title: HCT8-KD2

city: Nanjing

first: Peifen

last: Lu

address: Xianlin Street NO.163

institute: Nanjing University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform
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. All the downstream analyses were based on the clean data with high quality.
STAR is used to align clean reads to reference genome. STAR outperforms other aligners by a factor of >50 in mapping speed, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. [Dobin A1, Davis CA, Schlesinger F, Drenkow J, et.al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics. 2013 Jan;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.]
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated using Trizol reagent. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent  Technologies, CA, USA)
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: cell line

value: Colorectal Cancer Cell line


title: 7052: HLHS-Poor outcome scRNA-seq

status: Public on Apr 07 2022

type: SRA

city: Pittsburgh

first: Cecilia

middle: Wenya

last: Lo

state: United States

address: 530 45th St. 8120 Rangos Research Center

department: Developmental Biology

country: USA

institute: University of Pittsburgh

description: single cell total RNA

library_source: transcriptomic

data_processing:
Reads were processed using the Cell Ranger (version 3.1.0) count pipeline using the human reference genome GRCh38 and annotations from Ensembl (version 93).
Filtered data was read into a SingleCellExperiment object using the read10XCounts function of the R package DropletUtils [10.1186/s13059-019-1662-y] (v1.6.1). Quality control and filtering were performed using the R packages and scater [10.1093/bioinformatics/btw777] (v1.14.6). For each sample, cells with library size less than 500 and number of detected genes less than 300 or greater than 6,000 were excluded. Additionally, we used the automated outlier detection of scater to exclude cells with high mitochondrial percentage (greater than 3 times the median absolute deviation (MAD) from the median value).
Processed data files include the filtered feature barcode matrices for each sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: H5

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cell derived cardiomyocytes (iPSC-CM)

growth_protocol: Human fibroblasts or lymphoblastoid cells are transfected with four episomal plasmids71 (Addgene: 27077 (pCXLE-hOCT3/4-shp53-F), 27078 (pCXLE-hSK), 27080 (pCXLE-Hul), 27082 (pCXLE-EGFP)) using electroporation. After 7 days electroporated cells are switched to a 6-well plate with mTESR1 media and transferred to hypoxic conditions. After 21-40 days, islands of expanded iPSC clones were stained with Alkaline phosphatase, and positive colonies isolated onto 24well dishes.Isolated colonies are expanded in 24 well plates coated with feeder cells or BD Matrigel with mTESR1 media. After >15 passages, stable iPSC cells were seed on BD Matrigel pre-coated plates for 2-3 days under mTESR1 media then switched to CDM3 media consisting of RPMI 1640, BSA, 213 ug/ml Vitamin C and 6 uM CHIR9902172. After 2 days the media was replaced with CDM3 Media containing RPMI 1640, BSA, 10 uM XAV939, 213 ug/lm Vitamin C, and BSA. Finally,  beating cells were assayed by single cell RNAseq (Day20).

extract_protocol:
The iPSC-CMs were disaggregated using cold active protease [10 mg/ml Bacillus Licheniformis protease; Creative Enzymes NATE0633) and 125 U/ml DNAse (Applichem, A3778) incubated on ice with trituration for 5-7 minutes. Then 5% bovine serum albumin (BSA) was added, and cells were filtered through a 100 μm strainer and cetrifuged to pellet the cells and then re-suspended in 200ul PBS/5% BSA. Trypan blue exclusion was used to quantify cell viability, and the volume was adjusted to 200,000 cells/ml for 10X chromium single-cell RNA-seq.
Paired-end library preparation was carried out using the V3 version (10X Genomics). Single-cell droplet libraries from ~10K cells from each suspension were generated using the 10X Genomics Chromium controller with the Chromium Single Cell 3’ GEM Library and Gel Bead Kit v.3 and the Chromium Chip B Single Cell kit (1 GEMs per sample, expected recovery ~6k cells per GEM). All samples were barcoded with the Chromium i7 Multiplex Kit. All libraries were pooled and sequenced across two lanes of a HiSeq4000, 150bp paired-end reads with a target coverage of 20k fragments per cell.

treatment_protocol: The iPSC-CM from three patients and one control was prepared for single cell RNAseq.

tag: cell type

tag: day after differentation

tag: clinical outcome

value: HLHS-Poor outcome


title: HCT8-KD1

country: China

tag: treatment


title: HCT8-SCR2

value: shSCR


title: Mouse as control, biological rep4 [C24_Clariom_S_Mouse]

type: RNA

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description:
C24_(Clariom_S_Mouse)
Mouse as control for 4 weeks

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom_S_Mouse or Affymetrix miRNA-4_0 arrays. Arrays were washed and stained.

scan_protocol: Arrays were scanned.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Mus musculus

source_name: mouse as control

label_protocol: Biotinylated cRNA were prepared.

growth_protocol: Mice treated with PM2.5 for 4 weeks.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice in the experimental group were given melatonin orally (20 mg/kg•bw) every day for 28 days and PM2.5 (5 mg/kg•bw) via intratracheal instillation twice a week for 4 weeks. Mice in control group were intragastrically given equal volume of sterile water containing 0.5% ethanol, and intratracheal instillation with corresponding volume of blank filters eluted with saline.

tag: tissue

value: liver

value: control for 4 weeks


title: HCT8-SCR1


title: Mouse as control, biological rep3 [C21_Clariom_S_Mouse]

description:
C21_(Clariom_S_Mouse)
Mouse as control for 4 weeks


title: Unplated quiescent HSC [RSB21]

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description:
RSB21
Isolated HSC from uninjured liver.
Bulk RNA-seq
tpm_values_genes_kallisto_RSB19_to_RSB22.txt

data_processing:
Bulk RNA-seq:
20M paired-end 100bp sequencing was performed using the Illumina NovaSeq 6000.
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
A pseudoalignment to a kallisto index was created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Differentially expressed genes were tested using DESeq2. Normalization was done internally using DESeq2's specialized algorithm and normalization to compare across samples, was performed using the TPM (transcripts per million) method.
scRNA-seq:
10x Genomics' cellranger pipeline was used to process the data (v2.1.1).
BCL files were demultiplexed with 10x Cell Ranger's mkfastq command and analysis and alignment were performed using Cell Ranger's count command with Cell Ranger's reference mm10 (mouse).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bulk RNA-seq: Text files include TPM values for each Sample.
Supplementary_files_format_and_content: scRNA-seq: Raw counts in MatrixMarket (mtx) format, barcodes.tsv, genes.tsv.

source_name: liver

growth_protocol:
HSC were obtained perfusing and digesting the liver, followed by gradient centrifugation (Mederacke et al., Nat Protocol 2015).
For HSC that were not treated by UDP-glucose, further purification was achieved by FACS sorting for VitA and LratCre-induced TdTom and then centrifuged for RNA extraction.

extract_protocol:
Total RNA was column purified (Qiagen mini).
Construct libraries using Illumina TruSeq RNA Preparation Kit according to the manufacturer’s instructions.

tag: strain

value: LratCre+, TdTom+ in C57BL/6J

tag: liver damage

value: HSC


title: Wt-Female-Sal, 1 (RNA-seq)

city: North Chicago

first: Johnny

last: He

state: IL

address: 3333 Green Bay Road, Basic Science Building 2.300

department: Microbiology and Immunology

institute: Rosalind Franklin University

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
H1_S8

data_processing:
Reads were mapped to GRCm38 reference genomes with STAR (v2.7.9) (Dobin et al., 2013). The maximum number of multiple alignments allowed for a read is set to 10.
And, featureCounts (v 2.0.1.13) was used to quantify reads with the following parameters (-T 10 -t exon -s 1 -g exon_id).
The read count matrix were then normalized by countToFPKM package (v 1.0) to Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM/RPKM values for all Samples

source_name: Brain hippocampus

extract_protocol:
RNA was isolated by TRIzol reagent, and further purified using a RNA Clean & Concentrator Kit.
The RNA libraries were prepared from the RNA using a QIAseq Stranded mRNA Select kit.

value: Brain hippocampus

tag: genotype

value: WT

value: Saline i.p.

tag: Sex

value: Female


title: Wt-Female-Sal, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
H3_S23


title: Wt-Female-Sal, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
H2_S16


title: Animal4217-Array-8

city: Cambridge

first: Constantine

middle: Nicholas

last: Tzouanas

state: MA

address: 45 Carleton St

department: Harvard-MIT Health Sciences and Technology

institute: Massachusetts Institute of Technology

description:
Seq-Well
10Week_countsmatrix.mtx
10Week_countsfeatures.tsv
10Week_countsbarcodes.tsv
Updated10wk_alexandria_structured_metadata10.txt

data_processing:
Cell barcode and UMI tagging of transcript reads was performed using DropSeqTools v1.12 (Macosko et al., 2015)
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca fascicularis

source_name: Lung Tuberculosis Granuloma

extract_protocol:
Individual granulomas were enzymatically dissociated using the gentleMACS dissociator system.
Single-cell suspensions were loaded onto Seq-Well arrays and processed as according to Gierahn et al., Nature Methods (2017).
scRNA-seq

value: Lung Tuberculosis Granuloma

tag: infection

value: Mycobacterium tuberculosis

tag: time

value: 10weeks post-infection


title: Wt-Female-Coc, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
G3_S24

value: Cocaine i.p.


title: T-REx-293  siUPF1_2

city: Bethesda

first: J. Robert

last: Hogg

state: MD

address: 50 South Drive, Room 2341

department: Biochemistry and Biophysics Center

institute: National Heart, Lung, and Blood Institute

data_processing:
Reads were trimmed using fastp software, with options --detect_adapter_for_pe and --trim_poly_g.
Trimmed reads were aligned with Hisat2, using default parameters and the hg19/grch37 combined genome and transcriptome index provided by the authors.
Bam files from Hisat2 mapping were used for quantification with featureCounts, using Ensembl GRCh37 release 75 gene annotations.
Differential gene expression analysis was performed using limma/voom, implemented by degust.erc.monash.edu.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains log2 expression changes and FDRs for the indicated comparisons.

source_name: HEK-293 cells

growth_protocol: Flp-In T-REx-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Plus Mini RNA isolation kit
2 μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq Stranded RNA Library Preparation Kit (Illumina).

treatment_protocol: Flp-In T-REx-293 cells were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX. Forty-eight hours post-siRNA transfection, cells were replated at a density of 5x105 cells per well of a 6-well plate.

