title: BT3_ALBI_At_V

source_name: Anopheles albimanus Virgin Atria rep B 24 hr

value: Atria


title: DT3_ALBI_At_V

status: Public on Apr 20 2022

type: SRA

city: Boston

first: Flaminia

last: Catteruccia

state: MA

address: 655 huntington ave

country: USA

institute: Harvard University

library_source: transcriptomic

data_processing:
Alignment: hisat2/2.0.5. Parameters: -q -x --threads 4
Mapping quality filter: samtools/1.3.1. Parameters: view -bS -q 30
Sort mapped reads: samtools/1.3.1. Parameter: sort
Read count: htseq/0.9.1. Parameters: --stranded=no  --mode=union --quiet  -a 30
Assembly: Anopheles gambiae PEST AgamP4.12; Anopheles albimanus STECLA AalbS2.4
Supplementary files format and content: Processed data files format: Plain text file.  Content: Read counts

molecule: polyA RNA

organism: Anopheles albimanus

source_name: Anopheles albimanus Virgin Atria rep D 24 hr

extract_protocol:
Total RNA was extracted with TRI reagent (Thermo Fisher Scientific, MA) from pools of 10–12  tissues following the manufacturer’s instructions. RNA was treated with TURBO DNase (Thermo Fisher Scientific, MA), and purified with Qiagen RNeasy MinElute Cleanup Kit.
Illumina TruSeq Stranded mRNA kit

tag: tissue

tag: Sex

value: Female

tag: mating status

value: Virgin

tag: replicate

value: D

tag: time point

value: 24 hr post-mating or time-matching virgins


title: DT3_ALBI_At_M

source_name: Anopheles albimanus Mated Atria rep D 24 hr

value: Mated


title: BT3_ALBI_RB_M

source_name: Anopheles albimanus Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 24 hr

value: B


title: BT3_ALBI_At_M

source_name: Anopheles albimanus Mated Atria rep B 24 hr


title: WT + Acanthamoeba Rep 2

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

data_processing:
reads were aligned to the Acanthamoeba reference genome (Acanthamoeba castellanii strain NEFF GCA_000313135.1) using HiSat2
unused reads were then aligned to the bacterial reference genome (Pseudomonas fluorescens SBW25 GCA_000009225.1) using Bowtie2
Sequence reads were assigned to genomic features using featureCounts
Differential expression using GLM and count normalisation was calculated with edgeR, Counts were normalised by library size (counts per million, CPM) with log2 transformation.
Assembly: GCA_000313135.1, GCA_000009225.1
Supplementary files format and content: tab-delimited text files include CPM values per sample

molecule: total RNA

organism:
Pseudomonas fluorescens
Acanthamoeba sp.

source_name: Bacteria and Acanthamoeba

growth_protocol: Individual colonies of bacterial strains pre-cultured on LB agar were homogenised in LB broth and spread in single lines across PM agar plates using a 1ul transfer loop. Plates were allowed to dry before applying 2 ul of suspension containing ~103 Acanthamoeba cysts µl-1 at one end of the bacterial line. Plates were incubated at 28˚C for up to 1 week and the interaction zone was collected once the amoeba had formed a visible clearing. Pseudomonas fluorescens SBW25 strains were collected with Acanthamoeba from the bacteria-protozoa interaction zone and alone from the opposite end of the culture line with a transfer loop and immediately homogenised in RNA shield (n=4

extract_protocol:
Total RNA was extracted from bacterial and amoebae cells using the Quick-RNA MiniPrep Kit (Zymo Research, USA)
Preparations were dried in GenTegra RNA tubes according to manufacturer’s instructions (Gentegra, USA) and sent to the Microbial Genome Sequencing (MiGS, USA) Center for Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion and sequencing on the NextSeq 550 platform.

tag: strain

value: SBW25 + Acanthamoeba Sp


title: Wrinkly Fried Egg + Acanthamoeba Rep 4

value: SBW25 WFE + Acanthamoeba Sp


title: WT + Acanthamoeba Rep 3


title: WT + Acanthamoeba Rep 1


title: Wrinkly Speader1 + Acanthamoeba Rep 1

value: SBW25 WS1 + Acanthamoeba Sp


title: Root, PEG treatment for 120h rep2

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The consensus isoform obtained after ICE de-redundancy obtained by PacBio SMRT-seq was used as the reference sequence, and the Illumina RNA-seq data was compared with the reference sequence using RSEM (1.2.31) software.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Supplementary_files_format_and_content: fpkm

organism: Populus ussuriensis

source_name: Root

growth_protocol: Approximately 3 cm stem segments were excised from 4-week-old in vitro plants and cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
RNA was isolated using Trizol reagent
A total of 2 μg RNA per sample was used to generate sequencing libraries using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA). Libraries were sequenced in 150 bp paired-end mode, using an Illumina HiSeq X Ten platform.

treatment_protocol: For the PEG-induced drought stress treatment was performed in liquid media. Three-week-old P. ussuriensis seedlings with uniform root growth were then further transferred to liquid media containing 6% PEG 6000 (Sigma-Aldrich, St. Louis, MO, USA). After treatment at 0 h, 6 h, 12 h, 24 h, 48 h and 120 h, we harvested the roots at same time, and frozen in liquid nitrogen.

value: Root

tag: age

value: Three-week-old

value: Wild type

tag: agent

value: 6percent PEG


title: Root, PEG treatment for 48h rep2


title: Root, PEG treatment for 120h rep1


title: Wrinkly Fried Egg + Acanthamoeba Rep 1


title: Root, PEG treatment for 48h rep1


title: Root, PEG treatment for 24h rep2


title: Root, PEG treatment for 24h rep1


title: Wrinkly Speader1 + Acanthamoeba Rep 4


title: WT + Acanthamoeba Rep 4


title: Wrinkly Speader1 + Acanthamoeba Rep 2


title: Wrinkly Speader1 + Acanthamoeba Rep 3


title: Wrinkly Fried Egg + Acanthamoeba Rep 2


title: Root, PEG treatment for 6h rep3


title: Wrinkly Fried Egg + Acanthamoeba Rep 3


title: Root, PEG treatment for 24h rep3


title: Root, PEG treatment for 0h rep1


title: Sample_AE_F_1

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Odorrana tormota

source_name: brain

growth_protocol: 12 Samples of O. tormota were collected from the Huangshan mountain, Anhui province, China in April 2016.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA)

treatment_protocol: A total of adult individuals (eight males and four females) were collected and they were divided into two male (named M1 and M2) and two female (named F1 and F2) groups，brains were removed, stored at -80℃.

value: brain tissue

value: adult


title: Sample_AE_F_2


title: Root, PEG treatment for 12h rep3


title: Root, PEG treatment for 120h rep3


title: Root, PEG treatment for 48h rep3


title: Bovine mammary epithelial cells transfected with miR-29c inhibitor rep2

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

data_processing:
Illumina Novaseq 6000 used for basecalling.
After high-throughput sequencing, Raw data was stored in FASTQ file format. Clean reads were obtained after the quality control of Raw reads by perl, such as removal of linker sequence, filtering out low quality reads and filtering out reads with N ratio greater than 5%.
Clean reads were then compared to Mapped reads in the Bos taurus reference genome UMD3.1 (http://www.ensembl.org/Bos_taurus/Info/Index) using HiSAT2 software (http://daehwankimlab.github.io/hisat2/).
Differential expression analyses between 2 groups were conducted using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html). The DEGs were identified using P < 0.05 & | log2fold change | > 1 as standard.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Matrix table with information of gene and gene count for each sample.

organism: Bos taurus

source_name: Bovine mammary epithelial cells

growth_protocol: Bovine mammary epithelial cells (bMEC) previously frozen from our laboratory were cultured by DME/F12 in a 5% CO2 incubator when bovine mammary epithelial cell monolayers reached 60%~70% confluence, three wells were transfected with NC inhibitor (100 nM), and the remaining three wells were transfected with miR-29c inhibitor (100 nM), which were used as the negative control group and the experimental group, respectively.

extract_protocol:
Total RNA was extracted from bovine mammary epithelial cells transfected with NC inhibitor (100 nM) or miR-29c inhibitor (100 nM). using TRizol reagent (Takara Biomedical Technology Co., Ltd, Beijing, China) according to the manufacturer’s instructions.
RNA-seq library construction was used by ABclonal mRNA-seq Lib Prep Kit (ABclonal, Wuhan, Hubei, China), and the library were detected to ensure the quality of the library.

treatment_protocol: Bovine mammary epithelial cells were transfected with NC inhibitor (100 nM) or miR-29c inhibitor (100 nM). All treatment groups had three biological replicates. Continue culture for 48h and collecting cell, and stored at -80 °C for further analysis.

tag: cell type

value: Bovine mammary epithelial cells

tag: treatment

value: miR-29c inhibitor


title: Bovine mammary epithelial cells transfected with miR-29c inhibitor rep3


title: Bovine mammary epithelial cells transfected with NC inhibitor rep1

value: NC inhibitor


title: Root, PEG treatment for 12h rep2


title: GABA3

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: UT

institute: University of Utah

library_source: genomic

data_processing:
bcl2Fastq (v1.8.4)
Fastq reads aligned to BDGP 6 + ISO1 MT with Bowtie2 software
Aligned reads were filtered with Samtools to retain Chr2, 3, and X
Deduplication with Picard
Peak Calling with Macs2
Differential expression analysis with DESeq2
Peak annotation with ChipSeeker
Genome_build: BDGP release 6 + ISO1 MT
Supplementary_files_format_and_content: BigWig
Supplementary_files_format_and_content: peak
Supplementary_files_format_and_content: differential.csv

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: GABAergic nuclei from adult flies

growth_protocol: Flies were grown on standard cornmeal agar at 25 degrees C.

extract_protocol:
Adult flies expressing neuron-specific GFP were frozen at -80 degrees C for 5 min and the heads were removed by shaking. The heads were homogenized with a Dounce homogenizer, filtered through a 40 micron cell strainer, and washed several times. GFP-labeled nuclei were collected by flow cytometery.
Isolated nuclei were treated with Nextera Tn5 enzyme for 23 min at 37 degrees Celsius. The tagmented DNA was purified, amplified by PCR, and purified again using AMPure XP magnetic beads.

value: GABAergic nuclei


title: DT3_ALBI_H_V

source_name: Anopheles albimanus Virgin Head rep D 24 hr

value: Head

value: Female

value: Virgin

value: D


title: Bovine mammary epithelial cells transfected with NC inhibitor rep2


title: GABA2


title: Root, PEG treatment for 6h rep2


title: Root, PEG treatment for 6h rep1


title: Root, PEG treatment for 0h rep3


title: GABA1


title: TH1

source_name: Dopaminergic nuclei from adult flies

value: Dopaminergic nuclei


title: Root, PEG treatment for 12h rep1


title: PV8

city: Shanghai

first: Ning

last: Yu

state: Shanghai

address: Baode Road 1278

institute: Shanghai Skin Disease Hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
The read counts of each gene were obtained by htseq-count.
Supplementary files format and content: tab-delimited text files include gene read count for Samples in processed_data.txt

