title: Screen_IFN_2

city: Stanford

first: Shibin

last: Hu

state: CA

address: 240 pasteur drive, 4300

department: Genetics

institute: Stanford University

description:
CRISPR screen, guide RNA was amplified with sequencing adapters, seq data was analyzed by casTLE.
CRISPRscreen_rawcount.txt

data_processing:
Basecalls performed using illumina RTA v2.
Reads were mapped using STAR v2.4.2a with the reference genome hg19 for human (paremeters: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10).
The expression of known genes (measured in Transcripts Per Kilobase Million, TPM) was quantified using RSEM v1.2.21.
Assembly: hg19
Supplementary files format and content: Matrix table with TPM for every gene and every sample

extract_protocol:
Total RNA was extracted using Trizol Reagent.
The library was constructed using KAPA HyperPrep RNA-seq Kit (Kapa Biosystems, KK8540).

value: CRISPR library and IFNα

value: ADAR1 knockout


title: CR_control_1

status: Public on Oct 03 2023

type: SRA

city: New York

first: Rajal

last: Sharma

state: NY

address: 1425 Madison Ave., Room 16-52

country: USA

institute: ISMMS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by Trimmomatic 0.36
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.0.1
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

molecule: genomic DNA

organism: Homo sapiens

source_name: HCT116 cells

growth_protocol: WT HCT116 p53+/+ cells were cultured in RPMI-1640 (Gibco) contained 10% fetal calf serum (Gibco), 100 units of penicillin (Gibco) and 100 µg/ml streptomycin (Gibco). Cells were treated with 500 nM Doxorubicin or DMSO as noted prior to collection for further analysis.

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using TRIzol.
ChIP-sequencing for GAS41, c-Myc, H3K27cr and H3K27ac and RNA-sequencing in HCT116 cells with and without Dox treatment were performed on the Illumina HiSeq 2500v4 platform with 100bp read length under rapid run mode. Two to three biological replicates were prepared for each treatment condition. Specifically, for these genomic sequencing samples, ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. Additionally, RNA-sequencing for HCT116 GAS41 wt and GAS41 KO cells, or GAS41 KO cells stably expressing GFP-Flag-GAS41 wt (wt rescue), or GFP-Flag-GAS41 Y74A/W93A (mutant rescue), was performed using an BGISEQ-500 platform at BGI. Three biological replicates were prepared for each treatment. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA. nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method

tag: cell line

tag: replicate

tag: treatment

value: DMSO

tag: chip antibody

value: H3K27cr (PTM-Bio 526)


title: ME3_doxo_2

value: Dox 500 nM

value: H3K27me3 (Millipore 07-449)


title: Preadipocytes from iWAT (HFD-WT1) [WT1-RNA-seq]

city: California

first: Sona

last: Kang

state: Berkeley

address: Morgan Hall 321

department: Nutritional Sciences & Toxicology

institute: University of California, Berkeley

description: RNAseq.xlsx

library_source: transcriptomic

data_processing:
WGBS:
trim_galore, Version 0.6.6, trim_base1=10 trim_base2=15
mapping to the in silico bisulfite converted GRCm39, Bismark, Version 0.23.0
DMRs detection, DSS, version 2.44.0, p-value 0.01, minlen=200, minCG=5, dis.merge=50, pct.sig=0.5
Assembly: MM39 (WGBS); MM10 (RNA-seq)
Supplementary files format and content: WGBS.xlsx, DMRs for Pooled WT-WGBS, Pooled KO-WGBS
Supplementary files format and content: Readcount.xlsx, excel, readcount for WT1-RNA-seq, WT2-RNA-seq, WT3-RNA-seq, KO1-RNA-seq, KO2-RNA-seq, KO3-RNA-seq
RNA-seq:
RNA alignment, Hisat2, Version 2.2.1, Default
Feature count, Htseq, Version 0.9.1, Default
Differential gene expression analysis, Deseq2, Version 1.36.0, Default

molecule: polyA RNA

organism: Mus musculus

source_name: iWAT

extract_protocol:
WGBS: Preadipocytes were isolated from SVF of iWAT using flow cytometry and genomic DNA was purified using DNeasy blood & tissue kit (Cat#. 69506)
WGBS: Genomic DNA is sonicated and proceed to bisulfite conversion with ZYMO EZ DNA Methylation Lightning Kit (cat#11-338). The library is prepped with Swift Biosciences ACCEL-NGS MethylSeq DNA library kit Cat#30096)
RNA-seq:Preadipocytes were isolated from SVF of iWAT using flow cytometry and RNA was purified using RNAqueous®-Micro Kit (Cat#. AM1931)
RNA-seq:Poly(A) RNA Selection Kit V1.5

treatment_protocol:
WGBS: High fat diet (14 weeks)
RNA-seq: High fat diet (6 weeks)

tag: tissue

value: iWAT

tag: Sex

value: male

tag: cell type

value: preadipocytes (CD45-, CD31-, TER119-, PDGFRa+)

tag: genotype

value: Tet3 f/f

value: High fat diet (6 weeks)


title: ME3_doxo_1


title: Screen_untreat_2

molecule: total RNA

value: CRISPR library


title: Preadipocytes from iWAT (HFD-KO_pool) [Pooled KO-WGBS]

description: WGBS.xlsx

value: Pdgfra-Tet3 KO

value: High fat diet (14 weeks)


title: Screen_untreat_1


title: ME3_control_2


title: Preadipocytes from iWAT (HFD-WT_pool) [Pooled WT-WGBS]

description: WGBS.xlsx


title: ME3_control_1


title: Screen_Input


title: wild-type mouse testis day 21

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description: 10x Genomics Chromium Single Cell Gene Expression data

library_source: transcriptomic single cell

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-6.0.1).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference (refdata-gex-mm10-2020-A) and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: cellranger generated unfiltered feature-barcode matrix file.

