title: BT549_S6_GO-203_1


title: BT549_S6_cont_1

status: Public on Oct 11 2023

type: SRA

city: Buffalo

first: Henry

middle: G.

last: Withers

state: New York

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

country: USA

institute: Roswell Park Comprehensive Cancer Center

library_source: transcriptomic

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2)
Reads were mapped to human genome (GRCh38) by STAR (version 2.7.3a)
The number of fragments in each known gene from GENCODE (version 25) were quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2.
Assembly: GRCh38
Supplementary files format and content: Processed data in supplementary tab-delimited file contains a matrix of raw read counts for each gene accession number (rows) and sample (columns)

molecule: total RNA

organism: Homo sapiens

source_name: epithelial breast

growth_protocol: For 2D growth, human BT-549 BRCA1 wild-type TNBC (ATCC) cells were cultured in RPMI1640 medium (Thermo Fisher Scientific) containing 10% fetal bovine serum (GEMINI BioProducts), 100 µg/ml streptomycin, 100 U/ml penicillin and 10 µg/ml insulin. For culture of 3D mammospheres, BT-549 cells were seeded at 2.5-5×103/well in 6-well ultra-low attachment culture plates (Corning) using the MammoCult Human Medium Kit (Stemcell Technologies).

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
TruSeq Stranded mRNA (Illumina) was used for library preparation

tag: tissue

value: epithelial breast

tag: cell line

tag: cell type

value: TNBC cell line

tag: genotype

value: WT

tag: treatment

value: Control

tag: growth format

tag: shRNA

tag: shRNA info


title: BT549_S6_cont_2


title: BT549_S6_cont_3


title: BT549_S6_GO-203_2


title: BT549_2D_WT_1


title: BT549_2D_WT_2


title: PQN85_CA1200_1hrauxin_L3_rep1 [HW01]

status: Public on Sep 30 2023

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

library_source: genomic

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
Supplementary files format and content: ChIP-seq: input normalized bigwigs

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

tag: strain

tag: developmental stage

tag: antibody target

tag: antibody (vendor, cat#, lot#)


title: BT549_2D_WT_3


title: PQN85_JK05_1hrauxin_L3_rep1 [JK189]


title: SMC3_CA1200_1hrauxin_L3_rep1 [JK165]

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
Hi-C:  data was mapped to ce10 (WS220) reference genome or its variant that corrosponds to the perturbation using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016).
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
Supplementary files format and content: ChIP-seq: input normalized bigwigs
Supplementary files format and content: Hi-C:  hic matrix files

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima High Coverage Hi-C kit, which uses four 4-base cutters. The Arima manufacturer’s protocol was followed.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.
Hi-C: Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

tag: antibody (vendor, cat#)


title: BRG1_CUTnRUN_2i_(20210104_SB_MmScEc_2i_1217_BRG1_in)

status: Public on Oct 12 2023

city: Omaha

first: Sandipan

last: Brahma

state: NE

address: 985805 Nebraska Medical Center, DRCI 6054

institute: University of Nebraska Medical Center

description: CUT&RUN targeting BRG1 in mESCs in 2i

data_processing:
Genome_build: mm10
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to the UCSC mm10 Mus musculus reference sequence. 2. We extracted properly paired reads from the alignments. 3.We used bedtools 2.30.0 genomecov to make a normalized count mm10 track which is the fraction of counts at each base pair scaled by the size of the mm10 reference sequence (2725537669) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .bw)

organism: Mus musculus

source_name: CUT&RUN

extract_protocol:
CUT&RUN_Brahma.pdf
CUT&RUN_Brahma.pdf

tag: antibody

value: abcam ab110641, Antibodies Online ABIN101961

value: AB2.2 mouse embryonic stem cells ATCC SCRC-1023


title: SMC3_JK05_1hrauxin_L3_rep1 [JK163]


title: B6xPWK_MPac_hic_rep1

status: Public on Sep 23 2023

city: Beijing

first: Jing

last: He

state: Beijing

address: Room D110, Medical Science Building, School of Medicine, Tsinghua University

department: School of Medicine

country: China

institute: Tsinghua University

description: sisHi-C

data_processing:
For Hi-C samples: Hi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb or 10Kb bin size was used for compartment calling and a 40Kb bin size was used for TAD calling. The raw contact counts are normalized with iterative correction.
For RNA-Seq samples: Paired-end reads of RNA-seq libraries were quality confirmed by FastQC and then mapped to mm9 by Hisat2. Duplicated and multiple hit reads were discarded using SAMtools. The gene expression level was calculated by Python package HTSeq using the annotation file from the Gencode database. Only uniquely mapped reads were kept for raw counts matrix building.
For ATAC-Seq samples: Paired-end reads of ATAC-seq libraries were quality confirmed by FastQC and then mapped to mm9 by Hisat2. SAMtools was used for removing duplicates and multiple hit reads. Deeptools function bamCoverage was used for generates a bigwig coverage track.
Assembly: mm9
Supplementary files format and content: .hic files contain chromosomal contacts at different resolutions for each sisHi-C sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: bigwig files contain open chromatin regions for each ATAC-Seq sample

source_name: testis

extract_protocol:
FPGC, FLep, FZyg, FPac and FDip were isolated from ovaries of E11.5, E13.5, E15.5, E17.5 and E19.5 B6xPWK F1 female mice. For SGA, MLep, MZyg, MPac and MDip, we separated them from testes of 7dpp, 9dpp, 11dpp, 17dpp and 29dpp B6xPWK F1 male mice.
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification; RNA-Seq and ATAC-Seq libraries were constructed using TruSeq

value: testis

tag: Stage

value: pachytene spermatocyte

value: germ cells

value: FACS isolated


title: B6xPWK_MDip_hic_rep2

description: sisHi-C

value: diplotene spermatocyte


title: B6xPWK_MDip_hic_rep1

description: sisHi-C


title: B6xPWK_MPac_hic_rep2

description: sisHi-C

value: pachytene


title: B6xPWK_MZyg_hic_rep1

description: sisHi-C

value: zygotene spermatocyte


title: BT549-S6-t8-DOXplus_1

value: 500 ng/ml doxycycline

value: MISSION shRNA TRCN0000122938


title: B6xPWK_MLep_hic_rep2

description: sisHi-C

value: leptotene spermatocyte


title: BT549-S6-t8-DOX-_3

value: 0.1% DMSO


title: BT549-S6-t8-DOX-_2

value: epithelial breast


title: B6xPWK_MLep_hic_rep1

description: sisHi-C


title: B6xPWK_SGA_hic_rep2

description: sisHi-C

value: SGA


title: B6xPWK_SGA_hic_rep1

description: sisHi-C


title: B6xPWK_FDip_hic_rep2

description: sisHi-C

source_name: ovary

value: ovary

value: diplotene oocyte


title: B6xPWK_FPac_hic_rep1

description: sisHi-C

value: pachytene oocyte


title: B6xPWK_FZyg_hic_rep1

description: sisHi-C

value: zygotene oocyte


title: B6xPWK_FZyg_hic_rep2

description: sisHi-C


title: B6xPWK_FDip_hic_rep1

description: sisHi-C


title: B6xPWK_FLep_hic_rep2

description: sisHi-C

value: leptotene oocyte


title: B6xPWK_FPac_hic_rep2

description: sisHi-C


title: B6xPWK_FPGC_hic_rep2

description: sisHi-C

value: PGC


title: B6xPWK_FLep_hic_rep1

description: sisHi-C

value: germ cells


title: B6xPWK_FPGC_hic_rep1

description: sisHi-C

value: FACS isolated


title: CKD RASi/SGLT2i 3

status: Public on Sep 01 2023

city: München

first: ZHIHUI

last: ZHU

address: Geiselgasteigstr. 62, 2.0G

country: Germany

institute: LMU Klinikum

data_processing:
After QC, Fastq was mapped to the mm39 by hisat2. DESeq2 for downstream analyze.
Assembly: mm39
Supplementary files format and content: count, rpkm matrix

source_name: kidney

extract_protocol:
Total RNA was isolated using an RNA extraction kit (Life Technologies, Darmstadt, Germany) according to the manufacturer´s instructions, and RNA quality was assessed using agarose gels. RNA-seq of total RNA samples was conducted on the Illumina DNBSEQ-G400 platform, producing 100bp paired-end reads.
Strand-specific transcriptome library construction is completed by enriching mRNA from total RNA, sequenced by DNBSEQ high-throughput platform, and followed by bioinformatics analysis.

treatment_protocol: Col4a3-/- mice were treated with food admix of either vehicle, 10 mg/kg ramipril, 10 mg/kg ramipril plus 30 mg/kg empagliflozin, and 10 mg/kg ramipril plus 30 mg/kg empagliflozin plus 10 mg/kg finerenone. The different types of food preparations were marked by different food colors starting from 6 weeks of age for 8 weeks.

value: kidney

value: primary cell

value: Ramipril/Empagliflozin


title: CKD RASi/SGLT2i 1


title: CKD RASi/SGLT2i 2


title: SMC1_JK06_1hrauxin_L3_rep1 [JK161b]


title: UMA-18

status: Public on Jun 20 2023

city: Detroit

first: Adi

last: Tarca

state: MI

address: 3990 John R. St, 4 Brush South

institute: Wayne State University

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner in mapping-based mode.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Assembly: Ensembl GRCm38, release 101
Supplementary files format and content: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package (v. 1.10.1), and saved in .csv format.

source_name: Uterus

extract_protocol:
Pregnant Nlrp3+/+ and Nlrp3-/- dams were intra-amniotically injected with S100B or PBS on 16.5 days post coitum. Sixteen hours after the injection, the decidual and uterine tissues were collected, followed by the isolation of neutrophils and macrophages from these tissues using fluorescence activated cell sorting. Total RNA was extracted from the sorted cells using the Pico Pure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions. RNA concentrations, purity, and integrity were evaluated using the NanoDrop 1000 spectrophotometer and the Bioanalyzer 2100. Two to four biological replicates from each group were combined for the neutrophil samples to obtain quantities of RNA for RNA-seq. cDNA was synthetized using Smart-seq2.
The Nextera DNA Library Preparation Kit were used to prepare the RNA-seq library according to the manufacturer’s instructions.