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Blood

tag: disease status

value: Psoriasis vulgaris (PV)

value: Peripheral blood mononuclear cell (PBMC)


title: Sample_AE_M_2

value: Male


title: Sample_AE_M_1


title: Root, PEG treatment for 0h rep2

value: Root

value: Three-week-old

value: Wild type


title: Bovine mammary epithelial cells transfected with miR-29c inhibitor rep1


title: PV4


title: PV3


title: TH2


title: Bovine mammary epithelial cells transfected with NC inhibitor rep3


title: PV7


title: PV6


title: NN7

value: Healthy donor


title: NN4


title: NN1


title: NN3


title: NN6


title: PV5


title: PV1


title: NN5


title: GPP3

value: Generalized pustular psoriasis (GPP)


title: GPP8


title: NN2


title: GPP1


title: GPP5


title: GPP7


title: irCLIP-Seq data for IgG in hela cells

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
After obtaining the irCLIP-Seq raw datasets, we firstly used fastx_collapser to remove PCR duplicates with default parameters. Then clipped 5′ barcodes and 3′ adaptors using fastx_clipper, only the clipped reads which length larger than 15bp will be retained for further analysis. We have implemented STAR alignment algorithm to map reads to the genome (genome version hg38) with the parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNoverLmax 0.08 and --outFilterMultimapNmax 8. In addition, we only considered unique mapped reads, and used the parameter −q 30 in samtools to filter reads.
Then obtained the RT stop location of each read, and annotated the RT stop to transcripts. Transcripts’ annotation file was obtained from Gencode (Version 25). Then we obtained the significantly crossing-linking sites in Lnc2457 regions following the steps :(1) irCLIP RT-stops within Lnc2457 were extended ±25 nt surrounding regions.(2)The height of each nucleotide position is the number of reads that overlap that position.(3) We computed the background frequency after randomly placing the same number of extended reads within Lnc2457 for 100 iterations.(4)Then calculated the FDR for each height as the method described in (Gene W Yeo Nat Struct Mol Biol. 2009 February ). (5) Only the loci with height which FDR<0.05 will be assigned as significantly crossing-link sites.
Finally combined the two replicate irCLIP-Seq significantly crossing-link regions together, the 127-177nt part of Lnc2457 was defined as the CENPC bound regions.
Genome_build: hg38

source_name: Hela cell

growth_protocol: Hela Cells were grown in DMEM supplemented with 10% FBS

extract_protocol: irCLIP-seq was performed as previously described. Briefly, the 2× 108 isolated B cells were irradiated at 400 mJ/cm2 with 254 nm UV light. The cross-linked cells were lysed and 15 μg of anti-CENP-C antibody was applied to pull down specific protein-RNA complexes. After micrococcal nuclease treatment, 3′ RNA linker ligation and 5′ end 32P labeling, the immunoprecipitated complexes were fractionated on a 4–12% NuPAGE Bis-Tris gel and transferred to a nitrocellulose membrane. The autoradiographed CENP-C-specific smear bands were cut and treated with proteinase K (Takara, Catalog # 9034) prior to the extraction of respective RNA by phenol and chloroform. Strictly follow protocols from NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: Cells were UV-C crosslinked to fix in vivo RNA-protein interactions

tag: cell line

value: HeLa

tag: antibody

value: normal rabbit IgG (sc-2027, Santa Cruz)

tag: protocol

value: irCLIP-Seq


title: Input ChIRP-Seq control in hela cells

data_processing:
Library strategy: CHIRP-seq
Two Lnc-CCTT ChIRP-Seq libraries were combined before processing. Combined ChIRP-Seq and input datasets followed by adapter trimming and filtering low-quality reads with Trimmomatic using the parameters MINLEN: 80, ILLUMINACLIP: 2:30:10 and SLIDINGWINDOW: 4:20.
BamCoverage in deeptools was used to obtain the bigwig files using parameters --normalizeUsingRPKM --binSize 10 --ignoreDuplicates.
Enrichment peaks for ChIRP-Seq data were determined using SICER software using the input experiment as background. The parameters were referring to the previously processing for human CENP-A ChIP-Seq datasets. Only the high-quality peaks (raw reads count number > 20 and fold change > 2) were retained for the further analysis. Peaks were determined as centromeric peaks if they overlapped sites (BEDTools: intersect) in the genome previously annotated as centromere regions. In order to obtain the peaks enriched motifs, MEME suite was used to discover the motifs only using the peaks which fold change are larger than 5.
Genome_build: hg38

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS

extract_protocol: Each sample of beads were resuspended in 150 μL of DNA Elution Buffer (50 mM NaHCO3, 1% SDS) with RNases (1 0μL RNase A (10 mg/mL) and 10 μL RNase H (10 U/μl) per ml of DNA Elution Buffer) and DNA INPUT was resuspended in 140 μL. Samples were Incubated at 37 °C for 30min with shaking. Beads and supernatant were separated on DynaMag-2 magnetic strip. Repeat the previous step. All supernatant (should be ~300 μL) was collected and added 15 μL PK. Samples were incubated at 50 °C for 45 min with shaking. DNA samples were transfered to phase-lock gel tubes and followed protocols from Qiagen. Strictly follow protocols from NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.

treatment_protocol: We modified previously reported ChIRP-seq (chromatin isolation by RNA purification)  with a crosslinker 4’-aminomethyltrioxalen (AMT, a psoralen derivative), which allows fixation of nucleic acid interaction by ultraviolet light without crosslinking proteins. Briefly, antisense DNA probes against CCTT lncRNA were designed by ChIRP Probe Designer. The 3 ′-end Biotin-TEG-modified probes were synthesized by Invitrogen (Thermo, China). Hela cells were incubated with 0.5mg/ml AMT solution for 10 min and chilled on ice. The cells were placed on ice and irradiated the cells in a tissue culture dish for 10 min from a distance of 2.5cm with 365nm ultraviolet light. The cross-linked cells were lysed with lysis buffer (50 mM Tris-Cl, pH 7.5, 10 mM EDTA, 1% SDS, protease inhibitors, and SUPERase-In). The lysates were sonicated by Bioruptor (Diagenode, Denville, NJ) at 4 °C at high setting with 30 s on and 45 s off pulse intervals for a total of 15 min. The sonicated cell lysates were hybridized with the mixture of biotinylated DNA probes against human CCTT in hybridization buffer (50 mM Tris-Cl, pH 7.5, 750 mM NaCl, 1% SDS, 1 mM EDTA, 15% formamide, protease inhibitors and SUPERase-In) for 4hr at 37 °C. Then the binding complexes were recovered by streptavidin-conjugated magnet beads C1 (Invitrogen), and DNA was eluted with elution buffer (50 mM NaHCO3, 1% SDS).


title: GPP2


title: SHAPE-Map data denaturing control in in-cell condition

data_processing:
Library strategy: SHAPE-Map
ShapeMapper was used to processing the in-cell and cell-free SHAPE-MaP datasets separately. Only nucleotides with unique mapped read-depth larger than 10 were retained for modification detection. The distribution of mutation rates in the SHAPE-modified sample should be distinctly higher than that in the denaturing control and the no-reagent control sample.
After obtaining the SHAPE reactivities information, DeltaShAPE were used to obtain the significantly protein bound regions by comparing the difference between in-cell condition and cell-free condition. First, the absolute change in SHAPE reactivity is calculated at each nucleotide along the transcript of interest. Then the raw absolute difference was are smoothed by calculating the 50-nt sliding median. The regions were predicted as the significantly protein bound regions, which meet the following three criteria: (i) the Z-factor for a nucleotide is greater than zero, indicating that the 95% confidence intervals of measurements in the two conditions do not overlap, (ii) the standard score is greater than one standard deviation from the mean ΔSHAPE, and (iii) three of five nucleotides in a sliding window meet both Z-factor and standard score criteria.
Finally, based on the SHAPE-Map reactivity data, we predicted the RNA secondary structure through RNAstructure web server with default parameters.
Genome_build: hg38

growth_protocol: Hela cells were grown in DMEM supplemented with 10% FBS

extract_protocol: From each sample of RNA from Hela in-cell and cell-free probing experiments, 1-3 µg were subjected to mutational profiling (MaP) reverse transcription using a primer specific to CCTT. The cDNA generated was buffer exchanged over Illustra microspin G-50 columns (GE Healthcare). Output cDNA (5 µL) was used as a template for 50 µL PCR reactions (Q5 Hot-start polymerase, NEB) with primers made to amplify CCTT and add adapter sequences [1x Q5 reaction buffer, 250 nM each primer, 200 µM dNTPs, 3% DMSO, 0.02 Units/µL Q5 Hot-start polymerase]. PCR proceeded in a touchdown format and high-throughput sequencing library construction.

treatment_protocol: Hela cells were grown, and RNA was extracted and modified, both in cell and ex vivo, as described previously. In brief, In-cell modification was carried out by treating hela cells in fresh growth medium with 1M7 (10 mM final) and incubating at 37 °C for 5 min before RNA isolation. For ex vivo analyses, total cellular RNA was gently extracted from cells into RNA folding buffer (100 mM Hepes, pH 8.0, 100 mM NaCl, and 10 mM MgCl2), incubated at 37 °C for 20 min, and subjected to SHAPE modification with 1M7. RNA was subjected to MaP reverse transcription using CCTT-specific primers, followed by CCTT-specific PCR amplification.


title: SHAPE-Map data minus reagents in in-cell condition


title: ChIRP-Seq data for Lnc-CCTT in hela cells replicate2

description: Processed data files include data for rep1 and rep2 and are available on GSM4504493.


title: PV2


title: ChIRP-Seq data for Lnc-CCTT in hela cells replicate1

description: Processed data files include data for rep1 and rep2.


title: GPP6


title: NN8


title: irCLIP-Seq data for CENPC in hela cells replicate1

value: Rabbit monoclonal [EPR15939] to CENPC (ab193666, Abcam)


title: SHAPE-Map data minus reagents in cell-free condition


title: SHAPE-Map data plus reagents in in-cell condition


title: RIP-Seq using anti-CENPC antibody replicate1

data_processing:
After obtain RIP-Seq data, First, we used Trimmomatic to perform a sliding window trimming, cut once the average quality within the 4bp window falls below 20 and the trimmed read will be dropped if its length below 80. SortMeRNA(Kopylova et al., 2012) were used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version hg38) using STAR(Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtained the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES=true. We calculated the gene’s  reads counts using FeatureCounts(Liao et al., 2014) and converted the reads counts to RPKM using edgeR(Robinson et al., 2010) package in R language. Limma were used to obtain the differerntial expressed genes between CENPC and IGG RIP-Seq datasets. Only genes which FoldChange larger than 2 and P-Value below 0.01 were retained for further analysis.
The wig files of each RIP-Seq data set from sense strand and antisense strand were obtained through bamCoverage from DeepTools with the parameter --binSize 20, --smoothLength 100, --ignoreDuplicates and --normalizeUsingRPKM.
Genome_build: hg38

extract_protocol: Each RNA sample was treated with DNase I (Ambion, DNA-free TM kit). Strictly follow protocols from NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: RIP was carried out as previously described (Yin et al., 2012) with modifications. 1-1.2 ×107 cells were harvested, resuspended in lysis buffer (50mM Tris pH7.4, 150mM NaCl, 0.05% Igepal, 1mM PMSF, and 2mM VRC, with Protease Inhibitor Cocktail, Roche) and then subjected to two rounds of sonication. After incubation with anti-CENP-C (2μg, Abcam) or anti-IgG (Santa Cruz), the beads were washed once in lysis buffer and four times in washing buffer (50 mM Tris pH7.4, 150 mM NaCl, 1 mM MgCl2, 0.05% NP-40), followed by elution with extraction buffer C (100 mM Tris pH6.8, 4% SDS, 12% β-mercaptoethanol, 20% glycerol) at room temperature for 10 min. One-third of the RIP materials was used for immunoblotting and the other two-thirds was used for RNA extraction.