value: UPF1 siRNA


title: T-REx-293  siUPF1_3


title: Mouse as control, biological rep5 [C25_Clariom_S_Mouse]

description:
C25_(Clariom_S_Mouse)
Mouse as control for 4 weeks


title: Animal4217-Array-7


title: Mouse as control, biological rep2 [C20_Clariom_S_Mouse]

description:
C20_Clariom_S_Mouse)
Mouse as control for 4 weeks


title: Animal4217-Array-6


title: Mouse as control, biological rep1 [C19_Clariom_S_Mouse]

description:
C19_(Clariom_S_Mouse)
Mouse as control for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep5 [MP8_miRNA-4_0]

description:
MP8_(miRNA-4_0)
Mouse treated with PM2.5 and melatonin for 4 weeks

source_name: mouse treated with PM2.5+melatonin

value: PM2.5 and melatonin for 4 weeks


title: Wt-Female-Coc, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
G2_S15


title: T-REx-293  siUPF1_1


title: Wt-Female-Coc, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
G1_S7


title: Animal4217-Array-5


title: T-REx-293  siNT_3

value: non-targeting siRNA


title: Wt-Male-Sal, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
F3_S22

value: Male


title: Mouse treated with PM2.5+melatonin, biological rep2 [MP2_miRNA-4_0]

description:
MP2_(miRNA-4_0)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep3 [MP3_miRNA-4_0]

description:
MP3_(miRNA-4_0)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Animal4217-Array-4


title: Animal4217-Array-2


title: Animal4017-Array-13


title: T-REx-293  siNT_1


title: Wt-Male-Coc, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
E3_S21


title: Animal4017-Array-12


title: Wt-Male-Sal, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
F1_S6


title: Mouse treated with PM2.5+melatonin, biological rep1 [MP1_miRNA-4_0]

description:
MP1_(miRNA-4_0)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Mouse treated with PM2.5+melatonin, biological rep4 [MP4_miRNA-4_0]

description:
MP4_(miRNA-4_0)
Mouse treated with PM2.5 and melatonin for 4 weeks


title: Wt-Male-Coc, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
E2_S13


title: Mouse treated with PM2.5, biological rep3 [P14_miRNA-4_0]

description:
P14_(miRNA-4_0)
Mouse treated with PM2.5 for 4 weeks

source_name: mouse treated with PM2.5

value: PM2.5 for 4 weeks


title: NUP133-Mutant-2 repl.-1

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

data_processing:
Demultiplexing and adapter trimming were performed with bcl2fastq v2.19. No quality trimming was performed for deposited fastq files.
Sequenced reads were quality trimmed using fastp v0.20.1
Reads were mapped to hg38 whole genome using HISAT2 v2.2.1 with default settings for paired-end reverse strand specific libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.6 were applied for differential expression analysis
Genome_build: Human Dec. 2013 (GRCh38/hg38) (hg38)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for all Sample

source_name: human immortalized podocyte (AB8/13)

growth_protocol: Podocytes were cultured in RPMI 1640 cell growth medium supplemented with Glutamine (Thermo Fisher Scientific, #61870036), 10 % FCS (Merck, #S0615), 10 µg/ml ITS (Merck, #11074547001), 5 mM HEPES (Thermo Fisher Scientific, #15630-056), non-essential amino acids (MEM NEAA, Thermo Fisher Scientific, #11140050) 1:1000, 0.1 mM Sodium-Pyruvate (Thermo Fisher Scientific, #11360-039) and Penicillin-Streptomycin (Thermo Fisher Scientific, #15140122) at 33°C, 95% air and 5% CO2.

extract_protocol:
Cell were washed in PBS, scraped into PBS and pelleted by centrifugation. RNA was isolated from cell pellets using the Monarch Total RNA Miniprep Kit (T2010S, New England Biolabs) including gDNA depletion by gDNA binding columns and on column DNase-1 digest according to the supplier instructions. RNA quality number (RQN) was measured as 10.0 for all samples using an Agilent Fragment Analyzer system.
RNA libraries were prepared for sequencing using the NEBnext ultra II RNA kit. Libraries were sequenced on the Illumina NovaSeq 6000 sequencer following the manufacturer's protocols.

treatment_protocol: Podocytes were cultured on Collagen IV (C5533, Merck) precoated cell culture plates for 24 hours.

tag: background

value: NUP133 KO-1

value: podocyte


title: Thapsigargin_6h_siUPF1LL_2

data_processing:
Reads were trimmed using fastp software, with options --detect_adapter_for_pe and --trim_poly_g.
Trimmed reads were aligned with Hisat2, using default parameters and the hg19/grch37 combined genome and transcriptome index provided by the authors.
Bam files from Hisat2 mapping were used for quantification with featureCounts, using Ensembl GRCh37 release 75 gene annotations.
Differential gene expression analysis was performed using limma/voom, implemented by degust.erc.monash.edu.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file contains counts and normalized CPM values for all samples and log2 expression changes and statistics from limma/voom analysis of the indicated comparisons.

growth_protocol: HEK-293 cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml L-glutamine at 37°C and 5% CO2.

treatment_protocol: HEK-293 cells were reverse-transfected with 40 nM of the indicated siRNA using Lipofectamine RNAiMAX. Forty-eight hours post-siRNA transfection, cells were replated at a density of 5x105 cells per well of a 6-well plate. The next day, cells were treated with vehicle control, 25, 50, or 100 µg/mL puromycin (Sigma) for 4 hours, or 1 µM thapsigargin for 6 hours.

value: 1  μM thapsigargin

tag: sirna

value: UPF1LL-specific siRNA


title: Thapsigargin_6h_siUPF1LL_3


title: DMSO_6h_siUPF1LL_3

value: vehicle control


title: T-REx-293  siNT_2


title: Thapsigargin_6h_siUPF1LL_1


title: Wt-Male-Sal, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
F2_S14

value: Brain hippocampus

value: WT


title: Mouse treated with PM2.5, biological rep4 [P15_miRNA-4_0]

description:
P15_(miRNA-4_0)
Mouse treated with PM2.5 for 4 weeks

value: liver


title: Animal4017-Array-9

description:
Seq-Well
10Week_countsmatrix.mtx
10Week_countsfeatures.tsv
10Week_countsbarcodes.tsv
Updated10wk_alexandria_structured_metadata10.txt

value: Lung Tuberculosis Granuloma


title: Animal4017-Array-10

value: Mycobacterium tuberculosis


title: iTat-Female-Sal, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
D3_S20

value: iTat

value: Saline i.p.

value: Female


title: Wt-Male-Coc, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
E1_S5

value: Cocaine i.p.


title: Mouse treated with PM2.5, biological rep2 [P12_miRNA-4_0]

description:
P12_(miRNA-4_0)
Mouse treated with PM2.5 for 4 weeks


title: iTat-Female-Sal, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
D2_S12


title: DMSO_6h_siUPF1LL_2


title: Mouse treated with PM2.5, biological rep5 [P17_miRNA-4_0]

description:
P17_(miRNA-4_0)
Mouse treated with PM2.5 for 4 weeks


title: Mouse treated with melatonin, biological rep5 [M35_miRNA-4_0]

description:
M35_(miRNA-4_0)
Mouse treated with melatonin for 4 weeks

source_name: mouse treated with melatonin

value: melatonin for 4 weeks


title: Animal4017-Array-8

value: 10weeks post-infection


title: Animal4017-Array-6


title: DMSO_6h_siUPF1LL_1


title: Mouse treated with melatonin, biological rep4 [M34_miRNA-4_0]

description:
M34_(miRNA-4_0)
Mouse treated with melatonin for 4 weeks


title: Animal4017-Array-5


title: iTat-Female-Sal, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
D1_S4


title: Puromycin_50_siUPF1LL_3

value: 50 μg/ml puromycin


title: Puromycin_50_siUPF1LL_2


title: iTat-Female-Coc, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
C3_S19


title: iTat-Female-Coc, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
C2_S11


title: Animal4017-Array-4


title: Mouse treated with melatonin, biological rep3 [M33_miRNA-4_0]

description:
M33_(miRNA-4_0)
Mouse treated with melatonin for 4 weeks


title: Mouse treated with melatonin, biological rep2 [M31_miRNA-4_0]

description:
M31_(miRNA-4_0)
Mouse treated with melatonin for 4 weeks


title: iTat-Male-Sal, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
B3_S18

value: Male


title: iTat-Female-Coc, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
C1_S3


title: Animal4017-Array-2


title: Puromycin_50_siUPF1LL_1


title: iTat-Male-Sal, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
B2_S10


title: Puromycin_25_siUPF1LL_3

value: 25 μg/ml puromycin


title: Mouse treated with melatonin, biological rep1 [M28_miRNA-4_0]

description:
M28_(miRNA-4_0)
Mouse treated with melatonin for 4 weeks


title: Animal3917-Array-12

description:
Seq-Well
10Week_countsmatrix.mtx
10Week_countsfeatures.tsv
10Week_countsbarcodes.tsv
Updated10wk_alexandria_structured_metadata10.txt


title: Animal3917-Array-10


title: Puromycin_25_siUPF1LL_2


title: Mouse as control, biological rep4 [C24_miRNA-4_0]

description:
C24_(miRNA-4_0)
Mouse as control for 4 weeks

value: control for 4 weeks


title: Mouse as control, biological rep5 [C25_miRNA-4_0]

description:
C25_(miRNA-4_0)
Mouse as control for 4 weeks


title: iTat-Male-Sal, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
B1_S2


title: Animal3917-Array-9


title: Puromycin_100_siUPF1LL_3

value: 100 μg/ml puromycin

value: UPF1LL-specific siRNA


title: Mouse treated with PM2.5, biological rep1 [P10_miRNA-4_0]

description:
P10_(miRNA-4_0)
Mouse treated with PM2.5 for 4 weeks

value: PM2.5 for 4 weeks


title: Mouse as control, biological rep2 [C20_miRNA-4_0]

description:
C20_(miRNA-4_0)
Mouse as control for 4 weeks


title: Mouse as control, biological rep3 [C21_miRNA-4_0]

description:
C21_(miRNA-4_0)
Mouse as control for 4 weeks


title: Puromycin_25_siUPF1LL_1


title: pPMN Donor 3 (T)

city: Heidelberg

first: Guido

last: Wabnitz

address: Im Neuenheimer Feld 305

department: Institute of Immunology

institute: University of Heidelberg

description: Primed neutrophils

hyb_protocol: NanoString nCounter, a hybridization-based multiplex assay.

scan_protocol: According to Nanostring protocol

data_processing: Raw data were imported into nSolver 4.0.70 and analyzed via the nCounter Advanced Analysis plugin (version 2.0.115) to normalize the data. For downstream analysis, only genes with an expression value of ≥ 100 CodeSet counts in all three replicates of either rPMN or pPMN or both were considered. Differential expression analysis was performed using limma with P values adjusted for multiple comparisons according to Benjamini and Hochberg, corresponding to a false discovery rate. Genes with an expression of below this threshold were not further analysed.

source_name: Peripheral blood neutrophils

label_protocol: According to Nanostring protocol

extract_protocol: Total RNA was then purified from 10,000 cells using MagNA Pure (Promega, Mannheim, Germany) according to the manufacturer’s instructions. All RNA samples were quantified by using Qubit RNA assay kit (Thermo Fisher Scientific, Waltham, Massachusetts), and RNA integrity was assessed using Agilent 2100 Bioanalyzer system.

