title: Cytotrophoblast_control_Input-1

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using MACS2 v2.1.1 with -q 0.05 and --broad.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalization and 100 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig tracks; peak files (BroadPeak)

source_name: Cytotrophoblast

growth_protocol: Cytotrophoblast cells were isolated from term human placentas (n = 2) using an adaptation of the method developed by Kliman et al. (Endocrinology, 1986), as described in Desforges et al (Adv Exp Med Biol, 2015). Isolated cells were plated in culture medium (Dulbecco's modified Eagle's medium and Ham's F‐12 1:1, 10% heat inactivated fetal calf serum, 0.6% glutamine and the antibiotics 1% gentamicin, 0.2% penicillin and 0.2% streptomycin) onto 35 mm culture dishes, at a density of 2.5 × 10^6, and were maintained in primary culture at 37°C in a humidified incubator (95% air–5% CO2).

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 mins, followed by chromatin extraction and sonication. Immunoprecipitation was performed with 10 µg of chromatin for 2.5 µg of anti-H3K27ac or H3K4me3 antibody. DNA was purified using the GeneJET PCR purification kit (Thermo Fisher).
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.

treatment_protocol: At 66 hours of culture, matched cell samples had control media or 25(OH)D added to a final concentration of 20 μM and were cultured for a period of 24 hours before collection at 90 hours.

value: Cytotrophoblast

tag: treatment

value: Control

tag: chip antibody


title: Cytotrophoblast_control_H3K4me3-1

status: Public on Feb 25 2021

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

value: anti-H3K4me3 (Diagenode C15410003)


title: Cytotrophoblast_vitD_H3K27ac-1

value: anti-H3K27ac (Diagenode C15410196)


title: Cytotrophoblast_vitD_H3K4me3-1


title: spike for sgPofut1_ day 5 HWT004

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

description: spike for sgPofut1_ day 5

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: P14 cells transduced with indicatd sgRNAs were sorted from spleen after LCMV-Armstrong infection.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain

tag: sample type


title: sgPofut1_day 5 HWT003

description: sgPofut1_day 5

value: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen


title: Cytotrophoblast_control_H3K27ac-1


title: Col-0 infected by Fo5176 48HPI R1

city: Xi'an

first: Li

last: Guo

state: Shaanxi

address: 28 Xianning West Road

country: China

institute: Xi'an Jiao Tong University

description: 48 HOURS post inoculation

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
DATA FILTERING: java -jar trimmomatic-0.32.jar PE -phred33 control_a.fq control_b.fq control_aPaired.fq control_aUnpaired.fq control_bPaired.fq control_bUnpaired.fq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:25 MINLEN:36
Mapping using Tophat and bowtie
Transcript assembly using Cufflinks
Differential gene expression called using Cuffdiff
Genome_build: Arabidopsis thaliana TAIR10, Fusarium oxysporum 5176 genome, F. oxysporum 47 genome

organism: Arabidopsis thaliana

source_name: plant roots

growth_protocol: Arabidopsis thaliana Col-0 seeds (ARBC Ohio State University) were germinated on autoclaved MetroMix360® potting mix and allowed to grow in growth chamber with a photoperiod of 14-hour light and 10-hour dark at 24 C.

extract_protocol:
Total RNAs were extracted from leaves of healthy and infected basil plants using Trizol reagent (Thermo Fisher Scientific, MA) following manufacturer’s protocol. After removal of genomic DNA by DNase I (New England Biolabs, MA) treatment, RNA samples were quantified using NanoDrop 1000 (Thermo Fisher Scientific, MA) and assessed for integrity using Agilent Bioanalyzer 2100 (Agilent, MA).
Library construction was conducted using Illumina TruSeq mRNA library preparation kit (Illumina, CA)

treatment_protocol: For F. oxysporum infection, Arabidopsis plants of 14 days old were root-dipped for 30 seconds in 1x106 spores/ml fungal spore suspension of FO5176 or FO47 and sterile dH2O for control. Inoculated plants were planted in autoclaved potting mix and incubated in 28C growth chamber of the same photoperiod as above.

tag: tissue

value: roots

tag: ecotype

tag: pathogen

value: Fusarium oxysporum 5176


title: Col-0 infected by Fo5176 24HPI R3

description: 24 HOURS post inoculation


title: Col-0 infected by Fo47 24HPI R3

description: 24 HOURS post inoculation

value: Fusarium oxysporum 47


title: Col-0 infected by Fo5176 24HPI R2

description: 24 HOURS post inoculation


title: Col-0 infected by Fo5176 96HPI R3

description: 96 HOURS post inoculation


title: Col-0 infected by Fo5176 12HPI R3

description: 12 HOURS post inoculation


title: Col-0 infected by Fo5176 12HPI R2

description: 12 HOURS post inoculation


title: Col-0 infected by Fo5176 12HPI R1

description: 12 HOURS post inoculation


title: IgG_ChIP

city: Miwaukee

first: Katelyn

middle: Elizabeth

last: Heimbruch

state: Wisconsin

address: 8727 Watertown Plank Road

institute: Medical College of Wisconsin

description: H3K27me3 ChIP

data_processing:
Reads were aligned with Bowtie2 to mm10, using default parameters on basepairtech.com
Peaks were called using MACS2, using default parameters on basepairtech.com
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: murine BM

growth_protocol: Bone marrow was isolated from Smc3+/f or WT mice that were treated with pIpC to induced excision of one Smc3 allele. Cells were collected after one week in passage.

extract_protocol:
H3K27me3 antibody used: Millipore-Sigma 07-449. ChIP DNA was isolated by phenol-chloroform isolation.
ChIP libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: During passaing, cells were treated with 100uM DOT1L inhibitor (EPZ-5676) or vehicle (DMSO).

tag: genotype

tag: inhibitor or dmso

value: DMSO

value: IgG


title: spike for sgPofut1_ day 5 HWT002

description: spike for sgPofut1_ day 5


title: Input_ChIP

description: H3K27me3 ChIP

value: none (input)


title: Col-0 water control R3

description: 12 HOURS post inoculation


title: Col-0 water control R1

description: 12 HOURS post inoculation


title: Col-0 water control R2

description: 12 HOURS post inoculation


title: Smc3het_Inhibitor_ChIP_2

description: H3K27me3 ChIP

value: Inhibitor


title: Smc3het_Inhibitor_ChIP_3

description: H3K27me3 ChIP


title: Smc3het_DMSO_3

description: H3K27me3 ChIP


title: Smc3het_Inhibitor_ChIP_1

description: H3K27me3 ChIP


title: Smc3het_DMSO_1

description: H3K27me3 ChIP


title: A5HG Hindbrain

city: New York

first: Viviane

last: Tabar

state: New York

address: 1275 York Avenue

department: Department of Neurosurgery

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Quality of reads was checked for each sample using FastQC (XX)
After removing low-quality reads and library adaptors, reads were mapped to the human genome (hg38) using HISAT2 (Galaxy Version 2.0.5.2).
The number of reads for each gene was counted using featureCounts (Galaxy Versin 1.4.6.p5).
After removing small RNA (tRNAs, rRNAs, and snoRNAs) and transcripts shorter than 300 bp, values were normaliozed as TPM (Transcript Per Kilobase Million).
Genome_build: hg38
Supplementary_files_format_and_content: ProcessedDataMatrix_Final.txt (Tab-delimited text file containing TPMs)

source_name: Neural progenitor cells (NPCs)

growth_protocol: hESC-derived NPCs were maintained in neural differentiation medium (DMEM/F12, supplemented with N2, NeuroCult SM1, BDNF and ascorbic acid) as 3D neural spheroids.

extract_protocol:
Neural spheroids were dissociated using Papain Dissociation System (Worthington Biochemical) and HES5 reporter-positive cells were isolated by FACS. Total RNA was extracted using RNA Clean & Concentrator Kit (Zymo Research) following the manufacturer's instruction.
Poly A selected RNAs were subjected to paired-end library construction using TruSeq RNA Library Prep Kit

treatment_protocol: ATRX and/or p53 mutations were introduced into H1 hESCs by CRISPR/Cas9 gene editing. Expression casette that expresses wildtype or G34R-mutant histone H3.3 variant under HES5 promoter was lentivirally transduced into hESCs. Engineered hESC lines were differentiated into ventral forebrain NPCs or ventral hindbrain NPCs using chemically defined protocols.

value: hESC-derived Hindbrain NPCs

tag: mutations

value: H3.3 G34R + p53/ATRX DKO


title: WT_Inhibitor_ChIP_3

description: H3K27me3 ChIP


title: Smc3het_DMSO_2

description: H3K27me3 ChIP


title: 5HG Hindbrain


title: 5HW Hindbrain

value: H3.3 wildtype + p53 KO


title: A5HW Hindbrain

value: H3.3 wildtype + p53/ATRX DKO


title: A5HG Forebrain rep3


title: MHW Hindbrain

value: H3.3 wildtype


title: A5HG Forebrain rep2

value: hESC-derived Forebrain NPCs


title: WT_DMSO_ChIP_3

description: H3K27me3 ChIP


title: WT_Inhibitor_ChIP_1

description: H3K27me3 ChIP


title: MHG Hindbrain


title: WT_DMSO_ChIP_2

description: H3K27me3 ChIP


title: A5HW Forebrain rep3


title: WT_DMSO_ChIP_1

description: H3K27me3 ChIP


title: WT_Inhibitor_ChIP_2

description: H3K27me3 ChIP


title: A5HW Forebrain rep2


title: Cd4CrePofut1_WT 3

source_name: empty vector-transduced WT P14 cells at day 7.5 post-infection from spleen

growth_protocol: WT or Pofut1-null P14 cells with or without NICD co-expression were sorted from spleen after LCMV-Armstrong infection.

tag: transduction

value: empty vector

tag: genotype/variation

value: WT


title: Smc3het_Inhibitor_RNA_3_1repeat

data_processing:
Reads were aligned to mm10 using STAR, with default parameters on basepairtech.com
Cufflinks was used to estimate the transcript abundances
DESeq was used to identify differential gene expression
Genome_build: mm10
Supplementary_files_format_and_content: gtf files (output from cufflinks)

extract_protocol:
RNA was isolated using Trizol.
RNA libraries were created following the NEBNext Ultra RNA Library Prep Kit.