title: RIP-Seq using anti-CENPC antibody replicate2


title: RIP-Seq using anti-IgG antibody replicate2


title: STRS_2D

city: New York

first: David

middle: William

last: McKellar

state: NY

address: 101 6th Ave

institute: New York Genome Center

description: Two tibialis anterior sections (notexin-7dpi and notexin-5dpi) processed with in situ polyadenylation and Visium (spTotal, w/ SUPERase In Rnase Inhibitor)

data_processing:
3' polyA trimming with cutadapt v3.4
3' polyG trimming and 5' TSO trimming (CCCATGTACTCTGCGTTGATACCACTGCTT) with cutadapt v3.4
Alignment and quantitation with STAR v2.7.10a; used GRCm39 reference with GENCODE M28 annotations or the same reference appended with the Reovirus Type 1-Lang sequence/annotations
Pseudoalignment with  kallisto v0.48.0 and quantitation with bustools v0.41.0; used GRCm39 reference with GENCODE M28 annotations or the same reference appended with the Reovirus Type 1-Lang sequence/annotations
Assembly: GRCm39 (GENCODE M28 annotaitons)
Supplementary files format and content: Count matrices were uploaded in matrix market (.mtx) with the spot barcodes and feature names in separate tab-delimited .txt files (count matrices from the Reovirus-appended reference have "REO" in the filename)
Supplementary files format and content: Stitched and shading-corrected H&E images are uploaded as .tif files
Supplementary files format and content: Tissue section coordinates are uploaded as .json files, manually selected using the Loupe Browser software from 10x Genomics

organism: Mus musculus

source_name: muscle

extract_protocol:
In situ polyadenylation (yeast poly(A) polymerase) followed by Visium Spatial Gene Expression v1
Spatial Total RNA-sequencing

value: muscle

value: female

tag: genotype

value: Notexin (5dpi & 7dpi)

tag: injury


title: SHAPE-Map data plus reagents in cell-free condition


title: SHAPE-Map data denaturing control in cell-free condition


title: GPP4


title: RIP-Seq using anti-IgG antibody replicate1


title: irCLIP-Seq data for CENPC in hela cells replicate2


title: STRS_2A

description: Two tibialis anterior sections (uninjured and notexin-5dpi) processed with in situ polyadenylation and Visium (spTotal, w/ SUPERase In Rnase Inhibitor)

value: Notexin (Uninjured & 5dpi)

value: Uninjured


title: STRS_2B

description: Two tibialis anterior sections (uninjured and notexin-2dpi) processed with in situ polyadenylation and Visium (spTotal, w/ SUPERase In Rnase Inhibitor)

value: Notexin (Uninjured & 2dpi)


title: Neonatal_ATAC-seq_NV_male_1

city: Cold Spring Harbor

first: Melody

last: Wu

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
Fastq files were processed using the ENCODE ATAC-seq pipeline with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

source_name: Bed nucleus of the stria terminalis

growth_protocol: Esr1Cre/+; Sun1-GFP/+ male mice were treated on P0 and harvested on P4.

extract_protocol:
Tissue (4-5 animals pooled per replicate) was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer.The nuclei were diluted 2:1 with cold, supplemented homogenization buffer and immediately used for sorting. 30,000 GFP+ nuclei were collected into cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. After sorting, 0.1% Tween-20 was added, and the nuclei were centrifuged at 500 x g for 5 min at 4degC. The nuclei pellet was directly resuspended in transposition reaction mix.
library input: 30,000 nuclei
Nextera DNA Library Prep Kit

treatment_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) 4 days prior to brain dissection.

value: BNST

value: Vehicle


title: Neonatal_ATAC-seq_NE_female_3

growth_protocol: Esr1Cre/+; Sun1-GFP/+ female mice were treated on P0 and harvested on P4.

value: Female

value: Estradiol


title: Neonatal_ATAC-seq_NV_female_3


title: Neonatal_ATAC-seq_NE_female_2


title: Neonatal_ATAC-seq_NV_male_3

value: Male


title: Neonatal_ATAC-seq_NV_male_2


title: Neonatal_ATAC-seq_NV_female_2


title: Neonatal_ATAC-seq_NV_female_1


title: ATAC-seq_intact_female_1

source_name: Bed nucleus of the stria terminalis, posterior

growth_protocol: 8-12 week-old  Esr1Cre/+;Sun1-GFP/+ gonadally intact females.

extract_protocol:
Tissue (4 animals pooled per replicate) was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and then centrifuged at 500 x g for 15 min at 4degC. The pellet was resuspended in 0.5 ml homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and 1X EDTA-free PIC. 30,000 GFP+ nuclei were collected into cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. After sorting, 0.1% Tween-20 was added, and the nuclei were centrifuged at 500 x g for 5 min at 4degC. The nuclei pellet was directly resuspended in transposition reaction mix.
library input: 30,000 nuclei
Nextera DNA Library Prep Kit

value: BNSTp

value: Untreated


title: P0_ERa_neg_female_E2_CR

description: 150,000 nuclei

data_processing:
library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q<0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

source_name: Limbic system

growth_protocol: P0 Esr1Cre/+; Sun1-GFP/+ female mice were treated for 4 hr.

extract_protocol:
Tissue (4-5 animals pooled per replicate) was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer.The nuclei were diluted 2:1 with cold, supplemented homogenization buffer, and 2mM EDTA was added. The sample was immediately sorted using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. 150,000 GFP+ nuclei were collected into CUT&RUN wash buffer. GFP- events were collected into CUT&RUN wash buffer, and 150,000 nuclei were subsequently counted on the Countess II FL Automated Cell Counter for ERα- and IgG negative control CUT&RUN.
Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) 4 hours prior to brain dissection.

value: Brain


title: P0_ERa_female_veh_CR_2

description: 150,000 nuclei


title: ATAC-seq_intact_male_2

growth_protocol: 8-12 week-old  Esr1Cre/+;Sun1-GFP/+ gonadally intact males.


title: ATAC-seq_intact_male_1


title: Neonatal_ATAC-seq_NE_female_1


title: ATAC-seq_intact_female_2


title: P0_ERa_female_E2_CR_1

description: 150,000 nuclei


title: P0_ERa_female_veh_CR_1

description: 150,000 nuclei


title: P14_female_atac

description: Single-nucleus ATAC & RNA

data_processing:
ATAC and RNA reads were demultiplexed and aligned to the reference genome using cellranger ARC pipeline (v2.0.0)
Gene expression and ATAC matrices were constructed using the cellranger ARC pipeline (v2.0.0)
Predicted doublets and low-quality nuclei were removed using Seurat (v4.0.3)
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: RNA_matrix.mtx file contains the gene x cell matrix for all samples. Barcode suffix indicates sample ID: 1 = P4 male, 2 = P4 female, 3 = P14 male, 4 = P14 female.
Supplementary_files_format_and_content: RNA_features.tsv file contains the genes (matches row names of RNA matrix file).
Supplementary_files_format_and_content: RNA_barcodes.tsv file contains the cell barcodes (matches column names of RNA matrix file).
Supplementary_files_format_and_content: ATAC_matrix.mtx file contains the peak x cell matrix for all samples. Barcode suffix indicates sample ID: 1 = P4 male, 2 = P4 female, 3 = P14 male, 4 = P14 female.
Supplementary_files_format_and_content: ATAC_features.tsv file contains the peaks (matches row names of ATAC matrix file).
Supplementary_files_format_and_content: ATAC_barcodes.tsv file contains the cell barcodes (matches column names of ATAC matrix file).
Supplementary_files_format_and_content: atac_fragment.tsv file unique ATAC-seq fragments and their corresponding cell barcode for each sample. Duplicate reads are collapsed into a single fragment.

growth_protocol: P4 and P14 Esr1-Cre/+; Sun1-GFP/+ female and male mice

extract_protocol:
Tissue (4-5 animals pooled per replicate) was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, 1 U/ul Protector RNase inhibitor, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer. The nuclei were diluted 2:1 with cold, supplemented homogenization buffer and immediately used for sorting. 40,000-50,000 GFP+ nuclei were sorted into 1 ml of cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2), supplemented with 0.1% Tween-20, 0.01% digitonin, 2% sterile-filtered BSA, and 1 U/μl Protector RNase inhibitor. The nuclei were centrifuged in a swinging-bucket rotor at 500 x g for 10 minutes at 4degC. ~950 μl of supernatant was carefully removed, and 200 μl 10X Genomics Dilute Nuclei Buffer was added to the side of the tube without disturbing the pellet. The nuclei were centrifuged again at 500 x g for 10 minutes at 4oC. ~240 μl of supernatant was carefully removed, and the nuclei were resuspended in the remaining volume (~7 μl).
10X Genomics Single Cell Multiome ATAC + Gene Expression kit


title: P14_male_gex

description: Single-nucleus ATAC & RNA


title: P4_male_gex

description: Single-nucleus ATAC & RNA


title: P4_male_atac

description: Single-nucleus ATAC & RNA


title: P4_female_gex

description: Single-nucleus ATAC & RNA


title: P0_IgG_CR_veh

description: 150,000 nuclei


title: N5

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (read_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (read_counts.tsv)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. read_counts.tsv contains raw counts, with genes labeled by their gene names.

source_name: NPY-positive neuron

extract_protocol:
single cell cytosol extraction via patch pipette
Nextera XT

value: 3-8 weeks


title: N6


title: N7


title: N8


title: N52


title: N4X


title: N9


title: N51


title: N49


title: N48


title: N50


title: P14_male_atac

description: Single-nucleus ATAC & RNA


title: P0_ERa_female_E2_CR_2

description: 150,000 nuclei


title: N44


title: N43


title: P14_female_gex

description: Single-nucleus ATAC & RNA


title: N46


title: N45


title: P0_IgG_CR_E2

description: 150,000 nuclei


title: P4_female_atac

description: Single-nucleus ATAC & RNA


title: N42


title: N3X


title: N41


title: N38


title: N40


title: N47


title: N39


title: N36


title: N37


title: N33


title: N2X


title: N29


title: N26


title: N28


title: N4


title: N32


title: N22


title: N15


title: N14


title: N17


title: N12


title: N11


title: N10


title: N1


title: N30


title: N34


title: N23


title: N27


title: N16

source_name: NPY-negative neuron


title: N18


title: H-VMP1 KO rep3 [s_wx6vmp1ko]

