPLE 34_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine

value: FluB-att/IGIP

tag: time point

tag: extracted molecule


title: CSR_PQRXLF-2

description: Class Switch Recombination junctions

tag: genotype

tag: treatment


title: SAMPLE 33_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen

tag: mouse id


title: SAMPLE 32_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: RNA-seq_Microglia, SMAD4-conditional KO, Rep3

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

data_processing:
FASTQ files from sequencing experiments were mapped to mm10. RNA-seq files were mapped using STAR with default parameters. The gene expression raw counts were quantified by HOMER's (Heinz et al., 2020) analyzeRepeats command with the option “-condenseGenes -count exons -noadj”. Differential gene expression was calculated using the HOMER command “getDiffExpression.pl”. TPM (transcript per kilobase million) were quantified for all genes matching accession number to raw counts. Differentially expressed genes were assessed with DESeq2 (Love et al., 2014) at p-adj (adjusted pvalue) < 0.05 and FC (fold change) > 2 where indicated. Genes with TPM < 4 in all conditions were removed from analysis. Gene ontology enrichment analyses were performed using Metascape (Zhou et al., 2019)).
Assembly: mm10
Supplementary files format and content: SALL1SMAD4_RNAseq_RAW.txt, tab-delimited text file containing table of unnormalized read counts ffor all RNA-seq samples
Supplementary files format and content: SALL1SMAD4_RNAseq_TPM.txt, tab-delimited text file containing table of TPM counts for all RNA-seq samples

source_name: Brain

extract_protocol:
Mouse brains were homogenized as previously described by gentle mechanical dissociation (Gosselin et al, 2014) and stained with anti-mouse anti-CD11b-APC (BioLegend 101212), anti-CD45-Alexa488 (BioLegend 103122), and anti-CX3CR1-PE (BioLegend 149006). Microglia were sorted as DAPI negative, singlets, and CD11b+CD45lowCX3CR1+. Total RNA was extracted from sorted cells using the Direct-zol RNA MicroPrep Kit (Zymo Research R2052) and stored at -80°C until library preparation.
RNA-seq libraries were prepared as previously described (Sakai et al., 2019, Immunity)  with approximately 100,000 sorted live microglia. mRNAs were enriched from total RNA by incubation with Oligo d(T) Magnetic beads (NEB, S1419S) in 2X DTBB buffer (20 mM Tris-HCl pH 7.5, 1 M LiCl, 2mM EDTA, 1% lithium dodecyl sulfate, 0.1% Triton X-100) at 65°C for 2 minutes and were incubated at room temperature while rotating for 15 minutes. The beads were then washed 1x with RNA Wash Buffer 1 (10mM TrisHCl pH 7.5, 0.15M LiCl, 1mM EDTA, 0,1% lithium dodecyl sulfate 0.1% Triton X-100) and 1x with RNA Wash Buffer 3 (10mM Tris-HCl pH 7.5, 0.15 M NaCl, 1mM EDTA) before elution in RNA Elution Buffer (10mM Tris-HCl pH 7.5, 1mM EDTA) at 80°C for 2 minutes. PolyA selection was performed a second time, and samples were washed 1x with Wash Buffer 1, 1x with Wash Buffer 3, and 1x with 1x SuperScript III first-strand buffer. Beads were then resuspended in 10 µL 2x SuperScript III buffer plus 10 mM DTT, and RNA was fragmented at 94°C for 9 minutes and immediately chilled on ice before the next step. For first-strand synthesis, 10 µL of fragmented mRNA, 0.5 µL Random primers (50 µM)(Thermo Fisher), 0.5 µL SUPERase-In (Ambion), 1µL dNTPs (10mM), and 1µL of DTT (10mM) were heated for 50°C for one minute. At the end of incubation, 5.8 µL of water, 1 µL of DTT (100mM), 0.1 µL Actinomycin D (2µg/uL), 0.2uL of 1% Tween-20 (Sigma) and 0.5µL of SuperScript III (Thermo Fisher Scientific) were added and incubated in a PCR machine using the following conditions: 25°C for 10 minutes, 50°C for 50 minutes, and a 4°C hold. The product was then purified with RNAClean XP beads (Beckman Coulter) according to manufacturer’s instruction and eluted with 10 µL nuclease-free wate. The RNA/cDNA double-stranded hybrid was then added to 1.5 µL Blue Buffer (Enzymatics), 1.1 µL of dUTP mix (10mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µL RNase H (5U/uL), 1.05 µL of water, 1µL of DNA Polymerase I (Enzymatics) and 0.15 µL of 1% Tween-20. The mixture was incubated at 16°C overnight. The following day, the dUTP marked dsDNA was purified using 28 µL of SpeedBeads (GE Healthcare), diluted with 20% PEG8000, 2.5M NaCl to a final concentration of 13% PEG, eluted with 40 µL elution buffer (DNA elution buffer from Zymo ChIP Clean and Concentrator Kit). The purified dsDNA underwent end repair by blunting, A-tailing, and adaptor ligation as previously described 14 using barcoded adapters (NextFlex, Bioo Scientific). Libraries were PCR amplified for 16 cycles, size for 200-500bp size range, quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and sequenced on a HiSeq 4000 for 51 cycles according to the manufacturer’s instructions.