source_name: Single cells obtained from wild-type mouse testis

extract_protocol:
Single cells were obtained from enzymatic digestion of aging mouse ovary. Cell viability and concentration were measured by Countess II FL Automated Cell Counter (Life Technologies) targeting ≥90% cell viability. The cell emulsification is performed with the 10X Chromium Controller using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10X Genomics 1000092) and Chromium Chip B Single Cell Kit (10X Genomics 1000074).
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).

value: Testis

tag: genotype/variation

value: wild type


title: U937_ADAR1KO_PMA

value: phorbol myristate acetate treated


title: MYC_doxo_2


title: CR_control_2


title: wild-type mouse testis day 10


title: U937_ADAR1KO

value: untreated


title: MYC_doxo_1


title: MYC_control_2


title: stra8-deficient mouse testis day 21

source_name: Single cells obtained from stra8-deficient mouse testis


title: stra8-deficient mouse testis day 10


title: U937_WT_PMA


title: MYC_control_1


title: ELAC2 KO AP rep 3

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed with Trim Galore (--fastqc --paired --nextera --clip_R1 1 --clip_R2 1) using Cutadapt 1.18 and FastQC 0.11.9.
Trimmed reads were quantified with Salmon 1.5.2 using the selective alignment procedure (-l A --seqBias --qcBias --validateMappings) against the GENCODE vM27 transcriptome, with custom mitochondrial transcripts (properly merged bicistronic transcript sequences and corrected terminal sequences, and removal of mt-tRNAs).
Transcript quantifications were summarised to gene-level with tximport and analysed for differential gene expression changes with DESeq2, using the apeglm shrinkage estimator and an lfcThreshold of log2(1.5). Gene expression changes with an FSOS s-value < 0.01 were considered significant.
Normalized, strand-specific coverage profiles were generated with deepTools 3.5.0 bamCoverage (--filterRNAstrand [forward/reverse] --samFlagInclude 2 --samFlagExclude 256 --normalizeUsing CPM --exactScaling -bs 1 -of bigwig).
Assembly: mm39
Supplementary files format and content: tab-delimited txt files containing DESeq2 results and normalised counts tables
Supplementary files format and content: bigwig files containing per-sample, per-strand normalised coverage (in counts per million), sample group averages & log2 fold changes

source_name: blood

growth_protocol: Elac2 loxP/loxP (Siira et al., 2018), Ptcd1loxP/loxP (Perks et al., 2017), Mtif3 loxP/loxP (Rudler et al., 2019) and Pf4-Cre (Tiedt et al., 2007) transgenic mice have been previously described. Elac2 loxP/loxP, Ptcd1 loxP/loxP and Mtif3 loxP/loxP mice on a C57BL/6N background were crossed with Pf4-Cre mice to generate control (p/p) and megakaryocyte specific deletions of each of the three genes.  Mice were housed in standard cages (45 cm by 29 cm by 12 cm) under a 12-hour light/dark schedule (lights on 7:00 a.m. to 7:00 p.m.) in controlled environmental conditions of 22° ± 2°C and 50 + 10% relative humidity and fed a normal chow diet (Rat & Mouse Chow, Specialty Foods, Glen Forrest, Western Australia), and water was provided ad libitum.

extract_protocol:
RNA was isolated form megakaryocyte or platelet pellets using the Direct-zol RNA Microprep kit (Zymo Research) as per the manufacturer’s instructions.
Libraries were constructed from total RNA isolated from megakaryocytes, resting and activated platelets each from three control and three of each knockout mouse strains using an Illumina Stranded mRNA preparation kit and sequenced using a NovaSeq platform by the Australian Genome Research Facility (AGRF).

treatment_protocol: The platelet pellet was resuspended in 100 µl of 250 µM AYPGKF and incubated at 37°C for 15 min then centrifuged at 860 g for 5 min at room temperature to separate pellet and activated supernatant.

value: blood

value: Platelet (activated)

value: ELAC2 -/-

value: 250 µM AYPGKF


title: Screen_IFN_1

value: CRISPR library and IFNα

value: ADAR1 knockout


title: U937_WT


title: AC_doxo_1

value: Dox 500 nM


title: HEK293T_ADAR1KO_1


title: ELAC2 KO AP rep 2


title: HEK293T_ADAR1KO_2


title: AC_doxo_2


title: HEK293T_ADAR1E912A_1

value: ADAR1 RNA editing deficient


title: MTIF3 KO AP rep 3

value: MTIF3 -/-


title: MTIF3 KO AP rep 2


title: HEK293T_ADAR1E921A_2


title: AC_control_1

value: DMSO


title: Ninput_doxo_2

value: none (native input)


title: AC_control_2


title: MTIF3 KO AP rep 1


title: Ninput_doxo_1


title: HEK293T_WT_2


title: Ninput_control_2


title: PTCD1 KO AP rep 3

value: PTCD1 -/-


title: PTCD1 KO AP rep 2


title: Ninput_control_1


title: HEK293T_WT_1


title: PTCD1 KO AP rep 1


title: Xinput_doxo_2

value: none (x-linked input)