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

institute: University of Kansas Medical Center

data_processing:
Raw reads weredemultiplexed into Fastq format allowing up to one mismatch.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c), using Ensembl 96 gene models.
TPM values were generated using RSEM (version v1.3.0).
Pairwise differential expression analysis was performed using R package edgeR between the control and treatment group.
Genome_build: mm10
Supplementary_files_format_and_content: TPM tablef or every gene and every sample

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared with standard Illumina protocol

treatment_protocol: Flox VMP1 mice were intravenouly injected with AAV8-TBG or AAV8-TBG-cre for 2 weeks to generate WT or hepatocyte specific VMP1 KO mice.

value: Liver

value: floxed VMP1

value: AAV8-TBG-cre 2 weeks


title: N31


title: H-VMP1 KO rep1 [s_wx4vmp1ko]


title: WT rep2 [s_wx2wild]

value: AAV8-TBG-null 2 weeks


title: Bispecific_T24

first: Wenjing

last: Yanf

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

description:
Bisepcific
CD45+ cells sorted from Mc38 tumor after treated with CD47x PDL1 bispecific antibody

data_processing: none provided by the submitter

source_name: CD45+ cells sorted from MC38 tumor

growth_protocol: C57BL/6 mice were 6-10 weeks of age at time of MC38 tumor inoculation. MC38 murine cancer cells in serum-free PBS were inoculated in the right flank at 5 x 10^5 cells per implant and allowed to grow for 10 days.

extract_protocol:
MC38 tumors were mechanically dissociated by using the gentleMACS OCTO Dissociator and then filtered over 70uM nylon mesh filter. Spleens were treated for 25 minutes at 37 degrees with 25 ug Liberase TL (Roche) then mechanically dissociated by processing over a 70uM nylon mesh filter before treatment with ACK Lysis Buffer (Gibco) at room temperature for 3 minutes. Single cell suspension of the samples were then enriched for CD45+ cells using the Miltenyi mouse CD45(TIL) Microbeads Kit (Miltenyi BioTec) according to manufacturer’s instructions for the LS columns.
Single-cell emulsions were obtained using the 10X Genomics Controller and the v2 library and Gel Bead kit (10x Genomics). RNA-sequencing libraries were prepared as instructed by the 10x 3’ v2 kit protocol.
Resulting libraries were sequenced on an Illumina NextSeq using a NextSeq 500/550 v2.5 High Output Kit.

treatment_protocol: At day 10 post-tumor implant, vehicle control (PBS), CD47/PD-L1 mBisAb, amCD47, amPDL1, or the combination were administrated by I.P every 3 to 4 days. Tumors were then harvested at day 20 and day 24 post-tumor implant.

value: MC38 tumor bearing mice


title: WT rep3 [s_wx3wild]


title: N13


title: Bispecific_T23

value: treated with CD47x PDL1 bispecific antibody


title: Bispecific_T22


title: PDL1_T14

description:
PDL1
CD45+ cells sorted from Mc38 tumor after treated with PDL1 antibody

value: treated with PDL1 monoclonal antibody


title: Combo_T18

description:
Combination
CD45+ cells sorted from Mc38 tumor after treated with CD47 and PDL1 combination

value: treated with CD47 and PDL1 combination therapy


title: Bispecific_T20


title: Combo_T19


title: Combo_T16


title: PDL1_T12


title: Combo_T15


title: PDL1_T13


title: WT rep1 [s_wx1wild]


title: H-VMP1 KO rep2 [s_wx5vmp1ko]


title: PDL1_T11


title: CD47_T6

description:
CD47
CD45+ cells sorted from Mc38 tumor after treated with CD47 antibody

value: treated with CD47 monoclonal antibody


title: CD47_T8


title: Control_T4

description:
Control
CD45+ cells sorted from Mc38 tumor after treated with PBS

value: treated with PBS


title: CD47_T7


title: Bispecific_T21


title: CD47_T9


title: Control_T3


title: Control_T1


title: P4_BNST_Female_Veh_1

data_processing:
For adult dataset, reads were adapter trimmed and quality filtered (q>30) using the Fast-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit). For neonatal dataset, reads were adapter trimmed and quality filtered (q>30) using cutadapt.
Filtered reads were mapped to the mm10 reference genome using STAR.
The number of reads mapped to each gene (exons only) was calculated using featureCounts. For the neonatal dataset, technical duplicate reads were removed using the manufacturer's nudup.py script (https://github.com/tecangenomics/nudup). The number of reads mapping to each gene (including introns) was calculated using featureCounts.
Differential expression analysis was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content:
RNASeq_BNST: xls file with differential expression results and read counts for all samples.
Neonatal_BNST: xlsx file with differential expression results and read counts for all samples.

molecule: nuclear RNA

growth_protocol: Esr1Cre/+; ROSA26CAG-Sun1-sfGFP-Myc/+ female mice

extract_protocol:
Four days after injection, animals were rapidly decapitated, and 400-μm sections were collected in ice-cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 120 mM tricine-KOH, pH 7.8) on a microtome. The BNST was microdissected (4 animals pooled per condition) and collected in 1 ml of cold homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and 1X EDTA-free PIC, and 0.4 U/ml RNAseOUT. The tissue was dounce-homogenized 15x in a 1 ml glass tissue grinder (Wheaton) with a loose pestle. 0.3% IGEPAL CA-630 was added, and the suspension was homogenized 5x with a tight pestle. The homogenate was filtered through a 40-μm strainer then centrifuged at 500 x g for 15 min at 4oC. The pellet was resuspended in 0.5 ml homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X EDTA-free PIC, and 0.2 U/ml RNAseOUT. 12,000 GFP+ nuclei were collected into cold Buffer RLT Plus supplemented 1:100 with β-mercaptoethanol using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. Samples were stored at -80degC until RNA extraction. RNA extraction was performed with Qiagen RNeasy Plus Micro Kit.
Libraries were prepared using the Tecan Genomics Ovation SoLo RNA-seq kit

treatment_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) on the day of birth (P0)

value: Esr1Cre/+; ROSA26CAG-Sun1-sfGFP-Myc/+

value: BNST

value: Female

value: Vehicle

value: Postnatal day 4


title: P4_BNST_Female_E2_2

value: Estradiol


title: P4_BNST_Female_E2_1


title: Control_T2


title: P4_BNST_Female_Veh_2


title: P4_BNST_Female_E2_3


title: Combo_T17


title: ERa_female_E2_CR_1

description: 400,000 nuclei

data_processing:
Library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q < 0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

growth_protocol: 10-12 week-old C57/BL6 females or males were gonadectomized to clear circulating hormones for 3 weeks

extract_protocol:
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added.
Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) 4 hours prior to brain dissection

value: Brain


title: ERa_female_veh_CR_2

description: 400,000 nuclei


title: ATAC-seq_male_E2_3

growth_protocol: 8-12 week-old Esr1Cre/+;Sun1-GFP/+ females or males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, females or males were treated for 4 hr.

extract_protocol:
Tissue (4 animals pooled per replicate) was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and then centrifuged at 500 x g for 15 min at 4degC. The pellet was resuspended in 0.5 ml homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and 1X EDTA-free PIC. 30,000 GFP+ nuclei were collected into cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) using the Sony SH800S Cell Sorter (purity mode) with a 100-?m sorting chip. After sorting, 0.1% Tween-20 was added, and the nuclei were centrifuged at 500 x g for 5 min at 4degC. The nuclei pellet was directly resuspended in transposition reaction mix.
Nextera DNA Library Prep Kit

value: Male

value: BNSTp


title: P4_BNST_Female_Veh_3


title: ERa_male_veh_CR_2

description: 400,000 nuclei


title: ATAC-seq_male_E2_1


title: ERa_male_E2_CR_1

description: 400,000 nuclei


title: ERa_male_E2_CR_2

description: 400,000 nuclei


title: PDL1_T10


title: ERa_female_E2_CR_2

description: 400,000 nuclei


title: ERa_male_veh_CR_1

description: 400,000 nuclei


title: ERa_female_veh_CR_1

description: 400,000 nuclei


title: ATAC-seq_female_veh_2


title: ATAC-seq_female_E2_1


title: ATAC-seq_female_E2_3


title: ATAC-seq_male_veh_2


title: ATAC-seq_female_veh_3


title: ATAC-seq_female_E2_2


title: ATAC-seq_male_veh_3


title: ATAC-seq_male_E2_2


title: Adult_BNST_Female_E2_4

growth_protocol: 8-12 week-old Esr1Cre/+;Rpl22-HA/+ females or males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, females or males were treated for 4 hr.

extract_protocol:
Microdissected tissue from 8-9 mice was pooled and frozen at -80oC for each sample. Tissue homogenization, immunoprecipitation of polysomes from Esr1+ neurons, and mRNA extraction was performed as previously described (Heiman et al., 2014; Sanz et al., 2009).
Libraries were prepared according to instructions provided by NuGEN Ovation RNA-Seq kits (7102 and 0344).

value: 10-12 weeks old


title: ATAC-seq_male_veh_1


title: pooled_input-rep1

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

data_processing:
Raw reads were filter to retain only those with mean base quality score >20.
Cutadapt was used to remove adapter from 3' end of reads; only trimmed reads >30bp in length were used in analysis.
Reads were mapped against the mm10 reference assembly via Bowtie v1.2 with parameter -m 1, then deduplicated via Picard tools MarkDuplicates.jar v1.110.
uniquely-mapped non-duplicate reads from replicate samples  were aggregated with Picard tools MergeSamFiles.jar v1.110.
Peak calls were made via HOMER v4.10.3 with parameters "-style factor -fdr 0.00001 -tbp 0 -inputtbp 0", then re-defined as 300mers centered on the called peak midpoint.
For visualization purposes, uniquely-mapped non-duplicate fragments were extended to the estimate fragment length of 200nt, converted to bedGraph format via BEDtools genomeCoverageBed v2.24.0, normalized to 50M reads, then converted to bigWig format via UCSC utility bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: peak calls at BED files, normalized depth at bigWig files

source_name: E14.5 XX & XY mesonephroi

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols
ChIP-seq for RUNX1 and input on chromatin from pools of mouse CD1 fetal ovaries (E14.5).

