title: NIL_PRL5APO1_YP_2


title: Col-0-rep1

status: Public on May 23 2020

type: SRA

city: Shenzhen

first: Wenwen

last: Kong

state: Guangdong

address: 1066 Xueyuan Avenue, Nanshan District

department: College of Life Sciencesand Oceanography

country: China

institute: Shenzhen University

library_source: transcriptomic

data_processing:
All the data were analized with the pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
Genome_build: Araport11 genome
Supplementary_files_format_and_content: Processed data were combined into excel file which contained all the RPM value from each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown under long photoperiod conditions (16-h light/8-h dark; white light; light intensity, 120 mmol m22 s21) at 22°C.

extract_protocol:
Total RNAs were extracted from Arabidopsis inflorescence with TRIzol reagent (Ambion) and treated with DNase I (NEB).
Manufacturer of NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300)

treatment_protocol: No treatment

tag: genotype

value: wildtype

tag: ecotype


title: 1003_B14_3D_D15

city: Auburn

first: Michael

middle: W

last: Greene

state: AL

address: 260 Lem Morrison Dr

department: Nutrition

country: USA

institute: Auburn University

description: 3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture, batch 14

data_processing:
Sequencing reads were aligned to the human GRCh38 reference genome and counted with STAR using aRNApipe, a RNA-seq analysis pipeline developed at the HusdonAlpha Institute for Biotechnology
Human mapped raw counts obtained from STAR were used for differential expression analysis with the R package DESeq2. False discovery rates (FDR) p value less than 0.05 were considered significantly differentially expressed and genes with log2 fold change greater than 1.5 were used for downstream gene set analyses.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file with htseq gene counts for each Sample.

organism: Homo sapiens

source_name: PDX tumor

extract_protocol:
3D engineered CRC tissues and in vivo tumors were flash frozen in liquid nitrogen, and then stored at -80C.  RNA was isolated using RNeasy Plus Micro Kit (Qiagen). Illumina TruSeq RNA Stranded RNA Kit with Ribo-Zero Gold was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina NovaSeq protocols

tag: pdx model

value: In vitro

tag: crc stage

value: Stage II

tag: consensus molecular subtype

tag: batch

value: batch 14


title: NIL_PRL5APO1_YP_1

city: Nagoya

first: Tokunori

last: Hobo

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

data_processing:
convert .bcl files to .fastq using bcl2fastq
mask bases with QV < 25 using original script
align reads to cDNA reference provided from IRGSP1using bowtie with options "--all --best --strata"
count reads using linux commands (sort and uniq)
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.csv

organism: Oryza sativa

source_name: Oryza sativa

extract_protocol:
RNA was extracted from young panicle as described by Sambrook et al. (Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular cloning: a laboratory manual. Mol. cloning a Lab. manual. (1989).)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Young panicles

value: Prl5 and Pbl6 [APO1]


title: NIL_APO1_YP_3

value: Pbl6 [APO1]


title: HT6h_3

city: Shandong

first: Zhonghai

last: Ren

address: Daizong Road No.61,Taian

department: College of Horticulture Science and Engineering

institute: Shandong Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
Raw data of fastq format were firstly processed through perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the Cucumber (Chinese Long) v3 Genome was built using Hisat2 v2.0.5. The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM (expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Cucumber (Chinese Long) v3 Genome, http://cucurbitgenomics.org/organism/20
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Cucumis sativus

source_name: leaf

growth_protocol: The ‘Chinese long’ 9930，a cucumber typical of northern China, was used for expression analyses. The selected seeds after immersion and imbibition for 12h were seeded in pots containing vermiculite and matrix, and then cultivated in a growth chamber in temperature-controlled greenhouses with day and night temperature of 25 / 18 C and light cycle / dark period of 16h / 8h.

extract_protocol:
After heat treatment, leaves were collected and frozen in liquid nitrogen immediately and stored at − 80 °C prior to the assays. Total RNA of each sample was isolated using the Total RNA Extractor (TRIzol) kit (B511311, Sangon, China). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three-week-old seedlings were subjected to heat treatment at 42℃ and the leaves were collected at 0 (control), 3 and 6 h.

value: leaf

tag: treatment

value: Heat treatment at 42 C for 6 hours

tag: age

value: Three-week-old seedlings of cucumber


title: 1003_B12_4580

description: in vivo subcutaneously grown PDX CRC tumor, batch 12

value: In vivo

value: batch 12


title: HT6h_2


title: NIL_APO1_YP_2


title: 1003_B12_3D_D15

description: 3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture, batch 12


title: HT6h_1


title: HT3h_3

value: Heat treatment at 42 C for 3 hours


title: 1003_B20_3D_D15

description: 3D engineered CRC tissue, formed through PEG-fibrinogen encapsulation of PDX CRC cells, Day 15 of in vitro culture, batch 20

value: batch 20


title: NIL_APO1_YP_1


title: NIL_PRL5_YP_2


title: FoxQ1 3

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
For DESeq2 with biological replicates, differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.16.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 1 were set as the threshold for significantly differential expression.
Genome_build: Homo Sapiens(GRCh37/hg19)
Supplementary_files_format_and_content: FPKM represents Summary of gene expression level analysis by FPKM; Differential expression analysis

source_name: breast cancer

growth_protocol: The SUM1589 human breast cancer cell linespCMV6 empty vector (EV) or pCMV6-FoxQ1 (FoxQ1) were plated in 6-cm dish at a density of 5×105 cells/dish in triplicate and incubated overnight.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: no treatment

tag: cell type

value: human breast cancer

tag: cell line

tag: transfection

value: pCMV6-FoxQ1 (FoxQ1)


title: NIL_PRL5_YP_3


title: HT3h_2


title: FoxQ1 2


title: HT3h_1


title: FoxQ1 1


title: Col-0-rep2


title: EV_0 3

value: pCMV6 empty vector (EV)


title: HT0h_3

value: untreated


title: acinus pnn6

city: Stanford

first: Zhiyong

last: Wang

state: California

address: 260 panama street

department: Plant Biology

institute: Carnegie Institute for Science

data_processing:
Reads mapped with STAR and analyzed with Deseq2 for differential gene expression
To identify alternative splicing events, we used RACKJ following their online protocol to obtain raw read counts and then filtered by T-test p-vlaues and other selection criterion to identify significantly changes.
Genome_build: TAIR_10

source_name: 12-day-old light grown seedlings

growth_protocol: continuous light for 12 days at 22 degree

extract_protocol:
Total RNA extracted with RNeasy mini kit (Qiagen) following their protocol
cDNA constructed with NEBNext RNA Library Prep Kit for Illumina following the standard Illumina protocol

value: seedling

value: acinus-2 pnn


title: NIL_PRL5_YP_1


title: acinus pnn7


title: Koshihikari_YP_3

tag: cultivar

value: Koshihikari

value: WT


title: HT0h_2


title: WT5

value: wild-type


title: Koshihikari_YP_2

value: Young panicles


title: EV_0 2


title: EV_0 1


title: WT4


title: acinus pnn12


title: Koshihikari_YP_1


title: H3K27ac_2588_Tumor_1

status: Public on May 22 2020

city: Shanghai

first: Haojie

last: Chen

state: Shanghai

address: Yueyang Road 320

department: PICB

institute: CAS

library_source: genomic

data_processing:
Trim-galore was used to cut adaptor automatically
ChIP-seq reads were aligned to hg19 human genome using bowtie
Peaks were called using MACS(v.1.3.7) and select top 30,000 peaks in each samples
Reads count within peaks in each samples were calculated via MAnorm2-utils with bin size 2,000bp
Genome_build: hg19
Supplementary_files_format_and_content: bed file
Supplementary_files_format_and_content: raw read counts are included in the file GSE150976_ChIP-seq_raw_reads_count_profile_bins.xls

molecule: genomic DNA

source_name: lung

extract_protocol:
The tissue homogenate was filtered with a 70 µm cell strainer and fixed in 1% formaldehyde at room temperature for 10 min. The tissue pellet was collected through centrifugation, washed twice with cold PBS and then incubated with lysis buffer on ice for 20 min. The tissue lysate was sonicated, and DNA was sheared to an average size of 100-300 bp. Approximately 10% of the total tissue lysate was collected as input, while the other portion was first precleared with uncoupled Protein-A Dynabeads (Novex, 10002D) and incubated with H3K27ac-coupled Protein-A Dynabeads for 6 hours in a cold room. Then, the Dynabeads were collected using a magnet track, and chromatin was eluted.
The DNA was then processed for NGS library construction and sequenced.

treatment_protocol: H3K27ac ChIP-seq was performed using an anti-H3K27ac antibody (Abcam, ab4729). In brief, frozen LUAD and normal tissues were submersed in RPMI-1640 medium (Corning, 10-040-CVR), cut into small pieces and homogenized on ice with a Dounce homogenizer.

tag: chip antibody

value: anti-H3K27ac antibody (Abcam, ab4729)