title: Xinput_doxo_1


title: WT AP rep 3

value: Wild type


title: Xinput_control_2


title: Xinput_control_1


title: ELAC2 KO AP rep 1


title: MTIF3 KO MK rep 3

value: Megakaryocyte


title: WT AP rep 1


title: WT AP rep 2


title: Sample_15-12-GC

city: Ås

first: Gabriela

last: Carril

address: Oluf Thesens vei 30

country: Norway

institute: Norwegian University of Life Sciences

description: 150 bp paired-end

data_processing:
Raw reads from RNA sequencing were trimmed using BBDuk (v34.56)
HISAT (v2.1.0) was used for genome alignment
The fragments mapped were counted with featureCounts (v1.4.6-1)
Differentially expressed genes (DEGs) between groups were estimated using SARTools (v1.7.3)
Assembly: Genome Psal-013 LF-89 (ASM970875v1 - RefSeq assembly accession: GCF_009708755.1)
Assembly: Genome Psal-182 EM-90 (ASM970941v1 - RefSeq assembly accession: GCF_009709415.1)
Supplementary files format and content: count files/txt files

organism: Piscirickettsia salmonis

growth_protocol: FN2 broth medium for culture bacteria until reach OD600nm of 0.2, then nine semi-permeable implants were inserted into the abdominal cavity of Atlantic salmon for 6 days

extract_protocol:
Total RNA was extracted from all the samples using Qiagen RNeasy Mini Kit (Qiagen) and QIAseq FastSelect −5S/16S/23S (Qiagen) was used for rRNA depletion
Library preparation and RNA-seq were performed at the Norwegian Sequencing Center (UiO, Norway)
TruSeq Stranded mRNA library prep

tag: strain

tag: culture

value: single

tag: host

value: Salmo salar

tag: time

value: Day 6


title: Sample_14-11-GC

description: 150 bp paired-end


title: MTIF3 KO MK rep 2

value: blood


title: Sample_13-10-GC

description: 150 bp paired-end


title: MTIF3 KO MK rep 1


title: aPDL1_GFPpos, KT23

city: Melbourne

first: Kevin

middle: C

last: sek

state: VIC

address: 305 Grattan Street

department: Cancer Immunology

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the mouse reference genome (mm10)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Assembly: mm10
Supplementary files format and content: count file generated by featureCounts

extract_protocol:
Total RNA extracted from cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

value: Tumor infiltrating lymphocytes

tag: sorted cell type

value: CD8+ T cells

value: GFP positive

value: aPDL1 treatment


title: aPDL1_GFPneg, KT24

value: GFP negative


title: PTCD1 KO MK rep 3


title: aPDL1_GFPneg, KT22


title: aPDL1_GFPpos, KT21


title: PTCD1 KO MK rep 1


title: aPDL1_GFPneg, KT20


title: ELAC2 KO MK rep 3

value: ELAC2 -/-


title: aPDL1_GFPpos, KT19


title: Cell line-Ctrl-rep1

type: RNA

city: Kaohsiung

first: ChiaYi

last: Hsu

state: State...

address: No. 100, Shih-Chung 1

department: Graduate Institute of Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

hyb_protocol: Fluorescent targets with Cy5 dye (GE Healthcare) were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System.

scan_protocol: The slides were scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: The signal intensity was loaded into the Rosetta Resolver System® (Rosetta Biosoftware, USA) for data preprocessing and applied to the 75th percentile for centering normalization. The errors of the sample were estimated by using the error-weighted approach simultaneously. Both the fold change and p-value for pair-wise sample comparison were calculated to evaluate differentially expressed genes (DEGs). Criteria of a fold change of ≥ 2 or ≤ - 2 and p-value < 0.05 are strongly recommended for further analysis.

extract_protocol: Total RNA was extracted using TRIzol® (Invitrogen; Thermo Fisher Scientific, Inc.)

treatment_protocol: Human epithelial ovarian cancer cell lines were treated with or without HOXD10

value: epithelial ovarian cancer

value: control


title: NonTreated_GFPneg, KT18

value: No aPDL1 treatment


title: Sample_9-6-GC

description: 150 bp paired-end


title: Sample_8-5-GC

description: 150 bp paired-end


title: Sample_7-4-GC

description: 150 bp paired-end


title: ELAC2 KO MK rep 2


title: ELAC2 KO MK rep 1


title: NonTreated_GFPpos, KT17


title: Cell line-HOXD10-rep1

value: HOXD10 overexpression


title: NonTreated_GFPneg, KT16


title: Cell line-Ctrl-rep 2


title: Cell line-HOXD10-rep2


title: S. mutans deltaSMU.1147-3

city: Busan

first: Ryoo

last: SiUk

address: busandaehakro 63-2

department: Microbiology

country: South Korea

institute: Pusan univ.

data_processing:
Raw data of RNA-seq results were mapped to reference genome (S. mutans UA159) using NCBI gene.
Data processing was carried out through e-biogen (www.e-biogen.com), an outsourcing company.

organism: Streptococcus mutans

source_name: bacteria cell

growth_protocol: Cells were grown to late-exponential phase (OD600=0.6~0.7) in brain heart infusion (BHI) medium (BD Biosciences, New Jersey, USA) at 37℃ in 5% CO2 condition.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen). 1 μg of each RNA was used to construct the cDNA library.
cDNA libraries were prepared for sequencing using a Novaseq 6000 protocol


title: WT MK rep 4


title: WT MK rep 3


title: WT MK rep 2


title: NonTreated_GFPpos, KT15


title: PTCD1 KO MK rep 2

value: PTCD1 -/-


title: NonTreated_GFPneg, KT14


title: WT MK rep 1

value: Wild type


title: S. mutans WT-3

value: wild-type


title: NonTreated_GFPpos, KT13


title: PTCD1 KO RP rep 4

value: Platelet (resting)