value: Uterus

value: Macrophage


title: UMA-17


title: UMA-16


title: UMA-7


title: UMA-9


title: DMA-18

source_name: Decidua

value: Decidua


title: UMA-8


title: DMA-17


title: DMA-16


title: DMA-8


title: DMA-9


title: DMA-7


title: UN-11

value: Neutrophil


title: UN-12


title: UN-6


title: UN-5


title: DN-12


title: DN-6


title: DN-11


title: UMA-12

value: PBS


title: DN-5


title: B6xPWK_MZyg_hic_rep2

description: sisHi-C

value: testis

value: zygotene spermatocyte


title: UMA-11


title: UMA-2


title: UMA-1


title: UMA-10


title: DMA-11


title: DMA-3


title: DMA-10


title: DMA-1


title: DMA-12


title: DMA-2


title: UN-8


title: UN-1


title: DN-1


title: DN-2


title: UN-7


title: DN-8


title: UN-2


title: cdHFD_female_ZT20_rep_4

status: Public on Jun 16 2023

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Reference genome (GRCm38/mm10) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
All the downstream analyses were based on the clean data with high quality. FeatureCounts was used to count the reads numbers mapped to each gene. Normalized DESEq2 data in log values were used for all subsequent analyzes
Assembly: mm10
Supplementary files format and content: Raw counts and FPKM valuesv for each sample are shown

source_name: liver

extract_protocol:
Total RNA was extracted from livers using Trizol reagent (Thermofisher, Germany) and columns (Zymo Research, USA) according to the manufactory’s instructions. Trueseq RNAseq comprising 40 million reads per sample (12GB) was performed at Novogene (Germany).
Samples underwent quality control and only those with RNA integrity number (RIN) higher than 6.5 were used. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: liver

value: wild type (WT)


title: cdHFD_male_ZT20_rep_2


title: DN-7


title: cdHFD_male_ZT20_rep_1


title: cdHFD_male_ZT14_rep_3


title: UMA-3


title: cdHFD_male_ZT14_rep_2


title: cdHFD_male_ZT14_rep_1


title: cdHFD_female_ZT8_rep_4


title: cdHFD_female_ZT8_rep_3


title: cdHFD_female_ZT2_rep_3


title: cdHFD_female_ZT2_rep_4


title: cdHFD_male_ZT8_rep_1


title: cdHFD_male_ZT2_rep_1


title: chow_female_ZT20_rep_3


title: chow_female_ZT20_rep_4


title: chow_male_ZT20_rep_2


title: chow_female_ZT14_rep_4


title: chow_female_ZT14_rep_3


title: chow_male_ZT14_rep_2


title: cdHFD_female_ZT20_rep_3


title: chow_male_ZT8_rep_2


title: chow_male_ZT14_ep_1


title: chow_female_ZT8_rep_4


title: cdHFD_female_ZT14_rep_4


title: chow_female_ZT8_rep_3


title: chow_male_ZT2_rep_1


title: chow_male_ZT8_rep_1


title: chow_female_ZT2_rep_4


title: chow_male_ZT2_rep_2


title: cdHFD_male_ZT8_rep_2


title: cdHFD_male_ZT2_rep_2


title: chow_male_ZT20_rep_1


title: CWNIH012

status: Public on Mar 03 2023

type: protein

hyb_protocol: These SOMAmer reagents were then quantified by hybridization to custom DNA microarrays.

scan_protocol: The Cyanine-3 signal from the SOMAmer reagent was detected on microarrays. More details on all protocols are described in Gold L, et al. PLoS One. 2010;5(12):e15004 and Davies DR, et al. Proc Natl Acad Sci U S A. 2012;109(49):19971-6.

data_processing: The raw protein abundance data consisted of relative fluorescence units obtained from scanning the microarrays with a laser scanner. The proteomic data preprocessing, including an adaptive normalization by maximum likelihood (ANML) step and a calibration step, were performed by SomaLogic, Inc. The goal of these steps was to make data comparable across samples by calculating plate-specific and analyte-specific scale factors.

molecule: protein

source_name: Plasma

label_protocol: The photo-cleavage eluate, which contains all SOMAmer reagents (some bound to a biotin-labeled protein and some free), was separated from the beads and then incubated with a second streptavidin-coated bead that binds the biotin-labeled proteins and the biotin-labeled protein-SOMAmer complexes. The free SOMAmer reagents were then removed during subsequent washing steps. In the final elution step, protein-bound SOMAmer reagents were released from their cognate proteins using denaturing conditions.

extract_protocol: The plasma samples were diluted and then incubated with the respective SOMAmer mixes pre-immobilized onto streptavidin-coated beads. The beads were washed in order to remove all non-specifically bound proteins and other matrix constituents. Proteins that remained specifically bound to their cognate SOMAmer reagents were tagged using an NHS-biotin reagent. After the labeling reaction, the beads were exposed to an anionic competitor solution that prevents non-specific interactions from reforming after disruption.  Using this approach, pure cognate-SOMAmer complexes and unbound (free) SOMAmer reagents are released from the streptavidin beads using ultraviolet light that cleaves the photo-cleavable linker used to quantitate protein.

tag: individual

tag: age

tag: bmi

tag: chronic hypertension

value: Yes

tag: Sex

value: Female

tag: group

value: Controls

tag: clinical spectrum nih classification

tag: parity

tag: ga


title: CWNIH014

value: No


title: CWNIH010


title: CWNIH019


title: CWNIH018


title: CWNIH013


title: chow_female_ZT2_rep_3

tag: tissue

tag: genotype

tag: treatment


title: CWNIH015


title: CWNIH020


title: CWNIH016


title: CWNIH009


title: CWNIH007


title: CWNIH006


title: CWNIH008


title: CWNIH004


title: CWNIH005


title: CMNIH023

value: Male


title: CWNIH003


title: CMNIH022


title: CWNIH002


title: CMNIH020


title: CMNIH019


title: CMNIH021


title: CWNIH001


title: CMNIH024


title: CMNIH016


title: CMNIH017


title: CWNIH017


title: CMNIH018


title: CMNIH015


title: CMNIH011


title: CMNIH009


title: CMNIH008


title: CMNIH004


title: CMNIH006


title: CMNIH014


title: CMNIH012


title: CMNIH005


title: CMNIH007


title: WNIH027

value: Cases

value: Critical


title: WNIH030


title: WNIH028

value: Severe


title: CMNIH001


title: CMNIH010


title: CMNIH002


title: WNIH025


title: WNIH026


title: WNIH015


title: WNIH024


title: WNIH022


title: WNIH021


title: WNIH013


title: WNIH029


title: WNIH019


title: WNIH014


title: WNIH018

value: Moderate


title: WNIH016


title: WNIH017


title: WNIH012


title: WNIH010


title: WNIH009


title: WNIH007


title: WNIH006


title: WNIH023


title: WNIH005


title: WNIH008


title: WNIH001


title: MNIH030


title: WNIH002


title: WNIH003


title: WNIH020


title: WNIH004


title: MNIH031


title: MNIH028


title: MNIH025


title: MNIH027


title: MNIH018


title: MNIH023


title: MNIH026


title: WNIH011

value: Mild


title: MNIH019


title: MNIH015


title: MNIH012


title: MNIH014


title: MNIH013


title: MNIH011


title: MNIH010


title: MNIH001


title: PNI109001


title: MNIH006


title: CPN009001


title: MNIH022


title: PNI013001

value: Asymptomatic


title: CPN018001


title: CPN022001


title: PNI059001


title: PNI038001


title: CPN033001


title: PNI105001


title: PNI024001


title: MNIH008


title: MNIH007


title: MNIH004


title: CPN027001


title: CPN013001


title: CPN015001


title: PNI030001


title: PNI107001


title: PNI057001


title: MNIH002


title: PNI064001


title: CPN016001


title: CPN011001


title: CPN006001


title: PNI081001


title: PNI078001


title: PNI095001


title: CPN026001


title: CPN020001


title: PNI080001


title: CPN035001


title: PNI056001


title: CPN021001


title: PNI047001


title: PNI117001


title: PNI004001


title: CPN017001


title: CPN007001


title: PNI092001


title: PNI066001


title: PNI061001


title: PEN001001


title: PNI115001


title: CPN023001


title: CPN025001


title: PNI067001


title: PNI083001


title: PEN003001


title: CPN014001


title: PEN009001


title: PNI039002


title: PNI079001


title: PNI094001


title: PNI101001


title: PNI100001


title: PNI116001


title: PNI052001


title: PNI098001


title: PNI077001


title: CPN012001


title: PNI091001


title: CPN004001


title: PNI073001


title: CPN008001


title: PNI026001


title: PNI090001


title: CPN024001


title: PNI005001


title: PNI063001


title: PNI048001


title: PNI033001


title: PNI053001


title: PNI099001


title: PNI045001


title: PNI119001


title: PNI084001


title: PNI065001


title: PNI055001


title: PNI041002


title: PNI120001


title: PNI043001


title: PNI014001


title: PNI097001


title: PNI036001


title: PNI088001


title: PNI068001


title: PNI111001


title: CPN010001


title: PNI002001


title: PNI110001


title: PNI046001


title: PNI093001


title: PNI089001


title: PNI032001


title: PNI060001


title: CPN031001


title: PNI072001


title: PNI114001


title: PNI031001


title: SB_input_CHIP_rep2

status: Public on Jan 12 2023

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
ChIP-seq reads were mapped to the mm10 genome assembly using Bowtie version 1.1.1,allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6. Uniquely mapped and non-redundant reads were used for peak calling with MACS 1.4.2 (Zhang et al., 2008) with –p 1e-5 -B -S --nomodel. Bigwig files were generated with BedGraphToBigWig (Kent et al., 2010) and Bedtools/2.29.2 (Quinlan and Hall, 2010)
ATAC-seq reads were aligned to the mm10 genome assembly using Bowtie/1.1.1(Langmead et al., 2009),allowing two mismatches, after adapter sequences were removed using trimgalore version0.6.6.Redundant reads were removed using FastUniq (Xu et al.,2012), and customized Python scripts were used to calculate the fragment length of each pair of uniquely mapped pair-end reads. The regions of open chromatin were identified by MACS 1.4.2 (Zhang et al., 2008) with –p 1e-5 -B -S. Only regions called in both replicates were used in downstream analysis.
Hi-C  reads were mapped to the mm10 genome assembly using BWA (Li and Durbin, 2010),filtering reads that aligned to more than two places in the genome and low mapping quality score (MAPQ <30).Hi-C downstream analysis was performed with JUICER(Durand, et al 2016), HICEXPLORER(Wolff, et al 2018)
Assembly: mm10
Supplementary files format and content: peak files, txt, bin