value: lung

tag: disease state

value: tumor tissues


title: H3K27ac_2593_Tumor_1


title: H3K27ac_2627_Tumor_1


title: H3K27ac_2588_Normal_1

value: adjacent normal lung tissues


title: H3K27ac_2340_Tumor_1


title: H3K27ac_2340_Normal_1


title: H3K27ac_2593_Normal_1


title: H3K27ac_2627_Normal_1


title: H3K27ac_2300_Normal_1


title: H3K27ac_2469_Tumor_1


title: H3K27ac_2471_Normal_1


title: H3K27ac_2354_Normal_1


title: H3K27ac_2354_Tumor_1


title: H3K27ac_2300_Tumor_1


title: H3K27ac_2513_Normal_1


title: H3K27ac_2513_Tumor_1


title: H3K27ac_1823_Normal_1


title: HT0h_1

value: leaf

value: Three-week-old seedlings of cucumber


title: WT2


title: H3K27ac_3174_Tumor_1


title: H3K27ac_2539_Tumor_1


title: H3K27ac_3139_Normal_1


title: H3K27ac_2539_Normal_1


title: H3K27ac_2527_Normal_1


title: H3K27ac_2471_Tumor_1


title: H3K27ac_2527_Tumor_1


title: H3K27ac_3174_Normal_1


title: H3K27ac_2460_Tumor_1


title: H3K27ac_2624_Normal_1


title: H3K27ac_2320_Normal_1


title: H3K27ac_2514_Normal_1


title: H3K27ac_2320_Tumor_1


title: H3K27ac_2596_Tumor_1


title: H3K27ac_2624_Tumor_1


title: H3K27ac_2112_Normal_1


title: H3K27ac_2646_Tumor_1


title: H3K27ac_2646_Normal_1


title: H3K27ac_2112_Tumor_1


title: H3K27ac_2514_Tumor_1


title: H3K27ac_2499_Normal_1


title: H3K27ac_2499_Tumor_1


title: H3K27ac_2129_Tumor_1


title: H3K27ac_3139_Tumor_1


title: H3K27ac_2460_Normal_1


title: H3K27ac_1823_Tumor_1


title: H3K27ac_2505_Tumor_1


title: H3K27ac_2596_Normal_1


title: H3K27ac_2610_Tumor_1


title: H3K27ac_2505_Normal_1


title: H3K27ac_2655_Normal_1


title: H3K27ac_2129_Normal_1


title: H3K27ac_2610_Normal_1


title: H3K27ac_2655_Tumor_1


title: H3K27ac_2589_Tumor_1


title: H3K27ac_2589_Normal_1


title: H3K27ac_2445_Normal_1


title: H3K27ac_2496_Normal_1


title: H3K27ac_2445_Tumor_1


title: H3K27ac_1799_Normal_1


title: H3K27ac_2496_Tumor_1


title: H3K27ac_2524_Tumor_1


title: H3K27ac_1799_Tumor_1


title: H3K27ac_2118_Normal_1


title: H3K27ac_2118_Tumor_1


title: H3K27ac_2606_Tumor_1


title: H3K27ac_2428_Tumor_1


title: H3K27ac_2428_Normal_1


title: H3K27ac_2616_Normal_1


title: H3K27ac_1675_Tumor_2


title: H3K27ac_2606_Normal_1


title: H3K27ac_2658_Normal_1


title: H3K27ac_2658_Tumor_1


title: H3K27ac_2538_Tumor_1


title: H3K27ac_2478_Normal_1


title: H3K27ac_1821_Tumor_1


title: H3K27ac_2595_Normal_1


title: H3K27ac_1821_Normal_1


title: H3K27ac_2538_Normal_1


title: H3K27ac_2478_Tumor_1


title: H3K27ac_2136_Normal_1


title: H3K27ac_2573_Tumor_1


title: H3K27ac_2573_Normal_1


title: H3K27ac_2136_Tumor_1


title: H3K27ac_SPCA1_input_rep2

description: patient derived cell line

data_processing:
Trim-galore was used to cut adaptor automatically
ChIP-seq reads were aligned to hg19 human genome using bowtie
Peaks were called using MACS(v.1.3.7) and select top 30,000 peaks in each samples
Reads count within peaks in each samples were calculated via MAnorm2-utils with bin size 2,000bp
Genome_build: hg19
Supplementary_files_format_and_content: bed file
Supplementary_files_format_and_content: tab-delimited text files include reads count for each sample and each peak

treatment_protocol: H3K27ac ChIP-seq was performed using an anti-H3K27ac antibody (Abcam, ab4729).

tag: chip-antibody


title: H3K27ac_SPCA1_chip_rep2

description: patient derived cell line

value: anti-H3K27ac antibody (Abcam, ab4730)


title: H3K27ac_2524_Normal_1


title: H3K27ac_SPCA1_chip_rep1

description: patient derived cell line


title: H3K27ac_1153_input_rep2

description: patient derived cell line


title: H3K27ac_1153_input_rep1

description: patient derived cell line


title: H3K27ac_2616_Tumor_1


title: H3K27ac_1153_chip_rep2

description: patient derived cell line


title: H3K27ac_2595_Tumor_1


title: mouse embryonic stem cells - day 4 - column 10 - rows 1:40

city: Berlin

first: Guido

last: Pacini

address: Ihnestraße 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

description: HiSeq 2500: High Output

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. The C1-HT protocol uses a dual barcoding strategy, where read R1 contains a custom barcode (position 1-6, cell barcode) and a unique molecular identifier (position 7-11), read R2 maps to the cDNA sequence and read R3 contains a Nextera barcode.
Drop-seq version 1.12 (Macosko et al. 2015, Cell 161, 1202–1214.; https://github.com/broadinstitute/Drop-seq/releases), was used for read R1 cellular and molecular barcode extraction [TagBamWithReadSequenceExtended BASE_RANGE=1-6 BARCODED_READ = 1 BASE_QUALITY=10 NUM_BASES_BELOW_QUALITY=1; TagBamWithReadSequenceExtended BASE_RANGE=7-11 BARCODED_READ = 1 BASE_QUALITY=10 NUM_BASES_BELOW_QUALITY=1] and cell-wise FASTQ file demultiplexing [RowBarcodes.txt]
SNPsplit version 0.3.2 (Krueger and Andrews 2016,  F1000Res. 5, 1479.), was used to N-mask the mm10 genome using high confidence SNPs. [SNPsplit_genome_preparation --nmasking]
STAR version 2.5.2b (Dobin et al. 2013, Bioinformatics, 29(1), 15-21.), was used to align the R2 reads to the masked mm10 genome and the 96 ERCC spike-in sequences, allowing for unique alignments and a maximum of two mismatches. [ star --outFilterMismatchNmax 2 --outFilterMultimapNmax 1]
Drop-seq version 1.12 (Macosko et al. 2015, Cell 161, 1202–1214.; https://github.com/broadinstitute/Drop-seq/releases), was used for gene-wise read counting. Reads with the same unique molecular identifiers (UMIs) were collapsed for transcript counting (UMICountMatrix.txt.gz). [DigitalExpression EDIT_DISTANCE=0 OUTPUT_READS_INSTEAD=false]
The gene counting procedure was repeated for the two parental alleles (B6_UMICountMatrix.txt.gz, Cast_UMICountMatrix.txt.gz), using SNPsplit to assign reads overlapping a SNP locus to their parental genomes. [SNPsplit --SNPs_B6_CAST.txt]
The above procedures were repeated to quantify the number of spliced (Spliced_UMICountMatrix.txt.gz, relative to reads mapped to exonic regions only) and unspliced (Unspliced_UMICountMatrix.txt.gz, relative to reads mapped to intronic regions, or spanning exon-intron boundaries) transcripts, and their allele-specific counterparts (B6_Spliced_UMICountMatrix.txt.gz, B6_Unspliced_UMICountMatrix.txt.gz, Cast_Spliced_UMICountMatrix.txt.gz, Cast_Unspliced_UMICountMatrix.txt.gz)
Counts Per Million (CPM) values were computed using scran R package version 1.12.1 (Lun et al. 2016, Genome Biol. 17, 75) defining cell cluster independently for each time point [scran::computeSumFactors(clusters)]
Genome_build: GRCm38

organism: Mus musculus

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: Mouse embryonic stem (ES) cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901).

extract_protocol:
Cells were rinsed thoroughly with PBS, trypsinized for 7 minutes and resuspended in the respective growth medium at a concentration of 400 cells/μl. 30 μl cell suspension was diluted with 20 μl of suspension reagent (Fluidigm) and 10 μl of the dilution was loaded into one compartment of a Single-Cell mRNA Seq HT integrated fluidic circuit (IFC) 10-17 µm. A different cell type was loaded into the other compartment, which is not analyzed in this study. Cell viability staining was performed on the IFC using the LIVE/DEAD viability/Cytotoxicity Kit (Thermofisher) with 1 μM Ethidium and 0.05 μM Calcein. IFC loading and life/dead staining was analyzed with automated image acquisition using a Zeiss CellDiscoverer microscope (Zeiss) with a 20x objective. During the lysis step ERCC Spike-in Mix 1 (Thermofisher) was added with a final dilution of 1:200000. Lysis, reverse transcription and cDNA amplification was performed on the C1 machine.
Single-cell RNA-seq libraries were prepared with the C1-HT mRNA-seq v2 protocol according to the manufacturer’s recommendations (Fluidigm). cDNA pools were quantified by Qubit and Bioanalyzer HS. Around 2.25 ng of each pool were subjected to tagmentation and library preparation using the NexteraXT library preparation kit according to the C1-HT protocol. All pools were mixed in equal proportions and quantified with KAPA Library Quant-Kit. The libraries were sequenced on a HiSeq2500 instrument (Illumina) either in high output or in rapidrun mode, in asymmetric read length (Read1: 13bp, Index read: 8pb, Read2: 48bp), with 10pM loading concentration and 5% PhiX.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol at a density of 1.5*104cells/cm2 in fibronectin-coated (10 μg/ml) tissue culture plates

tag: strain

value: C57BL6/J x Cast/EiJ

value: female mESC

value: 4 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - day 4 - column 9 - rows 1:40

description: HiSeq 2500: High Output


title: NAE 18:3 rep1

city: Denton

first: Ashley

middle: Elisabeth

last: Cannon

state: TX

address: 1155 Union Circle #305220

department: Biological Sciences

institute: The University of North Texas

description:
Sample 4
S1-R1

data_processing:
Basecalls were made by NextSeq Control Software (NCS)
The Arabidopsis thaliana genome build 9, namely TAIR9, available at The Arabidopsis Information Resource (TAIR) database (https://www.arabidopsis.org/) was used as the reference genome for obtaining the read alignment using Tophat.
Transcript assembly and quantification was done by Cufflinks and CuffDiff (part of the Cufflinks package) was used for differential expression testing.
Genes with false discovery rate (FDR) adjusted p-value less than 0.05 were deemed significantly altered in expression, and were further examined for their abundance fold change between the conditions.
Genome_build: TAIR 9
Supplementary_files_format_and_content: The processed data file is Cufflinks output data including Transcript IDs, Gene IDs, TAIR transcript IDs, TAIR Gene IDs, FPKM values for individul samples and the average of the three samples, and TAIR Annotation information.

source_name: Seedlings

growth_protocol: Wild-type Arabidopsis (Col-0 ecotype) seeds were surface sterilized and plated on ½ MS with 1% sucrose media. Plates with seeds were stratified for 48 hours in 4°C and then incubated for 3 days in a growth room with 14-h-light/10-h-light/dark cycle (100 µmol.m-2.s-1) at 20 to 22°C. 3-d-old seedlings were then transferred to 12-well plates containing liquid ½ MS media with 1% sucrose, supplemented with 100 µM NAE 18:3 or 0.07% DMSO and incubated for 1 hour.

extract_protocol:
Seedlings of 3 biological replicates for each treatment were harvested in liquid nitrogen and total RNA was isolated with a RNeasy mini kit (Qiagen) as per manufacturer instructions, quantified with a nanodrop (ND-1000) and treated with TURBO DNA-free kit (Ambion) to remove contaminating genomic DNA
RNA quality was determined prior to library construction using an Agilent Bioanalzyer and RIN scores of 9.5 -10 was obtained for all samples. cDNA libraries were prepared using the Illumina’s TruSeq RNA sample preparation kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: 4-d-old seedlings were then transferred to 12-well plates containing liquid ½ MS media with 1% sucrose, supplemented with 100 µM NAE 18:3 or 0.07% DMSO and incubated for 1 hour

value: seedlings

value: 4 day-old

tag: treatment duration

value: 1 hour

value: 100 microM NAE 18:3


title: DMSO rep3

description:
Sample 3
S2-R3

tag: ecotype

value: DMSO


title: NAE 18:3 rep3

description:
Sample 6
S1-R3


title: DMSO rep2

description:
Sample 2
S2-R2


title: DMSO rep1

description:
Sample 1
S2-R1


title: NAE 18:3 rep2

description:
Sample 5
S1-R2


title: NOR-18-3

city: Guangzhou

first: Jiang

last: Guoxiang

address: No.723,Xingke Road

institute: South China Botanical Garden, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Tomato reference genome (version SL2.50)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Solanum lycopersicum

source_name: Ailsa Craig

extract_protocol:
Peel tissue was immediately collected after harvested, frozen in liquid nitrogen, and  RNA was harvested using Trizol reagent. mRNA Seq Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: At 55 days after anthesis (dpa)

value: Peel

tag: line


title: WT hMSCs [WGS]

city: Beijing

first: jiang

middle: xiao

last: yu

address: 15 Datun Road Chaoyang District

institute: institute of zoology, CAS

description: WGS sequencing of WT hMSCs.

data_processing:
Library strategy: WGS
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.wig file of  read cout for each 500000 bp bin size for WGS data.

source_name: Mesenchymal stem cell

extract_protocol: For WGS analysis, the sequencing libraries were constructed via the Next DNA Library Prep Reagent Set for Illumina (NEB).    For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Mesenchymal stem cell

tag: genotype

value: WT

tag: passage


title: ALKBH1 deficient hMSCs [WGS]

description: WGS sequencing of ALKBH1 deficient hMSCs.

value: ALKBH1 deficient


title: WT hMSCs 1

description: RNA sequencing of WT hMSCs.