title: S. mutans WT-2


title: 20,000 sorted CD45+ cells, 3

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Mapped filtered reads against GRCm38 reference genome using STAR (v2.5.2b) aligner allowing for soft clipping of adapter  sequences. For quantification, we used transcript annotation files from Ensembl version 86.
Quantify gene expression levels based on genome annotation files from Ensembl version 86 using RSEM (v1.3.0) and featureCounts (v1.5.1). For quality control use FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.2.2).
Perform variance stabilizing transformation (VST) using the function varianceStabilizingTransformation (DESeq2 v1.34.0)
Assembly: GRCm38
Supplementary files format and content: counts.csv comma separated csv file containing raw counts
Supplementary files format and content: tpm.csv comma separated csv file containing tpm normalized expression values

source_name: Liver

extract_protocol:
1. Thaw the samples from -80°C freezer on ice, homogenize them by gentle pipetting and transfer them to 2mL PhaseLock tubes.  2. Add half the volume of Chloroform: Isoamyl alcohol (24:1, v:v Honeywell, Cat. No. C2432-25ml) to each lysate and shake vigorously for 15 second  3. Incubate the samples for 5 min at room temperature.  4. Centrifuge at 12, 000g for 5 min at 4°C and transfer the upper aqueous phase to a pre-chilled 1.5 mL microtubes.  5. Add 1.5 volumes of Isopropanol to each tube and mix well by pipetting.  6. Transfer the lysates to RNeasy MinElute® spin columns and extract total RNA using miRNeasy Micro Kit (Qiagen, Cat. No. 217084), with on-column DNAse treatment (Qiagen, Cat. No. 79254)  7. For the final elution step, use 14ul and 30ul of nuclease-free water to elute RNA from leukocyte and liver tissue sample respectively.
Total RNA for cDNA synthesis following SMART-seq® v4 Ultra Low Input RNA kit’s  instruction (Takara Bio, #634891)with a maximum of 10 amplification cycles. The final sequencing libraries were created with the tagmentation-based DNA Prep Kit (#20018705) and the IDT® DNA/RNA UD Indexes Set A (#20026121), both Illumina®.

value: Liver

value: Liver immune cells

value: WT


title: S. mutans WT-1


title: 20,000 sorted CD45+ cells, 2


title: 20,000 sorted CD45+ cells, 1


title: G2ABL2EC

city: Maywood

first: wei

last: Qiu

state: IL

department: Surgery

institute: Loyola University Chicago

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: excel file contains read counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: transfection

value: EtOH


title: G2ABL2EB


title: PTCD1 KO RP rep 1

value: blood


title: PTCD1 KO RP rep 2


title: splenic Treg cells, Z5

city: tianjin

first: Teng

last: Zhang

address: nanjing road

country: China

institute: Tianjin Medical University General Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchword
Assembly: mm10
Supplementary files format and content: tab-delimited text file included FPKM, TPM, read counts for each Sample

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer`s protocols.

value: spleen

value: Cecum Ligation And Puncture+ ZM241385

tag: condition

value: sepsis CLP model


title: splenic Treg cells, Z6


title: splenic Treg cells, Z4


title: S. mutans deltaSMU.1147-2


title: ELAC2 KO RP rep 5

value: ELAC2 -/-


title: 10,000 sorted CD45+ cells, 2


title: ELAC2 KO RP rep 4


title: G2ABL2EA


title: S. mutans deltaSMU.1147-1


title: splenic Treg cells, Z3


title: G2SCR_EC

value: shSCR


title: 10,000 sorted CD45+ cells, 1


title: splenic Treg cells, Z2


title: G2SCR_EB


title: 5,000 sorted CD45+ cells, 3


title: ELAC2 KO RP rep 3


title: splenic Treg cells, Z1


title: PTCD1 KO RP rep 3


title: ELAC2 KO RP rep 2


title: G2SCR_EA


title: ELAC2 KO RP rep 1


title: splenic Treg cells, N5

value: Naive

value: control


title: 5,000 sorted CD45+ cells, 2


title: G2_ABL2C

value: Control


title: 10,000 sorted CD45+ cells, 3


title: MTIF3 KO RP rep 5

value: MTIF3 -/-


title: 2,500 sorted CD45+ cells, 3


title: G2_ABL2B


title: MTIF3 KO RP rep 4


title: 2,500 sorted CD45+ cells, 2


title: MTIF3 KO RP rep 3


title: G2_ABL2A


title: splenic Treg cells, N3


title: G2_SCR_C


title: splenic Treg cells, N1


title: MTIF3 KO RP rep 2


title: 2,500 sorted CD45+ cells, 1


title: Liver bulk,2

value: Liver cells


title: splenic Treg cells, C5

value: Cecum Ligation And Puncture


title: MTIF3 KO RP rep 1

value: Platelet (resting)


title: splenic Treg cells, C4


title: H9_EOS_rep_2, H9-4_2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
H9_EOS_R1.mLb.clN.bigWig
H9_EOS_R2.mLb.clN.bigWig
H9_EOS_R1.mLb.clN_peaks.xls
H9_EOS_R2.mLb.clN_peaks.xls

data_processing:
nf-core/atacseq v1.1.0 pipeline used to process the data
FastQC v0.11.8 used for quality control
TrimGalore v0.5.0 used for trimming low quality bases + adapter sequences
BWA  BWA v0.7.17-r1188 used for read mapping
Samtools v1.9 used for sorting bam files
BEDTools v2.27.1 used for converting sorted bam files into bedgraph files
MACS2 v2.1.2 used for calling peaks
Assembly: hg38
Supplementary files format and content: bigWig, XLS files with MACS2 peaks

source_name: H9-EOS (parental line for cR-H9-EOS)

extract_protocol:
To isolate nuclei, 50.000 cells were resuspended in 50ul cold lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal C-630), the mixture was pipetted up and down 16 times and immediately centrifuged at 500g for 10min at +4C.
The pellet was used for tagmentation reaction, which was performed with 2.5ul TDE1 in 50ul total volume (FC-121-1031, Nextera DNA Library Prep Kit, Illumina). The samples were then further amplified (Nextera kit FC-121-1030) and barcoded with the corresponding indices (FC-121-1011). The final libraries were then cleaned up with 1.2x vol AMPure XP beads.