source_name: Skin epidermis: suprabasal cells

extract_protocol:
Skin epidermis was dissected as described in Lichti et al., 2008, and then percoll gradient separation was employed to isolate the basal and suprabasal cells.
ChIP-seq libraries were prepared on the suprabasal cells according to Myers Lab ChIP-Seq protocol v011014.
ATAC-seq libraries were prepared according to Buenrostro et al., 2015.
HiC libraries were prepared according to manufacturer's protocol given by Arima HiC-kit using KAPA Hyper Prep kit.

value: WT

tag: strain

value: FvB

tag: transgene

value: not transgenic


title: SB_HIC

value: non transgenic


title: B_HIC

source_name: Skin epidermis: basal cells


title: SB_K4Me1_CHIP_rep1

tag: chip antibody


title: CPN019001


title: PNI087001


title: PNI015001


title: PNI034002


title: SB_input_CHIP_rep1


title: SB_K27Ac_CHIP_rep1


title: SB_K4Me3_CHIP_rep1


title: PNI062001


title: SB_Dlx3_CHIP_rep1


title: SB_WT_ATAC_rep2


title: SB_WT_ATAC_rep1


title: B_WT_ATAC_rep2


title: B_WT_ATAC_rep1


title: SB_Dlx3_WT_ATAC_rep2


title: SB_Dlx3_WT_ATAC_rep1


title: B_HIC_rep2

data_processing:
Hi-C  reads were mapped to the mm10 genome assembly using BWA (Li and Durbin, 2010),filtering reads that aligned to more than two places in the genome and low mapping quality score (MAPQ <30).Hi-C downstream analysis was performed with JUICER(Durand, et al 2016), HICEXPLORER(Wolff, et al 2018)
Assembly: mm10
Supplementary files format and content: bin

extract_protocol:
Skin epidermis was dissected as described in Lichti et al., 2008, and then percoll gradient separation was employed to isolate the basal and suprabasal cells
HiC libraries were prepared according to manufacturer's protocol given by Arima HiC-kit using KAPA Hyper Prep kit.

value: non-transgenic


title: SB_HIC_rep2


title: SB_Pol2_CHIP_rep1


title: PNI049001


title: SB_input_CHIP_rep3


title: 703807-neutrophils

status: Public on Jan 05 2023

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Assembly: GRCh37
Supplementary files format and content: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package, and saved in .csv format.

source_name: Neutrophils

extract_protocol:
Fluorescence-activated cell sorting was performed to obtain isolated amniotic fluid neutrophils and monocytes/macrophages. Isolated cells were kept in RLT buffer (Qiagen) prior to RNA isolation. RNA isolation was performed using the Qiagen Micro Rneasy kit, and RNA purity, concentrations, and integrity were assessed.
Low-input RNAseq libraries were constructed by Beijing Genomics Institute (BGI; Wuhan, China) using the Smart-Seq2 kit (Illumina).

tag: cell type

value: Neutrophils

tag: cell origin

value: maternal

tag: delivery status

value: Preterm

tag: fetal inflamatory response

value: strong


title: 703807-monocytes

source_name: Monocytes

tag: individual

value: Monocytes


title: SB_Klf4_CHIP_rep1


title: 703883-neutrophils

value: Term


title: 703854-monocytes

value: fetal

value: mild


title: 703672-monocytes


title: 703691-monocytes


title: 703672-neutrophils


title: 703883-monocytes


title: 703691-neutrophils


title: 702549-monocytes


title: 702549-neutrophils


title: SB_Dlx3_KO_ATAC_rep1

value: KO


title: X392_CON_WT

status: Public on Sep 28 2022

city: Chapel Hill

first: Rafia

last: Virk

state: NC

address: 135 Dauer Drive, Michael Hooker Research Center, Room 2204

institute: University of North Carolina at Chapel Hill

data_processing:
NovaSeq 6000 used for sequencing/base calling
Quality of sequencing files ran through FASTQC
FASTQ files aligned to the Mus musculus UCSC MM10 reference genome using Bowtie2
Gene counts were generated via the subread featureCounts package
DESeq2 was used for normalization and statistical analysis of the gene counts file output from the featureCounts program
Genome_build: UCSC MM10
Supplementary_files_format_and_content: DESeq2_results.csv:  CSV data table with DESeq2 output (statistics + normalized gene counts)
Supplementary_files_format_and_content: Featurecounts.txt:  raw counts

source_name: Whole Lung

extract_protocol:
Whole lung was removed from mouse and flash-frozen in liquid nitrogen and stored in -80C until shipment for further processing.
Total RNA-Seq library construction was performed from the RNA samples using the TruSeq Stranded RNA Sample Preparation Kit and bar-coded with individual tags following the manufacturer’s instructions (Illumina, Inc. San Diego, CA). An Agilent Bravo Automated Liquid Handling System was used to prepare libraries. Total RNA-Seq mRNA, 35 million reads per sample, 2 lanes per sample, paired-end run.

value: Lung

tag: dietary group

value: Lean control diet (10% kcal from fat)


title: X391_CON_WT


title: X185_CON_WT


title: SB_Dlx3_KO_ATAC_rep2


title: X183_CON_WT


title: X182_CON_WT


title: X184_CON_WT


title: X394_HF_WT

value: High fat diet (60% kcal from fat)


title: X263_HF_WT

value: WT


title: 703854-neutrophils


title: X154_HF_WT


title: X186_HF_WT


title: SB_K27Me3_CHIP_rep1

value: FvB


title: X187_HF_WT


title: X120_HF_WT


title: X131_HF_WT


title: X358_CON_WT


title: 258633818634_3

status: Public on Sep 26 2022

source_name: Maternal Plasma

tag: gestational age

tag: smoker

tag: maternal age

tag: nulliparous

tag: bmi

tag: fetal sex


title: 258633818627_4

tag: parity


title: 258633818632_3


title: 258633818626_7


title: X181_CON_WT

tag: tissue

tag: genotype


title: 258633818628_4


title: 258633818631_4


title: 258633818629_5


title: 258633818634_5


title: 258633818817_4


title: 258633818824_1


title: X251_HF_WT

tag: strain


title: 258633818670_2


title: 258633818822_2


title: 258633818632_7


title: 258633818822_1


title: 258633818824_6


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title: 258633818154_4


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title: 258633818346_6


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title: 258633818148_8


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title: 258633818343_8


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title: 258633818309_8


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title: 258633818330_8


title: 258633818502_2


title: 258633818541_2


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title: 258633818506_1


title: 258633818540_6


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title: 258633818540_3


title: 258633818503_4


title: 258633818504_4


title: 258633818509_4


title: 258633818502_4


title: 258633818500_4


title: 258633818506_6


title: 258633818508_7


title: 258633818505_5


title: 258633818504_1


title: 258633818509_8


title: 258633818505_8


title: 258633818502_8


title: 258633818270_2


title: 258633818272_2


title: 258633818279_2


title: 258633818275_1


title: 258633818276_3


title: 258633818270_4


title: 258633818275_3


title: 258633818270_3


title: 258633818181_6


title: 258633818181_4


title: 258633818277_4


title: 258633818275_7


title: 258633821231_1


title: 258633819029_7


title: 258633819030_4


title: 258633818276_7


title: 258633818273_2


title: 258633821238_1


title: 258633819029_4


title: 258633819031_1


title: 258633821164_7


title: 258633821238_5


title: 258633821163_7


title: 258633821236_4


title: 258633818276_6


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title: 258633821555_3


title: 258633821233_8


title: 258633821569_3


title: 258633821568_3


title: s105

scan_protocol: The Cyanine-3 signal from the SOMAmer reagent was detected on microarrays. More details on all protocols are described in Gold L, et al. PLoS One.

data_processing: The raw protein abundance data consisted of relative fluorescence units quantified by using the SOMAmer (Slow Off-rate Modified Aptamers) platform and its reagents.

source_name: Amniotic fluid

label_protocol: The amniotic fluid samples were diluted and then incubated with the respective SOMAmer mixes pre-immobilized onto streptavidin-coated beads. The beads were washed in order to remove all non-specifically bound proteins and other matrix constituents. Proteins that remained specifically bound to their cognate SOMAmer reagents were tagged using an NHS-biotin reagent. After the labeling reaction, the beads were exposed to an anionic competitor solution that prevents non-specific interactions from reforming after disruption.  Using this approach, pure cognate-SOMAmer complexes and unbound (free) SOMAmer reagents are released from the streptavidin beads using ultraviolet light that cleaves the photo-cleavable linker used to quantitate protein. The photo-cleavage eluate, which contains all SOMAmer reagents (some bound to a biotin-labeled protein and some free), was separated from the beads and then incubated with a second streptavidin-coated bead that binds the biotin-labeled proteins and the biotin-labeled protein-SOMAmer complexes. The free SOMAmer reagents were then removed during subsequent washing steps. In the final elution step, protein-bound SOMAmer reagents were released from their cognate proteins using denaturing conditions.