treatment_protocol: Peripheral blood human neutrophils were  analyzed immediately after isolation or after priming with 100 U/ml GM-CSF + 10 ng/ml IFNy or 20 ng/ml TNF for 2 days.

value: Primed neutrophils

tag: priming condition

value: TNF


title: iTat-Male-Coc, 3 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
A3_S17

value: Brain hippocampus


title: Animal3917-Array-8

value: Lung Tuberculosis Granuloma

value: Mycobacterium tuberculosis


title: Animal4017-Array-1


title: Puromycin_100_siUPF1LL_2


title: pPMN Donor 1 (T)

description: Primed neutrophils


title: pPMN Donor 2 (T)

description: Primed neutrophils


title: iTat-Male-Coc, 1 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
A1_S1

value: iTat


title: Puromycin_100_siUPF1LL_1


title: iTat-Male-Coc, 2 (RNA-seq)

description:
all_counts_byexon_geo.txt
all_counts_byexon_FPKM.txt
A2_S9


title: Mouse as control, biological rep1 [C19_miRNA-4_0]

description:
C19_(miRNA-4_0)
Mouse as control for 4 weeks

value: liver


title: pPMN Donor 3 (GI)

description: Primed neutrophils

value: GM-CSF and IFNg


title: Animal3917-Array-7


title: Vehicle_control_siUPF1LL_3

value: vehicle control


title: Vehicle_control_siUPF1LL_2


title: Animal24118-Array-6

description:
Seq-Well
4Week_countsmatrix.mtx
4Week_countsfeatures.tsv
4Week_countsbarcodes.tsv
Updated4wk_alexandria_structured_metadata3.txt

value: 4weeks post-infection


title: pPMN Donor 2 (GI)

description: Primed neutrophils


title: Animal3917-Array-4

value: 10weeks post-infection


title: Animal3917-Array-6


title: Vehicle_control_siUPF1LL_1


title: Animal3917-Array-5


title: Animal24118-Array-3


title: pPMN Donor 1 (GI)

description: Primed neutrophils


title: Animal3917-Array-2


title: rPMN Donor 3

description: Resting neutrophils immediately after purification

value: Resting neutrophils


title: Thapsigargin_6h_siNT_3

value: 1  μM thapsigargin

value: non-targeting siRNA


title: Animal3917-Array-1


title: Animal23118-Array-6


title: Thapsigargin_6h_siNT_2


title: Animal23118-Array-5


title: rPMN Donor 2


title: Animal23118-Array-4


title: Animal24118-Array-5


title: Thapsigargin_6h_siNT_1


title: Animal3817-Array-7


title: rPMN Donor 1


title: DMSO_6h_siNT_3


title: Animal3817-Array-5


title: Animal3817-Array-6


title: DMSO_6h_siNT_2


title: RVG_11: Crotalus viridis post-extraction venom gland ATAC-seq

city: Arlington

first: Blair

last: Perry

state: TX

address: 501 S. Nedderman Dr, Life Sciences Building RM 337

department: Biology

institute: The University of Texas at Arlington

library_source: genomic

data_processing:
Mapped to Prairie Rattlesnake genome using bwa with default settings; duplicates removed with picard-tools mark duplicates; non-unique and improperly paired reads removed
BAM files were randomly subsampled to the number of read pairs in the smallest sample using macs2 randsample, and narrow peaks were called using macs2 callpeak with -q 0.001
Raw bigwig files (.rawCov.bw) were generated with deeptools bamCoverage using --binSize 32, --smoothLength 96, --ignoreForNormalization scaffold-Z, --extendReads; a matrix of raw ATACseq counts in peak regions was generated using deeptools multiBigwigSummary
Scaling factors were calculated in R using calcNormFactors on the raw count matrix and TMM normalization, and these scale factors were used with deeptools bamCoverage to generate scale-factor normalized bigwig files (.scaleFactorNorm.bw) with --binSize 32, --smoothLength 96, --normalizeUsing none, --ignoreForNormalization scaffold-Z, --extendReads, and --scaleFactor N where N is the sample-specific scale factor calculated in R
Genome_build: GCA_003400415.2

molecule: genomic DNA

organism: Crotalus viridis

source_name: Venom gland (post-extraction)

extract_protocol: Tissue samples were extracted, snap frozen with liquid nitrogen, and sent to Active Motif for ChIP-seq/ATAC-seq data generation

value: Venom gland

value: post-extraction


title: Puromycin_50_siNT_3

value: 50 μg/ml puromycin


title: Control pDC

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: 5h treatment then single cell isolation

data_processing:
Samples were demultiplexed and aligned using Cell Ranger 2.2 (10X genomics)
Samples were processed and analyzed in R (3.6.0) using Seurat (v3)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data are matrices with raw counts for features in sequenced cells. A list of cell barcodes and detected genes is also included for each sample.

source_name: PBMC

growth_protocol: PBMC from buffy coats from healthy blood donors were isolated by density gradient centrifugation using SepMate tubes and Lymphoprep (both STEMCELL Technologies). pDC were negatively selected from PBMC using the plasmacytoid dendritic cell isolation kit II (Miltenyi Biotec).

extract_protocol:
Single cell RNA sequencing was performed using a 10X Genomics Chromium Controller.
Single cells were processed with GemCode Single Cell Platform using GemCode Gel Beads, Chip and Library Kits (v2) following the manufacturer’s protocol. Libraries were sequenced on HiSeq 3000 (Illumina)

treatment_protocol: Isolated pDC were maintained in RPMI (Gibco) supplemented with 10% FBS (HyClone), 4 mM L-Glutamine (Invitrogen), 100 U/ml Penicillin/Streptomycin (Invitrogen), 55μM β-Mercaptoethanol (Sigma) and, where indicated, 50 ng/ml IL-3 (Peprotech) or 50 ng/ml GM-CSF (Peprotech). Cells were stimulated with 5 μM CpG-A ODN (ODN2216, InvivoGen) for 5 hours.

value: CONTROL

value: plasmacytoid dendritic cell


title: RVG_1: Crotalus viridis post-extraction venom gland ATAC-seq


title: DMSO_6h_siNT_1


title: Mut-2-rep3

city: Guangzhou

first: Shanshan

last: Yin

state: Guangdong

address: 135 Waihuan Rd. E.

institute: Sun Yat-sen University

description:
mESC263
RC_ESC_genes.csv

data_processing:
Illumina bcl2fastq2 software used for converting base call files to fastq files. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. (--dta –t –p 4).
Reads Count for each gene in each sample was counted by HTSeq v0.6.0 (-i gene_id -f bam -s no -a 10 -q )
Genome_build: GRCm38_Ensembl
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured on MEFs in mESC medium with serum and LIF.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini kit from mESCs grown on MEFs.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tin2 S341X

value: Mouse blastocyte-derived ESCs


title: Crotalus viridis post-extraction venom gland H3K4me3 ChIP-seq

description:
1 day following manual extraction of venom
3_047W_00JKUTA_VenomGland-495_H3K4me3_CroVir_i89

data_processing:
Reads were mapped to the Prairie Rattlesnake genome using BWA with default settings
Fragment densities were determined in 32 bp windows, and peak regions were identified using MACS 2.1.0
To normalize between samples, the tag number of each sample was reduced by randomly sampling to the number of tags present in the sample with the fewest tags (separately for ATAC-seq and ChIP-seq samples)
Genome_build: UTA_CroVir_3.0 (GCA_003400415.2)
Supplementary_files_format_and_content: scores in bigwig files represent the number of tags identified in each 32 bp bin
Supplementary_files_format_and_content: peak text files

growth_protocol: adult animals were maintained under approved protocols for greater than 30 days prior to treatment and sample collection

extract_protocol:
Tissue samples were extracted, snap frozen with liquid nitrogen, and sent to Active Motif for ChIP-seq/ATAC-seq data generation
ATAC-seq and ChIP-seq libraries were prepared by Active Motif (Carlsbad, CA). ATAC-seq libraries were sequenced on an Illumina NextSeq500 using 42 bp paired-end reads, and ChIP-seq libraries were sequenced on an Illumina NextSeq 500 using 75 bp single-end reads.

treatment_protocol: "Post-extraction": venom glands were manually expressed and depleted either 1 day (ChIP-seq) or 3 days (ATAC-seq) prior to tissuing to stimulate venom production. "Unextracted": venom glands were not extracted prior to tissuing

tag: chip antibody


title: Animal3817-Array-1

value: Lung Tuberculosis Granuloma

value: Mycobacterium tuberculosis


title: Mut-2-rep2

description:
mESC262
RC_ESC_TE_genes.txt
RC_ESC_genes.csv

data_processing:
Illumina bcl2fastq2 software used for converting base call files to fastq files. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. (--dta –t –p 4).
Reads Count for each gene in each sample was counted by HTSeq v0.6.0 (-i gene_id -f bam -s no -a 10 -q )
Reads Count for each gene and repetitive elements in each sample was counted by TEtranscripts V2.2.0 (default parameters)
Genome_build: GRCm38_Ensembl
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Matrix table with raw gene counts for every gene or repetitive elements and every sample


title: Puromycin_50_siNT_2


title: Animal3817-Array-8


title: Mut-2-rep1

description:
mESC261
RC_ESC_genes.csv


title: Crotalus viridis post-extraction venom gland H3K27ac ChIP-seq

description:
1 day following manual extraction of venom
2_047V_00JKUTA_VenomGland-495_H3K27Ac_CroVir_i88


title: Scr-static_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content, and duplication rates with FastQC.
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned vs. the Ensembl human genome version hg38 (GRCh38) using STAR 2.6.9c with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1. Only genes with a minimum fold change of ±1.5 (log2 ± 0.59), a maximum Benjamini–Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: Count Matrix

source_name: Human Umbilical Vein Endothelial Cells

growth_protocol: HUVECs were obtained from Lonza and were cultured in endothelial growth medium (EGM-2; Lonza) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was isolated from endothelial cell monolayers using the Quick-RNA Micro prep kit according to the manufacturer’s protocol.
200ng of total RNA was used as starting material for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara).

treatment_protocol: HUVECs were seeded in µ-slide I0.4 Luer ibiTreat chambers and were transfected with control siRNA at 70% confluence. After transfection, HUVECs were exposed to 48 h laminar flow versus cells kept for 48 h under static conditions. Laminar flow was applied by using the ibidi pump system.