value: bone marrow

value: DOT1L inhibitor (EPZ-5676)


title: Smc3het_Inhibitor_RNA_1


title: A5HW Forebrain rep1


title: 5HG Forebrain rep1


title: Smc3het_DMSO_RNA_1


title: MHG Forebrain rep2


title: WT-Inhibitor_RNA_3_1repeat


title: 5HW Forebrain rep1


title: WT-Inhibitor_RNA_1


title: WT-Inhibitor_RNA_2


title: MHG Forebrain rep1


title: WT-DMSO_RNA3_1repeat


title: A5HG Forebrain rep1


title: MHW Forebrain rep2


title: MHW Forebrain rep1


title: WT-DMSO_RNA2


title: WT-DMSO_RNA1


title: Smc3het_Inhibitor_RNA_2


title: Ctl 7

city: Los Angeles

first: Yen-Wei

last: Chen

address: 650 Charles E. Young Dr. South  16-035 Center for Health Sciences

department: IDP Molecular Toxicology

institute: University of California, Los Angeles

data_processing:
Data quality checks were performed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and low quality reads were trimmed with Trim_Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
RNA-seq reads passing quality control were mapped to Rattus novegicus transcriptome (Rnor6) and quantified with Salmon.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab limited files containing raw counts of each sample

organism: Rattus norvegicus

source_name: Ctl_primary hippocampus tissue

growth_protocol: Juvenile male Sprague Dawley rats (Envigo; arrival post natal day (PN) 26-28; 50-70g) were housed individually in standard conditions with a 12:12 light/dark cycle. All rats had ad libitum access to water and Lab Diet 5001 (PMI Nutrition International, Brentwood, MO; 29.8 % kcal from protein, 13.4% kcal from fat, 56.7% kcal from carbohydrate), with modifications where noted. All experiments were performed in accordance with the approval of the Animal Care and Use Committee at the University of Southern California.

extract_protocol:
Total RNA was extracted according to manufacturer’s instructions using RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). Total RNA was checked for degradation in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA)
libraries were prepared from 1 ug of total RNA using a NuGen Universal Plus mRNA-seq Library Prep Kit (Tecan Genomics Inc. Redwood City, CA).

treatment_protocol: As shown in the sample 'characteristics: treatment'

value: Sprague Dawley

tag: Sex

value: male

tag: experitment design

value: Experitment design 1

tag: treatment group

value: Ctl

value: PN 26-28 rats  treated with an extra bottle of reverse osmosis-filtered water till PN104

value: Primary hippocampus tissue


title: IgG CUT&RUN

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

description: CUT&Tag followed by Illumina sequencing

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
The trimmed reads were aligned to the reference rat genome version Rn5 with the program BOWTIE v2.3.4.1.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8. Peaks were called using the program MACS v2.1.2 using the narrow and broad peaks mode for Cut&Run-Seq,
Rn5
bed files were generated by MACS1.4

source_name: OPC culture

growth_protocol: Mouse or rat OPCs were isolated from P6 cortices of mice by immunopanning with antibodies against Ran-2, GalC and O4 sequentially. Briefly, cerebral hemispheres were diced and digested with papain at 37°C. Following gentle trituration, cells were resuspended in a panning buffer containing insulin (5 µg/ml) and then incubated at room temperature sequentially on three immunopanning dishes: Ran-2, anti-GalC, and O4. O4+GalC− OPCs were released from the final panning dish with trypsin. To induce the differentiation of OPCs, mitogens in the culture medium (FGF and PDGFaa) were replaced with T3, NAC and CNTF.

extract_protocol:
Two million cells were harvested by centrifugation (600 g, 3 min) and cells were washed twice in 1 ml Wash Buffer (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1x Roche cOmpleteTM), followed by addition of 10 µl pre-activated concanavalin A coated magnetic beads (Bangs Laboratories-BP531). Tubes were held on mixing platform at RT for 10 mins, then placed on a magnet stand and pulled off the liquid. Cells were resuspended in 100 µl cold Antibody Buffer and 1 µl antibody (TET1, Active Motif #61943) was added for incubating on nutator overnight at 4ºC. Beads with cells were washed twice in 1 ml Digitonin Buffer (20 mM HEPES-KOH pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1x Roche cOmpleteTM,0.05% digitonin), and resuspended in 50 µl Digitonin Buffer with addition of 2.5 µl CUTANA pAG-MNase (20x stock). After 10 min incubation at RT, samples were washed twice in 1 ml Digitonin Buffer and changed to 50 µl cold Digitonin Buffer. Then tubes were placed in a metal block in ice-water and quickly mixed with 100 mM CaCl2 to a final concentration of 2 mM. The reaction was quenched by the addition of 50 µl Stop Buffer. Cleaved fragments were liberated into the supernatant by incubating the tube for 30 min at 37ºC. DNA fragments were purified by Qiagen MinElute PCR Purification Kit from the supernatant and used for the construction of sequencing libraries.
Libraries were prepared for Illumina sequencing with Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645).
CUT&Tag followed by  Illumina sequencing

tag: strain stage

value: OPC

tag: strain name

value: Wild Type


title: TET1 CUT&RUN

description: CUT&Tag followed by Illumina sequencing


title: Smc3het_DMSO_RNA_2

tag: treatment

value: DMSO


title: hMeDIP-seq-OL-1

description: hMeDIP-seq

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
After passing Solexa CHASTITY quality filter, the clean reads were aligned to Mus_musculus genome (UCSC MM10) using BOWTIE software (V2.1.0).
Aligned reads were used for peak calling, both mRNA and LncRNA associated hMeDIP enriched regions (peaks) with statistically significant were identified for each sample, using a q-value threshold of 10-4 by MACS v2.
mm10
wig files were generated by MACS14

source_name: OL culture

extract_protocol:
For hMeDIP-seq, genomic DNA was sonicated to ~200-800bp with a Bioruptor sonicator (Diagenode). 800 ng of sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina genomic DNA protocol (FC-102-1002, Illumina). After agarose size-selection to remove unligated adapters, the adaptor-ligated DNA was used for immunoprecipitation (IP) with a mouse monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode, C15200200). For this, DNA was heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μL primary antibody overnight at 4°C with rocking agitation in 400 μL IP buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 20 μL of magnetic beads were added and incubated for an additional 2 hours at 4°C with agitation. After IP, a total of five washes were performed with ice-cold IP buffer. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/mL proteinase K for 2 hours at 65°C and then allowed to cool down to room temperature. DNA was then purified using Qiagen MinElute columns and eluted in 16 μL EB (Qiagen).
14 cycles of PCR were performed on 5 μL of the immunoprecipitated DNA using the single-end Illumina PCR primers. The resulting products were purified with Qiagen MinElute columns, after which a final size selection (300-1,000 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Agilent 2100 Bioanalyzer.
hMeDIP-seq

value: Differentiated OPC


title: hMeDIP-seq-OL-2

description: hMeDIP-seq


title: 5HW Forebrain rep2

tag: cell type

value: H3.3 wildtype + p53 KO


title: MHCII KO CD8-3

city: Worcester

first: Samuel

last: Behar

state: MA

address: 368 Plantation street, AS8-2006

institute: University of Massachusetts Medical School

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
DESeq2 was used for differential gene expression analysis from the extracted gene hit counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Normalized counts after differential gene expression analysis by DESeq2

source_name: Lung CD8 T cells

extract_protocol:
RNA was extracted from purified CD8 T cells using Qiagen RNeasy mini kit.
Library was constructed by polyA selection using illumina protocol

treatment_protocol: WT or MHC II KO mice were infected with aerosolized Mtb (strain Erdman), and total CD8 T cells were purified from lungs unsing anti-CD8 beads at 8 weeks post infection.

tag: strain

value: Lung

value: CD8 T cells

value: MHCII KO

tag: infection

value: aerosolized Mtb (strain Erdman)


title: Sug 7

source_name: Sug_primary hippocampus tissue

value: Sug

value: PN 26-28 rats  treated with 11% weight-by-volume (w/v) solution containing monosaccharide ratio of 65% fructose and 35% glucose in reverse osmosis-filtered water till PN104

tag: tissue


title: MHCII KO CD8-2


title: MHCII KO CD8-1


title: WT CD8-3

value: WT


title: Sug 6

value: Sprague Dawley

value: male


title: Ctl 6

value: Experitment design 1

value: Ctl


title: Ctl 5

value: PN 26-28 rats  treated with an extra bottle of reverse osmosis-filtered water till PN104

value: Primary hippocampus tissue


title: 5HG Forebrain rep2

value: hESC-derived Forebrain NPCs


title: WT CD8-2


title: WT CD8-1


title: Tim3-CX3CR1+YFP+PD1+_54

city: St. Louis

first: Saravanan

last: Raju

email: sraju89@gmail.com, rajus@wustl.edu

state: MO

address: 660 S Euclid Avenue

institute: Washington University in St. Louis

description: ind11 GGCTAC 54-3

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Performance of the samples was assessed with Spearman correlations, and a Multi-Dimensional Scaling plot, and hierarchical clustering. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 and Pathview was used to display heatmaps or annotated KEGG graphs across groups of samples for each GO term or KEGG pathway (respectively) with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.
To find the most critical genes, the raw counts were variance stabilized with the R/Bioconductor package DESeq2 and was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA.  Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data.  An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coeffiecients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. For modules where the eigengene correlation exceeded 60%, edge networks were created and visualized with VisAnt and then filtered by a lower limit edge weight of 0.1 to find the most highly connected genes that act as hub genes. These hub genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler.  Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The hub genes for each significant module were then assessed for whether or not those features were also found to be significantly differentially expressed via Limma.
Genome_build: m_musculus reference build Ensembl_R76

source_name: Sorted T cells

growth_protocol: Prdm1-EYFP mice on a B6 background were infected with LCMV-c13. Splenocytes were harvested on Day 16 of infection, and purified using FACS

extract_protocol:
Cells were lysed in Trizol and processed using Zymo Direct-Zol Kit
Libraries were prepared using NEBNext Ultra II RNA Kit