tag: gender

value: female

tag: diagnosis

value: sonographic short cervix

value: Amniotic fluid

tag: gaamniocentesis

tag: gadelivery

tag: cervical length


title: s106


title: 258633821238_7

tag: individual


title: 258633821569_7


title: 258633821570_3


title: 258633818273_5


title: 258633818276_5


title: 258633821572_7


title: 258633821239_7


title: s104


title: s101


title: s103


title: 258633821573_6


title: s99


title: s102


title: 258633821237_8


title: s100


title: s97


title: s96


title: s95


title: s94


title: s93


title: s92


title: s91


title: s89


title: s88


title: s87


title: s98


title: s86


title: s85


title: s84


title: s83


title: s79


title: s78


title: s82


title: s81


title: s75


title: s74


title: s90


title: s76


title: s77


title: s80


title: s72


title: s70


title: s69


title: s73


title: s71


title: s67


title: s68


title: s64


title: s66


title: s62


title: s63


title: s61


title: s60


title: s58


title: s59


title: s56


title: s57


title: s54


title: s55


title: s65


title: s53


title: s52


title: s51


title: s45


title: s50


title: s47


title: s46


title: s48


title: s49


title: s43


title: s41


title: s39


title: s44


title: s42


title: s38


title: s36


title: s40


title: s34


title: s35


title: s33


title: s32


title: s29


title: s30


title: s28


title: s37


title: s27


title: s23


title: s24


title: s26


title: s22


title: s20


title: s15


title: s17


title: s18


title: s31


title: s19


title: s10


title: s13


title: s11


title: s16


title: s6


title: s14


title: s25


title: s21


title: s5


title: s8


title: ESCs: Input

status: Public on Aug 24 2022

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
Library strategy: SNS-Seq
The quality of sequencing reads was analysed with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Short sequences, adaptor sequences and read duplicates were removed. Reads were then analysed with the RUbioSeq pipeline v3.8 (Rubio-Camarillo et al., 2017), using BWA v0.7.10 (Li and Durbin, 2009), SAMtools v0.1.19 (Li et al., 2009), Picard tools v1.107 (http://broadinstitute.github.io/picard/) and MACS v2.0.10 (Feng et al., 2012), and the mouse reference genome GRCm38/mm10. When MACS algorithm was used, the peak calling was performed versus input. The algorithm described in Picard et al. (2014) was used to provide a second way to identify ORIs. Genome segmentation required by this algorithm was based on replication timing data from mESCs, which accurately matches the read coverage differences between segments. Common peaks were obtained using BedTools v2.23.0 (Quinlan, 2014) with parameters: -f 0.1 -r -wa –u. In stringent criteria, a peak was considered to be an origin when it was detected by both peak-calling algorithms (MACS/Picard) in both replicates. In relaxed criteria, a peak was considered to be an origin when it was detected by both peak-calling algorithms in at least one replicate. For common peaks between MACS and Picard the genomic coordinates defined by Picard were used. Read distribution around peak centres was generated using seqMINER v1.3.3e. For the comparative analysis with epigenomic features and chromatin states, genomic coordinates of origins were converted from mm10 to mm9 genome assembly with LiftOver (https://genome.ucsc.edu/util.html).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: BED files containing ORI genomic coordinates from MACS2 or PICARD programs.
Supplementary_files_format_and_content: bigWig files

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were cultured on 0.1% gelatin-coated plates in Dulbecco’s modified Eagle’s medium (DMEM) with Ultraglutamine 1 and 4.5 g/L glucose (Lonza) supplemented with 15% FBS (Sigma), 50 U/mL Penicillin - 50 mg/mL Streptomycin (Invitrogen), Minimum Essential Medium Non-Essential Aminoacids (MEM NEA; Invitrogen), 100 μM 2-mercaptoethanol (Invitrogen) and 103 U/mL ESGRO mLIF Medium Supplement (Millipore).

extract_protocol:
Exponentially growing mESCs (≈ 40x106) were washed twice in PBS and collected by scraping and centrifugation (3000 rpm, 7 min, 4 °C). Cells were lysed in lysis buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl ph 8.1) at a 2x107 cell/ml density. Sonication was performed in a Bioruptor device (Diagenode) for 25 min (30s sonication/30s pause mode). DNA was extracted with phenol/chloroform, ethanol- precipitated, air-dried and resuspended in 0.5x TE buffer. The size of DNA in the samples was monitored by 1% agarose gel electrophoresis
DNA libraries were prepared using standard Illumina protocols

tag: cell type

value: TetO-CDC6 mouse embryonic stem cells (mESCs) derived from the TetO-CDC6 mouse model (Munoz et al., 2017)

tag: treatment

value: No treatment


title: s7


title: ESCs: CDC6_I

description: short DNA replication intermediates

extract_protocol:
Cells were lysed and DNA was purified by phenol/cloroform extraction. DNA was denaturated (boiling) and size fractionated through a sucrose gradient centrifugation. Fractions containing the sizes of interest (F4 and F5) were digested three times with lambda-exonucleasa. Finally, ssDNA was converted into dsDNA prior library preparation.
DNA libraries were prepared using standard Illumina protocols

value: To induce CDC6 overexpression, 1 ug/ml doxycycline was added to the medium for 30 h


title: ESCs: WT_I

description:
short DNA replication intermediates
submitted previously as GSM2651111

growth_protocol: mES cells were grown at 37ºC and 5% CO2 in DMEM supplemented with 10% fetal calf serum, 1x non-essential aminoacids, 2 mM L-glutamine, 50 mM b-mercaptoethanol, 1 mM sodium piruvate, 100 U/ml penicillin, 100 ug/ml streptomycin and 10E3 U/ml LIF.

value: Embryonic stem cells

tag: genotype/variation


title: ESCs: CDC6_II

description: short DNA replication intermediates


title: ESCs: APH_II

description: short DNA replication intermediates

value: To induce mild replication stress, cells were treated with 0.5 uM aphidicolin for 2.5 h


title: ESCs: WT_II

description: short DNA replication intermediates


title: s3


title: s9


title: s12


title: s1


title: ESCs: APH_I

description: short DNA replication intermediates


title: s4


title: s2


title: CON, liver, ZT22, rep2

status: Public on Jul 26 2022

type: RNA

description: Microaaray gene expression

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Data was analyzed using Transcriptome Analyses Console (Thermo Fisher Scientific) and expressed in log2 values.

label: biotin

label_protocol: Standard Affymetrix protocol

extract_protocol: TRIzol (Thermofisher, Waltham, USA) and the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. Genome-wide expression analyses was performed using Clariom S arrays (Thermo Fisher Scientific) using 100 ng RNA of each sample according to the manufacturer’s recommendations.

treatment_protocol: To render mice hyperthyroid (i.e., high T3 levels) the animals received one week of 0.01 % BSA (Sigma-Aldrich, St. Louis, USA, A7906-50G) in their drinking water, followed by two weeks with water supplemented with T3 (0.5 mg/L, Sigma-Aldrich T6397, in 0.01 % of BSA). Control animals received only 0.01 % BSA in the drinking water over the whole treatment period.

value: Liver

value: CON

tag: time


title: MMI, liver, ZT22, rep4

description: Microaaray gene expression

value: MMI


title: T3, liver, ZT22, rep2

description: Microaaray gene expression


title: CON, liver, ZT22, rep4

description: Microaaray gene expression


title: T3, liver, ZT14, rep3

description: Microaaray gene expression


title: CON, liver, ZT18, rep4

description: Microaaray gene expression


title: T3, liver, ZT22, rep1

description: Microaaray gene expression


title: MMI, liver, ZT18, rep3

description: Microaaray gene expression


title: T3, liver, ZT18, rep4

description: Microaaray gene expression


title: CON, liver, ZT18, rep2

description: Microaaray gene expression


title: T3, liver, ZT22, rep3

description: Microaaray gene expression


title: MMI, liver, ZT22, rep3

description: Microaaray gene expression


title: CON, liver, ZT22, rep1

description: Microaaray gene expression


title: T3, liver, ZT14, rep2

description: Microaaray gene expression


title: MMI, liver, ZT18, rep1

description: Microaaray gene expression


title: MMI, liver, ZT22, rep2

description: Microaaray gene expression


title: T3, liver, ZT18, rep2

description: Microaaray gene expression


title: CON, liver, ZT18, rep1

description: Microaaray gene expression


title: T3, liver, ZT14, rep1

description: Microaaray gene expression


title: CON, liver, ZT22, rep3

description: Microaaray gene expression


title: MMI, liver, ZT22, rep1

description: Microaaray gene expression


title: T3, liver, ZT18, rep1

description: Microaaray gene expression


title: MMI, liver, ZT18, rep2

description: Microaaray gene expression


title: CON, liver, ZT14, rep2

description: Microaaray gene expression


title: CON, liver, ZT14, rep4

description: Microaaray gene expression


title: T3, liver, ZT18, rep3

description: Microaaray gene expression


title: T3, liver, ZT14, rep4

description: Microaaray gene expression


title: CON, liver, ZT18, rep3

description: Microaaray gene expression


title: CON, liver, ZT14, rep1

description: Microaaray gene expression


title: MMI, liver, ZT14, rep4

description: Microaaray gene expression


title: CON, liver, ZT14, rep3

description: Microaaray gene expression


title: MMI, liver, ZT14, rep1

description: Microaaray gene expression


title: MMI, liver, ZT14, rep2

description: Microaaray gene expression


title: T3, liver, ZT6, rep4

description: Microaaray gene expression


title: CON, liver, ZT10, rep2

description: Microaaray gene expression


title: T3, liver, ZT10, rep4

description: Microaaray gene expression


title: T3, liver, ZT10, rep1

description: Microaaray gene expression


title: CON, liver, ZT6, rep4

description: Microaaray gene expression


title: MMI, liver, ZT6, rep2

description: Microaaray gene expression


title: T3, liver, ZT10, rep3

description: Microaaray gene expression


title: MMI, liver, ZT10, rep1

description: Microaaray gene expression


title: T3, liver, ZT6, rep2

description: Microaaray gene expression


title: MMI, liver, ZT10, rep4

description: Microaaray gene expression


title: CON, liver, ZT10, rep3

description: Microaaray gene expression


title: T3, liver, ZT6, rep3

description: Microaaray gene expression


title: CON, liver, ZT10, rep1

description: Microaaray gene expression


title: MMI, liver, ZT6, rep3

description: Microaaray gene expression


title: CON, liver, ZT6, rep2

description: Microaaray gene expression


title: MMI, liver, ZT14, rep3

description: Microaaray gene expression


title: T3, liver, ZT2, rep4

description: Microaaray gene expression


title: T3, liver, ZT6, rep1

description: Microaaray gene expression


title: CON, liver, ZT6, rep3

description: Microaaray gene expression


title: T3, liver, ZT10, rep2

description: Microaaray gene expression


title: MMI, liver, ZT10, rep2

description: Microaaray gene expression


title: CON, liver, ZT6, rep1

description: Microaaray gene expression


title: MMI, liver, ZT6, rep1

description: Microaaray gene expression


title: CON, liver, ZT10, rep4

description: Microaaray gene expression


title: MMI, liver, ZT10, rep3

description: Microaaray gene expression


title: MMI, liver, ZT6, rep4

description: Microaaray gene expression


title: R5 Other CAR+ T2 [RNA-seq]