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC

tag: biological replicate

tag: day of_formative_transition

tag: culture condition


title: WT RP rep 2

value: Wild type


title: splenic Treg cells, C3

value: WT

tag: treatment


title: 5,000 sorted CD45+ cells, 1

value: Liver

value: Liver immune cells


title: Nav1 KO, snRNAseq

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

description:
Nav1
10x Genomics
snRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Brain (prefrontal cortex)

extract_protocol:
Brain tissue was obtained from aged-matched adult male Nav1 KO (n=4) and C57BL/6 (n=5) mice. The PFC was quickly dissected from the freshly extracted brain tissue and it was placed in chilled PBS with Hibernate AB Complete (HEB) medium (BrainBits LLC, Springfield, IL) at 4 0C. Freshly dissected PFC from each group were pooled in separate 50 ml conical tubes with a minimum amount of chilled Hibernate AB Complete (HEB) medium (BrainBits LLC, Springfield, IL). Then, 5 ml of chilled lysis buffer (2mM Tris-HCl, 2mM NaCl, 0.6 mM MgCl2 and 0.02% NonidetTM P40 Substitute in nuclease-free water) was added to the tubes, which were then incubated at 4 0C for 10 min. The amount of lysis buffer and the incubation time were optimized determining the amount of buffer and incubation time that produced high-quality nuclei. After adding 5 more ml of HEB medium to the tubes, the tissues were triturated with a fire-polished silanized Pasteur pipette for 10-15 passes and then strained with 30 um MACS strainer (Miltenyi Biotec Inc, Auburn CA). Nuclei were pelleted by centrifugation at 500xg centrifugation for 5 min at 4°C and were then resuspended in a chilled PBS with 1% BSA (Invitrogen AM2618, Thermo Fisher Scientific, Pittsburgh PA) wash buffer with 0.2 U/ul RNase inhibitor (#3335402001, Millipore Sigma, Darmstadt Germany). The nuclei were pelleted and resuspended twice, strained using a 30 um MACS strainer, and then centrifuged and resuspended in a chilled wash buffer. Mouse anti-NeuN antibody (MAB377, Millipore Sigma, Darmstadt Germany) was added at a 1:500 dilution, and the samples were incubated for 40 min at 4°C. Samples were then centrifuged at 400xg for 5 minutes at 4°C and the pelleted nuclei were resuspended with chilled wash buffer. Alexa 647 chicken anti-mouse antibody (A21463, Life technologies, Pittsburgh PA) was added to the preparations at a 1:500 dilution and the samples were incubated for 40 min at 4°C. After incubation, nuclei were pelleted and resuspended, and Hoechst 33342 (Invitrogen H3570, Thermo Fisher Scientific, Pittsburgh PA) was added to a final concentration of 0.25 ug/ml. Single nuclei sorting was conducted using a 6-laser BD Influx sorter (BD Biosciences, San Jose CA) with a 100-um nozzle in the Stanford Shared FACS Facility. Various control samples (unstained, Hochest33342+ or NeuN+) were examined to optimize the gating strategy. Nuclei were gated based on size, scatter properties and staining for Hoechst and NeuN. To ensure that we were able to analyze different types of cells, ~60% of the sorted nuclei were collected as NeuN+ and 40% were NeuN-. Single nuclei were sorted into collecting tubes and then visually inspected under a microscope for quality control; they were then pelleted and resuspended to produce a solution with 600 nuclei/ul in the final volume.
Single nuclei were captured in droplets with barcodes using the 10x Genomics Chromium system and cDNA libraries were produced using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10x Genomics, Pleasanton, CA) according to the manufacturer’s instructions. The samples were sequenced on the NovaSeq platform (Illumina, San Diego CA).

value: Neurons

value: Brain (prefrontal cortex)

value: Nav1 KO

tag: age

value: 6-8 weeks

value: male


title: H9_EOS_rep_2, H9-4_1

tag: cell line


title: splenic Treg cells, N2

tag: tissue

value: spleen

value: Naive

value: control


title: H9_EOS_rep_1, H9-3-A

tag: cell type


title: B6, snRNAseq

description:
B6
10x Genomics
snRNA-seq

tag: genotype

value: wild-type

tag: Sex


title: WT RP rep 1

value: blood


title: splenic Treg cells, C1

value: Cecum Ligation And Puncture

value: sepsis CLP model


title: BTBR, snRNAseq

description:
BTBR
10x Genomics
snRNA-seq

tag: strain

value: BTBR T<+> Itpr3<tf>/J


title: G2_SCR_B

value: shSCR

value: Control


title: G2_SCR_A


title: wingDisc-aH3K27ac-CnR-Rep2

city: Chapel Hill

first: Matthew

last: Niederhuber

state: NC

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

data_processing:
Adapters were trimmed using Bbmap BBDuk (v38.71)
Reads were aligned to the dm6 reference genome with Bowtie2 (v2.3.4.1) and the settings: "--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700"
Aligned reads were filtered on a custom CUT&RUN negative control exclusion list
Aligned reads were quality filtered (q > 5) with Samtools (v1.10)
Duplicate reads were filtered out with Picard (v2.2.4)
Reads were split by fragment size to keep only large fragments (150-700bp)
Coverage files were generated with deepTools (v2.4.1) and normalized to 1x genomic coverage (RPGC)
Coverage tracks were Z-normalized with a custom R script
Assembly: dm6
Supplementary files format and content: Z-normalized bigwig files from individual replicates
Library strategy: Cut & Run

organism: Drosophila melanogaster

source_name: wing

growth_protocol: Animals were raised at 25C.