value: splenocytes

tag: cell population


title: Sug 5


title: Sug 4


title: Tim3-CX3CR1-YFP-PD1+_54

description: ind12 CTTGTA 54-4


title: Tim3+CX3CR1-YFP+PD1+_54

description: ind9 GATCAG 54-1


title: Sug 3


title: Tim3+CX3CR1+YFP+PD1+_54

description: ind10 TAGCTT 54-2


title: Ctl 3


title: Sug 2


title: Tim3-CX3CR1+YFP+PD1+_49

description: ind7 CAGATC 49-3


title: Ctl 1


title: Tim3+CX3CR1-YFP+PD1+_49

description: ind5 ACAGTG 49-1


title: Tim3+CX3CR1+YFP+PD1+_49

description: ind6 GCCAAT 49-2


title: Tim3-CX3CR1-YFP-PD1+_49

description: ind8 ACTTGA 49-4


title: Tim3-CX3CR1+YFP+PD1+_45

description: ind3 TTAGGC 45-3


title: Sug 1


title: Abx_Sal 7

source_name: Abx_Sal_primary hippocampus tissue

value: Experitment design 2

value: PN 26-28 rats  treated twice daily gavage of a cocktail of antibiotics consisting of Vancomycin (50 mg/kg), Neomycin (100 mg/kg), and Metronidazole (100 mg/kg) along with 1 mg/mL of ampicillin in their drinking water for 7 days, followed by gavage of saline till PN 83


title: Abx_Sal 6


title: Tim3-CX3CR1-YFP-PD1+_45

description: ind4 TGACCA 45-4


title: Sal_Sal 7

source_name: Sal_Sal_primary hippocampus tissue

value: PN 26-28 rats treated twice daily of saline for 7 days and sacrified on PN 83


title: Abx_Sal 5


title: Tim3+CX3CR1+YFP+PD1+_45

description: ind2 CGATGT 45-2


title: Tim3+CX3CR1-YFP+PD1+_45

description: ind1 ATCACG 45-1


title: Ctl 4


title: Shiraz_Infected _5

city: Melbourne

first: Shiraz

last: Tyebji

state: Victoria

address: 1G Royal Parade

department: Infectious diseases and immune defence division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: CAGRF18125-Infected.vs.Control-all_genes.csv

data_processing:
Read quality was assessed using FastQC and per base read quality was determined to be above Q30 for >95% bases across all 10 samples.
Reads were then screened for the presence of any Illumina adapter/overrepresented sequences and cross-species contamination.
Cleaned sequence reads were aligned against the Mus musculus genome (build version mm10) using the STAR aligner (v2.5.3a) to map reads to the genomic sequences. Reads were mapped to each known gene and summarised using the Featurecounts (v1.5.3) utility of the subread package.
Multi-mapping was turned on and features mapped to the GRCm38 Gencode GTF containing small RNA annotations.
The transcripts were assembled with the Stringtie tool (v1.3.3) utilising the reads alignment with M6 and reference annotation based assembly option (RABT) which generates assembly for known and potentially novel transcripts. The Gencode annotation containing both coding and non-coding annotation for mouse genome version GRcm38 (Ensemble release 81) were used as a guide.
edgeR (v3.22.3) was used to perform normalisation and differential expression (DE) analysis using R-3.5.0.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet contains raw gene count for each sample, and includes Log Fold Change, Log Count Per Million, P value and False Discovery Rate value

source_name: Sperm

extract_protocol:
25 days post-infection, mature spermatozoa from control and infected mice was collected using the swim up method. Briefly, left and right cauda epididymis were dissected, placed into 20ul sterile PBS, chopped using a sterile scalpel and left for 5 min at room temperature for the sperm to be released. Fresh sperm samples were homogenised using the QIAzol lysis reagent and immediately processed for total RNA extraction using the miRNeasy Mini Kit (Qiagen, # 217004).
1000 ng of total RNA was used for library prep using NEB’s NEBNextÒ Multiplex Small RNA Library Prep Set (New England BioLabs Inc.)

treatment_protocol: Male mice were intraperitoneally injected with tachyzoites of Toxoplasma Prugniuand strain (Pru) that were maintained by passage in human foreskin fibroblast cell cultures. Parasites, harvested using a 27-guage needle, were pelleted and resuspended in phosphate-buffered saline (PBS) and then counted.Six- to eight-week-old male mice, randomly assigned to either control or infected groups, received 100ul PBS (vehicle control) or 50,000 tachyzoites resuspended in 100ul PBS, and were monitored and weighted daily for the next 21 days. Mice were housed with a 12-hr light-dark cycle, with access to food ad libitum. To establish a chronic infection, mice were provided with sulfadiazine sodium (Sigma) in drinking water (100ug/ul) from day 5 to 10 post-infection.

tag: week-post treatment

tag: infection status

value: Infected


title: Sal_Sal 6


title: HTHuGene11_050911K_MT230_Adult-Cb-3

city: Toronto

first: Michael

middle: David

last: Taylor

state: Ontario

address: 555 University Avenue

department: Division of Neurosurgery

country: Canada

institute: SickKids

hyb_protocol: As directed by affimetrix

scan_protocol: As directed by affimetrix

data_processing: Data were processed using software packages from R/Bioconductor. CEL files were read using functions from the oligo package. Quality control was performed using the arrayQualityMetrics package. Background correction, normalisation and summarisation was performed using RMA. Feature were then annotated with their gene symbols and Entrez IDs and probes mapping to multiple gene symbols were filtered out.

source_name: cerebellum

label_protocol: As directed by affimetrix

extract_protocol: RNA has been obtained from the Biochain company

value: cerebellum

tag: developmental stage

value: adult


title: Abx_Sal 3


title: Shiraz_Infected _2


title: Shiraz_Infected _4


title: Sal_Sal 4


title: Shiraz_Infected _3


title: Ctl 2


title: Shiraz_5

value: Uninfected


title: Abx_Sal 4


title: Abx_Sal 2


title: Shiraz_4


title: Shiraz_2


title: Sal_Sal 5


title: Sal_Sal 3


title: Sal_Sal 2


title: Abx_Pb 8

source_name: Abx_Pb_primary hippocampus tissue

value: PN 26-28 rats  treated twice daily gavage of a cocktail of antibiotics consisting of Vancomycin (50 mg/kg), Neomycin (100 mg/kg), and Metronidazole (100 mg/kg) along with 1 mg/mL of ampicillin in their drinking water for 7 days, followed by gavage of a 1:1 ratio of Parabacteroides distasonis and Parabacteroides johnsonii thirty six hours after the last ABX treatment till PN 83


title: Shiraz_1


title: Sal_Sal 1


title: Abx_Pb 5


title: OCP_ZA_8_run2: OCP_RNASeq - Osteoclast_precursors ZA_treatment replicate_8 run_2

city: Boston

first: Jessalyn

last: Ubellacker

address: 4 Blackfan Circle

institute: Harvard University

description: Sample used in batch correction and final comparison for OCP RNASeq experiment

data_processing:
Pseudoalignment with salmon, version ,0.8.2
Import and summarize salmon generated counts with tximport, version 1.6.0
Batch correct for sequencing run with RUVSeq and replicate samples, k=3(for OCP-RNASeq analysis), retain replicate sample with most reads
Analyze differential expression with DESeq2 BioConductor package, version 1.16.1 (using batch correction factors from RUVSeq in the OCP-RNASeq analysis)
Genome_build: mm10
Supplementary_files_format_and_content: comma separated format, rawCounts matrix file contains raw counts as generated by Salmon and imported by tximport (these counts were used for the DESeq2 analysis), tpm matrix contains transcripts per million normalized counts as calculated by tximport

source_name: Osteoclast precursors

growth_protocol: 6-7 week old C57BL/6J  female mice were purchased from The Jackson Laboratory (Bar Harbor, ME). All animal procedures were performed in accordance with the ethics and regulations of Brigham & Women’s Hospital Institutional Animal Care and Use Committee (protocol approval 2017N000056), Boston Children’s Hospital Institutional Animal Care and Use Committee (protocol approval 12-11-2308R), and Massachusetts General Hospital (protocol approval 2017N000023).

extract_protocol:
RNA isolated from mouse bone marrow was subject to quality control using the Bioanalyzer (Agilent). BMCs were prepared for flow cytometry by suspension in sterile PBS containing 2% FBS. Cells were labeled with appropriate antibodies for 30 minutes at 4°C. Gating was used to exclude debris, cell clumps, and dead cells (using 7-aminoactinomycin D; 7-AAD Viability Staining Solution (BioLegend, 420404).Prior to sorting of the M/OCP populations, the Murine Direct Lineage Cell Depletion Kit (Miltenyi Biotec Inc., 130-110-470) was used to enrich for Lin- populations, which was confirmed by flow cytometry for the markers in the lineage cocktail. Myeloid/osteoclast progenitor cell (M/OCP) populations were defined as Lineage- CD115+.  Antibody panel includes: Pacific BlueTM anti-mouse Lineage Cocktail (BioLegend, 133310: CD3-, Ly-6G/Ly6-C-, Cd11b-, CD45R-, TER119-) and Alexa Fluor® 488 anti-mouse CD115 (CSF-1R; BioLegend, 135511).
RNA was converted into a DNA library using the Ultra RNA Library Prep Kit for Illumina (New England BioLabs). After further quality control, libraries were sequenced on the HiSeq 2000 (Illumina).

treatment_protocol: Zoledronic acid (ZA) [1-hydroxy-2-(1H-imidazole-1-yl)ethylidene-bisphosphonic acid] (Novartis Pharmaceuticals, Cambridge, MA) was dissolved in 1X Hank’s Balanced Buffer Solution (Gibco) and stored at 4°C until use. ZA was administered to mice at a dose of 100 µg/kg (i.p.). Recombinant human granulocyte colony stimulating factor (G-CSF) (carrier-free, Biolegend #578604) was administered to nude mice each day for 3 days at a dose of 50 µg/kg (i.p.) beginning one day after administration of ZA, and C57BL/6 mice each day for 3 days at a dose of 50 µg/kg (i.p.) beginning 2 days after administration of ZA. For G-CSF depletion experiments, nude mice were treated with 100 µg/kg (i.p.) G-CSF antibody (R&D Systems, MAB414100) or the 100 µg/kg (i.p.) isotype control IgG (R&D Systems, MAB005) six hours prior to intracardiac injection of tumor cells.