status: Public on Dec 06 2021

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
CD8.IS.CAR+.R5.2
Adjusted_Counts_-_Exposure.txt
DESeq2_Results_-_Exposure.txt

data_processing:
Alignment: paired-end data were aligned to human genome assembly GRCh37/hg19 using STAR v2.5.2a with command-line parameters --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Post-processing: SAM files were converted to BAM format using samtools v1.1 (samtools view -bS)
Sorting: BAM files were sorted by position using samtools sort
Pooling of resequenced libraries: for replicate R2, several resequenced libraries were pooled after alignment to enhance coverage. This was accomplished using samtools merge as below:    R2 Control Day 0 CAR+ T1 - 4-Day0-CD8-CARpos_S7 with 16-Day0-CD8-CARpos_S5    R2 Control Day 0 CAR- T1 - 3-Day0-CD8-CARneg_S2 with 15-Day0-CD8-CARneg_S6    R2 Other CAR+ T1 - 21-IS-CD8-CARpos-10-24-2018_S11 with 12-IS-CD8-CARpos_S12 and 24-IS-CD8-CARpos_S10    R2 Continuous CAR+ T1 - 8-CS-CD8-CARpos_S9 with 20-CS-CD8-CARpos_S12    R2 Continuous CAR- T1 - 7-CS-CD8-CARneg_S6 with 19-CS-CD8-CARneg_S3
Tag counts per gene model: HTSeq v0.6.0 was used to count aligned tags over gene features with command-line python -m HTSeq.scripts.count -f bam -r pos -s no -t exon -i gene_id BAM_FILE GTF. The gene model GTF was constructed from RefSeq transcripts and UCSC Genome Browser's annotation of RefSeq transcript IDs to gene symbols.
Library size adjustment and significance testing: for the antigen exposure and time series analysis, DESeq2 was used to adjust library size and estimate significant differences at an FDR of 0.05.    Antigen exposure analysis: the Wald test was used to assess differences between control day 0 samples and continuous exposure samples. For this analysis we considered only CAR+ samples including control day 0, "other," and continuous exposure, with no day 16 time points. "Other" samples were included to adjust dispersions and library sizes but were not used for the contrast.    Time series analysis: the LRT was used to assess differences along the time course from day 0 to day 16 to day 28, with a full model of ~Replicate+Time and a reduced model of ~Replicate. For this analysis we considered only CAR+ samples including control day 0 and continuous exposure, with no "other" exposure.
Additional filtering: for the antigen exposure analysis, we removed genes which register as significantly different but which we expect to be artifacts due to SMART-seq's library construction; such genes fall along the extreme ends of a parabola in a volcano plot of the data. To remove these, we interpolated a line on the plot between IL22 and WDR63 (negative side) and another between ALK and INBHE (positive side). Any gene with a perpendicular < 1 to the lines was removed.
TPM calculation: to contrast CAR+ and CAR- samples, we calculated TPMs for each gene using the bioinfokit.analys module in python. Gene lengths were calculated from the GTF used to run HTSeq, taking the max of all summed exon lengths across multiple isoforms to be the length of each gene.
Genome_build: hg19
Supplementary_files_format_and_content: We include three tables of adjusted count data and two companion tables with DESeq2 significance testing results. For the antigen exposure analysis, we include the DESeq2 adjusted counts and DESeq2 significance results after processing to flag genes we deemed to be artifacts ("Additional filtering" above). For the time series analysis, we include the DESeq2 adjusted counts and DESeq2 significance results. For the CAR+ / CAR- analysis, we include a table of TPMs for all genes.

source_name: M5CAR T cells (PBMCs)

growth_protocol: Primary human CD4+ T and CD8+ T cells from normal donors were provided by University of Pennsylvania Human Immunology Core. CAR T cells were generated as previously described (Carpenito et al., 2009). Briefly, CD4+ and CD8+ T at 1:1 ratio at 1 x 10e6 cells/ml were activated with Dynabeads CD3/CD28 CTSTM (Gibco, Life Technologies) at a 3:1 bead-to-cell ratio. Approximately after 24 hours, T cells were transduced at a multiplicity of infection (MOI) of 5. At day 5 beads were removed from cultures. T cell cultures were maintained at 8 x 10e5 cells/ml. Cell number and volume were monitored daily using Multisizer 4 Coulter Counter (Beckmanwaslter). Transduced T cells were cryopreserved when reached the resting state, as determined by cell size.

extract_protocol:
For flow cytometry and sorting assays of CAE, M5 CAR T cells were stained in fluorescence-activated cell sorting (FACS) buffer consisting of PBS (Gibco), 0.5% bovine serum albumin (BSA) (GEMINI), 2 mM EDTA (Invitrogen), and 100ug/ml DNase (Roche). CountBrightTM Absolute Counting Beads, (ThermoFisher) were used as an internal standard according to the manufacturer's instructions to calculate absolute cell counts in cell suspensions.  Antibodies specific for human CD45 (ref 304032, clone HI30), CD3 (317322, OKT3), CD4 (357412, A161A1 / 317440), CD56 (304608, MEM-188), EpCAM (324226/324238, 9C4), CD94 (305520, DX22), KLRB1 (339918, HP-3G10), TIGIT (372716, A15153G), TCR Va24-Ja18 (342922, 6B11), PD-1 (329928, EH12.2H7) were purchased from BioLegend. Antibodies specific for human CD8 (560179, SK1) was purchased from BD Pharmingen. Antibodies specific for human NKG2A (FAB1059P, 131411) and Methothelin (FAB32652P, 420411) were purchased from R&D Systems. Antibodies specific for human CTLA-4 (12-1529-42, 14D3) was purchased from eBioscience. Antibody specific for human NKG2C (130-103-636, REA205) was purchased from Miltenyi.  M5 CAR expression was assessed using biotinylated goat anti-human IgG F(ab’)2 (Jackson ImmunoResearch, 109-066-006) followed by streptavidin (FITC or APC) (BioLegend) or using an anti-idiotype antibody provided by Novartis Pharmaceuticals. Live/dead staining was performed using a Live/Dead Fixable Aqua Dead Cell Stain Kit (Life Technologies following manufacturer’s protocol followed by cell surface staining for 20 minutes at room temperature in the dark. Intracellular staining was performed with the Foxp3/Transcription Factor Staining Buffer set (Thermo Fisher) according to the manufacturer’s instructions. Samples were acquired on an LSRII Fortessa Cytometer (BD Bioscience) and analyzed with FlowJo v10 software (FlowJo, LLC). Sorting assays were performed using a FACS Aria Cytometer (BD Bioscience).    Total RNA was extracted using Qiazol (Qiagen) from 300 cells for day 0, day 16 or day 28 for CD8+ T cells continuously stimulated with antigen (two sorted populations including surface CAR-positive and surface CAR-negative cells). Cells were recovered by RNA Clean and Concentrator spin columns (Zymo), followed by incubation with oligo-dT. The transcription reaction was carried out on 100pg of cDNA for 1min at 55°C.
RNA-seq libraries were made following the previously established SMARTseq2 protocol (Picelli et al., 2014). Libraries were uniquely barcoded (Buenrostro et al., 2013) and amplified for 14 cycles. Fragment size distribution was verified and paired-end sequencing (2 x 75 bp reads) was carried out on an Illumina NextSeq 500.

treatment_protocol: AsPC-1 cells were routinely seeded in 6-well plates at 1 x 10e6 cells/well the day preceding T cell seeding. M5 CAR T cells (30 - 50% of transduction efficiency) were thawed and rested at 1 x 10e6 cells/ml in T75 flasks with R10 media. After 24 hours, the T cell number (CD45+EpCAM-) was calculated and 2.5 x 10e5 T cells/well were transferred to the AsPC-1 plates. After 3 - 4 days, the cocultures were thoroughly suspended by frequent pipetting and 300 - 400µl of the cell suspension was used for T cell counting assessment and flow cytometry staining. The remaining cell suspension was spun down and the supernatant (conditioned media) was collected and filtered with a 0.45µm filter (Corning). The cells were resuspended in media containing equal amounts of conditioned and fresh R10. The resulting T cell suspension was transferred into AsPC-1-coated plates cells (2.5 x 10e5 T cells/well) for continuous co-culture. This process was repeated for 20-35 days.