value: mesonephroi

tag: sex chromosome

value: XX and XY (pooled)

tag: chip antibody


title: ATAC-seq_female_veh_1

tag: Sex

tag: tissue


title: E14.5_male_NR2F2-rep2

description:
E14.5_male_NR2F2.normalized_depth.bigWig
E14.5_male_NR2F2.peaks.bed.gz

source_name: E14.5 XY mesonephroi

value: XY

value: COUP-TFII rabbit antibody (Active Motif cat # 61213)


title: Adult_BNST_Female_Veh_3


title: Adult_BNST_Female_Veh_2


title: E14.5_male_NR2F2-rep1


title: Adult_BNST_Female_Veh_4


title: pooled_input-rep2


title: E14.5_female_NR2F2-rep2

description:
E14.5_female_NR2F2.normalized_depth.bigWig
E14.5_female_NR2F2.peaks.bed.gz

source_name: E14.5 XX mesonephroi

value: XX


title: E14.5_female_NR2F2-rep1


title: Adult_BNST_Female_E2_3


title: Adult_BNST_Female_Veh_1


title: Adult_BNST_Female_E2_1


title: Adult_BNST_Male_Veh_3

source_name: Bed Nucleus of the Stria Terminalis-principal nucleus


title: testis_30

city: Yangling

first: Lingkai

last: zhang

address: No. 3, Taicheng Road, Yangling District,  Xianyang 712100，Shaanxi Province，China.

institute: Northwest A&F University

data_processing:
scRNA-seq:  Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. Sample demultiplexing, barcode processing and single-cell 3’ gene countingby using the Cell Ranger pipeline and scRNA-seq data were aligned to Ensembl genome Sscrofa11.1, a total of 16,966 single cell captured from 150-day-old porcine testis were processed using 10X Genomics Chromium Single Cell 3’ Solution. The Cell Ranger output was loaded into Scanpy(version 1.7.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)

organism: Sus scrofa

source_name: testis cells

extract_protocol:
Testis cell suspensions were loaded into Chromium microfluidic chips with 3’ v3 chemistry and used to generate single-cell gel bead emulsions (GEMs) using the Chromium controller (10X Genomics), GEM-RT was performed in a T100 Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to manufacturer recommendations.
scRNA-seq:  Single-cell suspensions were loaded to 10x Chromium to capture a total 86,453 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 25,000 reads per cell.

value: testis cells

value: 30-days old


title: testis_60

value: 60-days old


title: Adult_BNST_Male_E2_4


title: Nfix_male_E2_CR_rep2

description: 200,000 nuclei

data_processing:
Library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700.
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q < 0.05). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent genomic binding events.

extract_protocol:
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added to improve binding to concanavalin A magnetic beads.
Takara SMARTer ThruPlex DNA-seq Kit


title: Adult_BNST_Male_E2_3


title: testis_7

value: 7-days old


title: Adult_BNST_Male_Veh_4


title: Adult_BNST_Female_E2_2

value: Female


title: Adult_BNST_Male_E2_2


title: Adult_BNST_Male_E2_1


title: Adult_BNST_Male_Veh_2

value: Vehicle


title: Adult_BNST_Male_Veh_1


title: Nfix_male_veh_CR_rep1

description: 200,000 nuclei


title: Nfix_male_E2_CR_rep1

description: 200,000 nuclei


title: shGPR81_rep2

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

country: Japan

institute: Osaka University graduate school of dentistry

data_processing:
Illumina Casava1.8.2 software was used for base-calling.
Sequenced reads were mapped to mm10 using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
FPKMs was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

extract_protocol:
Total RNA was isolated using Nucleo Spin RNA plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast cancer cell

tag: shRNA


title: shGPR81_rep3


title: Nfix_male_veh_CR_rep2

description: 200,000 nuclei


title: shNT_rep2

value: shNT


title: FFGC replicate 4

type: RNA

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was transformed using variance-stabilizing transformation before quantile normalisation using the lumi package in R

label: Biotin

source_name: spleen

label_protocol: Standard Illumina biotin labelling protocol

growth_protocol: direct flow cytometry sorting ex vivo

extract_protocol: trizol

treatment_protocol: no treatment

value: germinal center (GC) B cells

tag: genotype/variation

value: GC specific deletion of endogenous Myc and over-expression of MYC carrying a V394D mutation from the Rosa26 locus


title: Wild type replicate3

tag: strain

value: GC specific deletion of endogenous Myc and over-expression of MYC from the Rosa26 locus


title: FFGC replicate 2


title: shGPR81_rep1


title: FFGC replicate 1


title: FFGC replicate 3


title: Wild type replicate4


title: Wild type replicate2


title: Wild type replicate1


title: IgG_CR_veh

description: 400,000 nuclei

source_name: Cortex

value: Brain

value: Male


title: PAC139_RNA

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

description:
Placental Chorionic Villous tissue
PAC139

data_processing:
All sequencing data was firstly assessed for quality using FastQC and ngsReports (34, 35) to identify any failed and low-coverage samples.
Raw paired-end, stranded FASTQ files were then trimmed for sequence adapters using AdapterRemoval (36) and aligned to the 1000 genomes project GRCh37 (hs37d5) human reference genome using STAR (37) and gene counts were identified on raw alignments using featureCounts (38)
Analysis was limited to gene counts greater than 2 counts per million (CPM) in at least 55 samples (i.e. the size of the smallest sample group).
Differential gene expression (DGE) was carried out using edgeR (39) within the R/Bioconductor statistical framework, relying on sample-weight transformation contained in the voom functions (41). Linear models were then fitted with limma (42) along with empirical Bayes moderation(43).
Weighted gene correlation network analysis (WGCNA) was carried out using R package WGCNA (44) using two sets of early gestation RNA-seq samples. Low counts were removed similar to DGE, variance stabilisation and batch effects removed using DESeq2 (45) and low variability genes removed (i.e. genes in the lowest quartile of standard deviation). Signed network and adjacency matrix were constructed using a soft power threshold of 14 and modules with a minimum size of 50 generated and merged at distance cut-off of 0.25. Network graphs were constructed and visualised using Gephi (https://gephi.org/).
Genome_build: GRCh37 (hs37d5)
Supplementary_files_format_and_content: allCounts.xlsx

source_name: Chorionic Villous

extract_protocol:
Placental villous tissue was collected from women who were undergoing elective pregnancy terminations (6-23+6 weeks’ gestation) immersed in RNAlater solution (Invitrogen) within minutes of termination and placed at -4°C for 24 h prior to being stored at -80°C. RNA was extracted from each placental villous sample using the Qiagen RNeasy kit following the manufacturer’s protocols.
Sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation kits and all the ribosomal RNA was depleted using Ribo-Zero Gold.

tag: gestational age

value: male


title: Nfix_female_E2_CR_rep2

description: 200,000 nuclei

value: BNSTp

value: Estradiol


title: IgG_CR_E2

description: 400,000 nuclei


title: PAC134_RNA

description:
Placental Chorionic Villous tissue
PAC134

value: female


title: Nfix_female_veh_CR_rep2

description: 200,000 nuclei


title: shNT_rep1


title: Nfix_female_veh_CR_rep1

description: 200,000 nuclei


title: PAC129_RNA

description:
Placental Chorionic Villous tissue
PAC129


title: Nfix_female_E2_CR_rep1

description: 200,000 nuclei


title: PAC140_RNA

description:
Placental Chorionic Villous tissue
PAC140


title: Donor 1 Plasma cells (2020)_AT6p2b

city: Bellinzona

first: Ganesh

last: Phad

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine

data_processing:
Raw data obtained from illumina instrument demultiplexed and processed using standard cellranger-5.0.0 pipeline
Genome_build: GRCh38-2020-A
Supplementary_files_format_and_content: CellRanger output files (barcodes, features, counts files)

source_name: Peripheral blood

extract_protocol:
Plasma cells were FACS sorted from human peripheral blood and subjected to 10X single cell 5' gene expression protocol
RNA libraries were prepared for sequencing using standard 10X 5' immune profiling and Illumina protocols

value: Blood

value: Plasma cells

tag: donor id


title: shNT_rep3

tag: cell type


title: Donor 1 Plasma cells (2020)_AT6p1e


title: PAC124_RNA

description:
Placental Chorionic Villous tissue
PAC124


title: Donor 1 Plasma cells (2020)_AT6p2c


title: testis_90

value: testis cells

tag: age

value: 90-days old


title: P6.C

city: Singapore

first: Pavanish

last: Kumar

state: Not Applicable

address: 20 collage road, The Academia, Discovery Tower, Level-8 Translation Immunology Institute (TII)

country: Singapore

institute: Translational Immunology Institute (TII), SingHealth-DukeNUS

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.1.1
Aggregated Raw count matrix output files from CellRanger software were loaded in R software and Seurat package was used for analysis and to generate processed rds file
Assembly: Hg19
Supplementary files format and content: rds file with raw counts and clustering information

source_name: Lateral Temporal Gyrus

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


title: PAC118_RNA

description:
Placental Chorionic Villous tissue
PAC118


title: PAC109_RNA

description:
Placental Chorionic Villous tissue
PAC109


title: PAC114_RNA

description:
Placental Chorionic Villous tissue
PAC114


title: PAC127_RNA

description:
Placental Chorionic Villous tissue
PAC127


title: PAC131_RNA

description:
Placental Chorionic Villous tissue
PAC131


title: PAC111_RNA

description:
Placental Chorionic Villous tissue
PAC111


title: P5.A

source_name: Posteriar Mid Temporal Gyrus


title: Donor 1 Plasma cells (2020)_AT6p1d


title: P4


title: PAC107_RNA

description:
Placental Chorionic Villous tissue
PAC107


title: PAC105_RNA

description:
Placental Chorionic Villous tissue
PAC105


title: PAC103_RNA

description:
Placental Chorionic Villous tissue
PAC103


title: Donor 1 Plasma cells (2020)_AT6p1b


title: P3.A


title: Donor 1 Plasma cells (2020)_AT6p2a


title: PAC120_RNA

description:
Placental Chorionic Villous tissue
PAC120


title: PAC122_RNA

description:
Placental Chorionic Villous tissue
PAC122


title: P1.B

source_name: Occipital Core


title: PAC117_RNA

description:
Placental Chorionic Villous tissue
PAC117


title: P6.B

source_name: Posteriar Temporal Gyrus


title: P6.A

source_name: Mid Temporal Gyrus


title: PAC108_RNA

description:
Placental Chorionic Villous tissue
PAC108


title: Donor 1 Plasma cells (2020)_AT6p1c


title: P1.A

source_name: Occipital Cortex


title: P2

source_name: Frontal Lobe


title: P3.B

source_name: Superior frontal Gyrus


title: P5.B

source_name: Lateral Mid Temporal Gyrus


title: Donor 1 Plasma cells (2020)_AT6p1a


title: PAC088_RNA

description:
Placental Chorionic Villous tissue
PAC088


title: PAC091_RNA

description:
Placental Chorionic Villous tissue
PAC091


title: Hs#20 [Adrenal]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
We demultiplexed FASTQ files using the CellRanger 5.01 mkfastq command.
Primary data analysis (alignment, filtering, and UMI counting) was performed using GRC38 (human hg38) reference genome with CellRanger count.
Secondary analysis was performed using Seurat 4.0.1
Genome_build: hg38
Supplementary_files_format_and_content: raw count matrix

source_name: Adrenal

extract_protocol:
10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1
10X Genomics Chromium Next GEM Chip G Single Cell Kit

treatment_protocol: Isolated embryonic fragments were washed twice with PBS and then minced  with scissors in 500 μl of 0.1% trypsin/EDTA solution, then incubated for 9 min at 37°C   with gentle pipetting every 3 min. After quenching of the reaction by addition of 500 μl   of STO medium, cell suspensions were strained through a 70 µm nylon cell strainer and   centrifuged for 220 g for 5 min. Cell pellets were resuspended in 0.1% BSA in PBS and   counted. All samples were stained with trypan blue and confirmed to be >80% viable.   Cells were loaded into Chromium microfluidic chips and used to generate single cell   gelbead emulsions with a Chromium controller (10x Genomics) according to the   manufacturer’s protocol. Gelbead emulsion-RT was performed with a T100 Touch   Thermal Cycler (Bio-Rad). All subsequent cDNA amplification and library construction   steps were performed according to the manufacturer’s protocol.