extract_protocol:
20 male third larvale wandering wing discs were dissected per replicate
Libraries were prepared from the “pellet” fraction using the Takara ThruPLEX DNA-seq kit with unique dual-indexes and following the manufacturer’s specifications but with a modified amplification step (10s annealing, 68C extension)

value: wing

tag: developmental stage

value: third larval wandering

tag: antibody

value: Active Motif rabbit anti-H3K27ac #39135

value: yw


title: wingDisc-aH3K27ac-CnR-Rep1


title: F2, 70% ad lib, High Fat GP16.059

city: PORTLAND

first: Hillary

last: Le

state: OR

address: 3303 S Bond Ave

institute: Oregon Health & Science University

description:
F2, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.059

data_processing:
FastQC for quality check
Trimmomatic for trimming
STAR for alignment
DESeq2 for differential gene analysis
Assembly: CavPor3
Supplementary files format and content: GP_RNAseq_Processed_file.csv is the normalized counts following Deseq2 differential gene expression analysis

organism: Cavia porcellus

source_name: Carotid artery

extract_protocol:
At 20 weeks of age, 3 animals each from PC-C, PC-H, PR-C, PR-H, PC-C-C, PC-C-H, PR-C-C, PR-C-H were euthanized with intravenous overdose of commercial barbituate (Somnasol, 390mg/ml pentobarbital sodium). A carotid artery was rapidly cannulated in situ. The vessel was flushed with 1X PBS (Gibco) to remove blood, followed by 100uL of TRIzol Reagent (Invitrogen) to collect endothelial cell contents.
RNA was isolated using RNeasy Micro kit (Qiagen) and quality was assessed using Agilent 2100 Bioanalyzer with RNA 6000 Pico chip by the OHSU Gene Profiling Shared Resource. All samples had an RNA Integrity Number (RIN) score of above 5.0. Samples were stored at -80C until sequencing.

value: Carotid artery

value: endothelial cells


title: H9_EOS_rep_1, H9-1-A

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: cR_H9_EOS_d20X_rep_2, Z23X-2

description:
cR_H9_EOS_d20X_R1.mLb.clN.bigWig
cR_H9_EOS_d20X_R2.mLb.clN.bigWig
cR_H9_EOS_d20X_R1.mLb.clN_peaks.xls
cR_H9_EOS_d20X_R2.mLb.clN_peaks.xls

source_name: chemically reset cR-H9-EOS

value: chemically reset cR-H9-EOS

value: chemically reset hPSC after formative transition

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: F2, 70% ad lib, Control GP16.058

description:
F2, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.058


title: WT RP rep 3

value: blood

value: Platelet (resting)

value: Wild type


title: splenic Treg cells, N4

value: spleen

value: WT

value: Naive

value: control


title: KD-C57-Sp

city: shanghai

first: Qing

last: Li

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < 8000;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: spleen isolated CD8+T cells

extract_protocol:
For tumors established by i.v. injected tumor cells, lung tissues were digested by 2 mg/ml collagenase I for 30 minutes and homogenized by pressing through a 70 μm cell strainer to generate single cell suspensions. Cell suspensions of tumor tissues were subjected to a discontinuous Percoll gradient (70%/40%) by centrifugation at 2000 rpm without break at room temperature for 20 minutes. Mononuclear cells at the interface were collected and washed with PBS before further analysis.CD8+ T cells were isolated from the mononuclear cells or spleen using immunomagnetic separation beads according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard 10x genomics protocols

treatment_protocol: tumor bearing Kb-/-Db-/- mice were treated with MHC Ia+MCs or MHC Ia-MCs

value: CD8+T cells

value: B16F10 i.v and MHC Ia+ MC i.p.


title: Liver bulk,1

value: Liver

value: Liver cells


title: cR_H9_EOS_d20X_rep_2, Z23X-1


title: F2, 100% ad lib, Control GP16.055

description:
F2, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.055

value: Carotid artery

value: endothelial cells


title: small RNAs from w1118 testes

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

data_processing:
reads were trimmed by removal of the adaptor sequences, barcodes and random nucleotides.
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: table with counts for each sequenced small-RNA in all of the libraries

source_name: testis

growth_protocol: 25˚C, 12h dark/light

extract_protocol:
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)
Libraries were prepared by 3′ adaptors containing 6 random nucleotides plus a 5 nt barcode on their 5’ end and 5’ adaptors containing 4 random nucleotides at their 3’ end  followed by reverse transcription and amplification by PCR.

value: testis


title: C57-Tu

source_name: tumor infiltrated CD8+T cells

value: tumor


title: cR_H9_EOS_d20X_rep_1, W28X-2

value: chemically reset cR-H9-EOS

value: chemically reset hPSC after formative transition


title: small RNAs from CG2678[-/-] testes


title: F2, 100% ad lib, Control GP16.054

description:
F2, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.054


title: splenic Treg cells, C2

value: Cecum Ligation And Puncture

value: sepsis CLP model


title: C57-SP


title: small RNAs from rhino[G31D] testes


title: cR_H9_EOS_d20X_rep_1, W28X-1

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: KD-KD-Sp

value: spleen

value: B16F10 i.v and MHC Ia- MC i.p.