tag: replicate

tag: car presence

value: Present

tag: antigen exposure

value: Other

value: Day 28


title: T3, liver, ZT2, rep1

description: Microaaray gene expression


title: CLUES1-POOL23-2

status: Public on Dec 01 2021

city: San Francisco

first: Yang

last: Sun

state: CA

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

data_processing:
GEX/ADT: Cell ranger pipeline
GEX: Samples demultiplexed and doublets removedusing Freemuxlet
GEX: Scrublet used to remove additional doublets
GEX: Contaminated platelets were eliminated by removing all cells with > 1 count of platelet gene markers (PF4, SDPR, GNG11, PPBP)
GEX: Red blood cells (RBC) were removed using louvain community detection to identify a population with very high expression of RBC markers like hemoglobin genes
GEX: batch correction was carried out by COMBAT
GEX: total nUMIs and percentage mitochondrial UMIs were regressed out
GEX: After cell filtering and expression normalization using default parameters, we performed k-nearest neighbor (KNN) graph construction, louvain, and projected the data onto two UMAP dimensions
GEX: Each louvain community was assigned one of 11 cell types by comparing differentially expressed genes between communities and the most abundantly expressed genes for each community with known markers for each cell type. Cell type was confirmed using CITE-Seq dataset
ADT: ADTs were normalized using the CLR method, and used to confirm cell annotations
TCR: TRA and TRB CDR3 nucleotide reads were demultiplexed by matching reads to 10X barcodes from cells with existing expression data that passed filtering in the Cell Ranger pipeline. Following demultiplexing of the TRA and TRB CDR3s, reads were aligned against known TRA/TRB CDR3 sequences then assembled into clonotype families using miXCR (86) (Bolotin et al., 2015) with similar methodologies to a previous study (87) (Zemmour et al., 2018). For any given 10X barcode, the most abundant TRA or TRB clonotype was accepted for further analysis; if 2 TRA or TRB clonotypes were equally abundant for a given 10X barcode, the clonotype with the highest UMI reads was used for further analysis. Only cells with paired TRA and TRB were used for further downstream analysis.
Genome_build: hg19

source_name: PBMC

extract_protocol:
PBMCs isolated with Ficoll and cryopreserved in FBS with 10% DMSO. Frozen PBMCs were (stained with Abseq antibodies for batches 3/4) pooled as previously described in Kang et al, then loaded into the 10x Chromium Controller using 10X Chromium Single Cell 3’ v2 kit (PN 120236, 120237)
10X Chromium Single Cell 3’ v2 kit User Guide (PN GC00052, Rev E)
10% of the barcoded cDNA from the 10X workflow was further amplified with Template switch oligo (TSO) primer and the Truseq Read 1 primer with KAPA HiFi hotstart readymix (Kapa Biosystems, Thermo Fisher Scientific) for 12 cycles at the conditions 98°C for 15 seconds, 67°C for 20 seconds and 72°C for 1 minute. A pool of forward Valpha and Vbeta primers containing the Illumina read 2 primer sequence were used in conjunction with the Truseq Read 1 primer to amplify CDR3 sequences from the TCR alpha and beta loci with NEBNext Ultra II Q5 Master Mix (New England Biolabs Inc.) for 25 cycles at the conditions 98°C for 10 seconds, 68°C for 30 seconds and 72°C for 1 minute. An additional amplification step using primers containing the Illumina P5 adapter, i5 index sequences and Truseq Read 1 primer sequence with the Illumina P7 adapter, i7 index sequences and Truseq Read 2 with NEBNext Ultra II Q5 Master Mix was carried out for 8 cycles at the conditions 98°C for 15 seconds and 72°C for 1 minute and 20 seconds to create final TCR libraries for sequencing.

tag: 10x well

value: PBMC

tag: molecule

value: RNA, ADT


title: CON, liver, ZT2, rep4

description: Microaaray gene expression

tag: tissue


title: CLUES1-POOL23-4


title: T3, liver, ZT2, rep3

description: Microaaray gene expression

tag: strain


title: CLUES1-POOL22-3

value: RNA


title: CLUES1-POOL22-1


title: CLUES1-POOL21-4


title: CLUES1-POOL20-1


title: CLUES1-POOL20-4


title: CLUES1-POOL23-1


title: CLUES1-POOL23-3


title: CLUES1-POOL22-4


title: T3, liver, ZT2, rep2

description: Microaaray gene expression


title: CLUES1-POOL22-2


title: CLUES1-POOL21-1


title: CLUES1-POOL20-3


title: CLUES1-POOL19-2


title: CLUES1-POOL20-2


title: CLUES1-POOL19-3


title: MMI, liver, ZT2, rep4

description: Microaaray gene expression


title: MMI, liver, ZT2, rep3

description: Microaaray gene expression


title: CLUES1-POOL18-3


title: CLUES1-POOL21-2


title: MMI, liver, ZT2, rep2

description: Microaaray gene expression


title: CLUES1-POOL17-3


title: CLUES1-POOL17-4


title: CLUES1-POOL19-4


title: CLUES1-POOL19-1


title: CON, liver, ZT2, rep3

description: Microaaray gene expression


title: CLUES1-POOL17-1


title: CLUES1-POOL18-1


title: CLUES1-POOL21-3


title: CLUES1-POOL17-2


title: CLUES1-POOL16-4


title: CON, liver, ZT2, rep1

description: Microaaray gene expression


title: CLUES1-POOL16-3


title: CLUES1-POOL16-2


title: CLUES1-POOL16-1


title: MMI, liver, ZT2, rep1

description: Microaaray gene expression


title: CON, liver, ZT2, rep2

description: Microaaray gene expression


title: OT-1 T-ALL cell line

status: Public on Jun 28 2022

city: Columbia

first: Kimberly

middle: G

last: Laffey

state: Missouri

address: 1030 Hitt Street

department: Molecular Microbiology and Immunology

institute: University of Missouri

hyb_protocol: Labelled cDNA was hybridized to the array using GeneChip Hybridization Oven 640 for 16 hours at 45°C.

scan_protocol: The array was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw feature data were log2 transformed, background corrected and normalized using the RMA method with the 'oligo' package in R.

source_name: CD4-CD8- leukemic cells derived from OT-1 spontaneous murine T-ALL and adapted to in vitro culture

label_protocol: Biotinylated cDNA was prepared following standard procedures.

growth_protocol: Tot1si cells were maintained in RPMI-1640 supplemented with 10% Cosmic calf serum, 2 mM L-glutamine, 1% non-essential amino acids, 1 mM sodium pyruvate, and penicillin (100 U/ml)/streptomycin (100 μg/ml, and were cultured in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kit following manufacturer instructions.

tag: developmental stage

value: T-ALL


title: CLUES1-POOL15-2


title: CLUES1-POOL15-1


title: CLUES1-POOL18-2


title: CLUES1-POOL14-3


title: CLUES1-POOL13-4


title: CLUES1-POOL14-2


title: CLUES1-POOL13-3


title: CLUES1-POOL14-1


title: CLUES1-POOL13-1


title: CLUES1-POOL12-3


title: CLUES1-POOL12-1


title: CLUES1-POOL12-2


title: CLUES1-POOL18-4


title: CLUES1-POOL12-4


title: CLUES1-POOL11-2


title: CLUES1-POOL11-1


title: CLUES1-POOL10-4


title: CLUES1-POOL10-3


title: CLUES1-POOL10-2


title: CLUES1-POOL10-1


title: CLUES1-POOL09-1


title: CLUES1-POOL09-4


title: CLUES1-POOL08-3


title: CLUES1-POOL08-4


title: CLUES1-POOL08-2


title: CLUES1-POOL08-1


title: CLUES1-POOL07-4


title: CLUES1-POOL07-3


title: CLUES1-POOL14-4


title: CLUES1-POOL07-1


title: CLUES1-POOL13-2


title: CLUES1-POOL06-2


title: CLUES1-POOL06-1


title: CLUES1-POOL05-1


title: CLUES1-POOL07-2


title: CLUES1-POOL06-4


title: CLUES1-POOL06-3


title: CLUES1-POOL04-2


title: CLUES1-POOL03-4


title: CLUES1-POOL05-2


title: CLUES1-POOL05-4


title: CLUES1-POOL04-4


title: CLUES1-POOL03-3


title: CLUES1-POOL03-2


title: CLUES1-POOL09-3


title: CLUES1-POOL02-4


title: CLUES1-POOL03-1


title: CLUES1-POOL02-3


title: CLUES1-POOL02-1


title: CLUES1-POOL02-2


title: CLUES1-POOL09-2


title: CLUES1-POOL01-2


title: CLUES1-POOL01-3


title: CLUES1-POOL01-1


title: UMA-15

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner in mapping-based mode.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Genome_build: Ensembl GRCm38, release 101
Supplementary_files_format_and_content: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package (v. 1.10.1), and saved in .csv format.

extract_protocol:
Pregnant Nlrp3+/+ and Nlrp3-/- dams were intra-amniotically injected with LPS or PBS on 16.5 days post coitum. Sixteen hours after the injection, the decidual and uterine tissues were collected for the isolation of neutrophils and macrophages using fluorescence activated cell sorting. Total RNA was extracted from the sorted cells using the Pico Pure RNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions. RNA concentrations, purity, and integrity were evaluated using the NanoDrop 1000 spectrophotometer and the Bioanalyzer 2100. Two to four biological replicates from each group were combined for the neutrophil samples to obtain sufficient RNA quantities for RNA-seq.
Low-input RNA-seq libraries were constructed by Beijing Genomics Institute (BGI; Wuhan, China) using the Nextera DNA Library Preparation Kit (Illumina, San Diego, CA, USA). Library sequencing was performed by BGI.