value: Human Umbilical Vein Endothelial Cells

value: static conditions


title: Crotalus viridis post-extraction venom gland CTCF ChIP-seq

description:
1 day following manual extraction of venom
1_047U_00JKUTA_VenomGland-495_CTCF_CroVir_i87

value: CTCF (Active Motif, 61311, lot 17118005)


title: Puromycin_50_siNT_1


title: Mut-1-rep3

description:
mESC143
RC_ESC_TE_genes.txt
RC_ESC_genes.csv


title: RVG_4: Crotalus viridis post-extraction venom gland ATAC-seq


title: ODN treated pDC

description: 5h treatment then single cell isolation

value: ODN


title: Puromycin_25_siNT_3

value: 25 μg/ml puromycin


title: Mut-1-rep2

description:
mESC142
RC_ESC_genes.csv


title: Puromycin_25_siNT_2


title: Animal3817-Array-2

description:
Seq-Well
10Week_countsmatrix.mtx
10Week_countsfeatures.tsv
10Week_countsbarcodes.tsv
Updated10wk_alexandria_structured_metadata10.txt

value: 10weeks post-infection


title: Scr-flow_2

value: subjected to laminar shear stress


title: b83OX-15 +Fe Leaf

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

country: Japan

institute: Ishikawa Prefectural University

data_processing:
Preprocessing was performed using trimmomatic version 0.39
Mapping was performed using bowtie version 1.2.3
Quantification of expression was performed using RSEM version 1.2.21
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Text files including RPM values for each sample.

organism: Oryza sativa

source_name: iron-sufficient leaves

growth_protocol: Rice (Oryza sativa L.) cultivar Tsukinohikari and its transformants were germinated and cultured hydroponically based on the description in Kobayashi et al. (2019) Plant Mol. Biol. 101:471-486.

extract_protocol:
Total RNA was extracted from hydroponically grown roots and leaves using the RNeasy Plant Mini Kit (QIAGEN), treated with DNase I and reverse-transcribed using ReverTra Ace qRT-PCR RT Master Mix with gDNA Remover (TOYOBO).
RNA libraries were prepared for sequencing using Lasy-Seq v1.1 (Kamitani et al., 2019 Sci. Rep. 9: 7091).

treatment_protocol: Iron-sufficiency treatment (which was the same as preculture condition) was imposed after preculture in hydroponics

tag: cultivar

value: Tsukinohikari

value: leaves

value: OsbZIP83 overexpression line 15


title: Mut-1-rep1

description:
mESC141
RC_ESC_genes.csv


title: Scr-flow_1


title: D15_12_D_UNX: D-serine treated UNX mice_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: unilateral nephrectomy (UNX) mice treated with D-serine

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: D-serine treated UNX mice_rep3

extract_protocol:
RNA was extracted using TRIzol (15596018, Thermo Fisher Scientific, Waltham, USA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Mice were fed with a serine-free diet and water with or without 0.1% D-serine for one week, subjected to either UNX or sham operation, and then sacrificed two days after operation.

value: kidney

value: D-serine


title: NT +Fe Leaf (control)

value: non-transformant


title: b83OX-19 +Fe Leaf

value: OsbZIP83 overexpression line 19


title: Puromycin_25_siNT_1

value: non-targeting siRNA


title: WT-2-rep3

description:
mESC233
RC_ESC_genes.csv

value: wild type

value: Mouse blastocyte-derived ESCs


title: Puromycin_100_siNT_2

value: 100 μg/ml puromycin


title: Puromycin_100_siNT_3


title: D15_9_D_UNX: D-serine treated UNX mice_rep2

source_name: D-serine treated UNX mice_rep2


title: WT-2-rep2

description:
mESC232
RC_ESC_genes.csv


title: b83OX-13 +Fe Leaf

value: OsbZIP83 overexpression line 13


title: D15_8_D_UNX: D-serine treated UNX mice_rep1

source_name: D-serine treated UNX mice_rep1


title: WT-2-rep1

description:
mESC231
RC_ESC_genes.csv


title: Scr-static_1

value: Human Umbilical Vein Endothelial Cells

value: static conditions


title: Puromycin_100_siNT_1


title: b83OX-15 +Fe Root

source_name: iron-sufficient roots

value: roots


title: WT-1-rep3

description:
mESC153
RC_ESC_genes.csv


title: D15_6_V_UNX: vehicle treated UNX mice_rep3

description: unilateral nephrectomy (UNX) mice treated with vehicle

source_name: vehicle treated UNX mice_rep3

value: vehicle


title: b83OX-13 +Fe Root


title: Vehicle_control_siNT_3

value: vehicle control


title: WT-1-rep2

description:
mESC152
RC_ESC_genes.csv


title: Vehicle_control_siNT_2


title: NT +Fe Root (control)

value: Tsukinohikari


title: D15_5_V_UNX: vehicle treated UNX mice_rep2

source_name: vehicle treated UNX mice_rep2


title: D15_4_V_UNX: vehicle treated UNX mice_rep1

source_name: vehicle treated UNX mice_rep1


title: WT-1-rep1

description:
mESC151
RC_ESC_genes.csv


title: Vehicle_control_siNT_1

source_name: HEK-293 cells


title: b83OX-19 +Fe Root


title: Rh-Hippocampus-47_TC [Rh_20117]

status: Public on Apr 06 2022

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: processed data file: exp.Rh_Gestational_Hippocampus.txt

data_processing:
We combined the raw RNA-Seq data from the current study (n=110) with lung and brain samples sequenced in our prior study (n=17, preterm control and antenatal steroids), using the identical experimental protocols (Schmidt, 2019). To quantify gene expression, we applied pseudoalignment with the software Kallisto using the Ensembl 91 Rhesus Macaque reference transcriptome, using the software AltAnalyze version 2.1.4. For downstream-analyses, Rhesus gene symbols were converted to human gene symbols, where possible (Ensembl BioMart). To correct for seasonal differences in RNA collection and processing, fetal sex and treatment effect, we performed batch effects correction using NOISeq package in R, after excluding genes with strong sex-linked profiles (n=17). NOISeq was run using the ARSyNseq correction function, specifying the treatment group variable rather than a specific set of batch effect factors due to the number and inter-relatedness of candidate factors. Models fit for differential gene expression analyses included blocking by sample year, dichotomized to the earliest time-point group vs. other, to correspond to the two main treatment-by-year subsets. This ensured treatments were compared to (reasonably) contemporary pre-term controls and provided additional control for any year effects not removed in prior steps. Data from one amniotic fluid (AF) sample was not used because the distribution of expression values for this sample was markedly lower than for the other samples. Gene filtering was done on the basis of mean log2 expression values across samples, separately for Lung, Brain and amniotic fluid. Genes were retained for differential expression and correlation analyses if mean log2 expression values (prior to batch correction) were ≥ 1.0 TPM. Principal component analyses (PCA) were conducted using the pca function supplied in the PCAtools R package. The center & scale options were set to “TRUE”.
Genome_build: hg19
Supplementary_files_format_and_content: Gene-level Transcript Per Million (TPM) estimates (batch-corrected).

organism: Macaca mulatta

source_name: Hippocampus

growth_protocol: isolation protocol: Pregnant rhesus macaques were studied at the California National Primate Research Center at the University of California Davis with protocols and procedures approved by the Institutional Animal Care and Use Committee. Time-mated pregnant Rhesus macaques were delivered preterm at 132 days of gestation or near term at 155 days of gestation (full term is 165 days). Fetuses were delivered 5 days after the initiation of treatment with antenatal corticosteroids at 132  2 days of gestation by cesarean section with intact membranes (n=5-8 animals/group). After delivery, the amniotic fluid was sampled and immediately stored in AssayAssure tubes with standardized buffer (Sierra Molecular Corporation, Incline Village, NV) and frozen at -80 °C. After euthanasia, pressure-volume curves were measured by inflating lungs to 40 cmH2O and followed by deflation with measurements of lung volumes using a syringe and pressure manometer. Samples from the right lower lobe of fetal lung and the hippocampus were snap frozen for RNA-sequencing.

extract_protocol:
Approximately 10 mL of amniotic fluid from each animal was used for cell-free RNA extraction with the QIAamp Circulating Nucleic Acid Kit (QIAGEN, Valencia, CA). RNA from the lung and hippocampus was extracted with the RNeasy Universal Mini Kit (QIAGEN, Valencia, CA).
The RNAseq libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina).
RNA-Seq was performed at a target depth of 30 million reads, with paired-end 75 bp RNA-Seq performed with a HiSeq 2500 (Illumina). by the Cincinnati Children’s Hospital Sequencing Core.

treatment_protocol: For antenatal corticosteroid dosing studies, preterm pregnant rhesus macaques received one of the treatments. Oral drugs were given to animals habituated to receiving small treats as previously reported (Schmidt et al., 2019b). The IM betamethasone-acetate 0.125mg/kg and the oral betamethasone-phosphate have been previously shown to induce fetal lung maturation similar to the standard clinical treatment in preterm rhesus macaques, while the betamethasone-acetate 0.06mg/kg and the oral dexamethasone-phosphate did not (Schmidt et al., 2019a; Schmidt et al., 2019b).

tag: animal identifier

value: IA/IM Saline control

value: M

tag: gestational age

tag: body weigth

tag: pressure volume curve (pv40) value

tag: batch year

value: Hippocampus


title: Rh-Hippocampus-43_PTC [Rh_427-18]

tag: treatment

value: Control - Saline

tag: tissue


title: Rh-Hippocampus-44_PTC [Rh_430-18]


title: Rh-Hippocampus-45_PTC [Rh_432-18]


title: Rh-Hippocampus-40_PTC [Rh_21217]

value: F


title: Rh-Hippocampus-42_PTC [Rh_423-18]


title: Rh-Hippocampus-41_PTC [Rh_20917]


title: Rh-Hippocampus-34_POD [Rh_424-18]

value: PO Dexamethasone-phosphate 0.15mg/kg q12 x3 q12h


title: Rh-Hippocampus-35_POD [Rh_461-18]


title: Rh-Hippocampus-32_POD [Rh_421-18]


title: Rh-Hippocampus-33_POD [Rh_425-18]


title: Rh-Hippocampus-31_POD [Rh_418-18]


title: Rh-Hippocampus-36_POD [Rh_463-18]


title: Rh-Hippocampus-29_POD [Rh_414-18]


title: Rh-Hippocampus-30_POD [Rh_417-18]


title: Rh-Hippocampus-28_POB [Rh_462-18]

value: PO Betamethasone-phosphate 0.15mg/kg q12 x3 q12h

value: UNK


title: Rh-Hippocampus-27_POB [Rh_428-18]


title: Rh-Hippocampus-26_POB [Rh_422-18]


title: Rh-Hippocampus-25_POB [Rh_420-18]


title: Rh-Hippocampus-23_POB [Rh_416-18]


title: Rh-Hippocampus-24_POB [Rh_419-18]


title: Rh-Hippocampus-21_C2x [Rh_412-18]

value: Celestone 0.25mg/kg x2 q24h


title: Rh-Hippocampus-22_POB [Rh_415-18]


title: Rh-Hippocampus-19_C2x [Rh_410-18]


title: Rh-Hippocampus-18_C2x [Rh_409-18]