value: Brain

tag: strain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: SMAD4-conditional deletion


title: 110462_2_S35

tag: ID

tag: tr n

tag: visit

tag: group

value: Maintainer

tag: age ia


title: 110558_3_S70

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age


title: CSR_XLF-3

description: Class Switch Recombination junctions

tag: tissue

tag: cell line

tag: cell type

value: Xlf-/-


title: RNA-seq_Microglia, SMAD4 WT, Rep4

tag: genotype


title: SAMPLE 30_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

value: d14 dpc

tag: extracted molecule

value: IgG


title: 110496_2_S95

value: blood

tag: ID

tag: tr n

value: Progressor


title: SAMPLE 31_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: mouse id


title: RNA-seq_Microglia, SMAD4 WT, Rep3

tag: strain


title: SAMPLE 29_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: CSR_XLF-1

description: Class Switch Recombination junctions

value: Spleen

tag: treatment


title: RNA-seq_Microglia, SMAD4 WT, Rep2


title: CSR_XLF-2

description: Class Switch Recombination junctions

value: anti-CD40 and IL-4 activated B cell


title: RNA-seq_Microglia, SMAD4-conditional KO, Rep1


title: CSR_PQR-2

description: Class Switch Recombination junctions

value: B cells

value: DNA-PKcsPQR/PQR


title: SAMPLE 28_prime/boost challengeFluB-att/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array


title: RNA-seq_Microglia, SMAD4 WT, Rep1


title: SAMPLE 27_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP


title: 110576_3_S78

tag: visit

value: RNA 2

tag: group

tag: female yn

tag: nhw yn

tag: age ia


title: CSR_PQRXLF-1

description: Class Switch Recombination junctions

tag: tissue

tag: cell line

value: DNA-PKcsPQR/PQRXlf-/-

value: anti-CD40 and IL-4 for 4 days


title: RNA-seq_Microglia, SMAD4-conditional KO, Rep2

value: Brain

tag: cell type

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

tag: genotype

value: SMAD4-conditional deletion


title: RNA-seq_Microglia, SALL1 Enhancer KO, Rep3

value: Sall1 Enhancer Knockout


title: CSR_PQR-1

description: Class Switch Recombination junctions


title: 110477_3_S69

value: RNA 1

value: Reverter

tag: dr34 yn

tag: fdr yn

tag: age


title: CSR_XLF-4

description: Class Switch Recombination junctions

value: Xlf-/-


title: CSR_WT-3

description: Class Switch Recombination junctions

value: WT


title: 110596_3_S53

value: blood

tag: ID

value: Maintainer


title: SAMPLE 26_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: Serum

tag: vaccine regimen

value: prime/boost challenge

tag: vaccine

tag: time point

value: d14 dpc

tag: extracted molecule

value: IgG


title: 110432_2_S8

tag: tr n

tag: visit

value: Progressor


title: SAMPLE 25_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

value: FluB-RANS/IGIP

tag: mouse id


title: RNA-seq_Microglia, SALL1 Enhancer KO, Rep2

tag: strain


title: 110566_3_S45

tag: group

tag: female yn

tag: nhw yn

tag: age ia


title: CSR_WT-2

description: Class Switch Recombination junctions

tag: tissue

value: Spleen

tag: cell line

value: anti-CD40 and IL-4 activated B cell

tag: cell type

value: B cells

tag: genotype

tag: treatment

value: anti-CD40 and IL-4 for 4 days


title: SAMPLE 24_prime/boost challengeFluB-RANS/IGIPd14 dpc

description:
Fig. 5, 6 and 7
UGA#3 IBV-IGIP array

tag: vaccine regimen


title: 110529_3_S61

tag: ID

value: RNA 2

tag: dr34 yn

tag: fdr yn

tag: age


title: 110685_1_S60

tag: tr n

tag: visit

value: RNA 3


title: CSR_WT-1

description: Class Switch Recombination junctions


title: RNA-seq_Microglia, SALL1 Enhancer KO, Rep1

value: Brain

tag: strain

value: whole cell Microglia (CD45+ CD11b+ CX3CR1+)

value: Sall1 Enhancer Knockout