tag: genotype

value: Myometrium

value: Macrophage

value: LPS


title: CLUES1-POOL05-3


title: CLUES1-POOL04-1


title: UMA-14


title: UMA-13


title: UMA-12

value: PBS


title: UMA-11


title: CLUES1-POOL01-4


title: CLUES1-POOL04-3


title: UMA-10


title: UMA-6

source_name: Wild type_Myometrium_Macrophage_LPS

value: Wild type


title: UMA-5


title: UMA-4


title: UMA-3

source_name: Wild type_Myometrium_Macrophage_PBS


title: UMA-1


title: DMA-15

value: Decidua


title: UMA-2


title: DMA-14


title: DMA-11


title: DMA-4

source_name: Wild type_Decidua_Macrophage_LPS


title: DMA-10


title: DMA-5


title: DMA-12


title: DMA-1

source_name: Wild type_Decidua_Macrophage_PBS


title: DMA-6


title: DMA-2


title: UN-10

value: Neutrophil


title: UN-8


title: UN-4

source_name: Wild type_Myometrium_Neutrophil_LPS


title: UN-7


title: UN-3


title: UN-2

source_name: Wild type_Myometrium_Neutrophil_PBS


title: DN-10


title: DN-9


title: DN-8


title: DN-7


title: DN-3

source_name: Wild type_Decidua_Neutrophil_LPS


title: DMA-13


title: DN-4


title: DN-1

source_name: Wild type_Decidua_Neutrophil_PBS


title: CB-SA-11

status: Public on Nov 11 2021

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner in quasi-mapping-based mode.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Genome_build: Ensembl GRCh38, release 101
Supplementary_files_format_and_content: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package (v. 1.10.1), and saved in .csv format.

source_name: Cord blood

extract_protocol:
Total RNA was isolated from maternal blood and cord blood collected into PAXgene blood RNA tubes using the PAXgene Blood RNA Kit (Qiagen). The purity, concentration, and integrity of the RNA samples were assessed using the NanoDrop 1000 spectrophotometer and the Bioanalyzer 2100.
The RNA-seq library was prepared by BGI Genomics (ShenZhen, China) using the Oligo dT Stranded mRNA library preparation protocol (BGI, Hong Kong). Paired-end sequence reads (at least 50 million paired-end reads) of 150 bp length were generated using DNBseq (MGI-G400), and the raw data were provided by BGI.

tag: group

tag: age

tag: bmi

tag: nulliparous

tag: deliveryroute

value: Vaginal delivery

tag: labor

value: Yes


title: MB-SA-10

source_name: Maternal blood

value: No


title: DMA-3

tag: cell type

tag: treatment


title: MB-SA-11


title: CB-SA-8

value: Cesarean section


title: UN-9


title: MB-SA-9


title: CB-SA-7


title: MB-SA-8


title: MB-SA-6


title: CB-SA-5


title: MB-SA-5


title: CB-SA-4


title: MB-SA-4


title: CB-SA-6


title: UN-1


title: CB-SA-3


title: CB-SA-1


title: MB-SA-2


title: MB-SA-1


title: MB-SA-3


title: CB-C-10

value: Control


title: DN-2


title: MB-C-10


title: MB-C-9


title: CB-C-9


title: MB-C-7


title: CB-C-8


title: CB-C-6


title: MB-C-6


title: MB-C-5


title: CB-C-5


title: MB-C-4


title: CB-C-4


title: MB-C-3


title: MB-SA-7


title: MB-C-2


title: CB-SA-2


title: CB-C-1


title: MB-C-1


title: MB-C-8


title: CB-C-7


title: Delivery after 24 hours, Tarca_113

status: Public on Oct 01 2021

hyb_protocol: Hybridization of 200 μl of the hybridization cocktail was performed onto the GeneChip® Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA, USA) at 45°C, 60 rpm for 16 hours in a hybridization oven.

scan_protocol: Washing and staining of the arrays was done on a GeneChip® Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA) and scanning performed with a GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, USA). GeneChip® Command Console® Software (Affymetrix, Santa Clara, CA, USA) was used to generate the raw intensities from the array images.

data_processing: The Robust Multi-array Average104 method implemented in the R/Bioconductor's oligo package105 was applied to background correct, normalize, and summarize the raw probe-level microarray data into gene-level expression summaries based on probe-to-gene assignment provided by a custom chip definition file (hta20hsentrezgcdf, Brainarray)

source_name: Amniotic Fluid

label_protocol: Following the manufacturer protocol, we reverse-transcribed and amplified 10ng of RNA to cDNA using the GeneChip® WT Pico Reagent Kit (Affymetrix, Santa Clara, CA, USA). Using the same kit, fragmentation and labeling of 5.5μg sense–stranded cDNA was performed.

growth_protocol: Obstetricians used a 22-gauge needle to withdraw amniotic fluid transabdominally while monitoring with ultrasound or by aspirating directly through intact membranes during cesarean delivery. We collected 5 ml of AF from each woman and processed the samples according to recommended protocols.

extract_protocol: RNA was extracted from the AF samples with the Plasma/Serum RNA Purification Maxi Kit (Cat. No. 56200; Norgen BioTek, Thorold, ON, Canada) by following the manufacturer's protocol that included the DNAse treatment.  We applied the RNA Clean & Concentrator-5 Kit (Cat. No. R1015; Zymo Research, Irvine, CA, USA) to improve RNA quality and to concentrate each sample in a volume of 12 μl. RNA concentration and quality were assessed by using a DropSense spectrophotometer (Trinean NV, Gent, Belgium) and the Agilent 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA), respectively.

value: Delivery after 24 hours

tag: time to delivery

value: 4.7 wks

tag: sample type

value: Amniotic Fluid


title: Delivery after 24 hours, Tarca_034

value: 4.6 wks


title: Delivery after 24 hours, Tarca_147

value: 8.4 wks


title: Delivery after 24 hours, Tarca_131

value: 5.7 wks


title: Delivery after 24 hours, Tarca_168

value: 4 wks


title: Delivery after 24 hours, Tarca_156

value: 1 wks


title: Delivery after 24 hours, Tarca_164

value: 8.9 wks


title: Delivery after 24 hours, Tarca_018


title: Delivery after 24 hours, Tarca_138

value: 0.4 wks


title: Delivery after 24 hours, Tarca_015

value: 2.3 wks


title: Delivery after 24 hours, Tarca_122

value: 7.5 wks


title: Delivery after 24 hours, Tarca_186

value: 4.3 wks


title: Delivery after 24 hours, Tarca_199

value: 8 wks


title: Delivery after 24 hours, Tarca_154

value: 0.2 wks


title: Delivery after 24 hours, Tarca_104

value: 3 wks


title: Delivery after 24 hours, Tarca_201

value: 0.8 wks


title: Delivery after 24 hours, Tarca_175

value: Delivery after 24 hours

value: 6.1 wks


title: Delivery after 24 hours, Tarca_137

value: 1.6 wks

value: Amniotic Fluid


title: Delivery after 24 hours, Tarca_073

value: 0.7 wks


title: Delivery after 24 hours, Tarca_049

value: 5 wks


title: Delivery after 24 hours, Tarca_051

value: 0.3 wks


title: Delivery after 24 hours, Tarca_023

value: 5.6 wks


title: Delivery within 24 hours, Tarca_143

value: Delivery within 24 hours

value: 0.1 wks


title: Delivery after 24 hours, Tarca_035


title: Delivery after 24 hours, Tarca_145


title: Delivery after 24 hours, Tarca_006


title: Delivery after 24 hours, Tarca_189


title: Delivery after 24 hours, Tarca_022

value: 6.2 wks


title: Delivery within 24 hours, Tarca_085


title: 697276

status: Public on Aug 05 2021

data_processing:
Paired-end RNA-Seq sequence data in fastq format were processed using Salmon aligner (v. 0.12.0) in quasi-mapping-based mode.
Sequence count data inferred from Salmon gene abundance was imported into R using the tximport package.
Genome_build: Ensembl GRCh38, release 101
Supplementary_files_format_and_content: count_matrix.csv: Count matrix was generated by tximport function with "scaledTPM" option, from tximport package (v. 1.10.1), and saved in .csv (comma-separated) format.

source_name: Umbilical Cord Blood

extract_protocol:
Umbilical cord blood was collected into PAXgene tubes immediately after delivery of the placenta. RNA was isolated from cord blood in PAXgene tubes using the Qiagen PAXgene Blood miRNA kit, following the manufacturer’s instructions. The RNAseq library was prepared using the TruSeq RNA library prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Umbilical Cord Blood

tag: gestational age


title: Delivery after 24 hours, Tarca_109


title: 703448


title: 703374


title: 697156


title: 694781


title: 694846

value: Controls


title: Delivery within 24 hours, Tarca_126


title: Delivery within 24 hours, Tarca_066

value: 0 wks


title: Delivery within 24 hours, Tarca_160


title: 694612


title: Delivery within 24 hours, Tarca_159


title: Delivery within 24 hours, Tarca_078


title: Delivery within 24 hours, Tarca_158


title: Delivery within 24 hours, Tarca_030


title: 697286


title: 702689


title: 688857


title: 688573


title: 697226


title: 688339


title: 688341


title: 688116


title: Delivery within 24 hours, Tarca_045


title: 682899


title: 696927


title: 682867


title: 681702


title: 681557


title: 676358


title: 682650


title: 681630


title: 681624


title: 676000


title: 675012


title: 675873


title: 669600


title: 675272


title: 675364


title: 669268


title: 668801


title: 676160


title: 669180


title: 662077


title: 668712


title: 669212


title: 682732


title: s50

status: Public on May 24 2021

data_processing: The raw protein abundance data consisted of relative fluorescence units obtained from scanning the microarrays with a laser scanner. A sample-by-sample adjustment of the overall signal within a single plate (85 samples processed per plate/run) was performed in three steps: Hybridization Control Normalization, Median Signal Normalization, and Calibration, using the manufacturer’s protocol. Outlier protein abundance values above 2 × the 98th percentile of all samples, were replaced with 2 × the 98th percentile of all samples (data thresholding).