title: KD-C57-Tu


title: S2,NHS,ctrl,rep2

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

data_processing:
The PRO-seq reads were adaptor-clipped using cutadapt (Martin, 2011)and trimmed and filtered with fastx toolkit.
Reads were aligned to the Drosophila (dm6) and mouse (mm10) genomes using Bowtie 2.
Mapped reads were processed from bed files to coverage files, retaining only the 3′ end nucleotide (active sites of transcription) of each read.
Density normalized bedgraph files were adjusted by sample-specific normalization factors as described previously (Booth et al., 2018; Himanen et al., 2022).
dm6 and mm10
Supplementary files format and content: Density normalized bigwig files were adjusted by sample-specific normalization factors as described previously
Library strategy: Pro-Seq

source_name: embryo

growth_protocol: Schneider cell line (S2R+) cultured in Schneider’s Drosophila Medium (Thermo Fisher Scientific) supplemented with 10% heat inactivated fetal bovine serum (Thermo Fisher Scientific) and 1 x antibiotic-antimycotic solution (penicillin, streptomycin, Amphotericin B; Thermo Fisher Scientific) at +25°C incubator.

extract_protocol:
Chromatin from 10 million S2R+ cells was isolated with NUN buffer and fragmented with Diagenode Bioruptor using the high throughput power setting for five cycles. The solubilized chromatin was flash-frozen and stored at −80°C. Before run-on reaction, an equal amount of solubilized chromatin from untreated NIH3T3 cells was spiked into each sample, (counted to account for 1 % of the total chromatin).
Sample preparation for PRO-seq was conducted as previously described with slight modifications (Chu et al., 2018; Mahat et al., 2016a; Vihervaara et al., 2021)

treatment_protocol: Drug treatment was done for allocated timepoints (10 mins with the inhibitors at NH condition) followed by heat shock for 20 mins in 37°C waterbath.

value: embryo

tag: agent

value: DMSO

value: non-heat shock


title: F2, 100% ad lib, High Fat GP16.053

description:
F2, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.053


title: cR_H9_EOS_d20E_rep_2, Z23E_-2

description:
cR_H9_EOS_d20E_R1.mLb.clN.bigWig
cR_H9_EOS_d20E_R2.mLb.clN.bigWig
cR_H9_EOS_d20E_R1.mLb.clN_peaks.xls
cR_H9_EOS_d20E_R2.mLb.clN_peaks.xls


title: S2,NHS,CCG-1423,rep2


title: F2, 100% ad lib, Control GP16.052

description:
F2, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.052


title: small RNAs from rhino[-/-] testes


title: cR_H9_EOS_d20E_rep_1, W27E-2


title: cR_H9_EOS_d20E_rep_2, Z23E_-1


title: F2, 100% ad lib, High Fat GP16.051

description:
F2, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.051


title: F2, 100% ad lib, High Fat GP16.050

description:
F2, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.050


title: small RNAs from CG2678[-/-] ovaries

source_name: ovary

value: ovary


title: S2,HS,ctrl,rep2

value: heat shock


title: S2,HS,CCG-1423,rep2


title: small RNAs from w1118 ovaries


title: small RNAs from rhino[G31D] ovaries


title: F2, 70% ad lib, Control GP16.047

description:
F2, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.047


title: cR_H9_EOS_d20E_rep_1, W27E-1


title: S2,NHS,ctrl,rep1


title: small RNAs from rhino[-/-] ovaries


title: cR_H9_EOS_d10_rep_2, Z10A-2

description:
cR_H9_EOS_d10_R1.mLb.clN.bigWig
cR_H9_EOS_d10_R2.mLb.clN.bigWig
cR_H9_EOS_d10_R1.mLb.clN_peaks.xls
cR_H9_EOS_d10_R2.mLb.clN_peaks.xls

value: chemically reset hPSC during formative transition

value: N2B27 and 2uM XAV939


title: cR_H9_EOS_d10_rep_2, Z10A-1


title: F2, 70% ad lib, High Fat GP16.046

description:
F2, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.046

value: Carotid artery

value: endothelial cells


title: S2,HS,ctrl,rep1


title: S2,NHS,CCG-1423,rep1


title: w1118 input

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.3.0) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library for Illumina (NEB).

tag: corresponding input_sample


title: F2, 70% ad lib, High Fat GP16.043

description:
F2, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.043


title: cR_H9_EOS_d10_rep_1, W10A-2


title: w1118 Rhi-ChIP

value: anti-Rhi antibody (Rhino#1_3573gly)


title: S2,HS,CCG-1423,rep1


title: F2, 70% ad lib, Control GP16.041

description:
F2, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.041


title: cR_H9_EOS_d10_rep_1, W10A-1

value: chemically reset cR-H9-EOS


title: w1118 Kipf-ChIP


title: input

city: Atlanta

last: Armstrong

state: Georgia

address: 615 Michael St

institute: Emory University

data_processing:
Paired end reads were trimmed using Trimmomatic/0.36. Illumina adapters were removed from reads, bases with a pred score below 20 were trimmed off the end of the read, and a sliding window set at 4:15 was used to remove remaining low-quality bases.
owtie2 was used to align the paired-end reads to NCBI37v1/mm9 genome.
Samtools/1.9 was used to remove duplicate reads, sort, and index the reads mapped
5hmC peaks were called on grouped samples using the MACS2 peak calling software with 5hmC capture and non-pulldown input libraries (q <=0.05)
Differential peak analysis was performed using bdgdiff within the MACS2 peak calling software
Assembly: mm9
Supplementary files format and content: narrowPeak (except for Input sample)
Library strategy: 5hmC-Capture