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 human refference genome using bowtie2 or histat2 software.
Genome_build: hg19 for Homo sapiens
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.wig file of  read cout for each 500000 bp bin size for WGS data.


title: ALKBH1 deficient hMSCs 2

description: RNA sequencing of ALKBH1 deficient hMSCs.


title: WT hMSCs 2

description: RNA sequencing of WT hMSCs.


title: NOR-18-1

tag: tissue


title: ALKBH1 deficient hMSCs 1


title: H3K27ac_SPCA1_input_rep1

description: patient derived cell line


title: NOR-12-3


title: mouse embryonic stem cells - day 4 - column 7 - rows 1:40

description: HiSeq 2500: High Output

tag: treatment


title: mouse embryonic stem cells - day 4 - column 8 - rows 1:40

description: HiSeq 2500: High Output


title: H3K27ac_1153_chip_rep1

description: patient derived cell line

value: anti-H3K27ac antibody (Abcam, ab4729)


title: NOR-18-2


title: mouse embryonic stem cells - day 4 - column 5 - rows 1:40

description: HiSeq 2500: High Output


title: NOR-12-1


title: mouse embryonic stem cells - day 4 - column 4 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 4 - column 3 - rows 1:40

description: HiSeq 2500: High Output


title: NOR-12-2


title: mouse embryonic stem cells - day 4 - column 2 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 4 - column 6 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 4 - column 1 - rows 1:40

description: HiSeq 2500: High Output


title: nor-1

value: nor


title: mouse embryonic stem cells - day 3 - column 10 - rows 1:40

description: HiSeq 2500: High Output

value: 3 days after 2i/Lif withdrawal


title: SiPCF11_48_M_R3

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

description:
Illumina index 11
SiPCF11_48_M_R3_S6_L001

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stipped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 200 bases down-strand of a gene are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: h. sapiens ensembl version 93
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample. tail_count.csv contains count of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv. tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample. These files are sufficient for differential expression and differential tail length analysis.

growth_protocol: MDAMB231 cells were grown in RPMI (Gibco) containing 10% Fetal Bovine Serum (FBS) and 0.25% insulin. MCF7 breast cancer cells were grown in T75 flasks with Dulbecco's Modified Eagle's Medium (DMEM; Gibco) containing 10% FBS. Cells were kept in 5% carbon dioxide (CO2) incubator at 37ºC. Culture media was removed from flask at 70 - 90% confluent cells, cells were washed with 5 ml phosphate bufferer saline (PBS), and 2 ml of TrypLE for 2 mins at 37ºC was used to dissociate cells from flask. When 90% of cells dissociated, 4 ml of DMEM + 10% FBS added to flask, centrifuged for 5 min at 200 g. Cell pellet resuspended in 10 ml DMEM + 10% FBS. Cell counts and viability determined using the Countess Automated cell counter; 20 µl of Trypan blue mixed with 20 µl of cell suspension, 10 µl added to cell counter plate, repeated twice. Cells were seeded between 1:6 to 1:10 in new flask and DMEM + 10% FBS added to total 15 ml.

extract_protocol:
Medium was removed and wells were washed with 1 ml 1% PBS. For MDAMB231 cells, 600 µl of TRIzol was added to each well and incubated at RT for 10 mins before transfer to 2ml tubes and storage at -80ºC prior to RNA extraction. For MCF7 cells, 750 µl of TRIzol was added to each well and incubated at RT for 2 mins. Cells and TRIzol were transferred to a tube and 200 µl chloroform was added, vortexed for 15 sec, incubated at RT for 3 mins, and centrifuged at 4ºC for 5 mins at 13000 rpm. The aqueous phase was transferred to a fresh tube and an equal amount of 70% EtOH was added. RNA was then purified over Qiagen RNeasy spin columns according to manufacturer’s instructions. RNA was eluted in 40 µl RNase free H2O.  One microgram of total RNA was used for library preparation by the PAT-seq method (Harrison et al., 2015).
Library construction was by the PAT-seq approach (Harrison et al RNA 2015)
Cluster Generation: 9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
Sequencing chemistry: 1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: MDAMB231 cells were seeded at 100,000 cells/well (with RPMI + 10% FBS and 0.25% insulin) into 6 well plates and incubated at 37ºC for 48 hours to ~80% confluence. Cells were at passage 4 from thawing. MCF7 cells were seeded at 250,000 cells/well (with DMEM + 10% FBS media to 2.5 ml) into 6 well plates and incubated at 37ºC for 6 hrs. Media was removed and replaced with 2 ml of fresh media in each well. RNA interference (RNAi) was prepared for each well from 5 µM small interfering RNA (siRNA) stocks in total of 250 µl of opti-MEM (Gibco); positive control was LAMIN 6 µl/well, negative control scramble 6 µl/well, mock negative control 0 µl/well, hPCF11 1 and 2 siRNA 15 µl each/well, hCLP1 1 and 2 siRNA 15 µl each of each/well, hCLP1 3 and 4 siRNA 15 µl each/well. 5 µl in 245 µl of Lipofectamine RNAiMAX (Invitrogen) was added to each siRNA preparation and incubated at 10 - 20 mins at room temperature (RT). 500 µl of siRNA preparation was then added to the appropriate well.

value: Breast cancer cell line

value: Transfected with siRNA

tag: genotype/variation

value: PCF11 knockdown


title: SiPCF11_48_L_R4

description:
Illumina index  15
SiPCF11_48_L_R4_S9_L001

tag: cell type


title: mouse embryonic stem cells - day 3 - column 9 - rows 1:40

description: HiSeq 2500: High Output

value: C57BL6/J x Cast/EiJ

value: female mESC

tag: cell line


title: SiNT_48_M_R3

description:
Illumina index 10
SiNT_48_M_R3_S5_L001

value: Control Non-targeting siRNA


title: SiClp1_48_L_R3

description:
Illumina index 18
SiClp1_48_L_R3_S12_L001

value: CLIP1 knockdown


title: SiNT_48_L_R4

description:
Illumina index 14
SiNT_48_L_R4_S8_L001


title: mouse embryonic stem cells - day 3 - column 8 - rows 1:40

description: HiSeq 2500: High Output


title: SiNT_48_L_R5

description:
Illumina index 17
SiNT_48_L_R5_S11_L001


title: nor-3


title: MDAMD231_R2

description:
Illumina index  40
MDAMB231_R2_S6_L001

value: Cells growing in culture

value: Independent control for cell line dependent APA


title: mouse embryonic stem cells - day 3 - column 6 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 3 - column 5 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 3 - column 7 - rows 1:40

description: HiSeq 2500: High Output


title: MCF7_R2

description:
Illumina index 37
MCF7_R2_S2_L001


title: mouse embryonic stem cells - day 3 - column 2 - rows 1:40

description: HiSeq 2500: High Output


title: MDAMD231_R1

description:
Illumina index  34
MDAMB231_R1_S5_L001


title: MCF7_R1

description:
Illumina index 31
MCF7_R1_S1_L001


title: mouse embryonic stem cells - day 3 - column 1 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 3 - column 3 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 2 - column 9 - rows 1:40

description: HiSeq 2500: High Output

value: 2 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - day 2 - column 10 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 2 - column 8 - rows 1:40

description: HiSeq 2500: High Output


title: nor-2

value: At 55 days after anthesis (dpa)

value: Peel


title: SiClp1_48_M_R1

description:
Illumina index 13
SiClp1_48_M_R1_S7_L001


title: mouse embryonic stem cells - day 2 - column 7 - rows 1:40

description: HiSeq 2500: High Output


title: 3352CA3

city: Gainesville

first: Tom

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

data_processing:
ERCC analysis was performed with the ERCC analysis plugin in the Torrent. Spiked samples had an R2 above 0.9.
Ion Torrent derived reads were  aligned to the rattus norvegicus genome rn6 using STAR 2.5.3a in the in the Partek Flow servers Partek, Inc., St. Louis, MO.
Gene read counts were generated from Binary Alignment Map BAM files and annotated to the genome using Ensembl version 92; Partek, Inc..
Reads from FASTQ files produced by the Ion Torrent System were trimmed from both ends until all samples’ collective average Phred quality score was > 25. Reads shorter than 25 base pairs bps were also excluded.
Gene lists were filtered to exclude genes with an average count of 5 or less averaged across all samples included in a comparison.
Normalization and pairwise differential expression analysis were conducted using the DESeq2 package version 3.5 for comparisons by age, cognitive performance or hippocampal subregion. The threshold of significance was set at p<0.025 for differences by age.
Genome_build: Ensembl version 92; Partek, Inc..
Supplementary_files_format_and_content: Comma-separated values .csv files that contain the normalized counts for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: CA3 region of the hippocampus

extract_protocol:
Rats were briefly anesthetized with isoflurane Patterson Veterinary, Greenly, CO and swiftly decapitated. The brains were then rapidly removed, and the hippocampi were dissected according to previously described methods Lein 2004; Zeier 2011. The hippocampal regions DG, CA1, and CA3 were separated, placed in the tubes, and flash-frozen in liquid nitrogen. All samples were stored in at -80°C until processed. RNA was isolated from subregions of a hippocampus from a single hemisphere of each animal. RNA Isolation was performed according to methods previously described Ianov 2016; Barter 2019. Briefly, RNA was isolated using the RNeasy Lipid Tissue Mini kit Qiagen, catalog number 74804. Total RNA was treated with DNase using the RNase-Free DNase Set Qiagen, catalog number 79254. Concentration of total RNA was assessed using the NanoDrop 2000 spectrophotometer Thermo Fisher catalog number ND-2000 and the RNA integrity number RIN was quantified using the Agilent 2200 Tapestation system with High Sensitivity RNA Screen Tape Agilent Technologies, Santa Clara, CA. Mean RNA integrity across all samples was 9.05 SEM ± 0.02 with values ranging from 8.2 to 9.3. Poly-A-selection for mRNA was performed using 250 ng of isolated total RNA in the Dynabeads mRNA DIRECT Micro kit Thermo Fisher, catalog number 61021. External RNA Controls Consortium ERCC RNA Spike-In Control Mixes were included in all isolated mRNA samples Thermo Fisher, catalog number 4456740.
Library preparation was performed using the Ion Total RNA-seq Kit v2 Thermo Fisher, catalog number 4475936. Ion Xpress barcodes Thermo Fisher, catalog number 4475485 were included with libraries for multiplex sequencing. In summary, isolated mRNA was fragmented with RNase III then ligated to the Ion Adapter Mix v2. RNA samples were then reverse transcribed. cDNA from each biological replicate was uniquely barcoded and amplified with 16 PCR cycles. Library concentration from each sample was quantified using the Qubit dsDNA HS Assay Thermo Fisher, catalog number Q32851. DNA fragment size distribution was subsequently evaluated using High Sensitivity D1000 ScreenTape in the 2200 Tapestation system Agilent Technologies, Santa Clara, CA.   Templates were prepared using the Ion Chef system Thermo Fisher, catalog number 4484177 and sequencing was performed using the Ion Proton system Thermo Fisher, catalog number 4476610 or Ion GeneStudio S5 system Thermo Fisher, catalog number A38194.