source_name: maternal plasma

label_protocol: The serum samples were diluted and then incubated with the respective SOMAmer mixes pre-immobilized onto streptavidin-coated beads. The beads were washed in order to remove all non-specifically bound proteins and other matrix constituents. Proteins that remained specifically bound to their cognate SOMAmer reagents were tagged using an NHS-biotin reagent. After the labeling reaction, the beads were exposed to an anionic competitor solution that prevents non-specific interactions from reforming after disruption. Using this approach, pure cognate-SOMAmer complexes and unbound (free) SOMAmer reagents are released from the streptavidin beads using ultraviolet light that cleaves the photo-cleavable linker used to quantitate protein. The photo-cleavage eluate, which contains all SOMAmer reagents (some bound to a biotin-labeled protein and some free), was separated from the beads and then incubated with a second streptavidin-coated bead that binds the biotin-labeled proteins and the biotin-labeled protein-SOMAmer complexes. The free SOMAmer reagents were then removed during subsequent washing steps. In the final elution step, protein-bound SOMAmer reagents were released from their cognate proteins using denaturing conditions.

value: maternal plasma

tag: gadelivery

value: Control

tag: diagnosisga

tag: individual


title: s527

tag: tissue

value: sPTD


title: s465


title: s473


title: s51


title: s47


title: s519


title: 669006


title: s695


title: s58


title: s526


title: s508


title: s56


title: s468


title: s511


title: s510


title: s701


title: s700


title: s53


title: s517


title: s507


title: s1270


title: s694


title: s461


title: s516


title: s59


title: s57


title: s42


title: s46


title: s483


title: s485


title: s61


title: s487


title: s45


title: s688


title: s242

value: PPROM


title: s505


title: s474


title: s671


title: s493


title: s52


title: s60


title: s491


title: s504


title: s477


title: s310


title: s501


title: s238


title: s480


title: s514


title: s370


title: s55


title: s347


title: s321


title: s324


title: s373


title: s338


title: s341


title: s658


title: s332


title: s343


title: s371


title: s350


title: s655


title: s377


title: s383


title: s660


title: s380


title: s659


title: s645


title: s229


title: s334


title: s319


title: s227


title: s335


title: s361


title: s366


title: s305


title: s128


title: s328


title: s663


title: s342


title: s648


title: s654


title: s649


title: s93


title: s105


title: s653


title: s379


title: s323


title: s344


title: s96


title: s651


title: s336


title: s647


title: s346


title: s376


title: s143


title: s111


title: s360


title: s311


title: s304


title: s316


title: s313


title: s356


title: s368


title: s340


title: s327


title: s103


title: s657


title: s115


title: s367


title: s114


title: s381


title: s307


title: s375


title: s121


title: s365


title: s124


title: s355


title: s374


title: s357


title: s656


title: s652


title: s661


title: s134


title: s358


title: s322


title: s662


title: s317


title: s97


title: s151


title: s331


title: s228


title: s352


title: s329


title: s333


title: s650


title: s309


title: s138


title: s146


title: s384


title: s149


title: s339


title: s101


title: s82


title: s120


title: s351


title: s362


title: s337


title: s226


title: s325


title: s348


title: s364


title: s132


title: Tarca_917_P10E07

hyb_protocol: Labeled cDNA were hybridized to the arrays in a GeneChip™ Hybridization Oven 640 by rotating at 60 rpm, 45°C for 16 hours.

scan_protocol: Arrays were then washed and stained in the Affymetrix Fluidics Station 450 and scanned using the Affymetrix 3000 7G GeneChip™ Scanner with Autoloader.

data_processing: Probeset definitions are based on Brainarray’s custom CDFs version 23 and represent ENTREZ IDs. Microarray raw gene expression data was background corrected, quantile normalized and summarized at ENTREZ ID level using Robust Multi-array Average (RMA) implemented in the oligo package of Bioconductor.

source_name: Whole blood

label_protocol: Biotinylated cDNA were prepared from 20 - 50 ng total RNA.

growth_protocol: Plasma samples were collected and stored in PAXgene® Blood RNA collection tube (BD 762165)

extract_protocol: RNA was isolated from PAXgene® Blood RNA collection tubes (BD Biosciences, San Jose, CA; Catalog #762165), as described in the PAXgene® Blood miRNA Kit Handbook. Purified RNA was quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean, Gentbrugge, Belgium), and quality was assessed by microfluidics using the RNA ScreenTape on the Agilent 2200 TapeStation (Agilent Technologies, Wilmington, DE, USA).

value: Whole blood

tag: batch

tag: train

tag: lmp

tag: subgroup


title: Tarca_913_P10A07

tag: group


title: Tarca_904_P10H05


title: Tarca_897_P10A05


title: Tarca_910_P10F06


title: Tarca_911_P10G06


title: Tarca_762_P08B12


title: Tarca_868_P10D01


title: Tarca_907_P10C06


title: Tarca_908_P10D06


title: Tarca_886_P10F03


title: Tarca_885_P10E03


title: Tarca_914_P10B07


title: Tarca_918_P10F07


title: Tarca_912_P10H06


title: Tarca_919_P10G07


title: Tarca_880_P10H02


title: Tarca_916_P10D07


title: Tarca_915_P10C07


title: Tarca_920_P10H07


title: Tarca_870_P10F01


title: Tarca_888_P10H03

value: TL


title: Tarca_861_P8E12


title: Tarca_869_P10E01


title: Tarca_866_P10B01


title: Tarca_905_P10A06


title: Tarca_867_P10C01


title: Tarca_893_P10E04


title: Tarca_860_P8D12_3


title: Tarca_879_P10G02


title: Tarca_852_P8D11


title: Tarca_858_P8B12


title: Tarca_832_P9H08


title: Tarca_839_P9G09


title: Tarca_818_P9B07


title: Tarca_809_P9A06


title: Tarca_808_P9H05


title: Tarca_813_P9E06


title: Tarca_857_P8A12


title: Tarca_815_P9G06


title: Tarca_856_P8H11


title: Tarca_812_P9D06


title: Tarca_810_P9B06


title: Tarca_851_P8C11


title: Tarca_844_P8D10


title: Tarca_836_P9D09


title: Tarca_824_P9H07


title: Tarca_837_P9E09


title: Tarca_801_P9A05


title: Tarca_843_P8C10


title: Tarca_814_P9F06


title: Tarca_816_P9H06


title: Tarca_800_P9H04


title: Tarca_803_P9C05


title: Tarca_799_P9G04


title: Tarca_835_P9C09


title: Tarca_806_P9F05


title: Tarca_791_P9G03


title: Tarca_798_P9F04


title: Tarca_797_P9E04


title: Tarca_785_P9A03


title: Tarca_786_P9B03


title: Tarca_773_P9E01


title: Tarca_743_P8G09


title: Tarca_789_P9E03


title: Tarca_765_P8E12


title: Tarca_775_P9G01


title: Tarca_740_P8D09


title: Tarca_787_P9C03


title: Tarca_756_P8D11


title: Tarca_768_P8H12


title: Tarca_755_P8C11


title: Tarca_771_P9C01


title: Tarca_770_P9B01


title: Tarca_774_P9F01


title: Tarca_763_P8C12


title: Tarca_742_P8F09


title: Tarca_746_P8B10


title: Tarca_790_P9F03


title: Tarca_749_P8E10


title: Tarca_733_P8E08


title: Tarca_769_P9A01


title: Tarca_741_P8E09


title: Tarca_750_P8F10


title: Tarca_734_P8F08


title: Tarca_738_P8B09


title: Tarca_732_P8D08


title: Tarca_739_P8C09


title: Tarca_731_P8C08


title: Tarca_728_P8H07


title: Tarca_716_P8D06


title: Tarca_715_P8C06


title: Tarca_703_P8G04


title: Tarca_727_P8G07


title: Tarca_722_P8B07


title: Tarca_714_P8B06


title: Tarca_717_P8E06


title: Tarca_692_P8D03


title: Tarca_704_P8H04


title: Tarca_726_P8F07


title: Tarca_701_P8E04


title: Tarca_723_P8C07


title: Tarca_700_P8D04


title: Tarca_719_P8G06


title: Tarca_677_P8E01


title: Tarca_678_P8F01


title: Tarca_676_P8D01


title: Tarca_664_P7H11


title: Tarca_660_P7D11


title: Tarca_698_P8B04


title: Tarca_659_P7C11


title: Tarca_656_P7H10


title: Tarca_690_P8B03


title: Tarca_669_P7E12


title: Tarca_674_P8B01


title: Tarca_665_P7A12


title: Tarca_663_P7G11


title: Tarca_654_P7F10


title: Tarca_655_P7G10


title: Tarca_643_P7C09


title: Tarca_652_P7D10


title: Tarca_636_P7D08


title: Tarca_632_P7H07


title: Tarca_635_P7C08


title: Tarca_651_P7C10


title: Tarca_625_P7A07


title: Tarca_641_P7A09


title: Tarca_626_P7B07


title: Tarca_653_P7E10


title: Tarca_620_P7D06


title: Tarca_631_P7G07


title: Tarca_633_P7A08


title: Tarca_642_P7B09


title: Tarca_634_P7B08


title: Tarca_619_P7C06


title: Tarca_628_P7D07


title: Tarca_606_P7F04


title: Tarca_624_P7H06


title: Tarca_614_P7F05


title: Tarca_605_P7E04


title: Tarca_613_P7E05


title: Tarca_609_P7A05


title: Tarca_600_P7H03


title: Tarca_621_P7E06


title: Tarca_601_P7A04


title: Tarca_585_P7A02


title: Tarca_579_P7C01


title: Tarca_599_P7G03


title: Tarca_594_P7B03


title: Tarca_597_P7E03


title: Tarca_595_P7C03


title: Tarca_582_P7F01


title: Tarca_570_P6B12


title: Tarca_598_P7F03


title: Tarca_568_P6H11


title: Tarca_567_P6G11


title: Tarca_541_P6E08


title: Tarca_553_P6A10


title: Tarca_554_P6B10


title: Tarca_530_P6B07


title: Tarca_552_P6H09


title: Tarca_540_P6D08


title: Tarca_561_P6A11


title: Tarca_569_P6A12


title: Tarca_560_P6H10


title: Tarca_537_P6A08


title: Tarca_545_P6A09


title: Tarca_538_P6B08


title: Tarca_580_P7D01


title: Tarca_550_P6F09


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