tag: age

value: 6-7 weeks

value: Osteoclast precursors

value: ZA

tag: biological replicate

tag: sequencing batch


title: Abx_Pb 7

value: Sprague Dawley

tag: Sex

value: male


title: Abx_Pb 3

tag: experitment design


title: OCP_ZA_6_run2: OCP_RNASeq - Osteoclast_precursors ZA_treatment replicate_6 run_2


title: Shiraz_Infected _1


title: OCP_ZA_7_run2: OCP_RNASeq - Osteoclast_precursors ZA_treatment replicate_7 run_2


title: OCP_ZA_3_run1: OCP_RNASeq - Osteoclast_precursors ZA_treatment replicate_3 run_1


title: OCP_ZA_5_run2: OCP_RNASeq - Osteoclast_precursors ZA_treatment replicate_5 run_2


title: Abx_Pb 2

tag: treatment group


title: Abx_Pb 1


title: OCP_GCSF_3_run2: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_3 run_2

description: Sample used in batch correction for OCP RNASeq experiment

value: G-CSF


title: Shiraz_3


title: OCP_GCSF_4_run2: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_4 run_2


title: scRNA-seq_gata2b ko 1

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
The paired-end fastq files have been reorganized into a single-end raw file per sample. The read name contains the gel barcode and UMI. The gel barcode is composed of two sets of 8 sequences separate by a dash: NNNNNNNN-NNNNNNNN. The UMI is a 6 bp sequence that follows the gel barcode.
samples were processed by the Harvard Medical School Single Cell core (https://singlecellcore.hms.harvard.edu/) using inDrops single cell barcoding and sequencing methods. Library preparation with inDrop v3 was completed by the core. The libraries were sequenced on NextSeq system, with 75-cycle kit, with pair-end reads (Read1: 61 cycles, Read2: 14 cycles, Index 1: 8 cycles, Index 2: 8 cycles). BCL files were analyzed with the Cell Ranger pipeline (version 3.1.0). The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz10 reference and generated the single cell count matrix. Gene-level counts were imported into R using the Seurat suite version 3.0 (Stuart et al., 2019).
Genome_build: GRCz10
Supplementary_files_format_and_content: rds

organism: Danio rerio

source_name: sorted marrow cells

growth_protocol: Freshly isolated kidney marrow cells from euthanized adult zebrafish.

extract_protocol:
After euthanasia, the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin, placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40-μm nylon mesh. The samples were sorted into 1x PBS with 0.04% BSA while kept cold at 4C (both sample tube being sorted and collection tube). Samples were dissected and sorted in a staggered fashion, every 45-60min, were kept on ice after sorting and walked to the processing core every 45-60min for processing for inDrops single cell RNA sequencing.
Library preparation with inDrops v3 scRNA sequencing was performed by the Harvard Medical School single-cell core.  https://github.com/indrops/indrops

treatment_protocol: Cells were sorted into 1x PBS with 0.04% BSA over 30 minutes per sample and walked to the single-cell core at Harvard Medical school on ice, every 45-60 min for processing.

value: sorted marrow cells

value: 4 months old

tag: genotype

value: gata2b ko


title: scRNA-seq_gata2b ko 3


title: OCP_GCSF_2_run2: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_2 run_2


title: OCP_GCSF_5_run2: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_5 run_2


title: scRNA-seq_gata2b ko 2


title: OCP_GCSF_3_run1: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_3 run_1


title: OCP_GCSF_2_run1: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_2 run_1


title: OCP_GCSF_1_run1: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_1 run_1


title: scRNA-seq_gata2b het 2

value: gata2b het


title: scRNA-seq_wildtype 3

value: wildtype


title: scRNA-seq_gata2b het 1


title: OCP_GCSF_1_run2: OCP_RNASeq - Osteoclast_precursors G-CSF_treatment replicate_1 run_2


title: scRNA-seq_wildtype 2


title: Abx_Pb 4

value: Experitment design 2

value: Primary hippocampus tissue


title: OCP_CTL_2_run1: OCP_RNASeq - Osteoclast_precursors No_treatment replicate_2 run_1

value: No treatment


title: scRNA-seq_wildtype 1


title: OCP_CTL_2_run2: OCP_RNASeq - Osteoclast_precursors No_treatment replicate_2 run_2


title: OCP_BOTH_5_run2: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_5 run_2

value: ZA & G-CSF


title: ATAC-seq_gata2b ko 4

description:
isolated nuclei
10x Genomics scATACseq

data_processing:
two approaches of single-cell ATAC sequencing (scATAC-seq) – one method used in Jason Buenrostro’s lab called sci-ATAC-seq (LaFave et al. Cancer Cell 2020, in press), and the other using 10x Gemonics scATAC-seq platform.
Sci-ATAC profiles for all cells were first merged into a single alignment file. Merged sci-ATAC alignment file and 10x Genomics profiles for each sample were used as inputs for peak calling with MACS v2.1.2 (MACS2) (Zhang et al., 2008). All default options were used, with the following flags explicitly set: --nomodel, --nolambda, --keep-dup all, --call-summits. Only peak summits with FDR < 0.01 were retained. Next, the called peak summits were first padded with 150 base pairs (bp) at either end to obtain fixed-width peak windows. Using the generated peak region list, the number of reads overlapping a given peak window was determined for each unique cell barcode tag. This generated a peak by cell counts matrix corresponding to ATAC sequencing reads in peaks for each cell profiled. Only cells having FRIP > 0.3 and a minimum of 500 unique nuclear reads per cell were retained for downstream analyses, resulting in a total of 12,354 cells.
Genome_build: GRCz10
Supplementary_files_format_and_content: rds

source_name: unsorted whole kidney marrow cells

extract_protocol:
After euthanasia, the adult zebrafish were subjected to cardiac bleeding to remove most mature erythrocytes from the marrow. The zebrafish were then dissected at room temperature and the dissected marrow was placed into 500ul of 0.9x PBS with 2% FBS and 1 USP units/mL heparin, placed on ice. The marrow samples were then mechanically dissociated by repeated pipetting into single cell suspension and passed through a 40-μm nylon mesh. All 8 samples were washed by pelleting the cells at 350 x g for 5 min at 4C and resuspended in 300ul of 1x DPBS with 0.04% BSA (Gemini Bio-Products). Sci-ATAC samples were fixed and protocol for sample preparation was followed. 10x Genomics samples were subjected to nuclear isolation with lysis of 7 minutes, followed by 10x Genomics single-cell ATAC sequencing protocol as per manufacterer's recommendations.
Single-cell ATAC sequencing, sci-ATAC (LaFave et al. Cancer Cell 2020, in press) and 10x genomics. We followed the 10x genomics sample preparation protocol and the 10x genomics single cell ATAC sequencing V1 library preparation

treatment_protocol: No additional treatment for unsorted cells.

value: unsorted whole kidney marrow cells

value: 3 months old


title: ATAC-seq_gata2b ko 2

description:
isolated nuclei
10x Genomics scATACseq


title: OCP_CTL_7_run2: OCP_RNASeq - Osteoclast_precursors No_treatment replicate_7 run_2

value: 6-7 weeks


title: OCP_BOTH_3_run2: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_3 run_2

value: Osteoclast precursors


title: OCP_BOTH_4_run2: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_4 run_2


title: ATAC-seq_gata2b het 2

description:
isolated nuclei
10x Genomics scATACseq


title: ATAC-seq_gata2b ko3

description:
isolated nuclei
10x Genomics scATACseq


title: scRNA-seq_gata2b het 3


title: ATAC-seq_wildtype 3

description:
isolated nuclei
10x Genomics scATACseq


title: ATAC-seq_gata2b het 1

description:
isolated nuclei
10x Genomics scATACseq


title: ATAC-seq_wildtype 2

description:
isolated nuclei
10x Genomics scATACseq


title: OCP_BOTH_2_run1: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_2 run_1


title: ATAC-seq_wildtype 4

description:
isolated nuclei
10x Genomics scATACseq


title: sci-ATAC-seq_wildtype and ko

description:
isolated nuclei
sci-ATAC-seq

value: 11 months old

value: mixed sample (non-demultiplexed)


title: stage16a fetal skin scRNAseq

city: Huntsville

first: Christopher

middle: Bryan

last: Kaelin

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: 10x Genomics version 2 chemistry

data_processing:
Barcoded reads were aligned to the domestic cat genome using 10x Genomics CellRanger (v.3.1) software
Genome_build: felCat9
Supplementary_files_format_and_content: HDF5 with per-molecule information for validly indexed molecules

molecule: polyA RNA

organism: Felis catus

source_name: fetal skin

extract_protocol:
Embryos for single cell RNA sequencing were treated with dispase and the epidermis was removed with gentle scraping using a 15-blade scalpel. Epidermal sheets were dissociated with trypsin and gentle agitation. Red blood cells were removed with a red blood cell lysis solution. Single cell suspensions were incubated with a rat anti-CD49f antibody and enriched using a column-magnetic separation procedure.
Libraries were constructed using 10x Genomics protocol for version2 (stage16a) or version3 (stage15a/b) chemistry

value: fetal skin

value: stage16a (25-28 days post-coitus)

tag: enrichment

value: Enriched for basal keratinocytes with ITGA6 (CD49f)


title: OCP_BOTH_1_run1: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_1 run_1

tag: treatment


title: stage15b fetal skin scRNAseq

description: 10x Genomics version 3 chemistry

value: stage15b (23-25 days post-coitus)


title: stage15a fetal skin scRNAseq

description: 10x Genomics version 3 chemistry

value: stage15a (23-25 days post-coitus)


title: Pofut1_KO4

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

source_name: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen

growth_protocol: P14 cells transduced with indicated sgRNAs were sorted from spleen after LCMV-Armstrong infection.