value: CA3 region of the hippocampus

tag: age

value: 12 months

tag: Sex

value: male


title: 3352CA1

source_name: CA1 region of the hippocampus

value: CA1 region of the hippocampus


title: mouse embryonic stem cells - day 2 - column 6 - rows 1:40

description: HiSeq 2500: High Output


title: 3351DG

source_name: DG region of the hippocampus

value: DG region of the hippocampus


title: mouse embryonic stem cells - day 2 - column 3 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 2 - column 4 - rows 1:40

description: HiSeq 2500: High Output


title: 3351CA1


title: 3350DG


title: mouse embryonic stem cells - day 2 - column 2 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 2 - column 1 - rows 1:40

description: HiSeq 2500: High Output


title: 3352DG


title: mouse embryonic stem cells - day 1 - column 10 - rows 1:40

description: HiSeq 2500: High Output

value: 1 days after 2i/Lif withdrawal


title: 3349DG


title: 3350CA3


title: mouse embryonic stem cells - day 1 - column 9 - rows 1:40

description: HiSeq 2500: High Output


title: 3348CA3


title: 3349CA3


title: mouse embryonic stem cells - day 1 - column 9 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: 3348DG


title: 3348CA1


title: mouse embryonic stem cells - day 1 - column 8 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: 3347DG


title: mouse embryonic stem cells - day 1 - column 8 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 1 - column 7 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 2 - column 5 - rows 1:40

description: HiSeq 2500: High Output


title: 3347CA3


title: 3351CA3


title: mouse embryonic stem cells - day 1 - column 7 - rows 1:40

description: HiSeq 2500: High Output


title: 3346CA3


title: mouse embryonic stem cells - day 1 - column 6 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: 3346CA1


title: 3346DG


title: mouse embryonic stem cells - day 1 - column 5 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: 3345CA3


title: mouse embryonic stem cells - day 1 - column 6 - rows 1:40

description: HiSeq 2500: High Output


title: 3345CA1


title: mouse embryonic stem cells - day 1 - column 4 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 1 - column 4 - rows 1:40

description: HiSeq 2500: High Output


title: 3344CA3


title: 3344DG


title: mouse embryonic stem cells - day 1 - column 5 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 1 - column 3 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 1 - column 10 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 1 - column 3 - rows 1:40

description: HiSeq 2500: High Output


title: 3343DG


title: mouse embryonic stem cells - day 1 - column 1 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 1 - column 2 - rows 1:40 RapidRun

description: HiSeq 2500: Rapid Run


title: mouse embryonic stem cells - day 1 - column 2 - rows 1:40

description: HiSeq 2500: High Output


title: 3345DG


title: 3343CA3


title: 3350CA1


title: 3344CA1


title: 3342DG

value: 5 months


title: 3343CA1


title: 3342CA3


title: mouse embryonic stem cells - day 0 - column 10 - rows 1:40

description: HiSeq 2500: High Output

value: 0 days after 2i/Lif withdrawal


title: 3341DG


title: mouse embryonic stem cells - day 0 - column 9 - rows 1:40

description: HiSeq 2500: High Output

value: C57BL6/J x Cast/EiJ


title: mouse embryonic stem cells - day 1 - column 1 - rows 1:40

description: HiSeq 2500: High Output

value: female mESC


title: mouse embryonic stem cells - day 0 - column 8 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 0 - column 7 - rows 1:40

description: HiSeq 2500: High Output


title: 3341CA1


title: mouse embryonic stem cells - day 0 - column 6 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 3 - column 4 - rows 1:40

description: HiSeq 2500: High Output

value: 3 days after 2i/Lif withdrawal


title: 3340DG


title: 3339DG


title: mouse embryonic stem cells - day 0 - column 3 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 0 - column 4 - rows 1:40

description: HiSeq 2500: High Output


title: 3340CA3


title: mouse embryonic stem cells - day 0 - column 2 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 0 - column 5 - rows 1:40

description: HiSeq 2500: High Output


title: mouse embryonic stem cells - day 0 - column 1 - rows 1:40

description: HiSeq 2500: High Output


title: 3339CA1


title: 3340CA1


title: DBa28 KO-4J

city: Boston

first: David

middle: B

last: Sykes

state: Massachusetts

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: htseq_output.

source_name: Fetal liver hematopoietic progenitors

growth_protocol: ER-Hoxb8 GMPs are maintained in RPMI supplemented with 1% SCF-conditioned media (equivalent to ~50 ng/ml recombinant SCF), 10% FBS, penicillin/streptomycin and 0.5 uM beta-estradiol (E2).

extract_protocol: Total RNA was extracted from five million cells using RNeasy Plus Mini Kit (Qiagen, Cat# 74134).

value: fetal liver

value: GMP

value: Taz knockout


title: 3338DG


title: 3339CA3


title: DBa28 KO-3I


title: 3338CA3


title: 3338CA1


title: 3337DG


title: DBa28 KO-3H


title: 3337CA3


title: 3341CA3


title: DBa28 KO-3G


title: 3337CA1


title: DBa28 KO-4K


title: DBa28 WT-2E

value: wildtype


title: DBa28 WT-2F


title: DBa28 WT-2D


title: DBa28 KO-4L


title: KO-4L

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Genome_build: mm9
Supplementary_files_format_and_content: htseq_output

extract_protocol:
Total RNA was extracted from five million cells using RNeasy Plus Mini Kit (Qiagen, Cat# 74134) as well as on-column DNAse digestion.
NEBNExt Ultra Directional RNA Library Prep for Illumina (New England Biolabs)
polyA selection followed by strand-specific library construction


title: DBa28 WT-1B


title: KO-4K


title: KO-4J


title: KO-3I


title: KO-3H


title: #29_NAA 48h B

type: RNA

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: NAA-treated samples Samples; Berries collected after 48 h upon treatment; Replicate B

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: From a vineyard in the Adelaide Hills (Hahndorf, South Australia, -35.018223, 138.838220) 40 bunches at the pre-veraison stage were harvested from ten vines (Vitis vinifera L. cv. Shiraz). Bunches were harvested between 09:00 and 10:00 and rapidly transported to the lab for use. Fruit was harvested on 21 Dec 2009, 35 days before veraison.

extract_protocol: Total RNA was isolated from grape berry tissue according to Davies and Robinson (1996) and further purified as described by Symons et al. (2006).

treatment_protocol: Randomly picked berries from the sampled bunches were sterilized in 0.1% (v/v) Chemwet 1000 (Nufarm, Laverton, VIC, Australia) containing half a Milton antibacterial tablet L-1 (Milton Australia, Laverton North, Victoria) for 10 min and washed three times with sterile nanopure water. Any berries showing physical defects were discarded. All following procedures were carried out in a laminar flow under sterile conditions. A thin transverse slice of each berry was cut off from the brush area to facilitate compound absorption. Twenty berries were then placed on each petri dish containing 25 mL of Gamborg media, 0.025% (w/v) casein hydrosylate, 0.8% (w/v) agar, pH 5.7-5.8 alone (‘Control’) or also containing 0.5uM NAA (Gibo BRL Life Technologies, Grand Island, NJ, ‘NAA-treated’).

value: NAA-treated; 48 h

tag: cultivar

value: Shiraz


title: DBa28 WT-1C


title: #30_NAA 48h C

source_name: NAA-treated samples Samples; Berries collected after 48 h upon treatment; Replicate C


title: WT-2E


title: #28_NAA 48h A

source_name: NAA-treated samples Samples; Berries collected after 48 h upon treatment; Replicate A


title: WT-2D


title: WT-1C


title: WT-2F


title: DBa28 WT-1A


title: #27_CTRL 48h C

source_name: Control Samples; Berries collected after 48 h upon treatment; Replicate C

value: Control; 48 h


title: WT-1A


title: 1445 2019: shAPC 7d 3

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description: AKP Mouse tumoroids (7 days Apc restoration)

data_processing:
FastQ files were aligned against the mm10 (Ensembl GRCM38.97) genome with the STAR software v2.7.0e and default parameters
Aligned BAM files were sorted and indexed using Sambamba v0.6.7
Gene counts quantification carried out using featureCounts function from Rsubread R package
Differential expression was performed with DESeq2
Genome_build: mm10 (Ensembl GRCM38.97)
Supplementary_files_format_and_content: Counts per gene matrix (as derived from featureCounts function from Rsubread R package)

growth_protocol: AKP organoids were in vitro cultured as described in Dow et al., 2015

extract_protocol:
RNA was extracted using a PureLink® RNA Mini Kit (Thermo Fisher Scientific, Cat#12183025)
RNA libraries were prepared for sequencing using the kits NEBNext® Poly(A) mRNA Magnetic Isolation Module (Cat# E7490) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (Cat#E7770), following manufacturer´s instructions and 9 cycles of amplification.

treatment_protocol: Control AKP organoids were cultured with doxycycline. To induce differentiation doxycycline was removed during 2 days (2 days Apc restoration) or 7 days (7 days Apc restoration)

value: AKP organoids

tag: sample id

tag: technical replicate

tag: differentiation stage

value: Late stage differentiation


title: #26_CTRL 48h B

source_name: Control Samples; Berries collected after 48 h upon treatment; Replicate B


title: WT-1B

tag: strain


title: #22_NAA 24h A

source_name: NAA-treated samples Samples; Berries collected after 24 h upon treatment; Replicate A

value: NAA-treated; 24 h


title: #18_NAA 12h C

source_name: NAA-treated samples Samples; Berries collected after 12 h upon treatment; Replicate C

value: NAA-treated; 12 h


title: #25_CTRL 48h A

source_name: Control Samples; Berries collected after 48 h upon treatment; Replicate A


title: #21_CTRL 24h C

source_name: Control Samples; Berries collected after 24 h upon treatment; Replicate C

value: Control; 24 h


title: #23_NAA 24h B

source_name: NAA-treated samples Samples; Berries collected after 24 h upon treatment; Replicate B


title: #24_NAA 24h C

source_name: NAA-treated samples Samples; Berries collected after 24 h upon treatment; Replicate C


title: 1444 2019: shAPC 7d 2

source_name: AKP Mouse tumoroids (7 days Apc restoration)


title: 1442 2019: shAPC 2d 3

description: AKP Mouse tumoroids (2 days Apc restoration)

value: Early stage differentiation


title: #19_CTRL 24h A

source_name: Control Samples; Berries collected after 24 h upon treatment; Replicate A


title: 1440 2019: shAPC 2d 1

source_name: AKP Mouse tumoroids (2 days Apc restoration)


title: 1441 2019: shAPC 2d 2


title: 1439 2019: shAPC ctrl 3

description: AKP Mouse tumoroids (Apc OFF)

source_name: AKP Mouse tumoroids (Apc OFF)

value: Control


title: #14_CTRL 12h B

source_name: Control Samples; Berries collected after 12 h upon treatment; Replicate B

value: Control; 12 h


title: #16_NAA 12h A

source_name: NAA-treated samples Samples; Berries collected after 12 h upon treatment; Replicate A


title: #20_CTRL 24h B

source_name: Control Samples; Berries collected after 24 h upon treatment; Replicate B