title: Rh-Hippocampus-17_C2x [Rh_413-18]


title: Rh-Hippocampus-16_C2x [Rh_408-18]


title: Rh-Hippocampus-15_C1x [Rh_24517]

value: IM Celestone 0.25mg/k, 5d


title: Rh-Hippocampus-14_C1x [Rh_23817]


title: Rh-Hippocampus-10_B125 [Rh_23717]

value: IM Beta-Ac 0.125 mg/k, 5d


title: Rh-Hippocampus-9_B125 [Rh_23517]


title: Rh-Hippocampus-5_B060 [Rh_23117]

value: IM Beta-Ac 0.06 mg/k, 5d


title: Rh-Hippocampus-4_B060 [Rh_230-17]


title: Rh-Hippocampus-2_B060 [Rh_210-17]


title: Rh-Hippocampus-1_B060 [Rh_213-17]


title: Rh-Amniotic Fluid-47_TC [Rh_AF_201_17_17260]

description: processed data file: exp.Rh_Gestational_Amniotic-Fluid.txt

source_name: Amniotic Fluid

value: Amniotic Fluid


title: Rh-Amniotic Fluid-46_TC [Rh_AF_200_17_17259]


title: Rh-Amniotic Fluid-45_PTC [Rh_AF_432_18_17594]


title: Rh-Amniotic Fluid-43_PTC [Rh_AF_427_18_17591]


title: Rh-Hippocampus-20_C2x [Rh_411-18]


title: S2: ΔsbbA,48h

first: liyang

last: chu

address: haidian

institute: Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Genomic localization analysis of sequence using Bowtie 2.2.3
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were estimation of gene expression level (Trapnell, Cole, et al., 2010)
Genome_build: GCF_000092385.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Streptomyces bingchenggensis

source_name: High-yielding strain

extract_protocol:
The mycelia were collected,flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: sbbA deletion mutant


title: S6: ΔsbbA,192h


title: S5: ΔsbbA,144h


title: S4: ΔsbbA,96h


title: S3: ΔsbbA,72h


title: Rh-Amniotic Fluid-44_PTC [Rh_AF_430_18_17593]


title: S1: ΔsbbA,18h


title: Rh-Amniotic Fluid-42_PTC [Rh_AF_423_18_17588]


title: Rh-Amniotic Fluid-40_PTC [Rh_AF_212_17_17262]


title: Rh-Amniotic Fluid-36_POD [Rh_AF_463_18_17597]


title: W6: BC-101-4,192h

source_name: wild type


title: W5: BC-101-4,144h


title: Rh-Amniotic Fluid-35_POD [Rh_AF_461_18_17595]


title: W4: BC-101-4,96h


title: Rh-Amniotic Fluid-34_POD [Rh_AF_424_18_17589]


title: Rh-Hippocampus-3_B060 [Rh_20717]


title: Rh-Amniotic Fluid-33_POD [Rh_AF_425_18_17590]


title: Rh-Amniotic Fluid-32_POD [Rh_AF_421_18_17586]


title: W1: BC-101-4,18h


title: W2: BC-101-4,48h


title: Rh-Amniotic Fluid-31_POD [Rh_AF_418_18_17583]


title: H3K27me3_770CU_Rep2

city: Bologna

first: Cristian

last: Forestan

state: BO

address: Viale Fanin 44

department: Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)

country: Italy

institute: University of Bologna

data_processing:
Base-calling and demultiplexing with Bcl2Fastq 2.20.
Adapter clipping and quality filtering with Trimmomatic 0.39.
Mapping with bowtie2.
Peaks calling with MACS2 callpeak.
Differential enriched peaks detection with MACS2 bdgdiff.
Genome_build: Prunus persica Genome v2
Supplementary_files_format_and_content: bedGraph files of peaks called for each timepoint/antibody combination.

organism: Prunus persica

source_name: flower bud

growth_protocol: Buds were collected, during the autumn/winter vegetative arrest season, from 10-year-old trees of Fantasia (FAN) genotype in the experimental farm “Lucio Toniolo” of the University of Padova (45°21'04.8"N 11°57'01.3"E).

extract_protocol:
Chromatin was purified from frozen tissues, sonicated and immuno-precipitated with antibody.
Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN, Redwood City, CA) for Illumina sequencing.

value: Fantasia

value: Flower bud

tag: Stage

value: 770 chilling units

tag: sampling date

value: H3K27me3 (Millipore, Cat. 07-449)


title: Rh-Amniotic Fluid-30_POD [Rh_AF_417_18_17582]

tag: Sex

value: M


title: Rh-Amniotic Fluid-41_PTC [Rh_AF_209_17_17158]


title: H3K27me3_475CU_Rep3

value: 475 chilling units


title: parental cell gRNA_AAVS1 replicate 3

city: Vienna

first: Alexandra

last: Popa

state: Austria

address: Doktor-Boehringer-Gasse 5-11

country: Austria

institute: Boehringer Ingelheim

data_processing:
Base-calling was performed using the Real-Time Analysis (RTA)
Mapping of raw reads was performed with STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences.
Quantification of read counts to transcript annotations was implemented using RSEM(v1.3.0) and featureCounts (v1.5.1).
Normalization of read counts and differential analysis was implemented with the limma and voom R packages.
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for all samples.

source_name: KNS-42 cell line

growth_protocol: Cas9-expressing KNS-42 cells were grown in EMEM, 5% FCS, Glutamax, Sodium pyruvate, 1µg/ml Puromycin.

extract_protocol:
On day 7 after transduction, cells were washed with PBS, detached, lysed, treated with DNAse I (QIAGEN) and total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Next generation sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen) according to the manufacturer’s instructions.

treatment_protocol: Cells were transduced with 2ml unconcentrated gRNA-encoding lentiviral particles.

tag: cell line

tag: genotype

value: parental


title: H3K27me3_770CU_Rep1


title: H3K27me3_475CU_Rep2


title: parental cell gRNA_395  replicate 2


title: H3K27me3_475CU_Rep1


title: H3K4me3_770CU_Rep2

value: H3K4me3 (Active Motif, Cat. 39159)


title: Rh-Amniotic Fluid-29_POD [Rh_AF_414_18_17579]

value: PO Dexamethasone-phosphate 0.15mg/kg q12 x3 q12h


title: Rh-Amniotic Fluid-26_POB [Rh_AF_422_18_17587]

value: PO Betamethasone-phosphate 0.15mg/kg q12 x3 q12h

value: F


title: Rh-Amniotic Fluid-28_POB [Rh_AF_462_18_17596]

value: UNK


title: H3K27me3_0CU_Rep2

value: 0 chilling units


title: DDX3Yoes cell gRNA_AAVS1 replicate 2


title: W3: BC-101-4,72h


title: parental cell gRNA_395  replicate 3


title: H3K4me3_770CU_Rep1


title: H3K4me3_475CU_Rep3


title: parental cell gRNA_395  replicate 1


title: WholeChromatin

value: pool of the three samples


title: Rh-Amniotic Fluid-25_POB [Rh_AF_420_18_17585]


title: H3K4me3_475CU_Rep2


title: H3K4me3_475CU_Rep1


title: Rh-Amniotic Fluid-24_POB [Rh_AF_419_18_17584]


title: H3K4me3_0CU_Rep2


title: DDX3Xoe cell gRNA_395  replicate 3


title: H3K4me3_0CU_Rep1


title: Rh-Amniotic Fluid-23_POB [Rh_AF_416_18_17581]


title: H3K27me3_0CU_Rep1


title: DDX3Yoes cell gRNA_AAVS1 replicate 1


title: 770CU_Rep1

data_processing:
base-calling and demultiplexing
rRNA filtering with ERNE-filter
adapter clipping and quality filtering with Trimmomatic 0.39
mapping with hisat2.0.13; parameters: ' --dta --min-intronlen 20 --max-intronlen 10000 --rna-strandness RF
read counts with featureCounts
Differential expression analysis usignDESeq2 (v1.30)
Genome_build: Prunus persica Genome v2
Supplementary_files_format_and_content: tab-delimited matrix with normalized FPKM values for all the samples

growth_protocol: Buds were collected, during the autumn/winter vegetative arrest season, from 10 years old trees of Fantasia (FAN) genotype in the experimental farm “Lucio Toniolo” of the University of Padova (45°21'04.8"N 11°57'01.3"E)

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini kit (Qiagen)
Ribo-Zero rRNA removal; 150nt paired end Illumina sequencing

value: flower bud

tag: collection date


title: DDX3Xoe cell gRNA_AAVS1 replicate 2


title: Rh-Amniotic Fluid-22_POB [Rh_AF_415_18_17580]

value: Amniotic Fluid


title: 475CU_Rep1


title: parental cell gRNA_AAVS1 replicate 1


title: 200CU_Rep1

value: 200 chilling units


title: 0CU_Rep1

value: Fantasia


title: Rh-Amniotic Fluid-21_C2x [Rh_AF_412_18_17577]

value: Celestone 0.25mg/kg x2 q24h


title: Rh-Amniotic Fluid-20_C2x [Rh_AF_411_18_17576]


title: DDX3Yoes cell gRNA_AAVS1 replicate 3


title: 0CU_Rep2


title: Rh-Amniotic Fluid-18_C2x [Rh_AF_409_18_17574]


title: DDX3Xoe cell gRNA_AAVS1 replicate 3


title: MPH3_siCebpa

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Knock-down of Cebpa

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TPM abundance estimates and raw counts generated with kallisto.

