title: Scn1a_19

city: Davis

first: Alex

last: Nord

state: CA

address: 1544 Newton Court

department: Neurobiology, Physiology, & Behavior

institute: University of California, Davis

data_processing:
The transcriptomic analysis was performed as before. Reads from RNA-seq were aligned to the mouse genome (mm9) using STAR (version 2.7.2). Aligned reads mapping to genes were counted at the gene level using subreads featureCounts. The mm9 knownGene annotation track and aligned reads were used to generate quality control information using the full RSeQC tool suite. Unaligned reads were quality checked using FastQC.
Raw count data for all samples were used for differential expression analysis using edgeR43. Genes with at least 1 read per million in at least one sample were included for analysis, resulting in a final set of 15589, 14631, and 15002 genes for differential testing in P7 and P32 mice, respectively. Multidimensional scaling analysis indicated that Scn1a expression and sex were the strongest driver of variance across samples. Tagwise dispersion estimates were generated and differential expression analysis was performed using a generalized linear model with genotype as the variable for testing.
Effect of genotype was modelled as individual comparison of heterozygous and homozygous 1b deletion mice with the respective WT controls. Normalized expression levels were generated using the edgeR pseudocount and rpkm functions. Aligned reads contained in BAM files from each sample were counted to calculate the overlap of sequencing reads with each locus. The coordinates for each locus were m1a: chr2:66,278,753-66,278,887, the m1b deletion region: chr2:66245632-66248697, and m1c: chr2:66,249,400-66,249,514.
Mouse gene ontology (GO) data was downloaded from Bioconductor (org.Mm.eg.db). We used the goseq package to test for enrichment of GO terms indicating parent:child relationships. For GO analysis, we examined down- and up-regulated genes separately for genes meeting an FDR < 0.05. For the enrichment analysis, the test set of differentially expressed genes was compared against the background set of genes expressed in our study.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix file of gene counts

source_name: P7 Hippocampus

extract_protocol:
Cortex, hippocampus and cerebellum were regionally dissected from one hemisphere of P7, P32 and 3-month-old homozygous deletion, heterozygous and wildtype mice following anesthesia with isoflurane and decapitation. Total RNA was isolated using RNAqueous kit (Ambion) and assayed using an Agilent BioAnalyzer instrument.
Stranded mRNA sequencing libraries were prepared using TruSeq Stranded mRNA kits (Illumina).

value: Hippocampus

tag: genotype/variation

value: HT

tag: Sex

value: F


title: Scn1a_16

status: Public on Mar 26 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: Scn1a_18

value: KO


title: Scn1a_17

value: WT

value: M


title: Blood sample patient8 day 4

type: RNA

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 4

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the human Clariom D GeneChip according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 system.

data_processing: The microarray data were summarized applying the SST-RMA (signal space transformation - robust multi-array average) gene level method as implemented in the Transcriptome Analysis Console (TAC) 4.0 software (ThermoFisher Scientific).

label: Biotin

organism: Homo sapiens

source_name: Blood sample day 4

label_protocol: Biotinylated cRNA was prepared according to the protocol for the human Clariom D assay (ThermoFisher Scientific).

extract_protocol: PBMCs were isolated from blood samples taken from psoriatic patients and then total RNA from the PBMCs was isolated using the SV Total RNA Isolation System according to the manufacturer's instructions.

tag: patient diagnosis

value: psoriasis

value: blood

tag: gender

value: Male

tag: day


title: WT_rep1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Biotin-labeled cDNA (5 - 6 ug) was hybridized to an Affymetrix Clariom S Mouse Genechip Array (ThermoFisher Scientific, P/N 902930).

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

data_processing: Array signals were quantile normalized and transformed into log2 transcript expression values by using the robust multi-array average (RMA) algorithm (Affymetrix Expression Console v1.1).

source_name: CD45+CD3–B220–NK1.1–F4/80+CD11b+ TAMs from WT mouse

label_protocol: Total RNA (100 ng) was converted into biotin-labeled cDNA by using an Affymetrix Whole Transcript Plus Expression kit (ThermoFisher Scientific, P/N 902281).

growth_protocol: 6–12-week-old female or male BL/6 mice were shaved on their lower back and engrafted with B16-F10 melanoma cells by subcutaneously injecting 1 × 106 cells in 200 μl PBS. On day 15 post-injection, CD45+CD3–B220–NK1.1–F4/80+CD11b+ tumor-associated macrophages (TAMs) were isolated from spleen cells by Fluorescence Activated Cell Sorting (FACS).

extract_protocol: Total RNA was extracted using TRIzol reagent (P/N 15596026, Thermo Fisher Scientific)

tag: cell type

value: tumor-associated macrophages (TAMs)

tag: cell markers

tag: genotype


title: Blood sample patient8 day 0

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 0

source_name: Blood sample day 0


title: Blood sample patient7 day 42

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 42

source_name: Blood sample day 42


title: Blood sample patient7 day 84

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 84

source_name: Blood sample day 84


title: Scn1a_15


title: Blood sample patient7 day 14

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 14

source_name: Blood sample day 14


title: Blood sample patient7 day 4


title: Scn1a_14


title: Blood sample patient7 day 0


title: PA_PA0564_cycle4_Rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt

library_source: genomic

data_processing:
Library strategy: HT-SELEX
Illumina Casava v1.7 software used for basecalling.
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1, ASM676v1)
Supplementary_files_format_and_content: 0_PA_all_PWM_results.txt: Tab-delimited text file includes position weight matrix (PWM) results for each transcription factor (TF).
Supplementary_files_format_and_content: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt: Tab-delimited text file includes all TFs' genome wide target scan results based on the output of FIMO software.

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary Table3 and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul Promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary Table3, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer.

treatment_protocol: 0.5 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

value: wild type

tag: growth phase

value: exponential phase

tag: transcription factor


title: PA_PA0564_cycle2_Rep1


title: PA_PA0564_cycle3_Rep1


title: Scn1a_12


title: PA_PA0564_cycle1_Rep1


title: PA_PA0564_cycle0_Rep1

source_name: no protein

value: no protein


title: wild-type bisulfite-seq rep 4

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with parameters -q 25 -a AGATCGGAAGAG, and all other params default.
ChIP-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Pileup tracks of each ChIP-seq sample over its matched H3 sample (log2) were generated using the deeptools v.3.3.0 function bamCompare, while coverage tracks of input samples were generated using deeptools function bamCoverage; both functions used parameters --normalizeUsing CPM, --binSize 10.
ATAC-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only properly paired reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were obtained using Genrich (https://github.com/jsh58/Genrich) with parameters -p 0.01, -a 200, -l 100, -g 100. ChrM, ChrC, and several high-copy number rRNA regions were excluded from the analysis (provided as a supplementary file in the paper).
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.0c (parameters: --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 -outFilterMismatchNoverReadLmax 0.05, all others default). Only pairs with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.  Read counts for each gene and TE were obtained using htseq-count (parameters: --nonunique none -m intersection-strict) using the araport11 annotations (PMID: 27862469). Differential expression analysis was performed using DESeq2 (PMID: 25516281), and genes were considered differentially expressed with an adjusted p-value < 0.05 and abs[log2(fold change)] > 1.
BS-seq datasets: reads were trimmed, mapped to the TAIR10 genome, and methylation called using methylpy (version 1.4.3). Only uniquely mapping reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig tracks for all ChIP-seq samples (except for input samples) are provided, containing normalized sequencing depth of the IP sample vs. its matched input control. For input DNA samples, bigWig tracks contain coverage normalized by total library depth (CPM) instead. For ATAC-seq, normalized coverage tracks created by Genrich are provided. For RNA-seq, the output of DESeq2 analysis is provided, including overall per-gene/TE expression estimates (baseMean), log2(WT / mutant) (mutant = h2a.w-1 or h2a.w-2), and the adjusted p-value. Note that positive log2(FC) numbers indicate that mutant > WT, negative numbers indicate mutant < WT. For BS-seq, 'CGmap' text files containing all methylation data are provided, along with separate bigWig tracks of methylation levels for CG, CHG and CHH methylation. Only positions with 8+ coverage were used to generate the bigWig files.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
DNA was extracted from 10-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were prepared using the Nugen ultralow methyl-seq kit, and sequenced on NovaSeq 6000. WT reps 3 and 4 were processed alongsize h1 and h1 h2aw2 reps 1 and 2.

treatment_protocol: no treatment

tag: ecotype background

value: wild-type

tag: developmental stage

value: 10-day-old seedlings


title: MyD88-ko_rep3

source_name: CD45+CD3–B220–NK1.1–F4/80+CD11b+ TAMs from MyD88-ko mouse


title: MyD88-ko_rep2


title: Scn1a_13


title: 58_F4_S229

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

institute: Langston University

description: Blood cell-transcripts

data_processing: Several methods were utilized to conduct bioinformatic analysis of the obtained sequence data. For gene expression analyses, we used the Partek® Flow® software suites pipelines that include, but are not limited to the STAR algorithm, Normalization, and the gene set differential analysis method (GSA).

organism: Capra hircus

source_name: Blood, Infection only

extract_protocol:
Blood samples were collected from blood of five goats in four treatment groups (No infection, Infection, Infection ZA inject, and Infection AB inject), following seven (7) dpi. Blood samples included red blood cells, white blood cells (total and differential), hemoglobin, platelets, and plasma protein, from the jugular vein in EDTA tubes.Total RNA was collected from blood samples using a modified TRIzol reagent procedure.
The cDNA libraries were constructed by initial first strand synthesis using the Protocol for Non-directional RNA-seq Workflows and NEBNEXT® UltraTM II RNA First Strand Synthesis Module (E7771), according to a modified manufacturer’s protocol.