tag: Stage

value: 9 wpf

value: Adrenal


title: Hs#20 [Testis]

source_name: Testis

value: Testis


title: Hs#17 [Adrenal]

value: 6 wpf


title: PAC084_RNA

description:
Placental Chorionic Villous tissue
PAC084


title: Hs#15 [Testis]


title: PAC100_RNA

description:
Placental Chorionic Villous tissue
PAC100


title: PAC099_RNA

description:
Placental Chorionic Villous tissue
PAC099


title: PAC102_RNA

description:
Placental Chorionic Villous tissue
PAC102


title: PAC083_RNA

description:
Placental Chorionic Villous tissue
PAC083


title: Hs#14 [Adrenal]

value: 5 wpf


title: PAC098_RNA

description:
Placental Chorionic Villous tissue
PAC098


title: PAC093_RNA

description:
Placental Chorionic Villous tissue
PAC093


title: PAC078_RNA

description:
Placental Chorionic Villous tissue
PAC078


title: PAC097_RNA

description:
Placental Chorionic Villous tissue
PAC097


title: Hs#21 [Adrenal]

value: 12 wpf


title: PAC087_RNA

description:
Placental Chorionic Villous tissue
PAC087


title: Hs#19 [Adrenal]

value: 8 wpf


title: PAC086_RNA

description:
Placental Chorionic Villous tissue
PAC086


title: MCF7_ERa_Ab2_veh_CR_1

description: 25,000 cells

source_name: MCF7 cells

growth_protocol: Cells were maintained in stripped serum and phenol-red free media for 48 hours prior to treatment.

extract_protocol: Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: Cells were treated with either 20 nM 17-beta-estradiol or vehicle control (0.002% EtOH) for 45 min then harvested using trypsin.

value: Cell line

tag: treatment

value: Vehicle


title: Hs#14 [Testis]


title: PAC071_RNA

description:
Placental Chorionic Villous tissue
PAC071


title: PAC077_RNA

description:
Placental Chorionic Villous tissue
PAC077

value: male


title: PAC076_RNA

description:
Placental Chorionic Villous tissue
PAC076


title: MCF7_ERa_Ab2_E2_CR_2

description: 25,000 cells


title: PAC063_RNA

description:
Placental Chorionic Villous tissue
PAC063


title: PAC070_RNA

description:
Placental Chorionic Villous tissue
PAC070


title: PAC062_RNA

description:
Placental Chorionic Villous tissue
PAC062


title: MCF7_ERa_Ab1_E2_CR_1

description: 25,000 cells


title: PAC072_RNA

description:
Placental Chorionic Villous tissue
PAC072


title: PAC074_RNA

description:
Placental Chorionic Villous tissue
PAC074


title: PAC060_RNA

description:
Placental Chorionic Villous tissue
PAC060


title: MCF7_ERa_Ab1_E2_CR_2

description: 25,000 cells


title: Hs#19 [Testis]


title: MCF7_ERa_Ab2_veh_CR_2

description: 25,000 cells


title: PAC065_RNA

description:
Placental Chorionic Villous tissue
PAC065


title: PAC069_RNA

description:
Placental Chorionic Villous tissue
PAC069


title: PAC075_RNA

description:
Placental Chorionic Villous tissue
PAC075


title: PAC064_RNA

description:
Placental Chorionic Villous tissue
PAC064


title: MCF7_ERa_Ab2_E2_CR_1

description: 25,000 cells


title: Hs#3 [Testis/adrenal]

source_name: Testis/adrenal

value: 4 wpf

value: Testis/adrenal


title: PAC058_RNA

description:
Placental Chorionic Villous tissue
PAC058

value: female


title: MCF7_ERa_Ab1_veh_CR_1

description: 25,000 cells


title: PAC059_RNA

description:
Placental Chorionic Villous tissue
PAC059


title: MCF7_ERa_Ab1_veh_CR_2

description: 25,000 cells


title: 10000 ng/mL FA-treated SW480, biological rep1

city: Budapest

first: Sára

last: Zsigrai

state: --None--

address: Korányi Sándor utca 2/a

country: Hungary

institute: Semmelweis University

description:
gene expression data of folic acid-treated CRC cell lines
SW480_10000_1

hyb_protocol: Fragmented and labeled sscDNA samples (5.5 μg) were hybridized to Human Transcriptome Array 2.0 microarrays (Affymetrix, Santa Clara, CA, USA) for 16 h at 45 °C with 60 rpm rotation in the Hybridization Oven (Affymetrix).

scan_protocol: GeneChip Scanner 3000 (Affymetrix) was used for scanning.

data_processing: Signal space transformation–robust multi-array average (SST-RMA) algorithm was applied for background subtraction, normalization, and signal summarization. Gene expression alterations were evaluated using Transcriptome Analysis Console 4.0 (TAC 4.0; Affymetrix) software.

label: biotin

source_name: SW480 CRC cell line treated with 10000 ng/mL FA

label_protocol: Labeling was carried out according to the manufacturer's instruction using GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: HT-29 (ATCC HTB-39) and SW480 (ATCC CCL-228) human colon adenocarcinoma cell lines were cultured in RPMI 1640 medium (RPMI 1641, Biosera, Ringmer, UK) containing 10% fetal bovine serum (Biosera), 80 mg/2 mL gentamycin (Sandoz GmbH, Kundl, Austria), and 2 mM L-glutamine (Biosera). Cells were maintained at 37 °C in a 5% CO2 humidified atmosphere. Prior to FA treatment, 125000 cells were seeded in triplicates in each well of a 6-well plate (Sarstedt, Nümbrecht, Germany) and incubated for 24 h in 2.5 mL growth medium.

extract_protocol: Total RNA was purified with RNeasy Mini Kit (Qiagen), and isolated RNA concentration was measured by Qubit 1.0 fluorometer using RNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: Non-treated cells were kept in RPMI medium without any additional substances. In the case of treated cells 10,000 ng/mL FA concentrations were applied.

tag: cell line

value: colorectal cancer cell line

value: treated with 10000 ng/mL FA


title: 10000 ng/mL FA-treated SW480, biological rep3

description:
gene expression data of folic acid-treated CRC cell lines
SW480_10000_3


title: PAC057_RNA

description:
Placental Chorionic Villous tissue
PAC057


title: PAC056_RNA

description:
Placental Chorionic Villous tissue
PAC056


title: non-treated SW480, biological rep3

description:
gene expression data of folic acid-treated CRC cell lines
SW480_0_3

source_name: non-treated SW480 CRC cell line kept in FA-free medium

value: non-treated, kept in FA-free medium


title: PAC054_RNA

description:
Placental Chorionic Villous tissue
PAC054

source_name: Chorionic Villous


title: PAC055_RNA

description:
Placental Chorionic Villous tissue
PAC055


title: PAC053_RNA

description:
Placental Chorionic Villous tissue
PAC053


title: PAC051_RNA

description:
Placental Chorionic Villous tissue
PAC051


title: PAC049_RNA

description:
Placental Chorionic Villous tissue
PAC049


title: PAC050_RNA

description:
Placental Chorionic Villous tissue
PAC050


title: 10000 ng/mL FA-treated SW480, biological rep2

description:
gene expression data of folic acid-treated CRC cell lines
SW480_10000_2


title: PAC048_RNA

description:
Placental Chorionic Villous tissue
PAC048


title: PAC047_RNA

description:
Placental Chorionic Villous tissue
PAC047


title: PAC045_RNA

description:
Placental Chorionic Villous tissue
PAC045


title: PAC046_RNA

description:
Placental Chorionic Villous tissue
PAC046


title: non-treated SW480, biological rep2

description:
gene expression data of folic acid-treated CRC cell lines
SW480_0_2


title: PAC043_RNA

description:
Placental Chorionic Villous tissue
PAC043


title: PAC052_RNA

description:
Placental Chorionic Villous tissue
PAC052


title: 10000 ng/mL FA-treated HT-29, biological rep1

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_10000_1

source_name: HT-29 CRC cell line treated with 10000 ng/mL FA


title: PAC044_RNA

description:
Placental Chorionic Villous tissue
PAC044


title: non-treated SW480, biological rep1

description:
gene expression data of folic acid-treated CRC cell lines
SW480_0_1


title: 10000 ng/mL FA-treated HT-29, biological rep2

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_10000_2


title: non-treated HT-29, biological rep2

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_0_2

source_name: non-treated HT-29 CRC cell line kept in FA-free medium


title: non-treated HT-29, biological rep1

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_0_1


title: non-treated HT-29, biological rep3

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_0_3


title: SUIT-2_Acidic medium_4-5 months_rep1

city: Zhunan Town

first: Wun-Shaing

middle: Wayne

last: Chang

state: Miaoli County

address: 35, Keyan Road

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 4-5 months, biological rep1

hyb_protocol: cDNA was hybridized to Applied Biosystems GeneChip Human Transcriptome Array 2.0 according to the manufacturer’s instructions.