source_name: Mouse primary hepatocyte

growth_protocol: The freshly isolated hepatocytes were seeded on collagen-coated plates in Williams' E medium supplemented with 10% FBS, 2mM L-glutamine, 1% P/S, 100 nM dexamethasone, and 5% ITS

extract_protocol:
Total RNA was extracted using TRIzol method
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

treatment_protocol: Knock-down of siRNA for 48 hours

tag: cell type

value: primary hepatocyte

value: siCebpa


title: MPH3_siHnf4a

description: Knock-down of Hnf4a


title: Rh-Amniotic Fluid-17_C2x [Rh_AF_413_18_17578]

value: M


title: MPH3_siCon

description: Knock-down of control siRNA

value: siCon


title: MPH3_siHnf4a siCebpa

description: Knock-down of Hnf4a and Cebpa


title: 770CU_Rep2

value: 770 chilling units


title: parental cell gRNA_AAVS1 replicate 2

value: parental


title: Rh-Amniotic Fluid-16_C2x [Rh_AF_408_18_17573]


title: DDX3Xoe cell gRNA_395  replicate 2


title: 475CU_Rep2

value: 475 chilling units


title: DDX3Xoe cell gRNA_395  replicate 1


title: MPH2_siCebpa

description: Knock-down of Cebpa


title: Rh-Amniotic Fluid-15_C1x [Rh_AF_245_17_17269]

value: IM Celestone 0.25mg/k, 5d


title: MPH2_siCon

description: Knock-down of control siRNA


title: Rh-Amniotic Fluid-14_C1x [Rh_AF_238_17_17268]

value: F


title: MPH2_siHnf4a siCebpa

description: Knock-down of Hnf4a and Cebpa


title: 200CU_Rep2


title: MPH1_siHnf4a

description: Knock-down of Hnf4a


title: DDX3Yoes cell gRNA_395  replicate 1


title: Rh-Amniotic Fluid-10_B125 [Rh_AF_237_17_17267]

value: IM Beta-Ac 0.125 mg/k, 5d


title: DDX3Xoe cell gRNA_AAVS1 replicate 1


title: MPH1_siHnf4a siCebpa

description: Knock-down of Hnf4a and Cebpa


title: DDX3Yoes cell gRNA_395  replicate 3


title: MPH1_siCebpa

description: Knock-down of Cebpa


title: DDX3Yoe cell gRNA_395 replicate 2


title: Liver parenchymal cells-poly(I:C) 7h+LPS 12h

city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

institute: Third Xinagya Hospital

data_processing:
Sequencing data were processed into transcript count tables using the Cell Ranger Single Cell Software Suite version 2.2.0 by 10x Genomics (http://www.10xgenomics.com/).
Base calls from the MGISEQ-2000 were pre-processed into demultiplexed, processed reads.
The quality of the raw sequencing data were assessed with FastQC v0.11.7.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every single cell

source_name: liver parenchymal cells

extract_protocol:
Briefly, after anesthetization, mice were perfused through the portal vein with buffer solution lacking Ca2+ and Mg2+ and then perfused with 0.05% type IV collagenase at 37℃. The liver was then excised, minced and filtered through a 70 µm filter. Parenchymal cells were stored temporarily in Dulbecco's Modified Eagle Medium with 10% fetal bovine serum (FBS), 15 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 100 U/ml penicillin, and streptomycin after digestion. Parenchymal cells were separated by centrifugation at 50 × g for 2 min twice. Cell viability was typical > 90% by trypan blue exclusion.
Libraries generated using the 10× Genomics Chromium system require a conversion step using the MGIEasy Universal Library Conversion kit (App-A) (Part Number: 1000004155) before sequencing can be performed on the MGISEQ-2000 instrument.

treatment_protocol: A murine model of endotoxemia has been developed. Male mice were injected intraperitoneally (i.p.) with poly(I:C) and LPS solubilized in 0.9% sterile sodium chloride by sonication and vortexing. These mice were primed with poly(I:C) and then challenged 7 hour later with LPS. After fasting overnight, the mice were randomly divided into the following groups as designed: the control group received saline ; the poly(I:C) group received poly(I:C) only; the lps 3 hour group were primed with poly(I:C) for 7 hour and later received LPS for 3 hour; the lps 12 hour group were primed with poly(I:C) for 7 hour and later received LPS for 12 hour. All mice were randomly assigned to the treatment groups by random number via invoking computer. Blinding procedures were used to prevent researcher bias. No animals were excluded from the study.

value: Isolated liver parenchymal cells

value: liver

value: Male

value: Mice were primed with poly(I:C) for 7 hours and later received LPS for 12 hours


title: Liver parenchymal cells-poly(I:C) 7h+LPS 3h

value: Mice were primed with poly(I:C) for 7 hours and later received LPS for 3 hours


title: Rh-Amniotic Fluid-5_B060 [Rh_AF_231_17_17265]

value: IM Beta-Ac 0.06 mg/k, 5d

value: Amniotic Fluid


title: MPH2_siHnf4a

description: Knock-down of Hnf4a

value: primary hepatocyte


title: Liver parenchymal cells-control

value: Mice were injected with saline


title: FMB_3029_D8

city: New York

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: normalized.log2CPM.tsv (tab-delimited  file using log2-transformed CPM values for each sample)

organism: Mustela putorius furo

source_name: whole blood

extract_protocol:
RNA was extracted from ferret blood using the Mouse RiboPure-Blood RNA Isolation Kit (Ambion)
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer-supplied protocol. Libraries were sequenced 100 bp paired-end to a depth of approximately 40 million host genome reads on Illumina HiSeq 2500 instruments.

treatment_protocol: Adult ferrets were infected intranasally with the A/California/07/2009 virus at a dose of 106 plaque-forming units (PFU). The animals were monitored daily for the severity of clinical disease using weight loss.

tag: age

value: Adult

tag: ferretid

tag: day

tag: infectionagent

tag: viralload

tag: relweight

value: whole blood


title: FMB_3033_D1


title: Rh-Amniotic Fluid-3_B060 [Rh_AF_207_17_17157]

tag: animal identifier

tag: gestational age

tag: body weigth

tag: pressure volume curve (pv40) value

tag: batch year


title: FMB_3022_D8

tag: tissue


title: FMB_3002_D1

tag: Sex


title: Rh-Amniotic Fluid-9_B125 [Rh_AF_235_17_17266]

tag: treatment

value: M


title: cP2het1 [DE29NGSUKBR116536]

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

country: Spain

institute: INIA-CSIC

data_processing:
The samples were then mapped to the mouse genome (GRCm38.89) using HISAT2 2.1 (Kim et al. 2015).
StringTie 1.3.3 (Pertea et al. 2015) was used for transcript quantification and annotation. Gene annotation was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org)(GRCm38.89). The python script (preDE.py) included in the StringTie package was used to prepare DEseq2-compatible gene-level count matrices for analysis of differential gene expression.
Differential expression (DE) was analyzed using DESeq2 1.16.1 (Love et al. 2014). The adjusted p-value (Benjamini-Hochberg method) cutoff for DE was set at < 0.05, log2 fold change of expression (LFC) cutoff was set at > 1.
Assembly: GRCm38.89
Supplementary files format and content: comma-separated text files include raw counts

source_name: testis

extract_protocol:
RNA was extracted from testes after removal of the tunica albuginea using the RNeasy kit (Qiagen, Hilden, Germany).
RNA sample quality control and library preparation were performed by the University of Bonn Core facility for Next Generation Sequencing (NGS), using the QuantSeq 3'-mRNA Library Prep (Lexogen, Greenland, NH, USA).

value: testis

tag: genotype

value: het

tag: strain background


title: WT2 [DE34NGSUKBR116543]

value: WT


title: cP2het2 [DE02NGSUKBR116537]


title: Rh-Lung-47_TC [Rh20117Lung]

description: processed data file: exp.Rh_Gestational_Lungs.txt

source_name: Lungs

value: IA/IM Saline control

value: Lungs


title: FMB_3003_D1


title: FMB_3016_D2


title: MPH1_siCon

description: Knock-down of control siRNA

tag: cell type

value: siCon


title: FMB_3016_D3

tag: age


title: Rh-Amniotic Fluid-4_B060 [Rh_AF_230_17_17264]


title: FMB_3014_D1

tag: ferretid


title: Rh-Amniotic Fluid-1_B060 [Rh_AF_213_17_17263]


title: FMB_3030_D3

tag: day


title: FMB_3001_D8

tag: infectionagent


title: FMB_3033_D2

tag: viralload


title: cP2hom3 [DE88NGSUKBR116541]

value: hom


title: Rh-Lung-45_PTC [Rh-Lung-432-18]

value: Control - Saline


title: FMB_3005_D2

value: Male

tag: relweight


title: FMB_3003_D8


title: Rh-Lung-44_PTC [RhLung430-18]

tag: animal identifier


title: cP2hom2 [DE18NGSUKBR116540]


title: WT3 [DE07NGSUKBR116544]


title: FMB_3016_D1


title: FMB_3011_D3


title: cP2hom1 [DE45NGSUKBR116539]


title: FMB_3034_D5


title: Rh-Lung-46_TC [Rh20017Lung]

value: F

tag: gestational age


title: FMB_3011_D8

value: no sample


title: FMB_3009_D2


title: Rh-Lung-42_PTC [RhLung423-18]

tag: body weigth


title: Prm1_hom3

data_processing:
Samples were mapped to the mouse genome (GRCm38.89) using HISAT2 2.1 and transcripts were quantified and annotated using StringTie 1.3.3
Gene annotation was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org)(GRCm38.89). The python script (preDE.py) included in the StringTie package was used to prepare DEseq2-compatible gene-level count matrices for analysis of differential gene expression.
Differential expression was analyzed using DESeq2 1.16.1. The adjusted p-value (Benjamini-Hochberg method) cutoff for DE was set at < 0.05, log2 fold change of expression (LFC) cutoff was set at > 1.
Assembly: GRCm38.89
Supplementary files format and content: comma-separated text files include raw counts

extract_protocol:
RNA was extracted from whole testis of three individuals per genotype. After removal of the tunica albuginea, testes were homogenized in TRIzolTM and processed according to the manufacturers protocol (Thermo Fisher).
RNA sample quality control, library preparation (QuantSeq 3'-mRNA Library Prep (Lexogen, Greenland, NH, USA)) and RNAseq were performed by the University of Bonn Core facility for Next Generation Sequencing (NGS).


title: FMB_3005_D8


title: Prm1_hom2


title: FMB_3002_D8


title: Prm1_hom1


title: Rh-Lung-40_PTC [Rh21217Lung]

tag: pressure volume curve (pv40) value


title: WT1 [DE61NGSUKBR116542]


title: FMB_3035_D5


title: Rh-Lung-36_POD [Rh-Lung-463-18]

value: PO Dexamethasone-phosphate 0.15mg/kg q12 x3 q12h

tag: batch year


title: FMB_3003_D3

value: poor monolayer

tag: tissue


title: Prm1_het3


title: cP2het3 [DE72NGSUKBR116538]


title: Rh-Lung-35_POD [Rh-Lung-461-18]

tag: Sex


title: FMB_3011_D1


title: Prm1_het2


title: FMB_3014_D8


title: Rh-Lung-43_PTC [Rh-Lung-427-18]

tag: treatment


title: FMB_3006_D2


title: FMB_3027_D8


title: Rh-Lung-34_POD [Rh-Lung-424-18]


title: Prm1_het1

tag: genotype


title: FMB_3012_D8


title: Rh-Lung-33_POD [Rh-Lung-425-18]


title: FMB_3024_D1


title: FMB_3009_D5


title: Prm1_wt3

value: wt

tag: strain background


title: Rh-Lung-41_PTC [Rh20917Lung]


title: FMB_3027_D1

value: Adult


title: Rh-Lung-32_POD [Rh_Lung_421-18]


title: X819594204

data_processing:
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: tab-delimited  file using log2-transformed CPM values for each sample

value: Female

tag: ferret id

tag: illness severity

value: Moderate

tag: infection agent

tag: viral load

tag: rel. weight


title: X713427765

tag: age

tag: day

value: Uninfected


title: Prm1_wt1

value: testis


title: Rh-Lung-31_POD [Rh-Lung-418-18]

tag: animal identifier

value: M


title: X711216944


title: Prm1_wt2


title: X818068240


title: X812017553


title: FMB_3001_D1

tag: ferretid

tag: infectionagent

tag: viralload

tag: relweight

value: whole blood


title: Rh-Lung-29_POD [Rh-Lung-414-18]

tag: gestational age

tag: body weigth

tag: pressure volume curve (pv40) value

tag: batch year

tag: tissue

value: Lungs


title: X811116298

tag: Sex

tag: ferret id


title: X715857236

tag: illness severity

tag: infection agent


title: ko3

city: Shanghai

first: Fuhua

last: Wang

address: 800 Dongchuan RD. Minhang District

institute: SJTU

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were filtered using Cutadapt
Data was aligned to the mm10 mouse genome using HISAT2
Filtered reads were assigned to the annotated transcriptome and quantified using HTSeq
FPKM was used as normalization method
Assembly: mm10
Supplementary files format and content: CSV file include FPKM values for each Sample ...