tag: tissue type

value: Whole blood

tag: treatment

value: infection only

value: male


title: 57_E6_S164

description: Blood cell-transcripts

source_name: Blood, Infection, ZA inject

value: Infection ZA inject


title: Blood sample patient6 day 84

value: Female


title: PA_PA0547_cycle4_Rep1


title: 52_E3_S139

description: Blood cell-transcripts

source_name: Blood, No infection

value: No Infection


title: PA_PA0547_cycle3_Rep1


title: Scn1a_11

description:
Scn1a_9_F_Het_S153
Scn1a_GENE_MATRIX_2.txt

source_name: Adult Hippocampus

value: Hippocampus

value: HT

value: F


title: Scn1a_10

description:
Scn1a_16_M_WT_S159
Scn1a_GENE_MATRIX_2.txt

value: WT

value: M


title: PA_PA0547_cycle2_Rep1


title: Scn1a_9

description:
Scn1a_15_M_WT_S158
Scn1a_GENE_MATRIX_2.txt


title: Scn1a_8

description:
Scn1a_13_M_Het_S157
Scn1a_GENE_MATRIX_2.txt


title: 50_E10_S9

description: Blood cell-transcripts

source_name: Blood, Infection, AB inject

value: infection AB inject


title: 51_F5_S237

description: Blood cell-transcripts


title: 44_E2_S131

description: Blood cell-transcripts


title: 54_F2_S213

description: Blood cell-transcripts


title: PA_PA0547_cycle1_Rep1

value: wild type


title: Scn1a_7

description:
Scn1a_12_M_WT_S156
Scn1a_GENE_MATRIX_2.txt


title: MyD88-ko_rep1

value: tumor-associated macrophages (TAMs)


title: PA_PA0547_cycle0_Rep1

value: no protein


title: Scn1a_6

description:
Scn1a_11_M_Het_S155
Scn1a_GENE_MATRIX_2.txt


title: Scn1a_5

description:
Scn1a_10_M_Het_S154
Scn1a_GENE_MATRIX_2.txt


title: PA_PA0535_cycle4_Rep1

value: exponential phase


title: Blood sample patient6 day 4

value: psoriasis

value: blood


title: Blood sample patient6 day 0


title: PA_PA0535_cycle3_Rep1


title: WT_rep2


title: Hypoxia, P8, #4

city: Washington

first: Nikki

middle: Gillum

last: Posnack

state: Please select a region, state or province.

address: 111 Michigan Ave, NW

institute: Childrens National Hospital

description: gene expression

hyb_protocol: hybridized to affymetrix genchip mouse clariom s array for 16 hours at 48C

scan_protocol: affymetrix HCS3000 7G scanner

data_processing: quality control evaluated via affymetrix expression console software; data analyzed in Transcriptoe Analysis Console (applied biosciences), 1.5 Fold change relative to Normoxia p8, p<0.05,  0.1 FDR cutoff

label: biotin

source_name: Hypoxia, p8

label_protocol: biotin-labelled using WT Plus reagent kit

extract_protocol: Total RNA extracted with Qiagen Rneasy (fibrous) kit

treatment_protocol: Normoxia or hypoxia (11%)

value: Heart

tag: age

tag: oxygen status

value: hypoxia


title: 38_F9_S270

description: Blood cell-transcripts

value: Whole blood

value: Infection ZA inject

tag: Sex

value: male


title: Blood sample patient5 day 84

value: Female


title: Blood sample patient6 day 14


title: Blood sample patient5 day 4


title: Blood sample patient5 day 42


title: Blood sample patient5 day 0


title: 33_E9_S188

description: Blood cell-transcripts


title: 30_E7_S172

description: Blood cell-transcripts


title: PA_PA0535_cycle2_Rep1


title: 28_F1_S205

description: Blood cell-transcripts

value: No Infection


title: Blood sample patient4 day 42

value: Male


title: PA_PA0535_cycle1_Rep1


title: Scn1a_3

description:
DSRR00_11_S4
Scn1a_GENE_MATRIX_1.txt

tag: strain

value: Hippocampus

tag: genotype/variation

value: KO


title: Scn1a_1

description:
DSRR00_02_S1
Scn1a_GENE_MATRIX_1.txt

tag: tissue

value: WT

value: F


title: Blood sample patient4 day 84

tag: patient diagnosis

tag: gender


title: PA_PA0528_cycle4_Rep1

value: wild type


title: 20_E5_S155

description: Blood cell-transcripts

value: infection only


title: Scn1a_2

description:
DSRR00_05_S2
Scn1a_GENE_MATRIX_1.txt


title: 27_F8_S262

description: Blood cell-transcripts


title: 25_E8_S180

description: Blood cell-transcripts

value: infection AB inject


title: PA_PA0535_cycle0_Rep1

value: no protein


title: Blood sample patient4 day 4

value: psoriasis

value: blood

tag: day


title: 13_F3_S221

description: Blood cell-transcripts


title: Blood sample patient3 day 84


title: Blood sample patient4 day 0


title: Abl.2_control_resequenced_SMARTseq_kit_10ng_rep2

city: Boston

first: Saumya

last: Gupta

state: MA

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
Cell line Abl.2, in growth medium, Library preparation replicate 2, sequenced on a separate lane of HiSeq on a different day
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv

data_processing:
Reference preparation: we created two custom parental genomes (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014); or “pseudocontigs” when we have phasing by contigs) for each organism, we used a custom script (all custom software tools mentioned are available on Github https://github.com/gimelbrantlab/QCumber). We also created a vcf-file with one allele considered as a reference (maternal 129S1 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on the GATK pipeline (Castel et al., 2015).
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF files, GRCm38.68 and GRCh37.63, were downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts, allelic imbalance with confidence intervals

source_name: immortalised B cells

extract_protocol:
Total RNA was isolated using Trizol from a freshly collected kidney tissue of an adult female mouse of 129S1 x Cast/Ei F1 background. Isolated RNA was DNase-treated with RQ1 DNase (Promega).
Library preparation was done using NEBNext Ultra RNA Poly-A kit (mentioned as NEBNext in the sample name) or Clonetech SMARTseqv4 kit (mentioned as SMARTseq in the sample name), according to manufacturers’ instructions. Input RNA amount varied depending on the sample

value: 129S1/SvImJ x CAST/EiJ F1

tag: drug treatment

value: control

tag: library replicates

value: female


title: Blood sample patient6 day 42


title: 6_F6_S246

description: Blood cell-transcripts

value: Whole blood

value: Infection ZA

value: male


title: Blood sample patient3 day 42

value: Female


title: Abl.2_control_resequenced_SMARTseq_kit_10ng_rep1

description:
Cell line Abl.2, in growth medium, Library preparation replicate 1, sequenced on a separate lane of HiSeq on a different day
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv

growth_protocol: Total RNA was isolated using Trizol from a freshly collected kidney tissue of an adult female mouse of 129S1 x Cast/Ei F1 background


title: PA_PA0528_cycle3_Rep1

tag: genotype

tag: growth phase

value: exponential phase


title: 17_F10_S18

description: Blood cell-transcripts


title: PA_PA0491_cycle4_Rep1

tag: transcription factor


title: Blood sample patient3 day 4


title: Blood sample patient3 day 14


title: PA_PA0528_cycle2_Rep1


title: Abl.2_control_SMARTseq_kit_10ng_rep2

description:
Cell line Abl.2, in growth medium, Library preparation replicate 2
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv


title: Blood sample patient4 day 14

value: Male


title: Abl.2_control_SMARTseq_kit_10ng_rep1

description:
Cell line Abl.2, in growth medium, Library preparation replicate 1
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv


title: PA_PA0528_cycle1_Rep1


title: 8_E1_S123

description: Blood cell-transcripts

value: No Infection


title: PA_PA0528_cycle0_Rep1


title: Abl.1_control_SMARTseq_kit_10ng_rep1

description:
Cell line Abl.1, in growth medium, Library preparation replicate 1
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv


title: inflorescence meristems, GFP_MYB3R4_input_rep2

city: Cambridge

first: Weibing

last: Yang

state: Select...

address: 47 Bateman Street, Cambridge

country: United Kingdom

institute: Sainsbury Laboratory  University of Cambridge

data_processing:
The raw reads obtained from the sequencing facilities were analyzed in house. We first assessed the quality of reads using FastQC  (www.bioinformatics.babraham.ac.uk/projects/fastqc/).   Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 reference genome using Bowtie2 (Langmead et al., 2009). Potential optical duplicates were removed using Picard, as described earlier. The read counts mapped to each bp in each sample was normalized by the sample’s genome-wide mappable reads coverage per bp, and used in the subsequent statistical analyses.Peak calling was performed using MACS (Zhang et al., 2008).
Genome_build: TAIR10
Supplementary_files_format_and_content: narrowPeak

source_name: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4 inflorescence meristems

growth_protocol: Arabidopsis plants were grown in a growth chamber under the following conditions: long-day photoperiod (16-h light/8-h dark), light intensity 170 μmoles m-2 s-1, day/night temperature 21°C/17 °C. Shortly after bolting (with stem length ~1 cm), the shoot apices were cut and the SAMs were dissected by removing fully open flowers.

extract_protocol:
ChIP was performed as described (Gendrel et al., 2002) with minor modifications. In brief, chromatin was extracted from approximately 1 to 2 g of crosslinked materials. Chromatin was fragmented by sonication using a bioruptor (Diagenode) in lysis buffer (10 mM Tris-HCl [pH 8], 150 mM NaCl, 1 mM EDTA [pH 8], 0.1% deoxycholate, and 1X protease inhibitor cocktail). All ChIPs were performed in a buffer containing 20mM Tris-HCl (pH8), 150mM NaCl, 2mM EDTA, 1% triton X-100 and 1X protease inhibitor cocktail. ChIP were performed using Anti-inflorescence meristems, GFP antibody - ChIP Grade (Abcam, ab290) coupled to a 1/1 mix of protein-A and protein-G Dynabeads (life technologies, 10001D and 10003D). All ChIPs were performed in a buffer containing 10 mM Tris-HCl [pH 8.0], 5 mM EDTA [pH 8.0], 150 mM NaCl, 1% Triton X-100, and 1× protease inhibitor cocktail. The elution was done with elution buffer (1% SDS, 0.1M NaHCO3).
The efficiency of ChIP materials was assessed by qPCR in prior to in-house library preparation, using the TruSeq ChIP sample preparation kit (Illumina, IP-202-1012) following the manufacturer’s instructions.  Library preparation was performed by Novogene using another method for some of the samples. The libraries were sequenced on Illumina sequencer by Novogene using paired-end 150bp length reads, and on NextSeq500 at the Sainsbury Laboratory Cambridge University using single-end 75 bp length reads .