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

data_processing: Expression values were processed with Signal Space Transformation (SST) and Robust Multichip Average method, which included log2 transformation and quantile normalization.

source_name: Human PDAC SUIT-2 cells, Acidic medium, 4-5 months

label_protocol: RNA was amplified (in vitro transcription) and generate biotin labeled Single-stranded cDNA according to manufacturer's instructions.

growth_protocol: Cells were cultured as monolayers in RPMI-1640 medium supplemented with 23.8 mM NaHCO3 and 10% FBS at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: RNA was extracted using RNeasy mini kit (QIAGEN, Hilden, Germany) according to manufacturer's instructions.

treatment_protocol: The bicarbonated RPMI-1640 medium was further supplemented with 25 mM HEPES/PIPES followed by the addition of appropriate amount of 1N HCl to either pHe 7.4 for use as the buffer control medium, or to pHe 6.7 for use as the acidic culture medium. Each cell sample was adapted to the intended pHe by adding the corresponding pH-adjusted medium to freshly split cells, followed by intensive daily monitoring to ensure the desired pHe values were stably maintained within ± 0.1 unit.

value: Pancreatic ductal adenocarcinoma (PDAC)

tag: medium

value: Acidic medium

tag: phe

value: pHe 6.7

tag: time

value: 4-5 months


title: SUIT-2_Acidic medium_2-3 weeks_rep1

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 2-3 weeks, biological rep1

source_name: Human PDAC SUIT-2 cells, Acidic medium, 2-3 weeks

value: 2-3 weeks


title: SUIT-2_Acidic medium_10-12 months_rep1

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 10-12 months, biological rep1

source_name: Human PDAC SUIT-2 cells, Acidic medium, 10-12 months

value: 10-12 months


title: SUIT-2_Buff medium_10-12 months_rep1

description: Human PDAC SUIT-2 cells cultured in Buffered medium at pHe 7.4 for 10-12 months, biological rep1

source_name: Human PDAC SUIT-2 cells, Buff medium, 10-12 months

value: Buff medium

value: pHe 7.4


title: SUIT-2_Acidic medium_10-12 months_rep2

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 10-12 months, biological rep2


title: SUIT-2_Acidic medium_4-5 months_rep2

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 4-5 months, biological rep2


title: SUIT-2_Buff medium_10-12 months_rep2

description: Human PDAC SUIT-2 cells cultured in Buffered medium at pHe 7.4 for 10-12 months, biological rep2


title: SUIT-2_Acidic medium_2-3 weeks_rep2

description: Human PDAC SUIT-2 cells cultured in Acidic buffered medium at pHe 6.7 for 2-3 weeks, biological rep2


title: PAC040_RNA

description:
Placental Chorionic Villous tissue
PAC040


title: SUIT-2_Buff medium_2-3 weeks_rep2

description: Human PDAC SUIT-2 cells cultured in Buffered medium at pHe 7.4 for 2-3 weeks, biological rep2

source_name: Human PDAC SUIT-2 cells, Buff medium, 2-3 weeks


title: PAC041_RNA

description:
Placental Chorionic Villous tissue
PAC041


title: 24h_IFNAR_M3_Medium

city: Epalinges

first: Nicolas

last: Fasel

address: Chemin des Boveresses 155

department: Department of Biochemistry

institute: University of Lausanne

description: genes.htseq.normalized.logcpm.prior1_24h

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013)
Reads were aligned against the Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012). Reads were also aligned to the Mus musculus.GRCm38.92 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes independently in R (R version 3.4.4). Genes with low counts were filtered out according to the rule of 1 count(s) per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization. Subsequently, the normalized counts were transformed to cpm values, and a log2 transformation was applied, by means of the function cpm with the parameter setting prior.counts = 1 (EdgeR v 3.20.9; Robinson et al. 2010).

source_name: Bone marrow derived macrophages

growth_protocol: Macrophages were isolated from bone marrow of C57BL/6 mice (wild-type or knock-out). Hind leg bones were collected and the bone marrow was flushed out with complete DMEM medium, containing DMEM (Dulbecco’s modified Eagle’s medium, Gibco), supplemented with 10% heat-inactivated FBS (Gibco), 1% Penicillin-Streptomycin Solution (BioConcept) (i.e. 100 IU/ml and 100 µg/ml respectively), 1% HEPES (BioConcept) (i.e. 10mM). The cells were differentiated into macrophages for 6 days in complete DMEM medium containing 50 ng/ml recombinant mouse Macrophage Colony Stimulating Factor (rmM-CSF, ImmunoTools), at 37°C and 5% CO2, in Sterilin Petri Dish (Thermo Scientific). Then, the bone marrow-derived macrophages (BMDMs) were detached with 1X DPBS (Gibco) containing 5 mM EDTA, washed and resuspended with complete DMEM medium. The cells were plated in 12-well plates (TPP) with 1.95 million cells per well. They were finally put back in culture at 37°C and 5% CO2.

extract_protocol:
BMDMs were cleared out of supernatants and lysed with 350 µl RLT buffer (Qiagen) supplemented with 40 mM DTT (Dithiotreitol) for RNA extraction. Plates were then frozen at -80°C until the RNA purification. The RNA samples were purified with the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions. Purified RNA was eluted with 30 µl RNase-free water (Qiagen).
Library preparation and sequencing were performed at the Lausanne Genomic Technologies Facility (GTF), University of Lausanne (UNIL), Switzerland

treatment_protocol: One day after their plating, murine BMDMs were infected with stationary-phase Leishmania promastigotes with a multiplicity of infection of 5. Cells were also alternatively treated with Poly(I:C) (HMW), a TLR3 agonist (mimicking dsRNA), or FSL1, a TLR2 agonist.  As controls, non treated or non infected (Medium) wells were filled with complete DMEM medium alone. The cells were incubated at 35°C and 5% CO2 until 8 and 24 hrs post -infection or -treatment (h post-treatment).

tag: genotype

value: Ifnar-/-

tag: time-point

value: Non-treated


title: PAC038_RNA

description:
Placental Chorionic Villous tissue
PAC038

tag: Sex


title: PAC039_RNA

description:
Placental Chorionic Villous tissue
PAC039


title: 24h_IFNg_M2_Vpos

value: Ifng-/-


title: PAC042_RNA

description:
Placental Chorionic Villous tissue
PAC042

value: male


title: 24h_IFNg_M2_Vneg


title: 24h_WT_M3_Vpos_FSL1

value: WT

value: LgyLRV1+ and FSL1


title: 24h_WT_M3_Vneg_FSL1

value: LgyLRV+- and FSL1


title: PAC037_RNA

description:
Placental Chorionic Villous tissue
PAC037

value: female


title: 24h_IFNg_M2_Medium


title: 10000 ng/mL FA-treated HT-29, biological rep3

description:
gene expression data of folic acid-treated CRC cell lines
HT-29_10000_3

value: colorectal cancer cell line

value: treated with 10000 ng/mL FA


title: PAC036_RNA

description:
Placental Chorionic Villous tissue
PAC036


title: PAC035_RNA

description:
Placental Chorionic Villous tissue
PAC035


title: PAC034_RNA

description:
Placental Chorionic Villous tissue
PAC034


title: PAC033_RNA

description:
Placental Chorionic Villous tissue
PAC033


title: SUIT-2_Ctrl medium_rep2

description: Human PDAC SUIT-2 cells cultured in Ctrl medium at pHe 7.4, biological rep2

source_name: Human PDAC SUIT-2 cells, Ctrl medium

value: Pancreatic ductal adenocarcinoma (PDAC)

value: Ctrl medium


title: 24h_WT_M3_pIC

value: Poly IC


title: 24h_WT_M3_Vneg


title: PAC032_RNA

description:
Placental Chorionic Villous tissue
PAC032


title: PAC030_RNA

description:
Placental Chorionic Villous tissue
PAC030


title: PAC031_RNA

description:
Placental Chorionic Villous tissue
PAC031


title: PAC029_RNA

description:
Placental Chorionic Villous tissue
PAC029


title: 24h_WT_M3_Vpos


title: SUIT-2_Ctrl medium_rep1

description: Human PDAC SUIT-2 cells cultured in Ctrl medium at pHe 7.4, biological rep1


title: PAC027_RNA

description:
Placental Chorionic Villous tissue
PAC027


title: 24h_iNOS_M2_Vneg

description: genes.htseq.normalized.logcpm.prior1_24h

value: inos-/-


title: 24h_iNOS_M2_pIC


title: PAC026_RNA

description:
Placental Chorionic Villous tissue
PAC026


title: 24h_iNOS_M2_Vpos


title: PAC024_RNA

description:
Placental Chorionic Villous tissue
PAC024


title: PAC021_RNA

description:
Placental Chorionic Villous tissue
PAC021


title: 24h_IFNAR_M1_Vpos_FSL1


title: 24h_iNOS_M2_Medium


title: 24h_IFNAR_M1_Vneg_FSL1


title: SUIT-2_Buff medium_2-3 weeks_rep1

description: Human PDAC SUIT-2 cells cultured in Buffered medium at pHe 7.4 for 2-3 weeks, biological rep1