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

tag: genotype/variation

value: Pofut1 KO

tag: cell type


title: BM_GCSF_2_run2: OCP_RNASeq - Bone_marrow G-CSF_treatment replicate_2 run_2

source_name: Bone marrow

tag: strain

value: Bone marrow

value: G-CSF


title: Pofut1_KO3

value: sgRNA-transduced P14 cells from the dual-color transfer system at day 5 post-infection from spleen


title: BM_CTL_2_run2: OCP_RNASeq - Bone_marrow No_treatment replicate_2 run_2

tag: tissue

value: No treatment


title: BM_ZA_2_run2: OCP_RNASeq - Bone_marrow ZA_treatment replicate_2 run_2

value: ZA


title: Pofut1_spike4

value: Spike P14 cells


title: BM_ZA_2_run1: OCP_RNASeq - Bone_marrow ZA_treatment replicate_2 run_1


title: Pofut1_spike3


title: BM_GCSF_2_run1: OCP_RNASeq - Bone_marrow G-CSF_treatment replicate_2 run_1


title: OCP_BOTH_3_run1: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_3 run_1

value: ZA & G-CSF


title: OCP_BOTH_1_run2: OCP_RNASeq - Osteoclast_precursors Combined_treatment replicate_1 run_2

value: 6-7 weeks


title: Pofut1_spike2


title: Pofut1_spike1


title: Pofut1_KO2


title: BM_CTL_2_run1: OCP_RNASeq - Bone_marrow No_treatment replicate_2 run_1


title: ZA3: BM_RNASeq - Bone_Marrow ZA_treatment replicate_3

description: Sample used in bone marrow RNAseq comparison


title: Pofut1_KO1


title: ZA2: BM_RNASeq - Bone_Marrow ZA_treatment replicate_2


title: GCSF3: BM_RNASeq - Bone_Marrow G-CSF_treatment replicate_3


title: GCSF2: BM_RNASeq - Bone_Marrow G-CSF_treatment replicate_2


title: Epididyaml primary adipocytes - Prmt1 FKO_rep1

city: Seoul

first: Seung-Hoi

last: Koo

address: 145 Anam-Ro, Seongbuk-Gu

department: Life Sciences

country: South Korea

institute: Korea University

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the NCBI. And then, transcript assembly of known transcripts was processed by StringTie v1.3.4d.
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.
Genome_build: mm10

source_name: Epididyaml primary adipocytes

extract_protocol:
Total RNA concentration was calculated by Quant-IT RiboGreen(Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape(Agilent). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit (Illumina, Inc., San Diego, CA, USA). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T oligo‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.
The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase(Invitrogen) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the indexing adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation D1000 ScreenTape  (Agilent Technologies, Waldbronn, Germany). Indexed libraries were then sequenced using the HiSeq4000 platform (Illumina,San Diego, USA) by the Macrogen Incorporated.

value: Epididyaml primary adipocytes

value: Prmt1 adipocyte-specific KO


title: Epididyaml primary adipocytes - Prmt1 FKO_rep2


title: Epididyaml primary adipocytes - Prmt1 f/f_rep3

value: WT


title: NICD_overexpression_ day 7

data_processing:
The Cell Ranger 1.3 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

source_name: sgRNA-transduced P14 cells from the dual-color transfer system at day 7 post-infection from spleen

extract_protocol:
CD8+ T cells were sorted from sgRNA transduced P14 cells from the dual-color transfer system at day 7 post-infection from spleen and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: sgRNA transduced P14 cells

value: NICD-expressing vector- transduced P14


title: Epididyaml primary adipocytes - Prmt1 f/f_rep2


title: "spike for NICDOE"_ day 7

value: empty vector


title: CTL2: BM_RNASeq - Bone_Marrow No_treatment replicate_2


title: GCSF1: BM_RNASeq - Bone_Marrow G-CSF_treatment replicate_1


title: Epididyaml primary adipocytes - Prmt1 f/f_rep1


title: CTL1: BM_RNASeq - Bone_Marrow No_treatment replicate_1


title: sgPofut1_1_day 7

value: sgPofut1-transduced P14 cells


title: MKN-125b_48h_mimic

city: Tianjin

first: ben

last: liu

address: Huanhuxi Road

department: Department of Epidemiology and Biostatistics

institute: Tianjin Medical University Cancer Institute and Hospital

description: Gene expression of transfection after 48 hours after transfection

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for more than 30 minutes in a reaction volume containing 25x fragmentation buffer and 10X Blocking Agent following the manufacturers instructions of Agilent Gene Expression Hybridization Kit(Agilent). On completion of the fragmentation reaction, 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture.  After hybridization, microarrays were washed with GE wash buffer 1 and 2, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately using one color scan setting for 8x60K G3 Microarray Formats(Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)  by G2505 C Micro Array Scanner(Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (Agilent) using default Gene Expression protocol to obtain background. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: gastric cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the Agilent's Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by Qiagen’s RNeasy mini spin columns  (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer.

growth_protocol: The human gastric cancer MKN-45 cells were maintained in RPMI-1640 (GIBCO, USA) supplemented with 10% (v/v) fetal bovine serum (FBS) (GIBCO, USA). Cells were incubated at 37 °C in a humidified atmosphere with 5% CO2 (5 L CO2/95 L atmospheres).

extract_protocol: The whole RNA of MKN-45 cell lines was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for cRNA synthesis and hybridization.

treatment_protocol: 50nM miR-125b mimic or scrambled miRNA control (mimic control) (Shanghai GenePharma, China) were transfected to 50 thousand cells using the Lipofectamine RNAiMAX (Invitrogen, US) according to the manufacturer’s instruction. At 6 hours post-transfection, culture media were replaced with those containing 10% FBS.

tag: cell line

value: gastric cancer cell

value: miR-125b mimic


title: sgPofut1_2_day 7


title: "spike for sgPofut1_3"_ day 7

value: spike for sgPofut1


title: MKN-125b_48h_control

value: control


title: Intact replicate 4

city: Adelaide

first: John

middle: E

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

institute: The University of Adelaide

description: Gene expression data from endometrial total RNA of females 8 hour following mating with intact male

hyb_protocol: Genechips were hybridised overnight at 45 degrees celcius for 17 hours in an Affymetric Hybridisation Oven

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner

data_processing: The microarray data was analyzed using Partek Genomics Suite. .cel files were imported using RMA background correction, Partek's own GC content correction, and mean probe summarization

source_name: Endometrial tissue collected from CBAF1 females 8 hours following mating with intact BALB/c males

label_protocol: Total RNA (300ng) was labelled using the Ambion WT Expression Kit as per the manufacturers instructions

extract_protocol: RNA was extracted using the miRNeasy RNA extraction kit (Qiagen)

treatment_protocol: Females were separated into 3 treatment groups: 1 = Control (virgin unmated estrus females), 2 = Intact (Females mated with intact males), and 3 = Vasectomised (Females mated with vasectomised males).

tag: mating combination

value: Intact Balb/c male x CBAF1 female

value: Endometrium


title: Vasectomised replicate 2

description: Gene expression data from endometrial total RNA of females 8 hour following mating with vasectomised male

source_name: Endometrial tissue collected from CBAF1 females 8 hours following mating with vasectomised BALB/c males

value: Vasectomised Balb/c male x CBAF1 female


title: BOTH3: BM_RNASeq - Bone_Marrow Combined_treatment replicate_3

value: Bone marrow


title: "spike for sgPofut1_2"_ day 7


title: sgPofut1_3_day 7


title: Vasectomised replicate 3


title: Intact replicate 2


title: Vasectomised replicate 4


title: BOTH1: BM_RNASeq - Bone_Marrow Combined_treatment replicate_1

value: ZA & G-CSF


title: Control replicate 3

description: Gene expression data from endometrial total RNA of virgin estrus female mice

source_name: Endometrial tissue collected from virgin estrus CBAF1 females

value: Virgin estrus CBAF1 female


title: Intact replicate 1


title: Intact replicate 3


title: "spike for sgPofut1_1"_ day 7


title: Mut DRG Rep 2

city: Dallas

first: Mark

last: Landy

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Basecalls were performed using CASAVA
Reads were mapped to mouse genome (mm10)
Junctions were identified using tophat (v2.1.2)
Differential expression analysis was performed using cufflinks (v2.2.1)
Genome_build: mm10

source_name: DRG

extract_protocol:
DRGs were removed in oxygenated ACSF, and RNA was extracted with TRI reagent and the Direct-zol RNA Miniprep Plus Kit (Zymo R2071)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed

value: DRG

value: 10 weeks

value: Prdm12-/Fl; AvilCreERT2/+


title: Nanog_R_day5_-Dox_rep2

type: genomic

city: Barcelona

first: Ana

last: Sevilla

state: Barcelona

address: Avda Diagonal 643. Edificio Malagef 4rd Floor, Faculty of Biology

department: Departamento de Biologia Celular, Fisiologia e Inmunologia

country: Spain

institute: Universidad de Barcelona

description: Nanog_R_day5_-Dox_rep2. This sample is Nanog_rescue clone at Day 5 without Doxycycline replicate 2 of the three replicates.

hyb_protocol: Hybridization was performed by the Weill Cornell Medical College Epigenomics Core Facility using NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com. Section Two Color Sample Labeling.

scan_protocol: Scanning was performed with NimbleGen MS 200 by the Weill Cornell Medical College Epigenomics Core Facility using NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was processed as described in Thompson et al,(2008)

source_name: Embryonic Stem Cell

label_protocol: Labeling was performed with the NimbleGen Dual-color DNA labeling kit by the Weill Cornell Medical College Epigenomics Core Facility using NimbleGen Systems Inc., Madison, WI USA, standard operating protocol. See www.nimblegen.com.

extract_protocol: DNA extracted with Gentra Puregene Cell Kit (Qiagen) and digested with the isoschizomer enzymes HpaII or MspI (NEB, Ipswich, MA).

tag: rescue clone

tag: enzyme

value: MspI

tag: agent

value: no doxycycline

tag: day

value: HpaI


title: Vasectomised replicate 1


title: VitD-5

city: London

first: Miguel

last: Branco

address: 4 Newark Street

institute: Blizard Institute

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: EPIC BeadChip array were scanned using the Illumina iScan microarray scanner according to the manufacturer’s recommendations.

data_processing: Methylation markers on 65 single nucleotide polymorphism (SNP) and sex chromosomes were removed. Illumina background correction was applied to all intensity values. Any intensity values having detection p-values >= 10e-16 were set as missing data. Samples with call rate < 98% were excluded. A quantile normalization was applied using limma on intensity values separately based on six different probe-type categories (Type-I M red, Type-I U red, Type-I M green, Type-I U green, Type-II red, and Type-II green). Beta values were then calculated from these normalized intensity values.

label: Cy5 and Cy3

source_name: Placenta, vitamin D

label_protocol: Standard Illumina protocol.

growth_protocol: Villous tissue fragments of approximately 10 mg were dissected from the placenta and cultured at 37˚C in Tyrode’s buffer.

extract_protocol: DNA was extracted from placental fragments using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, UK) according to manufacturer’s instructions.

treatment_protocol: Villous fragments were incubated for 8 h at 37˚C in Tyrode’s buffer containing 20 µM 25(OH)D with 0.7 mM bovine serum albumin (BSA), or control buffer with 0.7 mM BSA.

value: Placenta

value: vitamin D


title: Nanog_R_day5_-Dox_rep3

description: Nanog_R_day5_-Dox_rep3. This sample is Nanog_rescue clone at Day 5 without Doxycycline replicate 3 of the three replicates.