value: inflorescence meristems

tag: replicate

tag: chip antibody


title: Blood sample patient2 day 42


title: 2_E4_S147

description: Blood cell-transcripts

tag: tissue type

tag: treatment


title: inflorescence meristems, GFP_MYB3R4_mNES_input_rep2

source_name: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4mNES inflorescence meristems


title: PA_PA0491_cycle3_Rep1

value: wild type


title: Abl.1_control_SMARTseq_kit_10ng_rep2

description:
Cell line Abl.1, in growth medium, Library preparation replicate 2
Abl1_Abl2_RNAseq_allelic_counts.csv
Abl1_Abl2_RNAseq_allelic_imbalance.csv


title: PA_PA0491_cycle2_Rep1


title: Blood sample patient2 day 84


title: PA_PA0491_cycle0_Rep1


title: Blood sample patient2 day 14


title: inflorescence meristems, GFP_MYB3R4_mNES_ChIP-seq_rep2

value: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4mNES

value: Anti-inflorescence meristems, GFP antibody - ChIP Grade (ab290)


title: PA_PA0491_cycle1_Rep1


title: inflorescence meristems, GFP_MYB3R4_mNES_ChIP-seq_rep1


title: inflorescence meristems, GFP_MYB3R1_input_rep3

source_name: Col0 pMYB3R1::inflorescence meristems, GFP-MYB3R1 inflorescence meristems


title: PA_PA0479_cycle3_Rep1


title: inflorescence meristems, GFP_MYB3R4_mNES_input_rep1


title: inflorescence meristems, GFP_MYB3R4_ChIP-seq_rep3

value: Col0 pMYB3R4::inflorescence meristems, GFP-MYB3R4


title: PA_PA0479_cycle4_Rep1


title: PA_PA0479_cycle2_Rep1


title: 201115557

city: Suzhou

first: Zhuang

last: Wenzhuo

state: Jiangsu

address: Ren Ai Road 199

institute: Soochow University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were normalized by RMA algorithm, Gene Spring Software 14.5 (Agilent technologies, Santa Clara, CA, US).
probe group file: HTA-2_0.r2.pgf
meta-probeset file: HTA-2_0.r2.Psrs.mps

source_name: lymph node

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n  AM1556 ) following the manufacturer's instructions.

tag: disease state

value: diffuse large B cell lymphoma (DLBCL)

tag: prognosis

value: favorable prognosis


title: 201403093

value: poor prognosis


title: inflorescence meristems, GFP_MYB3R1_ChIP-seq_rep3

value: Col0 pMYB3R1::inflorescence meristems, GFP-MYB3R1


title: human glomeruli_H3K27ac ChIP-seq

city: Nanjing

first: Jingping

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

data_processing:
raw reads were aligned to hg19 genome and call peaks using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: human glomeruli

extract_protocol:
The ChIP DNA was extract with Zymo DNA Clean & Concentrator-5 Kit (Zymo, D4013).
libraries were constructed according to the Illumina instruction

value: human glomeruli

value: H3K27ac, Abcam, ab4729


title: PA_PA0479_cycle1_Rep1


title: 201222161


title: In_112

city: Copenhagen

first: Helene

middle: Maria

last: Gylling

address: Ole maaløes vej 5

department: SUND/BRIC

data_processing:
Reads were trimmed using trimmomatic version 0.32 with parameters "ILLUMINACLIP:/path_to_adapter.fa:2:30:5 SLIDINGWINDOW:8:25 MINLEN:50 HEADCROP:8”.
Reads were mapped using RNA STAR Version 2.6.0b and samtools Version 1.8 (--outFilterMultimapNmax 10 --outFilterMismatchNoverReadLmax 0,2 --outFilterScoreMinOverLread 0,8)
PCR duplicates removed using RmDup Version 0.1.19.
BAM files were converted to BigWig ucsc-bedgraphtobigwig (Version 357) and bedtools (Version 2.27.1) and processed in DERfinder tool Version 1.8.5 for annotation free Expressed region identification and counting (cutoff=5, L=126)
Statistics were done in EdgeR Version 3.1 using an expressed region cutoff of min 6 counts in total in min 2 samples
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files used for DERfinder input, .txt files with EdgeR output for hg38 mapping including normalized counts and statistics

source_name: Hela S3

extract_protocol:
Samples were snap-frozen before sonication of chromatin in a Diagenode Bioruptor (4°C, 30s ON / 90s OFF x30 cycles on high) and checked for correct size on an agarose gel. Sonicated samples were pre-cleared before IP with Protein A dynabeads (Invitrogen 100-02D) by rotating 1h at 4°C. Biotinylated chromatin was isolated with T1 streptavedin magnetic beads (Invitrogen 656-01) in the presence of RNase inhibitors (100U/mL)(NEB M0314L) and decross-linked in TE buffer (incl. 0,5% SDS and Proteinase K) 37°C 10h followed by 65°C 6h (interval shaking) for RNA isolation. RNA was purified using a miRNeasy Purification Kit including an on-column DNAse digestion (QIAGEN, Hilden, Germany) as per kit protocol for low RNA amounts. RNA for the long RNA-seq was further purified and concentrated using a Clean and Concentrator-5 kit (Zymo Research, CA, USA) as per kit protocol.
Long RNA-seq: 10 ng of total RNA was used as input material for library preparation using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio, CA, USA formerly Clontech Laboratories) according to manufacturer’s instructions with the following modifications. Input and H3 samples were fractionated for 2 min while all other RNA samples were not fractionated at all given their already shorter fragment size, reflected by RNA integrity numbers (RIN) of 2 - 3. Final library PCR amplification cycles were increased to a maximum of 15 cycles. A negative control indicated no adverse effect to increased PCR cycles.

tag: timepoint

tag: sample label

value: b-dUTP


title: 201106713


title: 201116572


title: PA_PA0477_cycle4_Rep1


title: Blood sample patient2 day 4

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 4

source_name: Blood sample day 4

value: psoriasis

tag: tissue

value: blood


title: 201332289


title: Blood sample patient5 day 14

source_name: Blood sample day 14

tag: patient diagnosis

value: Female


title: Biopsy patient14 lesional skin day 84

description: Gene expression data from lesional psoriatic skin at day 84

source_name: Lesional skin punch biopsy day 84

extract_protocol: Total RNA from skin biopsies was isolated using the SV Total RNA Isolation System according to the manufacturer's instructions.

value: skin

tag: gender

tag: disease state (ls/nl)

value: LS


title: In_111


title: Blood sample patient3 day 0

description: Gene expression data from isolated PBMCs from blood samples from psoriatic patients day 0

source_name: Blood sample day 0

tag: day


title: Biopsy patient14 lesional skin day 4

description: Gene expression data from lesional psoriatic skin at day 4

source_name: Lesional skin punch biopsy day 4


title: Biopsy patient14 lesional skin day 0

description: Gene expression data from lesional psoriatic skin at day 0

source_name: Lesional skin punch biopsy day 0


title: PA_PA0479_cycle0_Rep1

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt

source_name: no protein

value: no protein


title: Biopsy patient14 lesional skin day 42

description: Gene expression data from lesional psoriatic skin at day 42

source_name: Lesional skin punch biopsy day 42


title: PA_PA0477_cycle2_Rep1

value: wild type

value: exponential phase


title: In_110


title: Biopsy patient14 nonlesional skin day 0

description: Gene expression data from nonlesional psoriatic skin at day 0

source_name: Nonlesional skin punch biopsy day 0

value: NL


title: In_109


title: PA_PA0477_cycle0_Rep1


title: PA_PA0477_cycle1_Rep1


title: H3_111

tag: ip


title: Blood sample patient2 day 0

value: Male


title: Biopsy patient14 lesional skin day 14

description: Gene expression data from lesional psoriatic skin at day 14

source_name: Lesional skin punch biopsy day 14


title: H3_110


title: tubule_4

hyb_protocol: Samples were prepared and hybridized to HTA 2.0 Array according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned according to manufacturer's instruction.

data_processing: The signal intensity data was normalized and quantified with Affymetrix Transcriptome analysis console (TAC) with SST-RMA.

source_name: kidney tubules

growth_protocol: Glomeruli or tubules were isolated by laser.

extract_protocol: RNA were extracted with Qiagen kit.

value: kidney tubules


title: tubule_5

label_protocol: Samples were prepared and hybridized to HTA 2.0 Array according to Affymetrix specifications.


title: PA_PA0477_cycle3_Rep1

tag: genotype


title: tubule_3


title: glomeruli_5

source_name: kidney glomeruli

value: kidney glomeruli


title: Biopsy patient13 lesional skin day 84


title: PA_PA0463_cycle3_Rep1

tag: growth phase


title: glomeruli_4


title: Biopsy patient13 lesional skin day 42


title: Scn1a_4

description:
DSRR00_17_S6
Scn1a_GENE_MATRIX_1.txt

source_name: Adult Hippocampus

tag: strain

value: Hippocampus

tag: genotype/variation

value: KO

tag: Sex

value: F


title: tubule_1


title: Biopsy patient13 lesional skin day 14


title: Biopsy patient13 lesional skin day 4


title: PA_PA0463_cycle1_Rep1

tag: transcription factor


title: PA_PA0463_cycle4_Rep1


title: H3_112


title: M10_112

value: T1 beads


title: tubule_2


title: PA_PA0463_cycle2_Rep1


title: H3_109


title: glomeruli_3


title: PA_PA0463_cycle0_Rep1


title: Biopsy patient12 lesional skin day 84


title: glomeruli_1


title: M10_111

value: b-dUTP


title: PA_PA0436_cycle4_Rep1


title: PA_PA0436_cycle3_Rep1


title: PA_PA0436_cycle2_Rep1


title: M10_110


title: PA_PA0436_cycle1_Rep1


title: M2_111


title: M2_112


title: Biopsy patient13 lesional skin day 0

value: psoriasis


title: M2_110


title: snRNA-seq plate #3

city: Wageningen

first: Michael

middle: D

last: Nodine

state: Gelderland

address: Radix West

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description: Single-end 50 base read mRNA-seq data from first plate of snRNA-seq from globular Col-0 embryos

data_processing:
Sequencing reads from each sample were preprocessed by trimming adapters using cutadapt v2.6 (Martin, 2011) in two steps. First, Nextera adapters (5′-CTGTCTCTTATACACATCTCCGAGCCCACGAGAC-3′) were trimmed from the 3′ end of reads, followed by trimming of template-switching oligos (TSO, 5′-AAGCAGTGGTATCAACGCAGAGTACATGGG-3′) and oligo-dT adapters (5′-AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′) from the 5′ and 3′ ends of reads, respectively. A Kallisto index was built from a combined FASTA file of all transcript models in EnsemblPlants TAIR10 v40 (ftp://ftp.ensemblgenomes.org/pub/plants/release-40/gff3/arabidopsis_thaliana/Arabidopsis_thaliana.TAIR10.40.gff3.gz), 96 ERCC spike-in transcripts and sGFP. Each trimmed sample FASTQ file was pseudoaligned to this index using the command kallisto quant with the options --single --fragment-length 200 --sd 100.
Genome_build: EnsemblPlants TAIR10 v40
Supplementary_files_format_and_content: Two TSV files for each plate of 93 single-nucleus RNA-seq libraries. 1) raw.counts_p{plate #}.tsv: Gene IDs (AGIs) are shown in the rows and estimated raw counts from Kallisto pseudoalignents of each 93 snRNA-seq library are shown in each column. 2) plate_{plate #}_barcodes.tsv: sample name is shown in first columnt and denoted by sn_p{plate #}s{sample #}, i7 barcoding index and i5 barcoding index.