value: 2-3 weeks


title: 24h_IFNAR_M1_Vneg


title: 24h_WT_M3_FSL1


title: PAC022_RNA

description:
Placental Chorionic Villous tissue
PAC022


title: PAC018_RNA

description:
Placental Chorionic Villous tissue
PAC018


title: 24h_IFNAR_M1_Vpos


title: 24h_IFNAR_M1_FSL1


title: PAC023_RNA

description:
Placental Chorionic Villous tissue
PAC023


title: 24h_IFNAR_M1_Medium


title: PAC020_RNA

description:
Placental Chorionic Villous tissue
PAC020


title: PAC015_RNA

description:
Placental Chorionic Villous tissue
PAC015


title: 24h_WT_M3_Medium


title: PAC017_RNA

description:
Placental Chorionic Villous tissue
PAC017


title: 24h_Prx5_M2_Vneg


title: 24h_Prx5_M2_Vpos


title: PAC014_RNA

description:
Placental Chorionic Villous tissue
PAC014


title: PAC012_RNA

description:
Placental Chorionic Villous tissue
PAC012


title: PAC013_RNA

description:
Placental Chorionic Villous tissue
PAC013


title: 24h_Prx5_M2_Medium


title: 24h_IFNg_M4_Vneg


title: PAC011_RNA

description:
Placental Chorionic Villous tissue
PAC011


title: 24h_IFNg_M4_Vpos


title: 24h_IFNg_M4_Medium


title: 24h_NOX2_M4_Vneg


title: PAC010_RNA

description:
Placental Chorionic Villous tissue
PAC010


title: 24h_NOX2_M4_Vpos


title: PAC007_RNA

description:
Placental Chorionic Villous tissue
PAC007


title: PAC008_RNA

description:
Placental Chorionic Villous tissue
PAC008


title: PAC025_RNA

description:
Placental Chorionic Villous tissue
PAC025


title: 24h_Prx5_M2_pIC

description: genes.htseq.normalized.logcpm.prior1_24h


title: 85_TTAGGC_L001

description:
Placental Chorionic Villous tissue
ADL0085


title: 24h_NLRX1_M1_Vneg


title: PAC016_RNA

description:
Placental Chorionic Villous tissue
PAC016


title: 24h_NLRX1_M1_Vpos


title: 24h_NLRX1_M1_pIC


title: 82_ACTGAT_L004

description:
Placental Chorionic Villous tissue
ADL0082


title: 24h_WT_M4_Vneg_FSL1


title: 81_GTGAAA_L003

description:
Placental Chorionic Villous tissue
ADL0081


title: 24h_NLRX1_M1_Medium


title: 83_CTTGTA_L006

description:
Placental Chorionic Villous tissue
ADL0083


title: 80_ATCACG_L005

description:
Placental Chorionic Villous tissue
ADL0080


title: 79_ATGTCA_L003

description:
Placental Chorionic Villous tissue
ADL0079


title: 24h_WT_M4_pIC


title: 24h_WT_M4_Vpos_FSL1


title: 24h_WT_M4_FSL1


title: 24h_WT_M4_Vneg


title: 24h_WT_M4_Vpos


title: PAC009_RNA

description:
Placental Chorionic Villous tissue
PAC009


title: 24h_NOX2_M4_Medium


title: 52_GCCAAT_L005

description:
Placental Chorionic Villous tissue
ADL0052


title: 55_TGACCA_L005

description:
Placental Chorionic Villous tissue
ADL0055


title: 51_GAGTGG_L004

description:
Placental Chorionic Villous tissue
ADL0051


title: 49_ATTCCT_L004

description:
Placental Chorionic Villous tissue
ADL0049


title: PAC006_RNA

description:
Placental Chorionic Villous tissue
PAC006


title: 24h_iNOS_M1_Vpos


title: 24h_iNOS_M1_pIC


title: 50_CGATGT_L005

description:
Placental Chorionic Villous tissue
ADL0050


title: 24h_iNOS_M1_Vneg


title: 47_GCCAAT_L001

description:
Placental Chorionic Villous tissue
ADL0047


title: 46_CCGTCC_L003

description:
Placental Chorionic Villous tissue
ADL0046


title: 24h_iNOS_M1_Medium

description: genes.htseq.normalized.logcpm.prior1_24h


title: 44_TTAGGC_L005

description:
Placental Chorionic Villous tissue
ADL0044


title: 24h_IFNAR_M4_Vneg_FSL1


title: 24h_IFNAR_M4_Vpos_FSL1


title: 24_CAGATC_L002

description:
Placental Chorionic Villous tissue
ADL0024


title: 24h_IFNAR_M4_FSL1


title: 36_CTTGTA_L002

description:
Placental Chorionic Villous tissue
ADL0036


title: 78_GTTTCG_L004

description:
Placental Chorionic Villous tissue
ADL0078


title: 24h_IFNAR_M4_Vpos


title: 24h_IFNAR_M4_Medium


title: 24h_Prx5_M4_pIC


title: 24h_WT_M4_Medium


title: 17_GTGGCC_L004

description:
Placental Chorionic Villous tissue
ADL0017


title: 16_ACAGTG_L001

description:
Placental Chorionic Villous tissue
ADL0016


title: 24h_Prx5_M4_Vneg


title: 15_CGATGT_L001

description:
Placental Chorionic Villous tissue
ADL0015


title: 24h_Prx5_M4_Vpos


title: 14_AGTCAA_L003

description:
Placental Chorionic Villous tissue
ADL0014


title: 12_ACTTGA_L002

description:
Placental Chorionic Villous tissue
ADL0012


title: 24h_IFNg_M3_Vneg


title: 24h_IFNAR_M4_Vneg


title: 6_AGTTCC_L003

description:
Placental Chorionic Villous tissue
ADL0006


title: 24h_IFNg_M3_Vpos


title: 24h_IFNg_M3_Medium


title: 24h_NOX2_M3_Vneg


title: 5_GATCAG_L002

description:
Placental Chorionic Villous tissue
ADL0005


title: 24h_NOX2_M3_Medium


title: 24h_NOX2_M3_Vpos


title: 24h_NLRX1_M4_pIC


title: 7_GGCTAC_L002

description:
Placental Chorionic Villous tissue
ADL0007


title: 26h_PRX5pos_M4_pIC_H2O2_4h

tag: gender

value: Ply I:C_H2O2_2h


title: 20_GTCCGC_L003

description:
Placental Chorionic Villous tissue
ADL0020


title: 19_ACAGTG_L005

description:
Placental Chorionic Villous tissue
ADL0019


title: 26h_PRX5pos_M4_Medium_H2O2_4h


title: 24h_NLRX1_M4_Vpos


title: 24h_Prx5_M4_Medium


title: 24h_iNOS_M3_Vneg


title: 26h_PRX5pos_M4_pIC_Medium_bis

value: Poly I:C_Non-treated


title: 24h_iNOS_M3_pIC


title: 24h_NLRX1_M4_Vneg


title: 26h_PRX5neg_M4_pIC_H2O2_4h


title: 26h_PRX5neg_M4_pIC_Medium_bis


title: 24h_iNOS_M3_Vpos


title: 24h_NLRX1_M4_Medium


title: 24h_iNOS_M3_Medium


title: 26h_PRX5pos_M4_Medium_Medium_bis


title: 3_ATCACG_L001

description:
Placental Chorionic Villous tissue
ADL0003


title: 26h_PRX5neg_M4_Medium_H2O2_4h


title: 4_TAGCTT_L002

description:
Placental Chorionic Villous tissue
ADL0004


title: 26h_PRX5neg_M4_Medium_Medium_bis


title: 26h_PRX5pos_M3_Medium_H2O2_4h


title: 24h_IFNAR_M2_Vneg_FSL1

description: genes.htseq.normalized.logcpm.prior1_24h

value: Ifnar-/-


title: 26h_PRX5pos_M3_pIC_Medium_bis


title: 26h_PRX5pos_M3_pIC_H2O2_4h


title: 24h_IFNAR_M2_FSL1


title: 26h_PRX5pos_M3_Medium_Medium_bis

value: Non-treated


title: 26h_PRX5neg_M1_pIC_Medium_bis


title: 24h_Prx5_M3_pIC


title: 26h_PRX5neg_M1_pIC_H2O2_4h


title: 24h_IFNAR_M2_Vpos


title: 24h_Prx5_M3_Vneg


title: 26h_PRX5neg_M1_Medium_H2O2_4h


title: 24h_Prx5_M3_Vpos


title: 26h_PRX5pos_M2_pIC_H2O2_4h


title: 26h_PRX5neg_M1_Medium_Medium_bis


title: 26h_PRX5pos_M2_pIC_Medium_bis


title: 24h_NOX2_M1_Vneg


title: 26h_PRX5pos_M2_Medium_H2O2_4h


title: 24h_Prx5_M3_Medium


title: 24h_NOX2_M1_Vpos


title: 24h_IFNAR_M2_Vpos_FSL1


title: 26h_PRX5neg_M2_pIC_Medium_bis


title: 26h_PRX5neg_M2_pIC_H2O2_4h


title: 26h_PRX5pos_M2_Medium_Medium_bis


title: 24h_NLRX1_M2_pIC


title: 26h_PRX5neg_M2_Medium_H2O2_4h


title: 24h_NOX2_M1_Medium


title: 24h_IFNAR_M2_Vneg


title: 24h_NLRX1_M2_Vneg


title: 24h_NLRX1_M2_Medium


title: 26h_PRX5neg_M2_Medium_Medium_bis


title: 24h_WT_M1_Vneg_FSL1


title: 24h_WT_M1_Vpos_FSL1


title: 24h_NLRX1_M2_Vpos


title: 26h_PRX5pos_M4_pIC_Medium


title: 24h_WT_M1_FSL1


title: 26h_PRX5pos_M4_Medium_Medium


title: 26h_PRX5pos_M4_Medium_H2O2_2h


title: 24h_WT_M1_pIC


title: 26h_PRX5neg_M4_pIC_H2O2_2h


title: 24h_WT_M1_Vneg


title: 24h_WT_M1_Vpos


title: 26h_PRX5neg_M4_pIC_Medium


title: 26h_PRX5neg_M4_Medium_Medium


title: 24h_WT_M1_Medium


title: 26h_PRX5pos_M4_pIC_H2O2_2h


title: 26h_PRX5neg_M4_Medium_H2O2_2h


title: 8h_iNOS_M2_Vneg


title: 8h_iNOS_M2_pIC


title: 8h_iNOS_M2_Vpos


title: 8h_IFNAR_M1_Medium


title: 8h_Prx5_M2_pIC


title: 8h_IFNAR_M1_Vneg


title: 8h_IFNAR_M1_Vneg_FSL1


title: 8h_IFNAR_M1_FSL1


title: 8h_iNOS_M2_Medium


title: 26h_PRX5pos_M3_pIC_Medium


title: 8h_Prx5_M2_Vneg


title: 8h_IFNAR_M1_Vpos_FSL1


title: 8h_IFNAR_M1_Vpos


title: 26h_PRX5pos_M3_Medium_H2O2_2h


title: 26h_PRX5neg_M1_pIC_H2O2_2h


title: 26h_PRX5neg_M1_Medium_H2O2_2h


title: 26h_PRX5pos_M2_pIC_H2O2_2h


title: 26h_PRX5pos_M3_pIC_H2O2_2h


title: 26h_PRX5pos_M2_Medium_H2O2_2h


title: 26h_PRX5pos_M2_Medium_Medium


title: 26h_PRX5pos_M3_Medium_Medium


title: 26h_PRX5pos_M2_pIC_Medium


title: 26h_PRX5neg_M1_pIC_Medium


title: 26h_PRX5neg_M2_pIC_Medium


title: 26h_PRX5neg_M2_Medium_H2O2_2h


title: 26h_PRX5neg_M2_pIC_H2O2_2h


title: 8h_Prx5_M2_Medium


title: 26h_PRX5neg_M1_Medium_Medium


title: 8h_IFNg_M4_Vneg

value: Ifng-/-


title: 8h_Prx5_M2_Vpos


title: 26h_PRX5neg_M2_Medium_Medium


title: 8h_IFNg_M4_Vpos


title: 8h_NOX2_M4_Vneg


title: 4h_WT-F_M6_H2O2_2h

value: H2O2 2h


title: 8h_NOX2_M4_Vpos


title: 8h_IFNg_M4_Medium


title: 4h_PRX5pos_M3_H2O2_4h

value: H2O2 4h


title: 4h_WT-F_M6_Medium

value: WT


title: 8h_NOX2_M4_Medium


title: 4h_WT-F_M6_H2O2_4h


title: 4h_PRX5neg_M1_H2O2_2h


title: 4h_PRX5pos_M3_H2O2_2h


title: 8h_NLRX1_M1_Medium


title: 8h_NLRX1_M1_pIC


title: 8h_NLRX1_M1_Vpos


title: 4h_PRX5pos_M3_Medium


title: Control_48hpf_Replicate-3

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

description:
Control_48hpf_3
Total RNA isolated from untreated control zebrafish embryos at 48 hpf.

data_processing:
SOAPnuke for read filter.
HISAT2 for genome mapping.
Bowtie2 for reference genome map.
DESeq2 for differential expression.
Genome_build: GCF_000002035.6_GRCz11
Supplementary_files_format_and_content: Excel files with compiled normalized count and clean read files for all samples.
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts.
Supplementary_files_format_and_content: FilterSummary.xlsx: Read percentages.
Supplementary_files_format_and_content: GeneExpressionSummary.xlsx: Clean read and mapping %.

organism: Danio rerio

source_name: Zebrafish embryonic total RNA

extract_protocol:
Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf.
Library prep and sequencing were done on a Beijing Genomics Institute DNBseq-G50 platform, with 100 bl PE.

treatment_protocol: Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6-48 hpf.

tag: tissue

value: whole embryos

tag: developmental stage

value: 48 hpf

value: Control


title: 8h_WT_M4_Vneg_FSL1

tag: strain

value: LgyLRV+- and FSL1


title: 4h_PRX5neg_M1_Medium

value: female


title: 8h_NLRX1_M1_Vneg


title: Control_48hpf_Replicate-4

description:
Control_48hpf_4
Total RNA isolated from untreated control zebrafish embryos at 48 hpf.