title: VitD-4


title: VitD-8


title: VitD-6


title: Control replicate 1


title: Control replicate 2


title: Nanog_R_day5_-Dox_rep1

description: Nanog_R_day5_-Dox_rep1. This sample is Nanog_rescue clone at Day 5 without Doxycycline replicate 1 of the three replicates.


title: Nanog_R_day3_-Dox_rep3

description: Nanog_R_day3_-Dox_rep3. This sample is Nanog_rescue clone at Day3 without Doxycycline replicate 3 of the three replicates.


title: Mut DRG Rep 1

tag: age


title: VitD-3


title: Control-7

source_name: Placenta, control


title: VitD-2


title: Control replicate 4


title: Esrrb_R_day3_-Dox_rep2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data was normalized using Robust Multichip Average (RMA) method using the Affymetrix Expression Console software

label_protocol: Biotinylated cRNA were prepared with the GeneChip WT cDNA Synthesis and Amplification Kit

growth_protocol: rtTA-expressing ES cells Aniv15 were used for derivation of rescue clones and were maintained on primary mouse embryonic fibroblasts with DMEM media

extract_protocol: total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Each rescue ES clone was grown in +Dox (1ug/ml) media; Dox withdrawal was performed for 5 days

value: AINV15 Esrrb Rescue Clone

tag: dox withdrawal

value: 3 days


title: Control-1

value: control


title: Control-8


title: Control-2


title: Esrrb_R_day3_-Dox_rep3


title: Esrrb_R_day5_-Dox_rep1

value: 5 days


title: VitD-1


title: WT DRG Rep1

value: wild type


title: TuMV-Rep2

city: Ningbo

first: Xinyang

last: Wu

state: Zhejiang

address: 818# Fenghua Road

institute: Ningbo University

data_processing:
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: transcriptome built with Trinity, FASTA on series record.
Supplementary_files_format_and_content: The file <transcript_expression_all> provides <transcript_ID> of each transcript. The sequence of each transcript are provided in the file <Trinity_transcript>.

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: N. benthamiana plants were grown in a greenhouse under a 16 h light/8 h dark regime at 25±2 °C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: N. benthamiana leaves were infiltrated with Agrobacterium tumefaciens carrying the TuMV-GFP vector.

value: TuMV infection

value: leaves


title: Esrrb_R_day1_-Dox_rep2

value: 1 days


title: VitD-7


title: Esrrb_R_day1_-Dox_rep3


title: TuMV-Rep3


title: TuMV-Rep1


title: ATACT3

city: Shanghai

first: Chunlai

address: 180 Fenglin Road

institute: Fudan University

data_processing:
Adaptor and low-quality sequences were trimmed from sequenced reads. For RNA-seq, the processed reads were mapped to hg38 genome reference using STAR v2.7.7. For ATAC-seq, the processed reads were also aligned to hg38 genome reference using BWA (v0.7.17-r1188).
For RNA-seq, read counts were generated using HTSeq v0.11.2. Differential gene expression analysis was conducted using DESeq2 R package (v1.26.0). For ATAC-seq, multiply mapped reads were removed using SAMtool v1.9. The bam file generated by the uniquely mapped reads were used for peak calling using MACS2 (v2.1.2) with q-value < 0.05. Differential peak analysis was conducted using DESeq2 R package (v1.26.0). Genomic features of peaks were annotated using ChIPseeker R package (v1.22.1).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include count values for each sample.
Supplementary_files_format_and_content: For ATAC-seq, MACS2 called narrow peak text files.
Supplementary_files_format_and_content: Count_matrix_RNA.txt: Count matrix for RNA-seq.
Supplementary_files_format_and_content: Count_matrix_ATAC.txt: Count matrix for ATAC-seq.

source_name: Tumor tissue from patient 3 (ATAC-seq)

extract_protocol:
For RNA-seq, total RNA were extracted from tissues using Trizol reagent. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocol.
For ATAC-seq, DNA sample preparation was performed as described in Corces et al., 2017. The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition reactions according to manufacturer’s instruction.

tag: patient

tag: diagnosis

value: Esophageal squamous cell carcinoma

value: Tumor tissue

tag: Stage

value: IIb

tag: smoking

value: Ever-smoker

tag: histological grade

tag: lymph node metastasis

value: No


title: Mock-Rep2

tag: treatment

value: Mock

tag: genotype


title: Nanog_R_day3_-Dox_rep2

description: Nanog_R_day3_-Dox_rep2. This sample is Nanog_rescue clone at Day3 without Doxycycline replicate 2 of the three replicates.

value: MspI

value: no doxycycline

value: HpaI


title: Control-5

tag: tissue

value: Placenta


title: Control-6


title: Control-4


title: WT DRG Rep2

tag: strain

value: Mixed

value: DRG

value: 10 weeks


title: Control-3

value: control


title: Mock-Rep3

value: wild type


title: ATACN2

source_name: Normal tissue from patient 2 (ATAC-seq)

value: Normal tissue

value: IIa


title: ATACT2

source_name: Tumor tissue from patient 2 (ATAC-seq)

value: Esophageal squamous cell carcinoma


title: ATACT1

source_name: Tumor tissue from patient 1 (ATAC-seq)

value: Tumor tissue


title: Esrrb_R_day3_-Dox_rep1

tag: cell line

value: AINV15 Esrrb Rescue Clone

value: 3 days


title: ATACN1

source_name: Normal tissue from patient 1 (ATAC-seq)

value: IIb

value: Ever-smoker

value: No


title: RT3

source_name: Tumor tissue from patient 3 (RNA-seq)


title: Nanog_R_day1_-Dox_rep3

description: Nanog_R_day1_-Dox_rep3. This sample is Nanog_rescue clone at Day1 without Doxycycline replicate 3 of the three replicates.

tag: rescue clone

value: MspI

value: no doxycycline


title: ATACN3

source_name: Normal tissue from patient 3 (ATAC-seq)


title: Nanog_R_day1_-Dox_rep1

description: Nanog_R_day1_-Dox_rep1. This sample is Nanog_rescue clone at Day1 without Doxycycline replicate 1 of the three replicates.

tag: enzyme

value: HpaI


title: Esrrb_R_day5_-Dox_rep3

value: 5 days


title: Mock-Rep1

value: Mock

value: leaves


title: Nanog_R_day3_-Dox_rep1

description: Nanog_R_day3_-Dox_rep1. This sample is Nanog_rescue clone at Day3 without Doxycycline replicate 1 of the three replicates.

tag: agent


title: Esrrb_R_day0_+Dox_rep2

value: 0 days


title: RT1

source_name: Tumor tissue from patient 1 (RNA-seq)


title: RT2

source_name: Tumor tissue from patient 2 (RNA-seq)


title: Nanog_R_day1_-Dox_rep2

description: Nanog_R_day1_-Dox_rep2. This sample is Nanog_rescue clone at Day1 without of Doxycycline replicate 2 of the three replicates.

tag: day


title: Nanog_R_day0_+Dox_rep2

description: Nanog_R_day0_+Dox_rep2: This sample is Nanog_rescue clone at Day0 in the presence of Doxycycline replicate 2 of the three replicates.

value: doxycycline


title: Esrrb_R_day1_-Dox_rep1

value: 1 days


title: RN2

source_name: Normal tissue from patient 2 (RNA-seq)

value: Normal tissue

tag: age

value: IIa


title: Nanog_R_day0_+Dox_rep3

description: Nanog_R_day0_+Dox_rep3: This sample is Nanog_rescue clone at Day0 in the presence of Doxycycline replicate 3 of the three replicates.


title: Esrrb_R_day5_-Dox_rep2

tag: dox withdrawal


title: Esrrb_R_day0_+Dox_rep3


title: WT+KMBA_root_replicate 3

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

description:
kmba_root_rep3
M_18_3255_Pool2-sample18_AD018_L002

data_processing:
RNA-seq was carried out on three independent biological replicates. Library preparation and sequencing was performed on HiSeq 4000 platform using Illumina 1.9 encoding resulting in 150 bps paired-end reads. About 50 million reads per sample was generated. Sequenced reads were checked for quality using FASTQC v0.11.5
Adapters and low-quality reads or bps were filtered using Trimmomatic 0.36 (Bolger, Lohse, & Usadel, 2014), retaining first 100 bps and by using the default settings available for paired-end reads in Trimmomatic. The trimmed reads were then cross-checked for quality and were aligned to the Arabidopsis thaliana reference genome (TAIR10) using Tophat v2.1.1with 2bp mismatches reporting one maximum hit. The annotation file was provided as reference for reads alignment. MultibamSummary from deepTools2 package
Summary of read counts per gene was calculated using featureCounts v1.5.1 (Liao, Smyth, & Shi, 2014). FPKM for individual replicates was calculated using Cufflinks v.2.2.1 (Trapnell et al., 2012). Differentially expressed genes between two conditions were identified using CuffDiff tool from Cufflinks package v2.2.1 (Trapnell et al., 2012) using quartile normalization. Genes with 2-fold change and P value <= 0.05 were considered as significantly different between samples with and without hrcc treatment, with and without SA187 treatment, under normal conditions against salt stress conditions.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file, FPKM values

extract_protocol:
root and shoot were cut, flash frozen in liquid nitrogen, and RNA was harvested using the Nucleospin RNA plant kit (Macherey-Nagel). Illumina Truseq_HT_hiseq4000 RNA Sample Prep Kit  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: after 5 days of germination seedlings were transferred to plates with 100nM of KMBA and 100mM NaCl for 16 days

tag: ecotype background

value: 21 days

value: KMBA

value: Root


title: WT+KMBA_shoot_replicate 3

description:
kmba_shoot_rep3
M_18_3256_Pool3-sample17_AD001_L003

value: Shoot


title: Esrrb_R_day0_+Dox_rep1

value: AINV15 Esrrb Rescue Clone


title: THP1 LPS rep2

city: Beijing

first: Xuefei

last: Guo

state: Bejing

address: Xueyuan road, haidian district

department: Institute of Systems Biomedicine

institute: Peking university health science center

description:
LPS_LDA_BAM
FPKM_anno.txt

data_processing:
fastqc, cutadapt and trim_galore were used for raw data quality control.
The R package, Rsubread, was used for mapping and counting the reads.
The GFOLD, a Linux program was used for analysed DEGs.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FPKM_anno.txt: Tab-delimited matrix table includes FPKM values for every gene and every sample.