source_name: Globular embryos

growth_protocol: Arabidopsis thaliana accession Columbia (Col-0) plants containing pWOX2::H2B-GFP, pWOX2::tdTomato-RCI2b (pWOX2::NLS-GFP) (Gooh et al., 2015) or no transgenes were grown at 20 to 22˚C and 16 h light/8 h dark cycles under incandescent lights (130-150 µmol/m2/s) in a climate-controlled growth chamber.

extract_protocol:
Each nucleus passing both DAPI and GFP gating was collected in 4 μL of cell lysis buffer (Picelli et al., 2014a) supplemented with 25 mM dithiothreitol (DTT) in single wells of 96-well plates.
Smart-seq2 libraries were prepared following the published SmartSeq2 single-cell protocol (Picelli et al., 2014a; Picelli et al., 2014b) with an additional 30-minute 37°C incubation before reverse transcription.
single-nucleus mRNA-seq (snRNA-seq)

tag: accession

value: Globular embryos


title: snRNA-seq plate #7


title: snRNA-seq plate #5


title: snRNA-seq plate #8


title: snRNA-seq plate #6


title: snRNA-seq plate #4


title: snRNA-seq plate #2


title: snRNA-seq plate #1


title: glomeruli_2


title: PA_PA0436_cycle0_Rep1


title: M2_109


title: Biopsy patient13 nonlesional skin day 0


title: Biopsy patient12 lesional skin day 4


title: Biopsy patient12 nonlesional skin day 0


title: Biopsy patient12 lesional skin day 14


title: Biopsy patient12 lesional skin day 42


title: Biopsy patient11 lesional skin day 84


title: M10_109


title: Biopsy patient11 lesional skin day 14


title: PA_PA0294_cycle4_Rep1


title: N_112


title: PA_PA0294_cycle3_Rep1


title: N_111


title: PA_PA5324_cycle4_Rep1


title: PA_PA0294_cycle1_Rep1


title: PA_PA0294_cycle0_Rep1


title: PA_PA0294_cycle2_Rep1


title: Biopsy patient11 lesional skin day 42


title: N_109


title: Biopsy patient12 lesional skin day 0


title: PA_PA5324_cycle3_Rep1


title: PA_PA0275_cycle3_Rep1


title: N_110


title: PA_PA0275_cycle4_Rep1


title: PA_PA5324_cycle2_Rep1


title: Biopsy patient11 lesional skin day 0


title: Biopsy patient11 lesional skin day 4


title: PA_PA0275_cycle1_Rep1


title: Biopsy patient10 lesional skin day 84


title: PA_PA5324_cycle1_Rep1


title: PA_PA0275_cycle2_Rep1


title: Biopsy patient10 lesional skin day 14


title: PA_PA3385_cycle4_Rep2


title: PA_PA0275_cycle0_Rep1


title: Biopsy patient10 lesional skin day 42


title: Biopsy patient11 nonlesional skin day 0


title: PA_PA3385_cycle3_Rep2


title: PA_PA0268_cycle2_Rep1


title: Αlpha6+/Sca1-_r3

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

country: Germany

institute: University of Cologne (UoC), Germany

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the murine reference assembly (mm10) using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated as TPMs.
Genome_build: GRCm38
Supplementary_files_format_and_content: Txt file containing Read count means, fold-change (FC) and p-values  calculated with Deseq for all mouse Ensembl genes. The file also contains gene expression values calculated as TPMs and dFH scores for all mouse Ensembl Genes.

molecule: polyA RNA

source_name: Αlpha6+/Sca1- cells isolated from back skin of P56 mice

growth_protocol: Αlpha6+/Sca1- cells were isolated from back skin of P56 mice (2nd telogen) by incubating skin pieces in 0.8% trypsin (Gibco) for 50 min at 37°C. After separating the epidermis from the underlying dermis, cells were passed through 70 µm and 45 µm cell strainers (BD Biosciences) and pelleted at 900 rpm for 7 minutes at 4 °C. Cells were resuspended in 250µl of FACS buffer (1 x PBS, 2.5% FBS or BSA and 2mM EDTA), afterward Alpha 6 conjugated antibody was added in each tube at concentration of 1:100. After vortex, samples were incubated at 4°C for 1 hr in the dark. The cells were washed twice with 1ml of FACS buffer and centrifuge at 900 rpm for 5 minutes at 4 °C. Cells were resuspended in FACS buffer. Cells were analysed in a BD FACS Canto II or sorted in either a BD FACSAria II or a BD FACSAria Fusion. Data were analysed using FlowJo software version 10. Expression of cell surface markers was analysed on live cells after exclusion of cell doublets and dead cells using 7AAD 1: 100 (eBioscience) or Fixable Viability Dye eFluor506 (eBioscience). The following antibody was used FITC-a6 Integrin (clone GoH3, eBioscience).

extract_protocol:
Accumulated cells were used to isolate total RNA using the RNeasy Plus Micro Kit after which the RNA quality was determined using an Agilent 2200 Tape Station.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Approximately 1 million Αlpha6+/Sca1- cells from back skin of P56 mice (2nd telogen) were isolated and collected (as biological duplicates) in 1.5 ml Eppendorf from 56 days old mice (P56: 2nd telogen).

value: WT

tag: age

value: back skin

tag: cell type

value: Alpha6+/Sca1- cells


title: PA_PA0268_cycle4_Rep1


title: PA_PA0268_cycle3_Rep1


title: Biopsy patient10 lesional skin day 4

value: skin

value: LS


title: Αlpha6+/Sca1-_r2


title: PA_PA3385_cycle1_Rep2

value: wild type

value: exponential phase


title: PA_PA0268_cycle1_Rep1


title: Αlpha6+/Sca1-_input

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Normalized bedGraph files were generated using DeepTools
Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

extract_protocol:
Αlpha6+/Sca1- cells were briefly homogenized in DMEM media with 10% FBS serum/1M sodium butyrate and cross-linked with 1% formaldehyde at room temperature with rotation for 15 min. Cross-linking was quenched with 0.125 M glycine, and HFSC were rinsed with cold 1 X PBS, re-suspended in 500 µl of sonication buffer (10 mM Tris, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycho-late, and 0.5% N-lauroylsarcosine) with 1% SDS, and incubated at 4C for 10 min. Chromatin was sonicated to generate DNA fragments of 200–500 bp. Sonicated chromatin was incubated overnight with 5 μg of antibodies against H3K27me3 (39536; Active Motif) or H3K4me3 (39159; Active Motif; Rada-Iglesias et al., 2011; Rehimi et al., 2016), followed by 4–6 hr incubation with Protein G Dynabeads (Life Technologies). Beads were washed four times with 1 mL of cold radioimmunoprecipitation assay buffer (RIPA) washing buffer (50 mM HEPES, 500 mM LiCl, 1 mM EDTA, 1% NP-40 and 0.7% Na-deoxycholate) and once with Tris/EDTA buffer (TE) containing 50mM NaCl. Immunoprecipitated chromatin was eluted from the beads by adding elution buffer (50 mM Tris, 10 mM EDTA, and 1% SDS) and vortexing at 65C for 15 min. Crosslinking was reversed by incubating the eluted samples at 65C overnight. Samples were then diluted (1:1) with TE and sequentially treated with RNase A (0.2mg/mL) and proteinase K (0.2mg/mL). DNA was purified using phenol:chloroform, followed by ethanol precipitation, and re-suspended in water.
DNA libraries from H3K27me3 ChIP, H3K4me3 ChIP, and corresponding input DNA samples were generated with the TruSeq kit (Illumina) as single reads

treatment_protocol: For each ChIP-seq experiment, 500,000 Αlpha6+/Sca1- cells isolated from back skin of P56 mice (2nd telogen) were used.