title: 1438 2019: shAPC ctrl 2

description: AKP Mouse tumoroids (Apc OFF)


title: #17_NAA 12h B

source_name: NAA-treated samples Samples; Berries collected after 12 h upon treatment; Replicate B


title: #13_CTRL 12h A

source_name: Control Samples; Berries collected after 12 h upon treatment; Replicate A


title: 1443 2019: shAPC 7d 1


title: 1437 2019: shAPC ctrl 1

description: AKP Mouse tumoroids (Apc OFF)


title: #12_NAA 6h C

source_name: NAA-treated samples Samples; Berries collected after 6 h upon treatment; Replicate C

value: NAA-treated; 6 h


title: #15_CTRL 12h C

source_name: Control Samples; Berries collected after 12 h upon treatment; Replicate C


title: #11_NAA 6h B

source_name: NAA-treated samples Samples; Berries collected after 6 h upon treatment; Replicate B


title: #7_CTRL 6h A

source_name: Control Samples; Berries collected after 6 h upon treatment; Replicate A

value: Control; 6 h


title: #10_NAA 6h A

source_name: NAA-treated samples Samples; Berries collected after 6 h upon treatment; Replicate A


title: #8_CTRL 6h B

source_name: Control Samples; Berries collected after 6 h upon treatment; Replicate B


title: S5_d1_dmso_2

city: Basel

first: Ilya

last: Lukonin

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute (FMI)

description: Day 1 organoids. DMSO vehicle control, sample 2

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were mapped to the GRCm38 mouse genome assembly and quantified (Genocode M23 gene annotation) using cellranger (version 3.1.0) using default parameters and in addition the parameter --nosecondary.
Sequencing data from multiple lanes corresponding to the same sample were pooled for alignment and quantification.
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: 'X.matrix.mtx':mtx file containing raw count data for sample X; 'X.barcodes.tsv':list of single-cell barcodes corresponding to count matrix; 'X.genes.tsv':list of genes corresponding to count matrix

source_name: Intestinal organoids

growth_protocol: Organoids were kept in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin for amplification and maintenance. From day 0 to day 3, organoids were cultured in ENR (advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin-Streptomycin, 1×Glutamax (Thermo Scientific), 1×B27 (Thermo Scientific), 1xN2 (Thermo Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (Thermo Scientific))  with 20% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (GSK3B inhibitor, STEMCELL Technologies). From day 3 to 5, ENR was used for organoid culture. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis)

extract_protocol:
Single cells were obtained from organoids by mechanical disruption and subsequent digestion with TRYPLE Express. Cells were used for FACS sorting to discard debris and dead cells. Obtained cellular suspensions were loaded on a 10x Genomics Chromium Single Cell instrument to generate single cell GEMs
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit according to CG00052_SingleCell3'ReagentKitv2UserGuide_RevB.

treatment_protocol: Organoids were treated either with DMSO, 10μm all-trans retinoic acid (atRA) or 5 μm RXR antagonist (RXRi) at day 0 of organoid culture, repeated treatment at day 3, concomitant with switching to ENR medium.

value: wild type

tag: mouse age

value: 8 weeks

tag: dnase treatment

value: Yes


title: S5_d1_dmso

description: Day 1 organoids. DMSO vehicle control, sample 1


title: S4_d4_novita

description: Day 4 organoids, cultured in VitaminA-free medium


title: S3_d4_atra

description: Day 4 organoids, atRA-treated


title: S2_d4_rxri

description: Day 4 organoids, RXRi-treated


title: StemA_C_mix_4

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

institute: Whitehead Institute

description: in vitro transcribed

data_processing:
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://codeocean.com/capsule/0380995/tree)
RNAstructure(v6.0.1) folding and VARNA (v3.93) visualization
Genome_build: Homo sapiens mitochondrial ribosomal protein S21 (MRPS21), accession number NM_018997.3
Supplementary_files_format_and_content: .sam files generated with bowtie2, .dot files generated by RNAstucture, _Mu.txt files produced by DREEM clustering algorithm. Multiple Mu files were generated for RREmutA and RREmutB by computationally mixing reads from the two samples in specified proportions in order to validate the ability of DREEM to accurately deconvolute the separate structures.

organism: synthetic construct

source_name: gBlock

growth_protocol: In vitro transcription

extract_protocol:
DMS-treated RNA was purified using phenol-chloroform
3'Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. rRNA was subtracted with RiboZero, and RT was performed with TGIRT-III. cDNAs were isolated by gelextraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer.

treatment_protocol: DMS-treatment for RNA secondary structure analysis, between 0.5-1% DMS at 37C for 5 minutes

tag: mixing proportion (stem a-stemc)

tag: molecule subtype

value: DMS-modified RNA


title: StemA_C_mix_5

description: in vitro transcribed


title: d5_RXRi_prep2_2

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were mapped to the UCSC mouse genome mm10 using STAR (version 2.5.2b) using parameters --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1.
Genes expression level were quantified with the QuasR Bioconductor package, using gene annotations from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package.
RPKM (reads per kilobase and million reads) of uniquely mapped reads were used to describe similarities and differences among the samples.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file with RPKM values for each Sample (columns)

extract_protocol:
RNA was isolated using Single Cell RNA Purification Kit (Norgen Biotek Corporation, Cat #51800) pooling 3 wells of 24 well plates (C57BL/6 wild type). Organoids were seeded as single cells at 50000 cells per well and cultured as described above. RNA purification was performed in duplicate for two organoid cultures (C57BL/6 wild type, male littermate mice) for all treatment conditions. A step of DNAse treatment was included (RNase-Free DNase I Kit, Cat #25710) for all samples.
RNA sequencing libraries were prepared using the TruSeq Illumina mRNA Library Prep

tag: genotype


title: #9_CTRL 6h C

source_name: Control Samples; Berries collected after 6 h upon treatment; Replicate C


title: StemA_C_mix_3

description: in vitro transcribed


title: d5_RXRi_prep2_1


title: d5_atRA_prep2_2


title: StemA_C_mix_2

description: in vitro transcribed


title: StemA_C_mix_1

description: In vitro transcribed


title: NPC48_D

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

data_processing:
Sequenced reads were trimmed using trimmomatic V0.36 to remove adapters and low quality bases. Ribosomal RNA were removed using SortMeRNA (v2.1).
Trimmed reads were aligned to the TAIR10 genome using STAR (2.5.2b).
Reads were counted using featureCounts from subreads package (v1.6.5) using strand specific mode.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited text files include raw count values by gene for each Sample.

source_name: 35S:NPC48 replicate 3

growth_protocol: Media = MS/10 +P (KH2PO4 500µM), hygrometry = 33% humidity, Temperature = 24°C day/ 21°c night, Light = 16 hours day / 8 hours night.

extract_protocol:
Roots 50µg (QuickRNA Zymo).
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq RNA.

treatment_protocol: No treatment.

tag: developmental stage

tag: tissue

value: roots


title: #6_NAA 3h C

source_name: NAA-treated samples Samples; Berries collected after 3 h upon treatment; Replicate C

tag: treatment

value: NAA-treated; 3 h

value: Shiraz


title: d5_atRA_prep2_1


title: NPC48_B

source_name: 35S:NPC48 replicate 2

tag: genotype/variation


title: #5_NAA 3h B

source_name: NAA-treated samples Samples; Berries collected after 3 h upon treatment; Replicate B


title: #3_CTRL 3h C

source_name: Control Samples; Berries collected after 3 h upon treatment; Replicate C

value: Control; 3 h


title: NPC48_A

source_name: 35S:NPC48 replicate 1


title: #2_CTRL 3h B

source_name: Control Samples; Berries collected after 3 h upon treatment; Replicate B


title: #4_NAA 3h A

source_name: NAA-treated samples Samples; Berries collected after 3 h upon treatment; Replicate A


title: #1_CTRL 3h A

source_name: Control Samples; Berries collected after 3 h upon treatment; Replicate A


title: d5_RXRi_prep1_2


title: Col0_B

source_name: Col0 replicate 2

tag: ecotype


title: Col0_A

source_name: Col0 replicate 1


title: d5_atRA_prep1_2


title: d5_RXRi_prep1_1


title: Col0_D

source_name: Col0 replicate 3


title: d5_atRA_prep1_1


title: S1_d4_dmso

description: Day 4 organoids, DMSO vehicle control


title: W82_Nodule_36dpi_Rep3_RNAseq

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

data_processing:
Quality of paired-ended reads was accessed using FastQC (version 0.11.4).
Adapter sequences and low-quality reads were removed using Trimmomatic (version 0.35).
TOPHAT v.2.0.13 was used to map the reads to the soybean reference genome (Wm82.a2.v1).
Reads mapped to multiple loci were discarded and numbers of uniquely mapped reads per gene were determined using HTSeq.
Differentially expressed genes were identified the R package DESEQ2.
Python-based package QoRTs was used for counting sequencing reads spanning exons for every gene.
Differentially spliced transcripts were identified using R package JunctionSeq.
Genome_build: Wm82.a2.v1

organism: Glycine max

source_name: Bradyrhizobium diazoefficiens USDA110

growth_protocol: The seeds were surface-sterilized in 50% bleach (2.5% NaClO). Approximately 200 seeds were planted in large plastic tray (50 x 28 x 15 cm deep) filled with vermiculite and the seeds were allowed to germinate in dark for 3 days.

extract_protocol:
mRNA was isolated using magnetic mRNA isolation kit (NEB).
RNA-seq libraries were prepared using NEBnext mRNA library prep master mix (NEB) following manufacturer’s protocol.

treatment_protocol: B. diazoefficiens USDA110 cultures (4.5 x 106 cells/ml) were poured over each tray. After inoculation, the trays were kept in a growth chamber that was maintained at a constant temperature of 28° C with a light intensity of 500 mmol of photons per square meter per second, and a 12-h light period.