source_name: THP-1 cell

growth_protocol: All animals were kept and bred in specific pathogen-free conditions.

extract_protocol:
THP-1 cells were centrifuged, and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: THP-1 cells were treated with or without SARS-CoV-2 Spike protein or LPS for 2h.

tag: cell type

value: human leukemia monocytic cell line

value: 5ng LPS for 2h


title: Esrrb_R_day5_-Dox_rep3

description: Esrrb_R_day5_-Dox_rep3. This sample is Esrrb_rescue clone at Day 5 without Doxycycline replicate 3 of the three replicates.

value: MspI

value: no doxycycline


title: THP1 LPS rep1

description:
LPS_1_BAM
FPKM_anno.txt


title: Esrrb_R_day5_-Dox_rep2

description: Esrrb_R_day5_-Dox_rep2. This sample is Esrrb_rescue clone at Day 5 without Doxycycline replicate 2 of the three replicates.

value: HpaI


title: RN1

last: Lu

source_name: Normal tissue from patient 1 (RNA-seq)

tag: patient

tag: diagnosis

value: Esophageal squamous cell carcinoma

tag: Stage

value: IIb

value: Ever-smoker

value: No


title: THP1 Spike rep1

description:
Spike_1_BAM
FPKM_anno.txt

value: 1nM SARS-CoV-2 Spike protein for 2h


title: THP1 Spike rep2

description:
Spike_LDA_BAM
FPKM_anno.txt


title: THP1 control rep2

description:
Control_LDA_BAM
FPKM_anno.txt

value: control


title: RN3

source_name: Normal tissue from patient 3 (RNA-seq)

value: Normal tissue

tag: smoking

tag: histological grade

tag: lymph node metastasis


title: WT+KMBA_root_replicate 2

description:
kmba_root_rep2
M_18_3254_Pool2-sample16_AD016_L002

value: 21 days

tag: treatment

tag: tissue


title: WT+KMBA_root_replicate 1

description:
kmba_root_rep1
M_18_3253_Pool2-sample14_AD014_L002

value: KMBA


title: THP1 control rep1

description:
Control_1_BAM
FPKM_anno.txt

tag: cell line


title: WT+ACC_root_replicate 3

description:
ACC_root_rep3
M_18_3267_Pool4-sample24_AD002_L004

treatment_protocol: after 5 days of germination seedlings were transferred to plates with 100nM of ACC and 100mM NaCl for 16 days

value: ACC

value: Root


title: WT+ACC_root_replicate 2

description:
ACC_root_rep2
M_18_3266_Pool4-sample22_AD022_L004


title: WT+KMBA_shoot_replicate 2

description:
kmba_shoot_rep2
M_18_3245_Pool1-sample15_AD015_L008

value: Shoot


title: S232_20201012171158_6

city: Naples

first: Gennaro

last: Gambardella

address: Via Campi Flegrei 34,

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

data_processing:
trimming with bbduk
alignment with star 2.6.0a
Expression quantification with htseq-count 0.9.1
Genome_build: cellRanger pre-build hg38 Ensembl Assembly 93
Supplementary_files_format_and_content: tab-delimited text files include avarege CPM values for each patient

source_name: Head and Neck Cancer tissue

growth_protocol: CUP stem-like cells were isolated and grown in ultra-low attachment flasks in DMEM/F12 supplemented with N2 (Gibco), BSA 0.5%, L-Glutamine 2mM, Pen/strep

extract_protocol:
Cell pellets of growing spheres were lysed in Triazol and RNA was extracted with RNeasy Micro Kit (Qiagen); FFPE tissue slices were  extracted with Maxwell® RSC RNA FFPE Kit (promega)
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Illumina NovaSeq 6000 with a read length of 100 bp

value: Early Metastatic Head and Neck Cancer FFPE Tissue

tag: type

value: tissue


title: S232_20201012171158_8

source_name: Breast Cancer tissue

value: Early Metastatic Breast Cancer FFPE Tissue


title: S232_20201012171158_5


title: WT+KMBA_shoot_replicate 1

description:
kmba_shoot_rep1
M_18_3244_Pool1-sample13_AD013_L008


title: S232_20201012171158_3


title: S232_20201012171158_4

source_name: Skin carcinoma tissue

value: Early Metastatic Skin Carcinoma FFPE Tissue


title: Nanog_R_day0_+Dox_rep1

description: Nanog_R_day0_+Dox_rep1: This sample is Nanog_rescue clone at Day0 in the presence of Doxycycline replicate 1 of the three replicates.

source_name: Embryonic Stem Cell

tag: rescue clone

tag: enzyme

value: MspI

value: doxycycline

value: HpaI


title: S232_20201012171158_2


title: WT+ACC_shoot_replicate 3

description:
ACC_shoot_rep3
M_18_3258_Pool3-sample23_AD023_L003


title: S232_20201012171158_10

source_name: CUP tissue

value: Cancer of Unknown Primary FFPE Tissue


title: S232_20201012171158_11


title: Esrrb_R_day5_-Dox_rep1

description: Esrrb_R_day5_-Dox_rep1. This sample is Esrrb_rescue clone at Day 5 without Doxycycline replicate 1 of the three replicates.

tag: agent

value: no doxycycline

tag: day


title: Esrrb_R_day3_-Dox_rep2

description: Esrrb_R_day3_-Dox_rep2. This sample is Esrrb_rescue clone at Day3 without Doxycycline replicate 2 of the three replicates.


title: Esrrb_R_day3_-Dox_rep1

description: Esrrb_R_day3_-Dox_rep1. This sample is Esrrb_rescue clone at Day3 without Doxycycline replicate 1 of the three replicates.


title: Esrrb_R_day1_-Dox_rep2

description: Esrrb_R_day1_-Dox_rep2. This sample is Esrrb_rescue clone at Day1 without of Doxycycline replicate 2 of the three replicates.


title: S232_20201012171158_9


title: Esrrb_R_day3_-Dox_rep3

description: Esrrb_R_day3_-Dox_rep3. This sample is Esrrb_rescue clone at Day3 without Doxycycline replicate 3 of the three replicates.


title: S232_20201012171158_1


title: Esrrb_R_day1_-Dox_rep1

description: Esrrb_R_day1_-Dox_rep1. This sample is Esrrb_rescue clone at Day1 without Doxycycline replicate 1 of the three replicates.


title: S232_20201012171158_7


title: Esrrb_R_day1_-Dox_rep3

description: Esrrb_R_day1_-Dox_rep3. This sample is Esrrb_rescue clone at Day1 without Doxycycline replicate 3 of the three replicates.


title: S232_20191113153626_4_bis


title: WT+SA187_shoot_replicate 3

description:
187_shoot_rep3
M_18_3243_Pool1-sample11_AD011_L008

treatment_protocol: after 5 days of germination and SA187 inoculation seedlings were transferred to plates with 100mM NaCl for 16 days

tag: age


title: WT+ACC_root_replicate 1

description:
ACC_root_rep1
M_18_3265_Pool4-sample20_AD020_L004

tag: ecotype background


title: S232_20191113153626_3_bis

tag: cell type


title: WT+ACC_shoot_replicate 1

description:
ACC_shoot_rep1
M_18_3246_Pool1-sample19_AD019_L008


title: WT+SA187_shoot_replicate 2

description:
187_shoot_rep2
M_18_3242_Pool1-sample9_AD009_L008


title: S232_20191113153626_2_bis

tag: patient


title: VitD4_L7.D707

data_processing:
Reads were mapped to hg38 using HISAT2 v2.0.5.
Raw read counts were generated with HTSeq v0.6.1p1 using union mode and stranded=reversed settings.
Genes were filtered based upon counts per million (CPM) and genes with < 1 CPM in at least half of the samples were removed.
Samples were normalized using the trimmed mean of M-values (TMM) method.
Differential expression analysis was carried out using EdgeR.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with differential expression analysis results, containing normalized gene expression values.

source_name: Placenta

extract_protocol:
RNA was extracted from 30 mg placental samples using the miRNeasy mini kit with the RNase-free DNase Set (Qiagen, UK) according to manufacturer’s instructions.
RNA samples (450 ng) were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit.

value: Placenta


title: VitD3_L7.D706


title: WT+ACC_shoot_replicate 2

description:
ACC_shoot_rep2
M_18_3257_Pool3-sample21_AD021_L003


title: R3h_L1

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Oncorhynchus mykiss

source_name: rainbow trout_R3h_liver

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 150 day

value: liver tissues


title: R3h_L2


title: Esrrb_R_day0_+Dox_rep2

description: Esrrb_R_day0_+Dox_rep2: This sample is Esrrb_rescue clone at Day0 in the presence of Doxycycline replicate 2 of the three replicates.


title: R3h_L3


title: Esrrb_R_day0_+Dox_rep1

description: Esrrb_R_day0_+Dox_rep1: This sample is Esrrb_rescue clone at Day0 in the presence of Doxycycline replicate 1 of the three replicates.


title: Esrrb_R_day0_+Dox_rep3

description: Esrrb_R_day0_+Dox_rep3: This sample is Esrrb_rescue clone at Day0 in the presence of Doxycycline replicate 3 of the three replicates.