tag: chip antibody


title: PA_PA3385_cycle2_Rep2


title: PA_PA0268_cycle0_Rep1

value: no protein


title: PA_PA3385_cycle0_Rep2


title: PA_PA1754_cycle4_Rep2


title: Αlpha6+/Sca1-_H3K4me3

value: H3K4me3 (39159; Active Motif)


title: PA_PA0248_cycle4_Rep1


title: PA_PA0248_cycle3_Rep1


title: PA_PA1754_cycle3_Rep2


title: PA_PA1754_cycle2_Rep2


title: Αlpha6+/Sca1-_H3K27me3

value: H3K27me3 (39536; Active Motif)


title: PA_PA0248_cycle2_Rep1


title: PA_PA1754_cycle1_Rep2


title: PA_PA0248_cycle1_Rep1


title: Biopsy patient10 lesional skin day 0

value: Male


title: Biopsy patient9 lesional skin day 14

value: Female


title: Biopsy patient10 nonlesional skin day 0

value: NL


title: Biopsy patient9 lesional skin day 84


title: Biopsy patient9 lesional skin day 42


title: Biopsy patient9 lesional skin day 4


title: Biopsy patient9 lesional skin day 0


title: PA_PA1431_cycle4_Rep2


title: PA_PA0248_cycle0_Rep1


title: PA_PA5324_cycle0_Rep1


title: Biopsy patient9 nonlesional skin day 0


title: FBXO44KD

city: San Diego

first: Jia

middle: Zack

last: Shen

address: 10901 North Torrey Pines Road

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Reads were aligned to the Homo sapiens genome (hg19) using STAR aligner with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM) gene expression matrix

extract_protocol:
RNA samples were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: FBXO44 knockdown cells


title: H3K9me3 FBXO44 Knockdown

data_processing:
ChIP-Seq reads were then aligned to the Homo sapiens genome (hg19) and peaks were called using Partek software with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using deeptools

source_name: MDA-MB-231 FBXO44 Knockdown

extract_protocol: Libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

tag: antibody

value: H3K9me3 antibody (Millipore no. 17-10242)

tag: cell line

tag: knockdown


title: H3K9me3 FBXO44 Control

source_name: MDA-MB-231 Control

value: control


title: PA_PA0236_cycle4_Rep1


title: PA_PA1431_cycle3_Rep2


title: Control

value: Control cells


title: PA_PA1431_cycle2_Rep2


title: PA_PA0236_cycle2_Rep1


title: PA_PA0236_cycle3_Rep1


title: PA_PA0236_cycle1_Rep1


title: FBXO44 ChIP-Seq

extract_protocol:
For FBXO44, cells were crosslined and sonicated. For H3K9me3 ChIP, native ChIP was performed.
Libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB)

value: FBXO44 antibody (Sigma-Aldrich no. HPA003363)


title: PA_PA0236_cycle0_Rep1

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary Table3 and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul Promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary Table3, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq X Ten or BGI MGISEQ-2000 sequencer.


title: H3K9me3 ChIP-Seq


title: Biopsy patient8 lesional skin day 14

data_processing: The microarray data were summarized applying the SST-RMA (signal space transformation - robust multi-array average) gene level method as implemented in the Transcriptome Analysis Console (TAC) 4.0 software (ThermoFisher Scientific).

tag: patient diagnosis

value: psoriasis

tag: tissue

tag: gender

tag: disease state (ls/nl)


title: PA_PA1431_cycle0_Rep2

tag: genotype

tag: growth phase


title: Biopsy patient8 lesional skin day 0

tag: day


title: Biopsy patient8 lesional skin day 84


title: Biopsy patient8 lesional skin day 4


title: Biopsy patient8 lesional skin day 42


title: Biopsy patient7 lesional skin day 84


title: PA_PA0225_cycle3_Rep1


title: h2a.w-2 bisulfite-seq rep 1

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with parameters -q 25 -a AGATCGGAAGAG, and all other params default.
ChIP-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Pileup tracks of each ChIP-seq sample over its matched H3 sample (log2) were generated using the deeptools v.3.3.0 function bamCompare, while coverage tracks of input samples were generated using deeptools function bamCoverage; both functions used parameters --normalizeUsing CPM, --binSize 10.
ATAC-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only properly paired reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were obtained using Genrich (https://github.com/jsh58/Genrich) with parameters -p 0.01, -a 200, -l 100, -g 100. ChrM, ChrC, and several high-copy number rRNA regions were excluded from the analysis (provided as a supplementary file in the paper).
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.0c (parameters: --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 -outFilterMismatchNoverReadLmax 0.05, all others default). Only pairs with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.  Read counts for each gene and TE were obtained using htseq-count (parameters: --nonunique none -m intersection-strict) using the araport11 annotations (PMID: 27862469). Differential expression analysis was performed using DESeq2 (PMID: 25516281), and genes were considered differentially expressed with an adjusted p-value < 0.05 and abs[log2(fold change)] > 1.
BS-seq datasets: analysis was performed as previously reported (Bourguet et al. 2018, PMID: 30574575). Briefly, different reads with identical sequences were presumed to be PCR duplicates and removed prior to mapping. Reads were mapped to TAIR10 using BS-Seeker2 v.2.1.5, allowing 4% mismatches, resulting in a 'CGmap file'. Methylation values were only called from uniquely-mapped reads. bigWig tracks were created from the CGmap files by retaining all cytosine positions with 8 or more read coverage, computing %methylation, and converting the resulting bedGraph files to bigWig using the UCSC bedGraphToBigWig function.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig tracks for all ChIP-seq samples (except for input samples) are provided, containing normalized sequencing depth of the IP sample vs. its matched input control. For input DNA samples, bigWig tracks contain coverage normalized by total library depth (CPM) instead. For ATAC-seq, normalized coverage tracks created by Genrich are provided. For RNA-seq, the output of DESeq2 analysis is provided, including overall per-gene/TE expression estimates (baseMean), log2(WT / mutant) (mutant = h2a.w-1 or h2a.w-2), and the adjusted p-value. Note that positive log2(FC) numbers indicate that mutant > WT, negative numbers indicate mutant < WT. For BS-seq, 'CGmap' text files containing all methylation data are provided, along with separate bigWig tracks of methylation levels for CG, CHG and CHH methylation. Only positions with 8+ coverage were used to generate the bigWig files.

source_name: h2a.w-2 bisulfite-seq_seedlings

extract_protocol:
DNA was extracted from 10-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Bisulfite conversion, library preparation and sequencing were performed at the Beijing Genomics Institute (Hong Kong). Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were sequenced PE 100 bp on HiSeq 4000.

tag: ecotype background

tag: developmental stage

value: 10-day-old seedlings


title: In_M10_e163

data_processing:
Reads were trimmed according to the CATS library recommendations using trimmomatic version 0.32 and cutadapt version 1.6
Reads were mapped using RNA STAR Version 2.6.0b and samtools Version 1.8 (--outFilterMultimapNmax 10 --outFilterMismatchNoverReadLmax 0,2 --outFilterScoreMinOverLread 0,8 --outSAMunmapped Yes) to Repbase repeats and quantified using IdxStats (samtools Version 1.2)
Unmapped reads were processed using BAM-toSAM, Filter SAM (samtools Version 1.2) (Type: The read is unmapped Flag: Yes), SAM to FASTQ picard Version 1.56.0 (Single or paired end: single, Re-reverse bases and qualities of reads on negative strand: True)
Proccessed reads were mapped to hg38 using RNA STAR Version 2.6.0b and samtools Version 1.8 (--outSAMunmapped No --outFilterMultimapNmax 10 --outFilterMismatchNoverReadLmax 0,2 --outFilterScoreMinOverLread 0,8)
BAM files were converted to BigWig (ucsc-bedgraphtobigwig Version 357 and bedtools Version 2.27.1) and processed in DERfinder tool Version 1.8.5 for annotation free Expressed region identification and counting (cutoff = 5, L = 76)
Statistics were done in EdgeR  Version 3.1 using an expressed region cutoff of min 6 counts in total in min 2 samples
Genome_build: repbase_comp, hg38
Supplementary_files_format_and_content: BigWig files used for DERfinder input, .txt files with EdgeR output for both Repbase and hg38 mapping including normalized counts and statistics

source_name: Hela S3

extract_protocol:
Samples were snap-frozen before sonication of chromatin in a Diagenode Bioruptor (4°C, 30s ON / 90s OFF x30 cycles on high) and checked for correct size on an agarose gel. Sonicated samples were pre-cleared before IP with Protein A dynabeads (Invitrogen 100-02D) by rotating 1h at 4°C. Biotinylated chromatin was isolated with T1 streptavedin magnetic beads (Invitrogen 656-01) in the presence of RNase inhibitors (100U/mL)(NEB M0314L) and decross-linked in TE buffer (incl. 0,5% SDS and Proteinase K) 37°C 10h followed by 65°C 6h (interval shaking) for RNA isolation. RNA was purified using a miRNeasy Purification Kit including an on-column DNAse digestion (QIAGEN, Hilden, Germany) as per kit protocol for low RNA amounts. RNA for the long RNA-seq was further purified and concentrated using a Clean and Concentrator-5 kit (Zymo Research, CA, USA) as per kit protocol.
Short RNA-seq: 10 ng RNA was used for library preparation with the Diagenode CATS small RNA-seq according to manufacturers protocol, using 10 PCR cycles. Library size selection was performed with AgencourtAMPure XP beads using a 1,4 volume ratio to remove primer-dimers. Libraries were pooled according to experimental replicates with 8 samples at equimolar concentrations including 2% phiX.

tag: timepoint

tag: dna label

value: b-dUTP


title: PA_PA1431_cycle1_Rep2

data_processing:
Library strategy: HT-SELEX
Illumina Casava v1.7 software used for basecalling.
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas aeruginosa PAO1 (GCF_000006765.1, ASM676v1)
Supplementary_files_format_and_content: 0_PA_all_PWM_results.txt: Tab-delimited text file includes position weight matrix (PWM) results for each transcription factor (TF).
Supplementary_files_format_and_content: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt: Tab-delimited text file includes all TFs' genome wide target scan results based on the output of FIMO software.

tag: transcription factor


title: In_M10_e161


title: WT bisulfite-seq rep 1

source_name: WT bisulfite-seq_seedlings

value: wild-type


title: In_M10_e160


title: PA_PA0225_cycle1_Rep1

value: wild type


title: h1 h2a.w-2 ATAC-seq rep 2

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with parameters -q 25 -a AGATCGGAAGAG, and all other params default.
ChIP-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Pileup tracks of each ChIP-seq sample over its matched H3 sample (log2) were generated using the deeptools v.3.3.0 function bamCompare, while coverage tracks of input samples were generated using deeptools function bamCoverage; both functions used parameters --normalizeUsing CPM, --binSize 10.
ATAC-seq datasets: reads were mapped to TAIR10 using bowtie2 v.2.3.4.3 (parameters: -N 0 -L 22, all others default). Only properly paired reads with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were obtained using Genrich (https://github.com/jsh58/Genrich) with parameters -p 0.01, -a 200, -l 100, -g 100. ChrM, ChrC, and several high-copy number rRNA regions were excluded from the analysis (provided as a supplementary file in the paper).
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.0c (parameters: --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 -outFilterMismatchNoverReadLmax 0.05, all others default). Only pairs with a single best alignment to the genome were kept for further analysis. Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite.  Read counts for each gene and TE were obtained using htseq-count (parameters: --nonunique none -m intersection-strict) using the araport11 annotations (PMID: 27862469). Differential expression analysis was performed using DESeq2 (PMID: 25516281), and genes were considered differentially expressed with an adjusted p-value < 0.05 and abs[log2(fold change)] > 1.
BS-seq datasets: reads were trimmed, mapped to the TAIR10 genome, and methylation called using methylpy (version 1.4.3). Only uniquely mapping reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig tracks for all ChIP-seq samples (except for input samples) are provided, containing normalized sequencing depth of the IP sample vs. its matched input control. For input DNA samples, bigWig tracks contain coverage normalized by total library depth (CPM) instead. For ATAC-seq, normalized coverage tracks created by Genrich are provided. For RNA-seq, the output of DESeq2 analysis is provided, including overall per-gene/TE expression estimates (baseMean), log2(WT / mutant) (mutant = h2a.w-1 or h2a.w-2), and the adjusted p-value. Note that positive log2(FC) numbers indicate that mutant > WT, negative numbers indicate mutant < WT. For BS-seq, 'CGmap' text files containing all methylation data are provided, along with separate bigWig tracks of methylation levels for CG, CHG and CHH methylation. Only positions with 8+ coverage were used to generate the bigWig files.