source_name: inguinal white adipose tissue

growth_protocol: Mice were grow under standard feeding conditions(chow diet and 22OC）

extract_protocol:
after homogenize the separated iWATs, isolate total RNA with trizol
Libraries were prepared according to the instructions of VAHTS® Stranded mRNA-seq Library Prep Kit for Illumina(Vazyme).Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 2 months old mice were exposed to  4OC enviroment for 7 days

tag: strain

tag: developmental stage

value: 2 months after birth

tag: genotype


title: X811038934

tag: age

tag: day

tag: viral load

tag: rel. weight


title: Rh-Lung-28_POB [Rh-Lung-462-18]

tag: animal identifier

tag: treatment

value: PO Betamethasone-phosphate 0.15mg/kg q12 x3 q12h

value: UNK


title: ko1


title: Rh-Lung-27_POB [RhLung428-18]

tag: gestational age

tag: body weigth


title: X812364893


title: X711407572


title: Rh-Lung-26_POB [RhLung422-18]

tag: pressure volume curve (pv40) value

tag: batch year


title: X819802467

tag: Sex


title: ct2


title: X810907388

tag: ferret id


title: X816558493

tag: illness severity


title: Rh-Lung-30_POD [Rh-Lung-417-18]

tag: tissue


title: Rh-Lung-25_POB [RhLung420-18]


title: X813836537

value: Severe

tag: infection agent


title: X813943816

value: Mild


title: ct3

tag: strain

tag: developmental stage


title: Rh-Lung-24_POB [Rh-Lung-419-18]

value: F


title: X814467556

tag: age


title: X714835455

tag: day


title: ko2

tag: genotype


title: SVF cells-Foxp4

data_processing:
Illumina Casava1.7 software used for basecalling.
Demultiplexed ChIP-seq reads were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012) with the parameter “--no-discordant --no-unal --no-mixed”
PCR duplicates and low-quality reads were removed by Picard.
Reads were processed using Samtools (Li et al., 2009)and subjected to peak-calling with MACS2 (Zhang et al., 2008) with a parameter “except -f BAMPE -p 0.01”
Bam files were converted to bw file using deeptools (v3.3.0).
Assembly: mm10
Supplementary files format and content: CSV file for peaks

source_name: SVF cells differentiated for 2 days in vitro

growth_protocol: The freshly isolated SVF cells were seeded and cultured in growth medium containing DMEM, 20% FBS, 1% penicillin/streptomycin (P/S) at 37 ℃ with 5% CO2 for 3 days, followed by feeding with fresh medium every 2 days to reach confluence.

extract_protocol:
Lysates were clarified from sonicated nuclei and Foxp4-DNA complexes were isolated with Foxp4 antibody(Millipore, #ABE74).
Libraries were prepared according to the instructions ofVAHTS Universal DNA Library Prep Kit for Illumina V3(Vazyme,ND607).Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Confluent SVF cells  were induced with induction medium contains DMEM, 10% FBS, 5 μg ml−1 insulin, 0.5 mM isobutylmethylxanthine (Sigma), 1 μM dexamethasone (Sigma), 50 nM T3 (Sigma) and 5 μM troglitazone (Sigma) for 48 h.

tag: cell type

value: iWAT derived SVF cells


title: SVF cells-input DNA


title: ct1


title: Rh-Lung-23_POB [RhLung416-18]

tag: animal identifier


title: beige adipocyte-H3K27AC

source_name: beige adipocytes

treatment_protocol: Confluent SVF cells  were induced with induction medium contains DMEM, 10% FBS, 5 μg ml−1 insulin, 0.5 mM isobutylmethylxanthine (Sigma), 1 μM dexamethasone (Sigma), 50 nM T3 (Sigma) and 5 μM troglitazone (Sigma) for 48 h, and further in growth medium supplemented with insulin, T3 and troglitazone for  six days.

value: Beige adipocytes differentiated from iWAT derived SVF cells

tag: agent


title: X712068156

tag: viral load

tag: rel. weight


title: X815367824


title: Rh-Lung-22_POB [Rh-Lung-415-18]

tag: treatment

tag: gestational age

tag: body weigth

tag: pressure volume curve (pv40) value


title: X814773057

tag: Sex

tag: ferret id

tag: illness severity


title: X819434402

tag: infection agent


title: X714451223


title: X811340071


title: Rh-Lung-21_C2x [RhLung412-18]

value: Celestone 0.25mg/kg x2 q24h

tag: batch year

tag: tissue


title: Rh-Lung-20_C2x [RhLung411-18]


title: X816250768

tag: age

value: Adult

tag: day


title: beige adipocyte-input DNA

tag: strain

tag: cell type


title: X816915655

value: Female


title: Rh-Lung-19_C2x [RhLung410-18]

tag: animal identifier


title: X818537863

tag: viral load


title: beige adipocyte-Foxp4

tag: agent


title: X814979993

tag: rel. weight


title: X715474744


title: Rh-Lung-18_C2x [RhLung409-18]

tag: treatment

tag: gestational age


title: YT-1111-09

city: Beijing

first: Minmin

last: Luo

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

description: Microglia in vitro - IL4 20ng/ml primed (bulk RNAseq) rep3

data_processing:
Illumina Casava used for base calling.
For 10x Chromium scRNA-seq, reads were aligned to mm10 reference genome with cellranger (v6.0.1) using "cellranger count" and all groups were aggregated using "cellranger aggr" commands with default parameters.
For Smart-seq2 scRNA-seq, we built a custom mm10 genome where the sequence and annotation of a transgene encoding mScarlet was added; read were aligned to this custom reference genome using STAR (v2.7.8a from snakemake-wrapper) with the following parameters --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNmax 6. umi_tools was used for preprocessing of barcoded reads and counting of umis per gene per cell. featureCounts from the subread package (v1.6.3) was used for gene assignment.
For bulk RNA-seq, reads were aligned to mm10 using Salmon (v1.6.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with raw/estimated counts for every gene in every sample

source_name: Brain

extract_protocol:
For scRNAseq datasets (in vivo), single cell suspension of microglia is obtained by a modified version of mechanical dissociation protocol as described in Bennett et al. Briefly, mice were perfused and brains were harvested and dounced. Microglia were enriched by Percoll density gradient centrifugation. For RNAseq datasets (in vitro), microglia were extracted from neonatal mouse by magnetic activated cell sorting (MACS) with Cd11b-beads and cultured
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For scRNAseq datasets (in vivo), mouse in the MG_S/MG_L/MG_P group was administered with saline/lipopolysaccharide/poly(i:c) i.p. 6 hours before microglia were harvested. Mice from the MG_AAV groups were injected with AAV variant AAV-MG.1.1 or AAV-MG.1.2 via stereotaxic surgery 2 weeks before microglia were harvested. For RNAseq datasets (in vitro), primary microglia were harvested from prenatal mice and cultured in TIC medium (Bohlen et al., 2017). treatment protocols were applied non-treated (homeostatic state), or treated with 200ng/ml LPS (reactive state), 20ng/ml IL4 (alternatively activation state), and AAV-MG.WPP.

value: Brain

value: cultured microglia


title: YT-1111-12

description: Microglia in vitro - LPS 200ng/ml primed (bulk RNAseq)


title: X813966637

value: Uninfected


title: X812715456


title: X817133065

value: Moderate


title: X810037336


title: Rh-Lung-17_C2x [Rh-Lung-413-18]

value: M

tag: body weigth

tag: pressure volume curve (pv40) value


title: Rh-Lung-16_C2x [Rh-Lung-408-18]

tag: Sex

value: Lungs


title: YT-1111-08

description: Microglia in vitro - IL4 20ng/ml primed (bulk RNAseq) rep2


title: X812976583

tag: ferret id

tag: illness severity


title: YT-1111-07

description: Microglia in vitro - IL4 20ng/ml primed (bulk RNAseq) rep1


title: X810694528

tag: infection agent


title: Rh-Lung-15_C1x [Rh24517Lung]

value: IM Celestone 0.25mg/k, 5d

tag: batch year

tag: tissue


title: X811159907

tag: age

tag: day


title: Rh-Lung-14_C1x [Rh23817Lung]


title: Rh-Lung-9_B125 [Rh23517Lung]

value: IM Beta-Ac 0.125 mg/k, 5d


title: X819548600


title: YT-1111-05

description: Microglia in vitro - LPS 200ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep2

tag: strain

tag: cell type


title: Rh-Lung-5_B060 [Rh23117Lung]

tag: animal identifier

value: IM Beta-Ac 0.06 mg/k, 5d


title: Rh-Lung-10_B125 [Rh23717Lung]


title: YT-1111-04

description: Microglia in vitro - LPS 200ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep1


title: X817354430

tag: viral load


title: X710912690

tag: rel. weight


title: YT-1111-03

description: Microglia in vitro - IL4 20ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep3


title: X818828878


title: Rh-Lung-4_B060 [RhLung_230-17]

tag: treatment


title: X818211697


title: YT-1111-06

description: Microglia in vitro - LPS 200ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep3


title: X711855826


title: Rh-Lung-3_B060 [Rh20717Lung]

tag: gestational age


title: X815439094


title: YT-1111-01

description: Microglia in vitro - IL4 20ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep1


title: X812044723


title: X810117899


title: YT-1111-02

description: Microglia in vitro - IL4 20ng/ml primed + cap18 mScarlet moi=50,000 (bulk RNAseq) rep2


title: yt0616_17

description: Microglia in vitro - AAV transduction cap18 mScarlet moi=50,000 (bulk RNAseq) rep2


title: X811240889


title: X711401590


title: yt0616_18

description: Microglia in vitro - AAV transduction cap18 mScarlet moi=50,000 (bulk RNAseq) rep3


title: X814036735


title: Rh-Lung-2_B060 [RhLung_210-17]

tag: body weigth


title: X815873604


title: Rh-Lung-1_B060 [RhLung-213-17]