value: Williams 82

value: Nodule

tag: age

value: 39 days


title: d5_DMSO_prep1_2


title: W82_Nodule_36dpi_Rep2_RNAseq


title: W82_Nodule_36dpi_Rep1_RNAseq


title: W82_Nodule_22dpi_Rep3_RNAseq

value: 25 days


title: d4_RXRi_prep2_1


title: d4_RXRi_prep2_2


title: d5_DMSO_prep1_1


title: d5_DMSO_prep2_2


title: d5_DMSO_prep2_1


title: W82_Nodule_22dpi_Rep1_RNAseq


title: W82_Nodule_22dpi_Rep2_RNAseq


title: d4_atRA_prep2_1


title: d4_atRA_prep2_2


title: d4_RXRi_prep1_2


title: d4_DMSO_prep2_2


title: W82_Root_36dpi_Rep3_RNAseq

source_name: Mock treated root tissue

value: Root


title: W82_Nodule_12dpi_Rep3_RNAseq

value: 15 days


title: d4_RXRi_prep1_1

source_name: Intestinal organoids


title: W82_Nodule_12dpi_Rep2_RNAseq


title: d4_atRA_prep1_2


title: W82_Root_36dpi_Rep2_RNAseq


title: d4_DMSO_prep1_1


title: d4_DMSO_prep1_2


title: d4_atRA_prep1_1


title: W82_Root_22dpi_Rep2_RNAseq


title: W82_Root_22dpi_Rep1_RNAseq


title: d3_RXRi_prep2_2


title: W82_Root_12dpi_Rep3_RNAseq


title: W82_Root_22dpi_Rep3_RNAseq


title: W82_Nodule_36dpi_Rep3_MethylC-seq

data_processing:
Library strategy: MethylC-Seq
Adapters and low quality reads below phred threshold of 33 were removed using Trimmomatic.
Reads were aligned to the soybean reference genome (Wm82.a2.v1) using Bismark.
Differentially methylated cytosines were identified using R bioconductor package methylKit.
Differentially methylated regions were mapped to various genic regions using R Bioconductor package rtracklayer.
Genome_build: Wm82.a2.v1

extract_protocol:
DNA was extracted using DNAeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions.
Whole genome methylC-seq libraries were constructed following the protocol from Illumina TruSeq Library Prep kit (Illumina, San Diego, CA)


title: d3_RXRi_prep2_1


title: W82_Nodule_36dpi_Rep2_MethylC-seq


title: d3_DMSO_prep2_2


title: d3_DMSO_prep2_1


title: d3_atRA_prep2_1


title: W82_Nodule_36dpi_Rep1_MethylC-seq


title: W82_Nodule_12dpi_Rep1_RNAseq


title: d3_RXRi_prep1_2


title: W82_Root_12dpi_Rep1_RNAseq


title: W82_Nodule_22dpi_Rep3_MethylC-seq


title: W82_Nodule_22dpi_Rep2_MethylC-seq


title: W82_Root_36dpi_Rep1_RNAseq


title: W82_Nodule_22dpi_Rep1_MethylC-seq


title: d3_atRA_prep1_2


title: W82_Nodule_12dpi_Rep3_MethylC-seq


title: d3_DMSO_prep1_1


title: d4_DMSO_prep2_1


title: d1_RXRi_prep2_2


title: W82_Nodule_12dpi_Rep1_MethylC-seq


title: W82_Root_12dpi_Rep2_RNAseq


title: d3_atRA_prep2_2


title: d1_RXRi_prep2_1


title: d3_DMSO_prep1_2


title: W82_Nodule_12dpi_Rep2_MethylC-seq


title: W82_Root_36dpi_Rep2_MethylC-seq


title: W82_Root_36dpi_Rep1_MethylC-seq


title: d1_DMSO_prep2_2


title: d1_DMSO_prep2_1


title: d1_atRA_prep2_1


title: W82_Root_22dpi_Rep2_MethylC-seq


title: W82_Root_22dpi_Rep3_MethylC-seq


title: W82_Root_22dpi_Rep1_MethylC-seq


title: W82_Root_12dpi_Rep3_MethylC-seq


title: d3_atRA_prep1_1


title: d1_atRA_prep1_2


title: d1_RXRi_prep1_1


title: W82_Root_12dpi_Rep2_MethylC-seq


title: d1_atRA_prep1_1


title: d1_RXRi_prep1_2


title: W82_Root_12dpi_Rep1_MethylC-seq


title: d1_DMSO_prep1_2


title: W82_Root_36dpi_Rep3_MethylC-seq


title: H3K27Ac ChIP-seq replicate 4 - KO control input

city: Baltimore

first: Weidong

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging/NIH

description: input for H3K27Ac-4 KO control, H3K9Ac-3 KO control

data_processing:
base_calling: generate fastq files from BCL reads by bcl2fastq
alignments, mapping and file format convertion: Reads are aligned to mm10 genome by Bowtie2, sorted by samtools 1.9; and are built index,  and transfer to bed format files by bamtools 2.5.1.
filtering, normalization and peakcalling: The bed files are filtered, normalized, and tested for peakcalling by SICER v1.1.
bedgraph generation/normalization: codes avalible upon request
functionl/phenotype analysis: Using bedtools 2.29.0 intersect function , the peak call change values with position information are mapped to the transcription Start Sites and EXON postions grouped by genes. These results are then used as input for PAGE algorithem  to analyze Gene Ontology gene set  and Broad Institute Pathway gene set to obtain functional change lists.  The same results are also used to analyze disease MESH term Gene Set  by the PAGE method to obtain phenotype change lists.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bedgraph files containing FPKM of normalized ChIP-seq

source_name: Brain

growth_protocol: 2-4 month old mice in standard growth condition

extract_protocol:
Mouse brain tissue was homogenized in 1 ml of 1% formaldehyde for 15 min. The sample was added of 50 ml of 2.5M glycine (final concentration 125 mM), incubated at room temperature for 5min, and centrifuged at 1,000 x g for 5 min at 4°C. The pellet was collected and washed with PBS. The pellet was then resuspended in 400 ml of RIPA buffer with protease inhibitor cocktail and 0.5 mM phenylmethylsulfonyl fluoride and centrifuge at 1,000 x g for 10 min at 4°C. The lysates were sonicated to shear the DNA to lengths between 200 and 400 bp, and were centrifuged at 1,000 x g for 10 min at 4°C. In order to pre-clear the chromatin, 100 ml of Protein A beads were added to the sample and incubated for 60 min at room temperature. During preclearing step, Protein A beads were incubated with blocking solution (0.5% BSA in PBS) for 60 min at room temperature. 5 ml of antibody and 20-30 ml of Protein A beads were added into the precleared lysate and incubated for 4 hrs at 4C and mixed on a rotator during all the incubation step. Each sample was washed one-time with 0.3 M NaCl/RIPA buffer, one-time with RIPA buffer, one-time with 0.25 M LiCl and twice with TE. The beads were incubated for 8 hrs at 65C with 100 ml TE, 3 ml of 10% SDS and 3ml of Protease K in a thermocycler, and the liquid was transferred into a new tube. 100 ml of TE was added to the beads, resuspended, and the supernatant was transferred again to the tube in order to reach a final volume of 200 ml.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were placed into the chamber (120 sec) for habituation, followed by 30 sec tone that co-terminated with a 2 -secondsec, 0.5 mA electric foot shock. This was repeated for a total of three tone-shock pairings with an interval of 30 seconds sec between tone presentations. The mice were culled by CO2 after 10 min.

value: no fear

tag: strain background

value: Top3b KO

value: brain


title: d1_atRA_prep2_2

value: wild type


title: d0_DMSO_prep2_2

value: 8 weeks


title: H3K27Ac ChIP-seq replicate 4 - WT control input

description: input for H3K27Ac-4 WT control, H3K9Ac-3 WT control

value: WT


title: d1_DMSO_prep1_1

value: Yes


title: d0_DMSO_prep1_2


title: d0_DMSO_prep2_1


title: d0_DMSO_prep1_1


title: H3K27Ac ChIP-seq replicate 4 - WT control

description: ChIP


title: H3K27Ac ChIP-seq replicate 3 - KO fear input

description: input for H3K27Ac-3 KO fear, H3K9Ac-2 KO fear

value: fear


title: H3K27Ac ChIP-seq replicate 4 - KO control

description: ChIP


title: H3K4me1 ChIP-seq replicate 2 - WT control

description: ChIP

data_processing:
CHIP SEQ fastq files are first passed fastqc to remove potentially low quality bases
Reads were mapped to mouse genome version mm10 using BOWTIE2 under “very sensitive” option and the maximum of 2 mismatches
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bedgraph file

tag: antibody


title: H3K27Ac ChIP-seq replicate 3 - WT fear input

description: input for H3K27Ac-3 WT fear, H3K9Ac-2 WT fear


title: H3K27Ac ChIP-seq replicate 3 - KO control input

description: input for H3K27Ac-3 KO control, H3K4me3-2 KO control, H3K4me2-1 KO control, H3K9Ac-2 KO control, H3K27me3-2 KO control, H3K9me3-2 KO control


title: H3K27Ac ChIP-seq replicate 3 - WT control input

description: input for H3K27Ac-3 WT control, H3K4me3-2 WT control, H3K4me2-1 WT control, H3K9Ac-2 WT control, H3K27me3-2 WT control, H3K9me3-2 WT control


title: H3K27Ac ChIP-seq replicate 3 - WT fear

description: ChIP


title: H3K4me1 ChIP-seq replicate 2 - WT control input

description: input for H3K4me1-2 WT control


title: H3K27Ac ChIP-seq replicate 3 - KO fear

description: ChIP


title: H3K27Ac ChIP-seq replicate 3 - KO control

description: ChIP


title: H3K27Ac ChIP-seq replicate 3 - WT control

description: ChIP


title: PR0549_94_a

city: Tokyo

first: Taku

last: Sato

address: 1-5-45 Yushima Bunkyo-ku

department: Department of Biodefense Research

institute: Medical Research Institute, Tokyo Medical and Dental University (TMDU)

data_processing:
bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using TopHat 2.0.14.
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using GeneData Expressionist for Genomic Profiling 9.1.4a.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: intestinal crypt epithelial cells

extract_protocol:
FCM-sorted single crypt epithelial cells were introduced into the cell input well of the C1 Single-Cell Auto Prep System (5–10 µm). Single cells captured on the IFC were microscopically inspected with a Keyence BZ-X700 to determine which C1 capture sites contained only a single cell. Reverse transcription and cDNA preamplification were performed using the SMARTer Ultra Low RNA kit (Clontech).
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera Index Kit (Illumina), according to the manufacturer’s instructions. The preparation and sequencing of cDNA libraries and the extraction of multiple expression data were performed by Takara Bio, Inc.

treatment_protocol: 48 hrs after 10 Gy TBI

tag: cell type

value: tdTomato+ Sca1- crypt epithelial cells

value: Tamoxifen injected 24 hrs before TBI, 48 hrs after 10 Gy TBI


title: PR0549_92_a


title: PR0549_95_a


title: PR0549_86_a


title: H3K27Ac ChIP-seq replicate 2 - WT fear

description: ChIP


title: PR0549_83_a


title: PR0549_79_a


title: H3K27Ac ChIP-seq replicate 2 - WT control

description: ChIP


title: H3K27Ac ChIP-seq replicate 1 - KO fear

description: ChIP


title: PR0549_76_a


title: H3K27Ac ChIP-seq replicate 1 - KO control

description: ChIP


title: hybrid (Berlin and Agnostic(ts3))_rep2

city: Moscow

first: Sergei

last: Funikov

state: Moscow

address: Vavilov str. 32

country: Russia

institute: Engelhardt Insitute of Molecular Biology

description: Gel extraction of small RNAs

data_processing:
3’-adapter cropping, filtration of reads by length filtration (>18 nt) and quality (80% of nt have ≥ 20 Phred quality) using Trim Galore.
Pre-processed reads were further subjected to subtraction of reads matching to all ribosomal RNA sequences.
The selected reads were mapped to the dm6 release of D. melanogaster genome by  Bowtie with the following settings: “--best --strata -m 1 -v 0”, retaining only uniquely mapped reads with zero mismatches.
The number of reads mapped to miRNAs was counted using the HTseq-count and dm6 annotation.
Genome_build: dm6
Supplementary_files_format_and_content: counts text files

organism: Drosophila melanogaster

source_name: whole fly

extract_protocol:
Total RNA was isolated using Tri-reagent (Sigma-Aldrich, USA). A total of 25 µg of total RNA were separated using 15% polyacrylamide gel electrophoresis containing 8 M of urea. After incubation in ethidium bromide solution (0.5 µg/ml), gel fragments corresponding to small RNAs fraction were excised. We used chemically synthesized RNAs (Syntol, Russia) corresponding to 21 and 27 nucleotides as size markers.
Cloning of small RNA libraries was performed by Illumina TruSeq Small RNA prep kit (Illumina, USA) according to the manufacturer’s protocol.