source_name: seedlings

extract_protocol:
Nuclei were extracted from 0.5 g fresh 10-day-old seedlings, DAPI stained and sorted on FACS Aria III (BD Biosciences)
ATAC-seq was performed as described in Lu et al. 2017 (PMID: 27903897). Tagmentation reaction was carried out on 50,000 sorted nuclei using Tn5 transposase (Nextera cat. no. 15027865), and tagmented DNA was isolated using the MinElute PCR purification kit (Qiagen). Libraries were amplified using NEBNext 2x master mix (NEB) and Nextera primers, and sequenced on NextSeq 550 (Illumina).


title: PA_PA0225_cycle4_Rep1

value: exponential phase


title: Biopsy patient8 nonlesional skin day 0

value: skin


title: PA_PA0225_cycle2_Rep1


title: PA_PA0225_cycle0_Rep1

value: no protein


title: h1 ATAC-seq rep 2


title: In_M2_e160


title: In_M2_e161


title: PA_PA0191_cycle4_Rep1


title: Biopsy patient7 lesional skin day 42

value: LS


title: Biopsy patient7 lesional skin day 4

source_name: Lesional skin punch biopsy day 4

value: Male


title: Biopsy patient7 nonlesional skin day 0


title: Biopsy patient7 lesional skin day 0

source_name: Lesional skin punch biopsy day 0


title: Biopsy patient6 lesional skin day 84

source_name: Lesional skin punch biopsy day 84

value: Female


title: h2a.w-2 ATAC-seq rep 2


title: h2a.w-2 ATAC-seq rep 1


title: PA_PA0191_cycle3_Rep1


title: In_N_e163


title: h1 h2a.w-2 ATAC-seq rep 1


title: wild-type ATAC-seq rep 2


title: In_N_e161


title: h1 ATAC-seq rep 1


title: In_N_e160


title: PA_PA0191_cycle2_Rep1


title: wild-type ATAC-seq rep 1


title: PA_PA0191_cycle0_Rep1

source_name: no protein


title: no b-dUTP_e163

tag: ip

value: T1 beads


title: h2a.w-2 input rep 2

source_name: h2a.w-2 input_seedlings

extract_protocol:
3 g 10-day-old seedlings were fixed in 1% PFA and ground into powder. Nuclei were isolated and chromatin was sheared using a Covaris E220 for 15 min. IP, washes, and DNA isolation were carried out as in Yelagandula et al. 2017 (PMID: 28439859).
(Rep 2) NEBNext Ultra II DNA preparation kit (NEB), sequenced on Illumina NextSeq 550


title: PA_PA0181_cycle4_Rep1


title: In_M2_e163


title: no b-dUTP_e161


title: Biopsy patient6 lesional skin day 0


title: PA_PA0181_cycle2_Rep1


title: Biopsy patient7 lesional skin day 14

source_name: Lesional skin punch biopsy day 14


title: PA_PA0181_cycle3_Rep1


title: PA_PA1754_cycle0_Rep2


title: Biopsy patient6 lesional skin day 14


title: H3_e163


title: h2a.w-2 H3K27me1 ChIP-seq rep 1

source_name: h2a.w-2 H3K27me1 ChIP-seq_seedlings

extract_protocol:
3 g 10-day-old seedlings were fixed in 1% PFA and ground into powder. Nuclei were isolated and chromatin was sheared using a Covaris E220 for 15 min. IP, washes, and DNA isolation were carried out as in Yelagandula et al. 2017 (PMID: 28439859).
(Rep 1) Ovation Ultralow Library System V2 (NuGen), sequenced on Illumina NextSeq 550

tag: chip antibody

value: anti-H3K27me1 (17-643, Millipore)


title: Biopsy patient5 lesional skin day 84


title: Αlpha6+/Sca1-_r1

value: WT

tag: age

value: back skin

tag: cell type

value: Alpha6+/Sca1- cells


title: Biopsy patient6 lesional skin day 42

source_name: Lesional skin punch biopsy day 42


title: H3_e161


title: PA_PA0181_cycle1_Rep1


title: Biopsy patient5 lesional skin day 14


title: Biopsy patient5 lesional skin day 4


title: H3_e160


title: PA_PA0181_cycle0_Rep1


title: h2a.w-2 H3K27me1 ChIP-seq rep 2


title: h2a.w-2 H3K9me2 ChIP-seq rep 1

source_name: h2a.w-2 H3K9me2 ChIP-seq_seedlings

value: anti-H3K9me2 (ab1220, Abcam)


title: M10_e163


title: Biopsy patient6 lesional skin day 4

value: psoriasis


title: PA_PA0159_cycle4_Rep1


title: Biopsy patient5 lesional skin day 0


title: PA_PA0159_cycle3_Rep1


title: M10_e161


title: Biopsy patient6 nonlesional skin day 0

source_name: Nonlesional skin punch biopsy day 0

value: NL


title: h2a.w-2 H3K9me1 ChIP-seq rep 1

source_name: h2a.w-2 H3K9me1 ChIP-seq_seedlings

value: 10-day-old seedlings

value: anti-H3K9me1 (ab8896, Abcam)


title: PA_PA0159_cycle2_Rep1

value: wild type


title: h2a.w-2 H3K9me1 ChIP-seq rep 2


title: Biopsy patient5 nonlesional skin day 0


title: M10_e160

value: b-dUTP


title: M2_e163


title: Biopsy patient4 lesional skin day 84

value: skin


title: h2a.w-2 H3 ChIP-seq rep 2

source_name: h2a.w-2 H3 ChIP-seq_seedlings

value: anti-H3 (ab1791, Abcam)


title: PA_PA0159_cycle0_Rep1

value: no protein


title: PA_PA0159_cycle1_Rep1

value: exponential phase


title: h2a.w-2 H3 ChIP-seq rep 1


title: M2_e161


title: M2_e160


title: Biopsy patient4 lesional skin day 14

value: Male

value: LS


title: h2a.w-2 H3K9me2 ChIP-seq rep 2


title: PA_PA0123_cycle3_Rep1


title: PA_PA0123_cycle4_Rep1


title: h2a.w-2 H2A.Z ChIP-seq rep 2

source_name: h2a.w-2 H2A.Z ChIP-seq_seedlings

value: custom anti-H2A.Z (Yelagandula et al. 2014)


title: h2a.w-2 H2A.Z ChIP-seq rep 1


title: PA_PA0123_cycle2_Rep1


title: N_e163

value: T1 beads


title: Biopsy patient4 lesional skin day 0


title: N_e161


title: h2a.w-2 input rep 1


title: N_e160


title: Biopsy patient4 lesional skin day 4


title: h2a.w-2 H2A ChIP-seq rep 2

source_name: h2a.w-2 H2A ChIP-seq_seedlings

value: custom anti-H2A (Yelagandula et al. 2014)


title: h2a.w-2 H2A.X ChIP-seq rep 2

source_name: h2a.w-2 H2A.X ChIP-seq_seedlings

value: custom anti-H2A.X (Yelagandula et al. 2014)


title: PA_PA0123_cycle0_Rep1


title: Biopsy patient3 lesional skin day 42

value: Female


title: PA_PA0120_cycle4_Rep1


title: Biopsy patient4 nonlesional skin day 0

value: psoriasis


title: NAF20

city: Suwon

first: Hoon

last: Hur

address: 164 Worldcup-ro, Yeongtong-gu

department: Department of Surgery

country: South Korea

institute: Ajou University School of Medicine

data_processing:
Illumina bcl2fastq-1.8.4 software
Reads for each sample were mapped to the reference genome (human hg19) by Tophat(v2.0.13).
The aligned results were added to Cuffdiff(v2.2.0) to report differentially expressed genes.
For library normalization and dispersion estimation, geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods were applied.
Cuffdiff data were added to CummeRbund(v2.8.2) to visualize RNA-Seq data.
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output

source_name: Gastric normal associated-fibroblasts cell

growth_protocol: All cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml), amphotericin b (1.25 mg/L).