tag: pressure volume curve (pv40) value


title: X719715015

tag: Sex


title: X813424683

tag: ferret id


title: X715251858

tag: illness severity


title: yt0616_16

description: Microglia in vitro - AAV transduction cap18 mScarlet moi=50,000 (bulk RNAseq) rep1


title: X812869806

tag: infection agent


title: X719065003


title: X715580993


title: yt0616_9

description: Microglia in vitro - IL4 20ng/ml (bulk RNAseq) rep3


title: aCO2_1930_rep2

city: Sendai

first: Yonghyun

last: Kim

state: Miyagi

address: Aramaki, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

data_processing:
After sequencing, the raw sequence reads are filtered based on quality.
The adapter sequences are also trimmed off the raw sequence reads.
The trimmed reads are gathered forming a unique cluster.
Unique clustered reads are sequentially aligned to reference genome, miRBase v21 and non-coding RNA database, Rfam9.1 to classify known miRNAs and other type of RNA such as tRNA, snRNA, snoRNA etc.
the reads for each miRNA are normalized by the total reads of each individual sample as the standardized to reads per million.
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Rice

growth_protocol: Rice plants were grown at high nitrogen (0.5g N/plant) and ambient CO2 condition (320-360 ppm) in two identical growth chambers up to eCO2 treatment (28/23°C, 14/10h, day/night, 60% humidity, light intensity: about 900 PPFD)

extract_protocol:
Total RNA was isolated from the leaf samples using Plant RNeasy mini kit (QIAGEN, Hilden, Germany) as described in the manufacturer’s instruction with modification for small RNA isolation (Miller et al., 2013, Methods). Total RNA was quantified using a NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA). The total RNA integrity was analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Small RNA libraries were prepared for sequencing using TruSeq small RNA Library Prep Guide.

treatment_protocol: eCO2 (1000 ppm) begun at 6:00 am (beginning daytime) when plant age of leaf number was 7.1-7.3. Lower part of 7th leaf sheath including 9th immature leaf was fixed in EtOH:HOAc (3:1) 7 h and 13.5 h after elevated CO2 treatment. 9th leaf was isolated the fixed 7th leaf sheath for total RNA isolation.

value: Leaf blade

tag: cultivar

value: Nipponbare

tag: condition

value: ambient CO2

tag: time


title: X613994300

tag: age

tag: day


title: eCO2_1930_rep1

tag: tissue

value: elevated CO2


title: eCO2_1930_rep2


title: aCO2_1930_rep1


title: X619124270


title: yt0616_7

description: Microglia in vitro - IL4 20ng/ml (bulk RNAseq) rep1

tag: strain

tag: cell type


title: X719514677

tag: viral load

tag: rel. weight


title: X818146119


title: yt0616_8

description: Microglia in vitro - IL4 20ng/ml (bulk RNAseq) rep2


title: yt0616_6

description: Microglia in vitro - LPS 200ng/ml (bulk RNAseq) rep3


title: eCO2_1300_rep2

value: 7 hr


title: X614186888


title: eCO2_1300_rep1


title: X615959225


title: X514069465


title: yt0616_5

description: Microglia in vitro - LPS 200ng/ml (bulk RNAseq) rep2


title: X519259756


title: yt0616_4

description: Microglia in vitro - LPS 200ng/ml (bulk RNAseq) rep1


title: aCO2_1300_rep2


title: yt0616_3

description: Microglia in vitro - blank ctrl (bulk RNAseq) rep3


title: X518601389


title: X515227389


title: aCO2_1300_rep1


title: X516076286


title: X516297813


title: X612999343


title: yt0616_2

description: Microglia in vitro - blank ctrl (bulk RNAseq) rep2


title: X512432078


title: X514905365


title: X516575947


title: yt0616_1

description: Microglia in vitro - blank ctrl (bulk RNAseq) rep1


title: X517682181


title: CC_Setd2het_ATACseq_repl3

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Sequencing and base calling was performed by GeneWiz (https://www.genewiz.com/)
Raw reads were subjected to adapter trimming using NGmerge with option “-a”.  Trimmed reads were aligned to mm10 reference genome using bowtie2 with options “-X2000 –local”. Alignments were filtered using samtools v1.8 to retain only uniquely mapping read pairs and to discard mitochondrial mapping reads. Read duplicates were detected and removed using the MarkDuplicates program in Picard Tools 2.18.11.
ATAC-seq peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited

source_name: Germinal center centrocytes

extract_protocol: ATACseq was performed following the Omni-ATAC protocol as described in manuscript. Library was prepared as described in manuscript.

value: Germinal center centrocytes

tag: genotype

value: CD19-cre Setd2WT/-

tag: isolation strategy


title: X518278892

value: Female

value: Adult


title: CC_Setd2het_ATACseq_repl2


title: CC_Setd2het_ATACseq_repl1


title: X512428263


title: X517047725


title: Sample_22_CC_Setd2het_RNAseq_repl3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNAseq reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Cut&Run reads were aligned using BWA-MEM and peaks were called using SICER2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited TPM or SICER2 peak

growth_protocol: not applicable

extract_protocol:
Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).
CUT&RUN was performed following CUTANA protocol v1.5.2 (Epicypher).  Enriched DNA was purified using Monarch DNA cleanup kit (NEB; T1030S).

tag: tissue/cell type


title: Sample_23_CC_Setd2het_RNAseq_repl4


title: CC_cre_ATACseq_repl3


title: X510357203

tag: Sex


title: X517913927

tag: ferret id


title: Sample_20_CC_Setd2het_RNAseq_repl1


title: X511359086

tag: illness severity


title: Sample_21_CC_Setd2het_RNAseq_repl2


title: CC_cre_ATACseq_repl2


title: X416676021

tag: infection agent


title: Sample_19_CB_Setd2het_RNAseq_repl4

value: Germinal center centroblasts


title: X418687465


title: X415917679

value: Uninfected


title: CC_cre_ATACseq_repl1


title: Sample_18_CB_Setd2het_RNAseq_repl3


title: CB_Setd2het_ATACseq_repl3

source_name: Germinal center centroblasts


title: X410384235


title: X416004464


title: CB_Setd2het_ATACseq_repl1


title: X411099113


title: X412229433


title: X315356295


title: Sample_17_CB_Setd2het_RNAseq_repl2


title: X313553109


title: X316986775


title: Sample_16_CB_Setd2het_RNAseq_repl1


title: X318975971


title: Sample_15_NB_Setd2het_RNAseq_repl3

value: Naive B cells


title: X210827733


title: CB_cre_ATACseq_repl3


title: CB_cre_ATACseq_repl2


title: CB_cre_ATACseq_repl1


title: X217055661


title: Sample_31_GCB_Setd2het_CutAndRun_H3K36me3_repl4

data_processing:
library strategy: CUT&RUN
Illumina Casava1.8.2 software used for basecalling.
RNAseq reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Cut&Run reads were aligned using BWA-MEM and peaks were called using SICER2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited TPM or SICER2 peak

value: Germinal center B cells

value: PNA


title: Sample_13_NB_Setd2het_RNAseq_repl1


title: X218439682


title: X212112621


title: X213011252


title: CB_Setd2het_ATACseq_repl2


title: Sample_12_CC_cre_RNAseq_repl4


title: X217445575


title: Sample_11_CC_cre_RNAseq_repl3


title: X214546104


title: Sample_29_GCB_Setd2het_CutAndRun_H3K36me3_repl2


title: X210519198


title: X219848274


title: Sample_10_CC_cre_RNAseq_repl2


title: X211964298


title: Sample_9_CC_cre_RNAseq_repl1


title: Sample_14_NB_Setd2het_RNAseq_repl2


title: X213494946


title: X415995462


title: Sample_27_GCB_cre_CutAndRun_H3K36me3_repl4


title: Sample_8_CB_cre_RNAseq_repl4


title: Sample_26_GCB_cre_CutAndRun_H3K36me3_repl3


title: X615508695


title: X616434678


title: Sample_7_CB_cre_RNAseq_repl3


title: Sample_25_GCB_cre_CutAndRun_H3K36me3_repl2


title: X619090480


title: Sample_30_GCB_Setd2het_CutAndRun_H3K36me3_repl3


title: X618383248


title: Sample_6_CB_cre_RNAseq_repl2


title: X613284312


title: Sample_5_CB_cre_RNAseq_repl1


title: Sample_24_GCB_cre_CutAndRun_H3K36me3_repl1


title: X218972810


title: Sample_28_GCB_Setd2het_CutAndRun_H3K36me3_repl1


title: Sample_4_NB_cre_RNAseq_repl4


title: X616068525


title: X612483341


title: Sample_3_NB_cre_RNAseq_repl3


title: 14Rik #3 gDNA

city: Boston

first: Hanneke

last: Vlaming

address: 45 Shattuck St

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: 14Rik #3 gDNA

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

source_name: Mouse embryonic stem cells

growth_protocol: mESCs were cultured in KO-DMEM media (Gibco) supplemented with 15% KO Serum replacement (Gibco), GlutaMAX, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, 1000 U/ml LIF (Cell Guidance Systems), 1µM MEK inhibitor (PD0325901; Stemgent), and 3µM GSK3 inhibitor (CHIR99021; Stemgent). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
In a first round of PCR, the 14Rik lincRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

tag: cell line

value: F121-9 wt mESCs

tag: library integration location

value: 4930461G14Rik TSS + 102 (CAST allele)

tag: assay

value: RNA-based INSERT-seq

value: Untreated


title: X616911017

tag: age


title: 14Rik #2 gDNA

description: 14Rik #2 gDNA

tag: condition


title: X611843253

tag: day


title: Sample_2_NB_cre_RNAseq_repl2


title: X614053499


title: X614215843


title: 14Rik #2 total-RNA

description: 14Rik #2 total-RNA

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences plus spliced versions of these inserts as called by STAR. STAR v2.7.0 was run on replicates 2-4 using flags --outSJfilterOverhangMin 10 4 4 4 --peOverlapNbasesMin 10 --peOverlapMMp 0.08 --alignEndsType EndToEnd --outFilterMismatchNmax 5 --scoreDelOpen -10 --scoreInsOpen -10. The detected splice junctions were filtered down to only junctions on the + strand with >10 read counts and >25% of the maximum counts for other junctions detected in the same insert. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
For total-RNA, >5M library-containing cells was pelleted and resuspended in Trizol (Ambion). RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer that annealed 287nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: X611902721


title: 14Rik #3 total-RNA

description: 14Rik #3 total-RNA


title: FMB_3030_D5

value: Male

tag: ferretid

tag: infectionagent

tag: viralload

tag: relweight

tag: tissue

value: whole blood


title: Sample_1_NB_cre_RNAseq_repl1

tag: genotype

tag: isolation strategy


title: X617337041

tag: Sex

tag: viral load

tag: rel. weight


title: X619260119

tag: ferret id

tag: infection agent


title: FMB_3028_D2