value: whole fly

value: Agnostic(ts3) and Berlin


title: hybrid (Berlin and Agnostic(ts3))_rep1

description: Gel extraction of small RNAs


title: PR0549_72_a


title: H3K27Ac ChIP-seq replicate 1 - WT control

last: Wang

description: ChIP


title: PR0549_96_a


title: PR0549_93_a


title: PR0549_71_a


title: PR0549_67_a


title: hybrid (Agnostic(ts3) and Berlin)_rep1

description: Gel extraction of small RNAs


title: PR0549_66_a


title: H3K27me3 ChIP-seq replicate 1 - KO fear

description: ChIP


title: H3K27me3 ChIP-seq replicate 1 - KO control

description: ChIP


title: H3K27me3 ChIP-seq replicate 1 - WT fear

description: ChIP


title: Canton_S_heat_shocked_rep2

description: Gel extraction of small RNAs

value: Canton

value: heat shocked


title: Canton_S_heat_shocked_rep1

description: Gel extraction of small RNAs


title: H3K27me3 ChIP-seq replicate 1 - WT control

description: ChIP


title: H3K9me3 ChIP-seq replicate 2 - KO control

description: ChIP


title: H3K9me3 ChIP-seq replicate 1 - KO fear

description: ChIP


title: H3K27Ac ChIP-seq replicate 1 - WT fear

description: ChIP


title: PR0549_63_a


title: Canton_S_rep2

description: Gel extraction of small RNAs


title: H3K9me3 ChIP-seq replicate 2 - WT control

description: ChIP


title: PR0549_101_a


title: H3K27me3 ChIP-seq replicate 2 - KO control

description: ChIP


title: PR0549_60_a


title: H3K27me3 ChIP-seq replicate 2 - WT control

description: ChIP


title: H3K9me3 ChIP-seq replicate 1 - WT control

description: ChIP


title: hybrid (Agnostic(ts3) and Berlin)_rep2

description: Gel extraction of small RNAs


title: H3K9Ac ChIP-seq replicate 3 - KO control

description: ChIP


title: H3K9me3 ChIP-seq replicate 1 - KO control

description: ChIP


title: Canton_S_rep1

description: Gel extraction of small RNAs


title: PR0549_56_a


title: H3K9me3 ChIP-seq replicate 1 - WT fear

description: ChIP


title: PR0549_54_a


title: PR0549_65_a


title: H3K9Ac ChIP-seq replicate 2 - KO fear

description: ChIP


title: H3K9Ac ChIP-seq replicate 2 - KO control

description: ChIP


title: PR0549_52_a


title: H3K9Ac ChIP-seq replicate 2 - WT fear

description: ChIP


title: Berlin_heat_shocked_rep2

description: Gel extraction of small RNAs

value: Berlin


title: Berlin_rep2

description: Gel extraction of small RNAs


title: H3K9Ac ChIP-seq replicate 2 - WT control

description: ChIP


title: H3K9Ac ChIP-seq replicate 1 - KO fear

description: ChIP


title: Berlin_rep1

description: Gel extraction of small RNAs


title: PR0549_48_a


title: H3K9Ac ChIP-seq replicate 1 - KO control

description: ChIP


title: H3K9Ac ChIP-seq replicate 1 - WT control

description: ChIP


title: PR0549_46_a


title: H3K9Ac ChIP-seq replicate 1 - WT fear

description: ChIP


title: H3K4me3 ChIP-seq replicate 2 - KO control

description: ChIP


title: Agnostic(ts3)_heat_shocked_rep1

description: Gel extraction of small RNAs


title: H3K9Ac ChIP-seq replicate 3 - WT control

description: ChIP


title: H3K4me3 ChIP-seq replicate 2 - WT control

description: ChIP


title: PR0549_39_a


title: Agnostic(ts3)

description: Gel extraction of small RNAs


title: PR0549_43_a


title: H3K4me3 ChIP-seq replicate 1 - KO fear

description: ChIP


title: H3K4me3 ChIP-seq replicate 1 - WT fear

description: ChIP


title: H3K4me2 ChIP-seq replicate 2 - KO control

description: ChIP


title: mRNA-seq-for-normalization-Siadat2-replicate_2

city: Dallas

first: xueliang

last: lyu

state: Texas

address: 6001 Forest Park Road

department: Physiology

institute: UT Southwestern Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using tophat2 with parameters --library-type fr-firststrand --min-intron-length 20 --max-intron-length 50000 --read-mismatches 4.
Fragments Per Kilobase Million (FPKM) were calculated using cufflinks with parameters --library-type fr-firststrand --multi-read-correct --min-intron-length 20 --max-intron-length 50000 --frag-bias-correct
Genome_build: For the ribosome profiling, the reference sequences are all mRNAs with upstream and downstream 100 bp respectively; for the mRNA-seq, the reference sequence is whole genome sequence with gtf annotation file from NCBI database.
Supplementary_files_format_and_content: For the mRNA-seq, tab-delimited text files include FPKM values for each sample; for the ribosome profiling, tab-delimited text file includes absolute codon occupancy values.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For the ribosome profiling and accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of adat2-silenced mutant and wild-type strain were cultured in plates with 50 ml growth medium (1 × Vogel’s, 0.1% glucose, 10-2 M QA) at room temperate for three days. The cultures were cut into small discs with a diameter of 1 cm and then were transferred into flasks with the same medium and grown with orbital shaking (200 rpm) under constant light for one day. For the independent mRNA-seq, the culture condition was identical to that described above, except that CHX was not added.

extract_protocol:
For the ribosome profiling and accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq™ Ribosome Profiling Kit (Catalog Number: RPYSC12116). For the independent mRNA-seq, total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase (Turbo DNase, Ambion) according to standard RNA extraction protocol.
For the ribosomal profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq™ Ribosome Profiling Kit (Catalog Number: RPYSC12116). For the independent mRNA-seq, libraries were constructed using Illumina TruSeq reagents. All RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For the ribosome profiling and accompanying mRNA-seq, CHX (final concentration of 50 g/ml) was added 10 min before collecting the samples. For the mRNA-seq, no special treatment was performed.

value: mycelia

value: adat2-silenced mutant

tag: molecule

value: mRNA


title: PR0549_36_a


title: Berlin_heat_shocked_rep1

description: Gel extraction of small RNAs


title: mRNA-seq-for-normalization-WT-replicate_2


title: PR0549_51_a


title: PR0549_34_a


title: H3K4me2 ChIP-seq replicate 1 - WT control

description: ChIP

value: no fear


title: H3K4me2 ChIP-seq replicate 2 - WT control

description: ChIP

value: brain


title: Agnostic(ts3)_heat_shocked_rep2

description: Gel extraction of small RNAs


title: H3K4me1 ChIP-seq replicate 1 - WT fear input

description: input for H3K4me1-1 WT fear, H3K27Ac-2 WT fear


title: PR0549_30_a


title: Ribosome-profiling-Siadat2-replicate_2

molecule: other

value: ribosome protected fragments


title: H3K4me1 ChIP-seq replicate 1 - WT control input

description: input for H3K4me1-1 WT control, H3K27Ac-2 WT control


title: H3K4me1 ChIP-seq replicate 1 - WT control

description: ChIP


title: PR0549_29_a


title: PR0549_22_a


title: TDRD3 ChIP-seq replicate 2 - WT fear

description: ChIP


title: TDRD3 ChIP-seq replicate 2 - WT fear input

description: input for TDRD3-2 WT fear


title: mRNA-seq-for-normalization-Siadat2

data_processing:
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using tophat2 with parameters --library-type fr-firststrand --min-intron-length 20 --max-intron-length 50000 --read-mismatches 4.
Fragments Per Kilobase Million (FPKM) were calculated using cufflinks with parameters --library-type fr-firststrand --multi-read-correct --min-intron-length 20 --max-intron-length 50000 --frag-bias-correct
Genome_build: For the ribosome profiling, the reference sequences are all mRNAs with uptream and dowmstream 100 bp respectively; for the mRNA-seq, the reference sequence is whole genome sequence with gtf annotation file from NCBI database.
Supplementary_files_format_and_content: For the mRNA-seq, tab-delimited text files include FPKM values for each sample; for the ribosome profiling, tab-delimited text file includes absolute codon occupancy values.

extract_protocol:
For the ribosome profiling and accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, total RNA was extracted using Trizol reagents (Invitrogen) and treated with DNase (Turbo DNase, Ambion) accoding to standard RNA extraction protocal.
For the ribosomal profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq™ Ribosome Profiling Kit(Catalog Number: RPYSC12116). For the independent mRNA-seq, libraries were constucted using Illumina TruSeq reagents. All RNA libraries were prepared for sequencing using standard Illumina protocols.


title: Ribosome-profiling-WT-replicate_2

value: wild type


title: TDRD3 ChIP-seq replicate 2 - WT control input

description: input for TDRD3-2 WT control

value: WT


title: mRNA-seq-for-normalization-WT


title: H3K4me2 ChIP-seq replicate 1 - KO control

description: ChIP

value: Top3b KO


title: TDRD3 ChIP-seq replicate 2 - WT control

description: ChIP


title: PR0549_18_a


title: TDRD3 ChIP-seq replicate 1 - KO fear

description: ChIP

value: fear


title: Ribosome-profiling-WT


title: TDRD3 ChIP-seq replicate 1 - KO control

description: ChIP


title: Ribosome-profiling-Siadat2


title: PR0549_16_a

value: tdTomato+ Sca1- crypt epithelial cells


title: PR0549_17_a

value: Tamoxifen injected 24 hrs before TBI, 48 hrs after 10 Gy TBI


title: TDRD3 ChIP-seq replicate 1 - WT fear

description: ChIP


title: TDRD3 ChIP-seq replicate 1 - WT control

description: ChIP


title: Pol2ser5 ChIP-seq replicate 3 - KO fear

description: ChIP


title: Pol2ser5 ChIP-seq replicate 3 - KO control

description: ChIP


title: PR0549_14_a


title: Pol2ser5 ChIP-seq replicate 3 - WT fear

description: ChIP


title: H3K4me1 ChIP-seq replicate 1 - WT fear

description: ChIP


title: Pol2ser5 ChIP-seq replicate 3 - WT control

description: ChIP


title: Nevus_5

city: Salt Lake City

first: Robert

middle: L

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

description:
small RNA-Sequencing
McNeal_GEO_processed.txt

data_processing:
fastq files were aligned to GRCh37 using Bowtie.
BAM files resulting from the alignments were summarized to small RNA reference group (miRBase 21) and counted using the feature counts algorithm of DESEq2 in R.
Expression data was normalized using the DESeq2 package's median of ratios method in R.
Differentially expressed genes (£5% false discovery rate) were identified by DESeq2's General Linear Modeling and Bayesian statistics.
Genome_build: human reference genome GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene count values from DESeq2 for each sample.

source_name: adult nevus-derived melanocytes

growth_protocol: Melanocytes were plated in 10cm culture-treated dishes and placed in a 5% CO2 37 °C incubator.

extract_protocol:
RNA was isolated using the Trizol Reagent (Ambion/ThermoFisher Scientific) and processed as per manufacturer’s instructions. Resulting RNA was then processed using the RNeasy Power Clean Pro Cleanup kit (Qiagen) and processed as per manufacturer's instructions.
MicroRNA Library Preparation was performed by SeqMatic using the SeqMaticMicroRNA Library Preparation Kit and protocols.