title: WT+SA187_shoot_replicate 1

description:
187_shoot_rep1
M_18_3241_Pool1-sample7_AD007_L008

value: 21 days


title: VitD2_L1.D705_508


title: WT_shoot_replicate 2

description:
col_shoot_rep2
M_18_3239_Pool1-sample3_AD003_L008

treatment_protocol: after 5 days of germination seedlings were transferred to plates with 100mM NaCl for 16 days

value: none (control)


title: S232_20191219123658_32

value: Melanoma FFPE Tissue


title: S232_20191113153626_1_bis


title: H24h_L3

source_name: rainbow trout_H24h_liver


title: H24h_L2


title: H24h_L1


title: Control4_L4.D711

value: control


title: VitD1_L8.D704


title: Control3_L5.D710


title: H12h_L3

source_name: rainbow trout_H12h_liver


title: WT_shoot_replicate 1

description:
col_shoot_rep1
M_18_3238_Pool1-sample1_AD001_L008

value: Shoot


title: S232_20191219123658_30


title: Control2_L7.D709


title: L0416-473

city: University of Helsinki

first: Aapo

last: Kahilainen

address: P.O. Box 65

department: Research Centre for Ecological Change

country: Finland

institute: University of Helsinki

data_processing:
Sequenced reads were first trimmed for adaptor sequence using Trimmomatic.
To verify the family structure, the trimmed sequence reads were mapped against an existing Melitaea cinxia genome by Ahola et al. (Nature Communications 2014) using STAR, and the SNPs called using the software package SAMtools. The genetic distances between samples and clustering based on neighbour-joining trees were then determined using the R packages “ape” (version 5.1) and “adegenet” (version 2.1.1). One sample (sample name S29, title L0416-218) was identified as not belonging to the family it was assigned to originally and it was removed from further analyses.
To build one complete and diverse de novo transcriptome, two transcriptomes were built using both the Trinity (v2.6.5) and Velvet/Oases pipelines. The two transcriptomes were then combined using EvidentialGene to yield a single transcriptome of 69 182 putative transcripts. The combined transcriptome was then mapped against the genome of M. cinxia (Ahola et al., Nature Communications, 2014) using GMAP (v. 2018-07-04) to identify transcripts that exhibited any probability to map to the mitochondrial genome (29 transcripts in total).
Read counts of transcripts in the de novo transcriptome were obtained using RSEM (v. 1.3.0) with parameters --paired-end --strandedness reverse. In this process bowtie was used as the aligner with parameters --seed-length 25 -n 2 -e 99999999 -m 200 -I 1 -X 1000.
After obtaining a matrix of raw read counts, transcripts with > 1 counts-per-million in a minimum of four samples were kept, the 29 mitochondrial genome mapping transcripts were discarded, and the remaining raw read counts normalized according to TMM normalization as implemented in in the Bioconductor R-package edgeR (Robinson et al. Bioinformatics 2010).
Genome_build: De novo transcriptome
Supplementary_files_format_and_content: De novo transcriptome, fasta sequence for each transcript.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every transcript and every sample.
Supplementary_files_format_and_content: Matrix table with TMM-normalized transcript counts for a filtered set of transcripts and every sample.

organism: Melitaea cinxia

source_name: full organism

growth_protocol: Melitaea cinxia larvae reared in 28 deg. Celsius day temperature (08:00-20:00) and 15 deg. Celsius night temperature (20:00-08:00). Larvae fed daily with ad libitum Plantago lanceoalta.

extract_protocol:
Larvae were frozen in liquid nitrogen at 4th larval instar and stored at -80 deg. Celsius until extraction. The frozen larvae were subsequently homogenized in dry ice in their entirety, followed by RNA and DNA extraction following a TRIzol-chloroform purification protocol.
RNA libraries were prepared by using Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: In addition to a control treatment, in which the larvae were fed with well watered Plantago lanceolata (40 ml water per day), the larvae experienced three different treatments with feeding on water limited P. lanceolata (20ml water per day). In these three treatments the larvae were fed with water limited P. lanceolata at different stages during pre-diapause development: (1) at late pre-diapause development during 3rd and 4th larval instars ("late water limitation"), (2) at early pre-diapause development during 1st and 2nd larval instars ("early water limitation"), and (3) throughout their pre-diapause development from the 1st to the 5th larval instar ("constant water limitation").

tag: full-sib family

tag: egg clutch

value: late water limitation


title: S232_20191219123658_33

value: tissue


title: H12h_L1


title: Control1_L7.D708


title: H12h_L2


title: WT_shoot_replicate 3

description:
col_shoot_rep3
M_18_3240_Pool1-sample5_AD005_L008


title: L0416-468


title: S232_20191113153626_6

value: Early Metastatic Merkeloma FFPE Tissue


title: S232_20191113153626_10

value: Early Metastatic Skin Carcinoma FFPE Tissue


title: shA2_3 (EphA2 shRNA cells RNA-seq)

city: Maywood

first: Wei

last: Qiu

state: IL

address: 2160 S 1st Ave

department: Surgery

institute: Loyola University Chicago

data_processing:
The original reads were mapped to human genome (UCSC hg38) using HISAT2 (version 2.0.4), and then the number of reads unambiguously mapped to each RefSeq gene was counted using HTSeq (version 0.6.1). Genes with less than five reads per sample were removed. Then the count data was normalized by the samr.norm.data function in R package samr (version 2.0).
Genome_build: UCSC hg38
Supplementary_files_format_and_content: The normalized data is in FPKM

source_name: Huh7 cells

growth_protocol: DMEM culture medium

extract_protocol:
RNA extration with Qiagen kit
250~300 bp insert cDNA library

tag: tag

value: Two weeks after puromycin selection

value: Huh7 Liver cancer cells

tag: shRNA

value: EphA2 shRNA


title: L0416-467


title: H3h_L3

source_name: rainbow trout_H3h_liver


title: shA2_2 (EphA2 shRNA cells RNA-seq)


title: shA2_1 (EphA2 shRNA cells RNA-seq)


title: H3h_L1


title: L0416-466


title: S232_20191113153626_7

value: Cancer of Unknown Primary FFPE Tissue


title: shCtrl_3 (Scrambled cells RNA-seq)

value: shCtrl


title: L0416-462


title: S232_20191113153626_9


title: L0416-448

value: constant water limitation


title: H3h_L2

value: 150 day


title: S232_20191113153626_14


title: S232_20191219123658_31

value: Early Metastatic Melanoma FFPE Tissue


title: shCtrl_2 (Scrambled cells RNA-seq)


title: N_L3

source_name: rainbow trout_N_liver

value: N

value: liver tissues


title: L0416-447


title: N_L2


title: L0416-472


title: S232_20191113153626_8


title: N_L1


title: S232_20191113153626_13


title: S232_20191113153626_15


title: L0416-442

value: early water limitation


title: shCtrl_1 (Scrambled cells RNA-seq)


title: L0416-441


title: S232_20191113153626_5


title: h+ rpb1-CTD-WT29::NatMX

city: New York

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: control for GSM4886769; GSM4886770; GSM4886771; GSM4880437; GSM4880438; GSM4880439; GSM4880440; GSM4880441; GSM4880442; GSM4880443; GSM4880444; GSM4880445; GSM4880446; GSM4880447; GSM4886772; GSM4886773

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Genome_build: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts

organism: Schizosaccharomyces pombe

source_name: h+ rpb1-CTD-WT29::NatMX

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

tag: lab strain number

tag: genotype/variation

value: h+ rpb1-CTD-WT29::NatMX

tag: growth conditions

value: log phase culture, YES medium

tag: developmental stage

value: vegetative growth


title: rpb1-CTD-T4A29 rep3 [re-analysis]

description:
This is duplicated sample record of GSM4708517 for the convenient retrieval of the complete raw data from SRA
control used: GSM5012302
DESeq2_T4A_vs_markWT.xlsx

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA Seq

value: BS 1


title: L0416-438

tag: treatment

value: control


title: S232_20191113153626_4

tag: type

value: tissue


title: L0416-436


title: S232_20191113153626_3


title: XB3

city: Fuzhou

first: Jing-Hao

last: Huang

state: Fujian

address: Wusi Road

department: Pomological Institute

institute: Fujian Academy of Agricultural Sciences

description: long-term Boron toxic treatments

data_processing:
The raw reads obtained from high-throughput sequencing were subjected to the Illumina pipeline filter for removement of adapter dimers, junk and low-complexity sequences, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Clean reads were subjected to BLAST searches against miRBase 21 (http://www.mirbase.org/) to identify known miRNAs.
The remaining non-annotated sequences of 18-30 nucleotides (nt) in length were mapped to the Citrus clementina genome (JGI version 1.0, http://www.phytozome.org/clementine.php) with the MTide program (http://bis.zju.edu.cn/MTide) to identify novel miRNAs.
Both the fold-change and P-value of each miRNA identified in each library were calculated using DESeq software, and the P-value was then adjusted to the false discovery rate (FDR) according to the Benjamini Hochberg Method. A 1.5-fold cut-off was set for determination of up- and down-regulated miRNAs, in addition to a FDR of less than 1.
Target genes of miRNAs obtained were predicted using TargetFinder.

organism: Citrus sinensis

source_name: 400 uM H3BO3 for 15 weeks

growth_protocol: 11-week-old Citrus sinensis and C. grandis seedlings were sand cultured in ceramic pots, grown in a greenhouse under natural photoperiod and environmental temperature.

extract_protocol:
Root total RNA was extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Approximately 1 μg of mixed total RNA from five replicates was used to prepare a small RNA (sRNA) library with the TruSeq Small RNA Sample Prep Kit (Illumina, USA) according to the manufacturer’s protocol. The sRNA libraries were gel-purifid in 6% PAGE gels, and their concentration was then diluted to 2 ng/μl. The insert size of the sRNA libraries was tested with an Agilent 2100 bioanalyser. Aftr accurate quantifiation via qRT-PCR, single-end sequencing was performed on an Illumina HiSeq 2500.

treatment_protocol: Plants were irrigated with Hogland’s nutrient solution containing 10 (control) or 400 (B-toxic) μM H3BO3 every other day for 15 weeks

tag: tissue

value: Root tips


title: XC3

description: Control treatments

source_name: 10 uM H3BO3 for 15 weeks


title: XC2

description: Control treatments


title: S232_20191113153626_1


title: XB2

description: long-term Boron toxic treatments


title: rpb1-CTD-T4A29 rep1 [re-analysis]

description:
This is duplicated sample record of GSM4708515 for the convenient retrieval of the complete raw data from SRA
control used: GSM5012302
DESeq2_T4A_vs_markWT.xlsx


title: XC1

description: Control treatments


title: L0416-429


title: XB1

description: long-term Boron toxic treatments


title: h+ rpb1-CTD-(ALT-P6A)29::NatMX [ALT-P6A-3]

description:
control used: GSM5012302
DESeq2_ALT_P6A_vs_markWT.xlsx

source_name: h+ rpb1-CTD-(ALT-P6A)29::NatMX

value: h+ rpb1-CTD-(ALT-P6A)29::NatMX


title: rpb1-CTD-T4A29 rep2 [re-analysis]

description:
This is duplicated sample record of GSM4708516 for the convenient retrieval of the complete raw data from SRA
control used: GSM5012302
DESeq2_T4A_vs_markWT.xlsx


title: L0416-427


title: h+ rpb1-CTD-(ALT-P6A)29::NatMX [ALT-P6A-2]


title: S232_20191113153626_2


title: L0416-412


title: S232_20200114180155_6

source_name: CUP cells

value: Cancers of Unknown Primary cells

value: Cell


title: h+ rpb1-CTD-(ALT-P6A)29::NatMX [ALT-P6A-1]