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit. mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
mRNA Sequencing using Illumina Truseq Stranded mRNA Library prep kit

treatment_protocol: All cells were incubated at 37°C in 5% CO2

value: Gastric normal tissue-derived fibroblasts cell

tag: passage


title: CAF20

source_name: Gastric cancer associated-fibroblasts cell

value: Gastric cancer tissue-derived fibroblasts cell


title: h2a.w-2 H2A.X ChIP-seq rep 1

value: 10-day-old seedlings


title: PA_PA0120_cycle3_Rep1

value: wild type


title: h2a.w-2 H1 ChIP-seq rep 2

source_name: h2a.w-2 H1 ChIP-seq_seedlings

value: anti-H1 (AS111801, Agrisera)


title: PA_PA0120_cycle2_Rep1


title: PA_PA0123_cycle1_Rep1


title: h2a.w-2 H2A ChIP-seq rep 1


title: h2a.w-2 H1 ChIP-seq rep 1


title: WT input rep 2

source_name: WT input_seedlings

value: wild-type


title: PA_PA0120_cycle1_Rep1


title: Biopsy patient3 lesional skin day 84

source_name: Lesional skin punch biopsy day 84

tag: patient diagnosis

value: skin


title: Biopsy patient3 lesional skin day 14

tag: tissue


title: 2nd Fis1-4

first: Yae-Huei

last: Liou

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Primary hepatocyte

growth_protocol: All sample are 48hr post-infected primary hepatocyte.

extract_protocol:
RNA was harvest by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: Ad-LacZ, Ad-Fis1 and Ad-Drp1 infected

tag: strain

tag: treatment

value: Ad-Drp1 infected

tag: mouse


title: Biopsy patient3 lesional skin day 0

source_name: Lesional skin punch biopsy day 0

tag: gender

tag: disease state (ls/nl)


title: 2nd Fis1-3

tag: genotype


title: 2nd Fis1-2


title: 2nd Fis1-1


title: PA_PA0120_cycle0_Rep1

source_name: no protein

value: no protein

tag: growth phase


title: Biopsy patient3 lesional skin day 4

source_name: Lesional skin punch biopsy day 4

tag: day


title: PA_PA0191_cycle1_Rep1

value: exponential phase


title: PA_PA0048_cycle4_Rep1


title: Biopsy patient3 nonlesional skin day 0

value: NL


title: PA_PA0048_cycle3_Rep1


title: WT H3K27me1 ChIP-seq rep 2

source_name: WT H3K27me1 ChIP-seq_seedlings

tag: ecotype background

tag: developmental stage

value: anti-H3K27me1 (17-643, Millipore)


title: 2nd LacZ-4

value: Ad-Lacz infected


title: WT H3K27me1 ChIP-seq rep 1


title: 2nd LacZ-3


title: WT H3K9me2 ChIP-seq rep 2

source_name: WT H3K9me2 ChIP-seq_seedlings

value: anti-H3K9me2 (ab1220, Abcam)


title: PA_PA0048_cycle2_Rep1

tag: transcription factor


title: WT input rep 1


title: Biopsy patient2 lesional skin day 14

source_name: Lesional skin punch biopsy day 14

value: Male

value: LS


title: Biopsy patient2 lesional skin day 42

source_name: Lesional skin punch biopsy day 42

value: psoriasis


title: Biopsy patient2 lesional skin day 4


title: WT H3K9me2 ChIP-seq rep 1

tag: chip antibody


title: no b-dUTP_e160

source_name: Hela S3

tag: timepoint

tag: ip

value: T1 beads


title: PA_PA0048_cycle1_Rep1


title: 2nd LacZ-2


title: 2nd LacZ-1


title: PA_PA0048_cycle0_Rep1


title: WT H3K9me1 ChIP-seq rep 2

source_name: WT H3K9me1 ChIP-seq_seedlings

value: anti-H3K9me1 (ab8896, Abcam)


title: 1st Fis1-3

value: Ad-Fis1 infected


title: Biopsy patient2 lesional skin day 84


title: Biopsy patient2 lesional skin day 0


title: Biopsy patient2 nonlesional skin day 0

source_name: Nonlesional skin punch biopsy day 0


title: 1st Fis1-2

value: wild type


title: WT H3 ChIP-seq rep 2

source_name: WT H3 ChIP-seq_seedlings

value: 10-day-old seedlings

value: anti-H3 (ab1791, Abcam)


title: PA_PA0037_cycle3_Rep1


title: WT H3K9me1 ChIP-seq rep 1

value: wild-type


title: WT H3 ChIP-seq rep 1


title: 1st Fis1-4


title: WT H2A.Z ChIP-seq rep 2

source_name: WT H2A.Z ChIP-seq_seedlings

value: custom anti-H2A.Z (Yelagandula et al. 2014)


title: PA_PA0037_cycle4_Rep1


title: 1st LacZ-4


title: PA_PA0037_cycle0_Rep1

value: no protein


title: Biopsy patient1 lesional skin day 14

value: skin


title: 1st LacZ-3


title: WT H2A.Z ChIP-seq rep 1


title: 1st Fis1-1


title: PA_PA0037_cycle1_Rep1

value: exponential phase


title: PA_PA0037_cycle2_Rep1


title: WT H2A.X ChIP-seq rep 2

source_name: WT H2A.X ChIP-seq_seedlings

value: custom anti-H2A.X (Yelagandula et al. 2014)


title: scRNA-seq of liver Lin-CD122+CD49a+ cells

city: Hefei

first: Hui

last: Peng

address: 443 Huangshan Road

institute: University of Science and Technology of China

data_processing:
FASTQs generated from the Illumina sequencing output were aligned with the mouse genome, version GRCm38, with the STAR algorithm.
Gene-barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell-associated barcodes.
The output for a gene-barcode matrix containing the barcoded cells and gene expression counts was then imported into the Seurat (v2.3.0) R toolkit for quality control and downstream analysis.
We selected genes with a high variance, using the FindVariableGenes function with the “vst” method and nfeatures set to 2,000.
Dimensionality of the data was reduced by principal component analysis (PCA), and the FindNeighbors and FindClusters functions (20 pcs and a resolution of 0.5) were used for clustering analysis.
RunUMAP was applied for visualization, the samples were integrated with the FindIntegrationAnchors and IntegrateData functions, and cluster markers were identified with FindMarkers.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Purified Lin-CD122+CD49a+ cells from adult mouse liver

extract_protocol:
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation. After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription.
The library construction were performed according to the standard manufacturer's protocol (CG000206 Rev D).

tag: age

value: 7-10 weeks

value: Liver

tag: cell type

value: CD45+Lin-CD122+CD49a+ cells


title: 1st LacZ-2

value: Ad-Lacz infected


title: scRNA-seq of liver LSM cells

source_name: Purified LSM cells from adult mouse liver

tag: tissue

value: CD45+Lin-Sca-1+Mac-1+ cells


title: PA_PA0032_cycle4_Rep1


title: PA_PA0032_cycle3_Rep1


title: 1st LacZ-1

tag: strain


title: Biopsy patient1 lesional skin day 84

first: Thomas

address: Blegdamsvej 3C

source_name: Lesional skin punch biopsy day 84

extract_protocol: Total RNA from skin biopsies was isolated using the SV Total RNA Isolation System according to the manufacturer's instructions.

tag: patient diagnosis

value: psoriasis

value: Male

value: LS


title: WT H2A ChIP-seq rep 2

source_name: WT H2A ChIP-seq_seedlings

value: custom anti-H2A (Yelagandula et al. 2014)


title: PA_PA0032_cycle2_Rep1

value: wild type


title: Biopsy patient1 lesional skin day 0

source_name: Lesional skin punch biopsy day 0


title: Biopsy patient1 lesional skin day 4


title: Biopsy patient1 lesional skin day 42


title: RNA-Seq Pneumocystis infection 4W

city: Beijing

first: Zhaohui

last: Tong

state: Beijing

address: NO. 8, Gong Ti South Road

department: Department of Respiratory and Critical Care Medicine

institute: Beijing Chaoyang Hospital

data_processing:
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package
Protein-protein interaction was obtained from STRING database with combine_score >=400. For each cluster, the interaction of top 20 marker genes was extracted from the database and the results were visualized using Cytoscape software, respectively.
Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. The gene and TF network for each cluster was visualized using Cytoscape software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung CD45+ cells

extract_protocol:
Single cell suspensions were isolated from mouse lungs by collagenase digestion.
CD45+ cells were sorted by BD FACS ARIA II cell sorter from lung cell suspensions. Single-cell 5’ RNA-Seq libraries were generated using Single Cell 5’ Library and Gel Bead Kit and Chromium Controller (10x Genomics) according to the manufacturer’s protocol.
single-cell RNA Seq

treatment_protocol: For Pneumocystis infection, 1×106 Pneumocystis cysts contained in 100μl PBS were injected through trachea of each mouse. Control mice were transtracheally injected with 100μl PBS.

value: Lung-derived CD45+ cells

value: 6-8 week

tag: duration of infected with pneumocystis

value: 4 weeks


title: RNA-Seq Pneumocystis infection 3W

value: 3 weeks


title: PA_PA0032_cycle1_Rep1

first: Jian

address: 83 Tat Chee Avenue, Kowloon


title: RNA-Seq Pneumocystis infection 2W

value: 2 weeks


title: WT H1 ChIP-seq rep 2

first: Colette

address: 610 Charles E Young Dr East, Room 4045

source_name: WT H1 ChIP-seq_seedlings

value: wild-type

value: 10-day-old seedlings

value: anti-H1 (AS111801, Agrisera)


title: mouse_kidney_control_SMARTseq_kit_100pg_rep4

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 4
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

data_processing:
Reference preparation: we created two custom parental genomes (“pseudogenomes” (Crowley et al., 2015; Zou et al., 2014); or “pseudocontigs” when we have phasing by contigs) for each organism, we used a custom script (all custom software tools mentioned are available on Github https://github.com/gimelbrantlab/QCumber). We also created a vcf-file with one allele considered as a reference (maternal 129S1 or first phased allele) and the other as an alternative allele. Only heterozygous sites were used.
Alignment: RNA-seq reads were aligned with STAR aligner v.2.5.4a (Dobin et al., 2013) on each of two pseudogenomes, with default threshold on quality of alignment. Only uniquely alligned reads were used.
Allele assigment. Given vcf file with heterozygous positions, coverage over each SNP was calculated using custom script based on samtools mpileup and parsed to obtain the table with allelic counts. Data processing steps from read alignment to allelic counts were based on the GATK pipeline (Castel et al., 2015).
Allele counting per gene. All exons belonging to the same gene were merged into a single gene model based on GTF file (RefSeq GTF files, GRCm38.68 and GRCh37.63, were downloaded from Ensemble ftp://ftp.ensembl.org/pub/release-68/gtf/ (Zerbino et al., 2018)), excluding overlapping regions that belong to multiple genes. This step was based on the GATK pipeline (Castel et al., 2015).
AI point estimate per gene obtained as a proportion of maternal gene counts to total allelic gene counts
Genome_build: mm10
Supplementary_files_format_and_content: allelic counts, allelic imbalance with confidence intervals

source_name: mouse left kidney tissue

extract_protocol:
Total RNA was isolated using Trizol from a freshly collected kidney tissue of an adult female mouse of 129S1 x Cast/Ei F1 background. Isolated RNA was DNase-treated with RQ1 DNase (Promega).
Library preparation was done using NEBNext Ultra RNA Poly-A kit (mentioned as NEBNext in the sample name) or Clonetech SMARTseqv4 kit (mentioned as SMARTseq in the sample name), according to manufacturers’ instructions. Input RNA amount varied depending on the sample

value: 129S1/SvImJ x CAST/EiJ F1

tag: drug treatment

value: control

tag: library replicates

tag: Sex

value: female


title: Biopsy patient1 nonlesional skin day 0

city: Copenhagen N

last: Litman

institute: University of Copenhagen

value: skin

tag: gender

tag: disease state (ls/nl)

value: NL


title: RNA-Seq Pneumocystis infection 1W

value: 1 week


title: RNA-Seq Pneumocystis infection 5W

value: 5 weeks


title: WT H2A ChIP-seq rep 1

tag: ecotype background

tag: genotype

value: custom anti-H2A (Yelagandula et al. 2014)


title: mouse_kidney_control_SMARTseq_kit_100pg_rep3

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 3
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: RNA-Seq Pneumocystis uninfection

value: uninfected


title: WT H2A.X ChIP-seq rep 1

tag: developmental stage

value: custom anti-H2A.X (Yelagandula et al. 2014)


title: mouse_kidney_control_SMARTseq_kit_100pg_rep2

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 2
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: mouse_kidney_control_SMARTseq_kit_100pg_rep5