value: BRAF V600E


title: Nevus_6


title: Pol2ser5 ChIP-seq replicate 2 - KO fear

description: ChIP


title: Nevus_8


title: PR0549_07_a


title: PR0549_09_a


title: Nevus_4


title: PR0549_05_a


title: Pol2ser5 ChIP-seq replicate 2 - WT fear

description: ChIP


title: Pol2ser5 ChIP-seq replicate 2 - WT control

description: ChIP


title: Pol2ser5 ChIP-seq replicate 2 - KO control

description: ChIP


title: Pol2ser5 ChIP-seq replicate 1 - KO fear

description: ChIP


title: PR0549_02_a


title: Nevus_2


title: PR0549_04_a


title: Pol2ser5 ChIP-seq replicate 1 - WT fear

description: ChIP


title: Nevus_3


title: Pol2ser2 ChIP-seq replicate 3 - KO fear

description: ChIP


city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

description:
Germinal center B cells from WT mice, ATACseq, replica1
ATACseq_WT_GCB_1

data_processing:
1. RNASeq: Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Epigenomics Core Facility at Weill Cornell Medicine using a HiSeq2500
2. RNASeq: 50-bp paired-end reads at a depth of ~ 22-30 million reads per sample. Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to the mouse genome (mm10) and reads in exons were counted against Gencode v27 with STAR2.6
3. RNAseq: Differential gene expression analysis was performed in R using edgeR3.24.3. Genes with low expression levels (<2 counts per million in at least one group) were filtered from all downstream analyses. Replica-associated batch correction was performed by directly incorporating a batch-specific term into a linear model. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an unadjusted p-value less than 0.01 were considered differentially expressed
4. ATACseq: The nuclei of sorted WT and CD23-Rock2 GC B cells were prepared by incubation of cells with nuclear preparation buffer (0.30M sucrose, 10mM Tris, pH 7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.1% NP40, 0.15mM spermine, 0.5mM spermidine, and 2mM 6AA)
5. The libraries has been constructed as in PMID:24097267
6. ATACseq: Paired-end 50bp sequences were generated from samples with an Illumina HiSeq2500 and, following adapter trimming with FastP, were aligned against mouse genome (mm10) using bowtie2 with --local -q -p options. Peaks were called with MACS2 with --macs2 callpeak -f BAMPE --nomodel --shift -100 --extsize 200 –B --SPMR -g $GENOMESIZE -q 0.01 options
Genome_build: mm10
Supplementary_files_format_and_content: edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx : unfiltered count matrix, filtered  count matrix, log-transformed normalized matrix, differential expression statistics
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_cKO_GCB_1_treat_pileup.bw: bigWIG of aligned cKO_GCB_replica 1 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_cKO_GCB_2_treat_pileup.bw: bigWIG of aligned cKO_GCB replica 2 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_WT_GCB_1_treat_pileup.bw: bigWIG of aligned WT GCB replica1 ATACseq
Supplementary_files_format_and_content: Sample_GRCF-Pernis-ER-6879_WT_GCB_2_treat_pileup.bw: bigWIG of aligned WT GCB replica 2 ATACseq

source_name: Germinal center B cells

extract_protocol:
1. RNA-seq: Total RNA was isolated using QIAGEN RNeasy Plus Mini Kit from FACS sorted FoB or GCB cells; 2. ATAC-seq: the nuclei of sorted GCB cells were prepared by incubation of cells with nuclear preparation buffer (0.3M sucrose, 10mM Tris pH7.5, 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.1% NP40, 0.15mM spermine, 0.5mM spermidine, 2mM 6AA)
1. RNA-seq: sequence-compatible libraries were prepared by Nextera library preparation at a the Weill Cornell Epigenomics core. Quality of all RNA and library preparations were evaluated with BioAnalyzer 2100 (Agilent). Sequencing libraries were sequenced by the Epigenomics Core Facility at Weill Cornell Medicine using a HiSeq2500; 2. ATAC-seq: sequencing libraries were constructed as described in PMID: 26083756: Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23;523(7561):486-90. doi:10.1038/nature14590. Epub 2015 Jun 17.

treatment_protocol: WT and CD23-Cre.Rock2 mice were immunized for 7d with 100ug NP-CGG in alum

value: Rock2 flox/flox

value: spleen

value: Germinal center B cells

value: 10 weeks


title: Pol2ser5 ChIP-seq replicate 1 - WT control

description: ChIP


title: Pol2ser2 ChIP-seq replicate 3 - KO control

description: ChIP


description:
Germinal center B cells from WT mice, ATACseq, replica2
ATACSeq_WT_GCB_2


title: Pol2ser2 ChIP-seq replicate 3 - WT control

description: ChIP


title: Pol2ser2 ChIP-seq replicate 3 - WT fear

description: ChIP


title: Pol2ser2 ChIP-seq replicate 2 - KO fear

description: ChIP


title: FS063L

source_name: neonatal foreskin-derived melanocytes

value: BRAF WT


description:
Germinal center B cells from Rock2 conditional KO mice, ATACseq, replica2
ATACseq_cKO_GCB_2

value: Rock2flox/flox CD23-Cre


title: FS057LM


title: FS056L


title: Pol2ser2 ChIP-seq replicate 2 - KO control

description: ChIP


title: Pol2ser2 ChIP-seq replicate 2 - WT fear

description: ChIP


title: FS046LM


title: Pol2ser2 ChIP-seq replicate 2 - WT control

description: ChIP


title: Pol2ser2 ChIP-seq replicate 1 - KO control

description: ChIP


title: Pol2ser5 ChIP-seq replicate 1 - KO control

description: ChIP


description:
Germina center B cells from WT mice, RNAseq, replica3
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_GCB_3


title: FS065L


title: Pol2ser2 ChIP-seq replicate 1 - WT fear

description: ChIP


title: A1030

source_name: adult skin-derived melanocytes


title: Pol2ser2 ChIP-seq replicate 1 - WT control

description: ChIP


title: Pol2CTD ChIP-seq replicate 5 - KO fear

description: ChIP


title: A1019LM


title: Pol2CTD ChIP-seq replicate 5 - KO fear input

description: input for Pol2CTD-5 KO fear, H3K27me3-1 KO fear, H3K9me3-1 KO fear


title: d3_RXRi_prep1_1

value: 8 weeks

value: Yes


description:
Germinal center B cells from WT mice, RNAseq, replica2
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_GCB_2


description:
Germinal center B cells from WT mice, RNAseq, replica1
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_GCB_1


title: Pol2CTD ChIP-seq replicate 5 - WT fear

description: ChIP

value: brain


title: Pol2CTD ChIP-seq replicate 4 - KO fear input

description: input for Pol2CTD-4 KO fear, Pol2ser2-2 KO fear, Pol2ser5-2 KO fear, H3K27Ac-1 KO fear, H3K9Ac-1 KO fear


description:
Folicular B cells from WT mice, RNAseq, replica3
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_FoB_3

source_name: Folicular B cells

value: Folicular B cells


description:
Germinal center B cells from Rock2 conditional KO mice, ATACseq, replica1
ATACseq_cKO_GCB_1


title: Pol2ser2 ChIP-seq replicate 1 - KO fear

description: ChIP


description:
Folicular B cells from WT mice, RNAseq, replica2
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_FoB_2


title: Pol2CTD ChIP-seq replicate 4 - KO control input

description: input for Pol2CTD-4 KO control, Pol2ser2-2 KO control, Pol2ser5-2 KO control, H3K27Ac-1 KO control, H3K9Ac-1 KO control

value: no fear


title: Pol2CTD ChIP-seq replicate 4 - KO control

description: ChIP


title: Pol2CTD ChIP-seq replicate 4 - KO fear

description: ChIP


description:
Folicular B cells from WT mice, RNAseq, replica1
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
WT_FoB_1


title: Patient5-I_CD4Treg-TCRseq

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

description: TCR-enrich polyA RNA

data_processing:
Library strategy: TCR-seq
TCRβ data were aligned and quantified using MixCR (version 2.1.5).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.TRB.clones.txt: TCRseq; Tab-delimited text files with counts and VDJ-CDR3 description for all clonotypes for each sample.

growth_protocol: Ex-vivo

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

tag: disease status

value: Luminal breast cancer

value: Invaded Lymph Node

tag: patient


title: Pol2CTD ChIP-seq replicate 4 - WT fear input

description: input for Pol2CTD-4 WT fear, Pol2ser2-2 WT fear, Pol2ser5-2 WT fear, H3K27Ac-1 WT fear, H3K9Ac-1 WT fear

value: fear

value: WT


description:
Germina center B cells from Rock2 conditional KO mice, RNAseq, replica3
edgeR_DEGs_for ver1.3.2_2019-03-15.xlsx
cKO_GCB_3

tag: strain


title: Pol2CTD ChIP-seq replicate 4 - WT fear

description: ChIP


title: MDA-MB-231_JQ1_neg_ChIP_Brd4_L

first: Cheng-Ming

last: Chiang

address: 5323 Harry Hines Blvd. ND2.210H

department: Simmons Comprehensive Cancer Center

data_processing:
Raw reads were trimmed by TrimGalore for ChIP-seq or FASTP for CUTandRUN.
Reads were mapped to hg19 using BWA for BRD4 CUTandRUN and BWA-MEM for ChIP-seq and EN1 datasets.
Alignments with mapping quality less than 15 were filtered out.
Duplicate alignments were removed using Sambamba or SAM/BAM RmDuP.
Peaks were called using MACS2 following the Galaxy default configuration (effective genome size 2.45e+09, band width 300, model fold [5, 50], q-value cutoff 0.05, larger dataset scaled towards smaller dataset, range for calculating regional lambda 1000 bps and 10000 bps) for BRD4 CUTandRUN or (p cutoff 0.01 --nomodel --shift 0 --extsize 90 --keep-dup all -B --SPMR) for ChIP-seq and EN1 data sets.
Supplementary_files_format_and_content: ChIP-seq bigwig files containing relative signal fold change (fc) of sample/control were generated by BICF ChIP-seq Analysis Workflow.  CUTandRUN bigwig files contain spike-in-normalized signals were generated using Galaxy bamcompare.
Genome_build: hg19

growth_protocol: MDA-MB-231 and its derived 3F:BRD4-S(a) line were maintained in high-glucose DMEM + 10% heat-inactivated FBS + Penicillin (100 units/ml) & Streptomycin (0.1 mg/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated by IP with anti-BRD4-L or BRD4-S [i.e., S(a)] antibody or with Abcam EN1 antibody (Cat# ab108598).
Sequencing libraries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocol.

treatment_protocol: Cells were either untreated (unt) or treated with 1 µM inactive JQ1(-) (i.e., JQ1-neg) or active JQ1(+) (i.e., JQ1-pos) for 4 hours.

tag: cell line

value: breast cancer cell line MDA-MB-231

tag: er/pr/her2 statue

value: triple negative – ER-; PR-; HER2-

tag: chip antibody

tag: bet inhibitor jq1 treatment

value: inactive enantiomer JQ1, i.e. JQ1_neg or JQ1(-)


title: MDA-MB-231_JQ1_pos_ChIP_Brd4_L

value: active JQ1, i.e. JQ1_pos or JQ1(+)