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 5
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: PA_PA0032_cycle0_Rep1

source_name: no protein

value: no protein

tag: growth phase

tag: transcription factor


title: Biopsy patient5 lesional skin day 42

value: psoriasis

value: Female

value: LS

tag: day


title: h2a.w-2 RNA-seq rep 3

description:
h2aw2_3_RNA
processed data file:
RNAseq_WT_vs_h2aw2_stats.txt.gz

source_name: h2a.w-2 RNA-seq_seedlings

extract_protocol:
Total RNA was isolated from 10-day-old seedlings using the Rneasy Mini kit (Qiagen), DNase treated using the DNA-free kit (Invitrogen), and rRNA depleted using the RiboZero kit (Illumina)
NEBnext Ultra II directional RNA library prep kit, sequenced on NextSeq 550 (Illumina)


title: Biopsy patient4 lesional skin day 42

source_name: Lesional skin punch biopsy day 42

value: Male


title: h2a.w-2 RNA-seq rep 2

description:
h2aw2_2_RNA
processed data file:
RNAseq_WT_vs_h2aw2_stats.txt.gz

value: 10-day-old seedlings


title: h2a.w-2 RNA-seq rep 1

description:
h2aw2_1_RNA
processed data file:
RNAseq_WT_vs_h2aw2_stats.txt.gz


title: WT H1 ChIP-seq rep 1

value: wild-type

tag: chip antibody

value: anti-H1 (AS111801, Agrisera)


title: mouse_kidney_control_SMARTseq_kit_100pg_rep1

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 1
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

value: 129S1/SvImJ x CAST/EiJ F1

value: control


title: mouse_kidney_control_SMARTseq_kit_10ng_rep6

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 6
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

value: female


title: NC_NgCtrl3_cycle1_Rep1

source_name: Negative Control 3


title: mouse_kidney_control_SMARTseq_kit_100pg_rep6

description:
mouse left kidney, control sample, RNA input 100pg, library sequenced using SMARTseq kit, library preparation replicate 6
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: Pneumocystis infection 3W

data_processing:
Library strategy: TCR-seq
The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest. Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package
Protein-protein interaction was obtained from STRING database with combine_score >=400. For each cluster, the interaction of top 20 marker genes was extracted from the database and the results were visualized using Cytoscape software, respectively.
Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. The gene and TF network for each cluster was visualized using Cytoscape software.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Single cell suspensions were isolated from mouse lungs by collagenase digestion.
CD45+ cells were sorted by BD FACS ARIA II cell sorter from lung cell suspensions. Full-length TCR V(D)J segments were generated by using the Chromium Single-Cell V(D)J Enrichment kit following the manufacturer’s protocol.

tag: cell type

value: Lung-derived CD45+ cells

tag: age

value: 6-8 week

value: 3 weeks


title: mouse_kidney_control_SMARTseq_kit_10ng_rep5

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 5
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

tag: strain


title: mouse_kidney_control_SMARTseq_kit_10ng_rep4

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 4
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: Pneumocystis infection 1W

value: 1 week


title: Pneumocystis infection 2W

value: 2 weeks


title: NC_NgCtrl3_cycle3_Rep1

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt


title: NC_NgCtrl2_cycle3_Rep1

source_name: Negative Control 2


title: h2a.w-1 RNA-seq rep 2

description:
h2aw1_2_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz

source_name: h2a.w-1 RNA-seq_seedlings


title: Pneumocystis uninfection

value: uninfected


title: NC_NgCtrl2_cycle4_Rep1

value: no protein


title: Pneumocystis infection 4W

value: 4 weeks


title: h2a.w-1 RNA-seq rep 1

description:
h2aw1_1_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz


title: mouse_kidney_control_SMARTseq_kit_10ng_rep3

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 3
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: WT RNA-seq rep 3

description:
WT_3_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz
RNAseq_WT_vs_h2aw2_stats.txt.gz

source_name: WT RNA-seq_seedlings


title: Raw 264.7 gV sPLA2 knockdown cell transfected with gV sPLA2 (H48Q)-Myc

city: Chuo

first: Daisuke

last: Fujioka

state: Yamanashi

address: 1110 Shimokato

country: Japan

institute: University of Yamanashi

description: gV sPLA2 knockdown cells reconstituted with gV sPLA2 (H48Q, enzymatic activity-deleted)-Myc

data_processing:
ChIP-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v1.1.2.
ChIP-Seq peaks were called using the MACS2 v2.1.1.20160309, then annotated with the use of ChIPseeker v1.16.1.
Genome_build: mm10

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's TruSeq ChIP Sample Preparation Guide 15023092 Rev.B using TruSeq DNA Sample prep Kit. Briefly, DNA was end-repaired to convert the overhangs resulting from fragmentation into blunt ends. The blunt ends were treated with dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 18 cycles and library fragments were purified with magnetic beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

tag: cell line

value: macrophage; Abelson murine leukemia virus transformed

value: BALB/c

value: Myc-tag

tag: treatment

value: untreated


title: NC_NgCtrl3_cycle2_Rep1

city: Hong Kong

last: Yan

institute: City University of Hong Kong


title: mouse_kidney_control_SMARTseq_kit_10ng_rep2

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 2
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

tag: drug treatment


title: NC_NgCtrl2_cycle2_Rep1


title: Raw 264.7 gV sPLA2 knockdown cell transfected with gV sPLA2-Myc

description: gV sPLA2 knockdown cells reconstituted with gV sPLA2-Myc


title: NC_NgCtrl2_cycle1_Rep1


title: WT RNA-seq rep 2

city: Los Angeles

last: Picard

institute: University of California - Los Angeles

description:
WT_2_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz
RNAseq_WT_vs_h2aw2_stats.txt.gz

value: wild-type

value: 10-day-old seedlings


title: WT RNA-seq rep 1

description:
WT_1_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz
RNAseq_WT_vs_h2aw2_stats.txt.gz


title: NC_NgCtrl3_cycle0_Rep1


title: h2a.w-1 RNA-seq rep 3

description:
h2aw1_3_RNA
processed data file:
RNAseq_WT_vs_h2aw1_stats.txt.gz


title: Raw 264.7 gV sPLA2 knockdown cell

description: gV sPLA2 knockdown cells


title: NC_NgCtrl2_cycle0_Rep1


title: mouse_kidney_control_NEBNext_kit_rep6

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 6
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

value: 129S1/SvImJ x CAST/EiJ F1

tag: library replicates


title: Raw 264.7 Input control-gV sPLA2 knockdown cell transfected with gV sPLA2-Myc


title: mouse_kidney_control_NEBNext_kit_rep5

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 5
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

value: control

tag: Sex


title: inflorescence meristems, pMYB3R4::GFP-MYB3R4mNES_rep3

data_processing:
The raw reads obtained from the sequencing facilities were analyzed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).Read were aligned to the TAIR10 transcriptome using Salmon (Patro et al., 2017). For each gene, read abundance were computed.
Genome_build: TAIR10
Supplementary_files_format_and_content: rna-seq_combined_read.txt

extract_protocol:
Total RNA was isolated from 36 dissected inflorescence meristems using RNeasy Mini Kit (QIAGEN Cat No./ID: 74104), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries,  rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using  mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the  second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and  PCR enrichment.The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume.

tag: tissue

value: inflorescence meristems

tag: shift experiment


title: inflorescence meristems, pMYB3R4::GFP-MYB3R4mNES_rep2


title: mouse_kidney_control_NEBNext_kit_rep3

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 3
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv

value: female


title: NC_NgCtrl1_cycle3 Rep1

source_name: Negative Control 1


title: mouse_kidney_control_NEBNext_kit_rep4

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 4
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: NC_NgCtrl1_cycle2 Rep1


title: inflorescence meristems, pMYB3R4::GFP-MYB3R4mNES_rep1


title: NC_NgCtrl1_cycle1 Rep1


title: mouse_kidney_control_SMARTseq_kit_10ng_rep1

description:
mouse left kidney, control sample, RNA input 10ng, library sequenced using SMARTseq kit, library preparation replicate 1
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: inflorescence meristems, myb3r1myb3r4_rep3

source_name: myb3r1myb3r4 inflorescence meristems


title: NC_NgCtrl1_cycle0 Rep1


title: mouse_kidney_control_NEBNext_kit_rep1

description:
mouse left kidney, control sample, RNA input 100ng, library sequenced using NEBNext kit, library preparation replicate 1
kidney_RNAseq_allelic_counts.csv
kidney_RNAseq_allelic_imbalance.csv


title: inflorescence meristems, myb3r1myb3r4_rep2


title: inflorescence meristems, myb3r1myb3r4_rep1


title: NC_NgCtrl1_cycle4 Rep1

description:
processed data file: 0_PA_all_PWM_results.txt
processed data file: 1_PA_all_PWM_FIMO_genome_scan_results_reshaped_bed6_plus.sorted.txt