source_name: cortex

extract_protocol:
Cells were lysed with 600ul of lysis buffer contaning 100mM Tris-HCl, Ph8.5, 5mM EDTA, 0.2% SDS, 200mM NaCl, and 25ul of protease K.Following lysis, RNase A was added and phenol:chloroform:isoamyl alcohol (25:24:1) was used to extract DNA. The Covaris ME220 was used to sonicate gDNA into ~200-300bp fragments. 5hmC was labeled with UDP-6-N3-Glu βGT and biotin. Invitrogen Dynabeads® MyOne™ Streptavidin C1 were used to pull down the biotin labeled 5hmC.
5hmC capture libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® manufacturers protocol

value: cortex

value: WT

value: male


title: HNES1_d10_rep_2, D10A-2

description:
HNES1_d10_R1.mLb.clN.bigWig
HNES1_d10_R2.mLb.clN.bigWig
HNES1_d10_R1.mLb.clN_peaks.xls
HNES1_d10_R2.mLb.clN_peaks.xls

source_name: embryo-derived HNES1

value: embryo-derived HNES1

value: embryo-derived naive hPSC during formative transition


title: RhinoG31D homozygous mutant input


title: biol FAD/Tet1(+/-)_3


title: HNES1_d10_rep_2, D10A-1


title: biol FAD/Tet1(+/-)_4


title: F1, 100% ad lib, High Fat GP16.034

description:
F1, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.034


title: RhinoG31D homozygous mutant Rhi-ChIP


title: HNES1_d10_rep_1, C10A-2


title: RhinoG31D homozygous mutant Kipf-ChIP


title: F1, 70% ad lib, High Fat GP16.031

description:
F1, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.031


title: F1, 100% ad lib, Control GP16.028

description:
F1, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.028


title: HNES1_d10_rep_1, C10A-1


title: RhinoG31D mutant input


title: cR_H9_EOS_d0_rep_2, Z0A-2

description:
cR_H9_EOS_d0_R1.mLb.clN.bigWig
cR_H9_EOS_d0_R2.mLb.clN.bigWig
cR_H9_EOS_d0_R1.mLb.clN_peaks.xls
cR_H9_EOS_d0_R2.mLb.clN_peaks.xls

value: chemically reset hPSC


title: biol FAD/Tet1(+/-)_2


title: F1, 100% ad lib, Control GP16.027

description:
F1, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.027


title: RhinoG31D mutant Rhi-ChIP


title: biol FAD/Tet1(+/-)_1


title: cR_H9_EOS_d0_rep_2, Z0A-1


title: F1, 70% ad lib, Control GP16.025

description:
F1, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.025


title: RhinoG31D mutant Kipf-ChIP


title: biol Tet1(+/-)_1


title: F1, 70% ad lib, High Fat GP16.023

description:
F1, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.023


title: F1, 70% ad lib, Control GP16.036

description:
F1, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.036


title: biol Tet1(+/-)_2


title: cR_H9_EOS_d0_rep_1, W0A-2


title: biol 5xFAD2


title: F1, 100% ad lib, High Fat GP16.021

description:
F1, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.021


title: cR_H9_EOS_d0_rep_1, W0A-1


title: F1, 70% ad lib, Control GP16.017

description:
F1, 70% ad lib, Control
generation, maternal diet, offspring diet
GP16.017


title: Appl deleted, replicate 2, scRNAseq

city: Frederick

first: Anthony

last: Cicalo

state: MD

address: 8400 Research Plaza

department: Neurology

institute: NMRC BDRD

description: 10 X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cellranger, version 6.0, 10x Genomics.(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Control 3  libraries were sequenced twice to get enough sequencing depth.
Assembly: Drosophila Melanogaster
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
20 male and 20 female Drosophila brain of the appropriate geneotype were dissected on ice cold Schneider’s medium. After a brief wash with PBS, the brains were incubated with 0.05% trypsin-EDTA (Fisher scientific) for 30 minutes, with continuous pipetting every 5 minutes. The dissociated tissue were filtered through a 10um cell strainer to get a single cell suspension.
10x libraries were constructed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1).

value: Brain

value: Brain cells

value: Appl[d] w[*]

value: Appl deleted


title: HNES1_d0_rep_2, D0A-2

value: embryo-derived naive hPSC


title: biol WT4


title: F1, 70% ad lib, High Fat GP16.016

description:
F1, 70% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.016


title: Appl deleted, replicate 1, scRNAseq

description: 10 X genomics


title: biol WT3


title: HNES1_d0_rep_1, C0A-2


title: Appl deleted, replicate 3, scRNAseq

description: 10 X genomics


title: Control, replicate 2, scRNAseq

description: 10 X genomics

value: Control


title: F1, 100% ad lib, High Fat GP16.011

description:
F1, 100% ad lib, High Fat
generation, maternal diet, offspring diet
GP16.011


title: HNES1_d0_rep_1, C0A-1

value: N2B27 and 2uM XAV939


title: biol 5xFAD1


title: biol WT1


title: Control, replicate 1, scRNAseq

description: 10 X genomics


title: 3 hour, crotonate, rep1

status: Public on Oct 02 2023

city: Clayton

first: Rachael

last: Turner

state: Victoria

address: Wellington Road

department: Biochemistry and Molecular Biology

institute: Monash University

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0Ahttps://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 2000 bases for mouse and 500 bases for Candida 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.
Assembly: Mm39 (Ensembl 107) and SC5314 assembly 21
Supplementary files format and content: comma-separated values files containing the mouse or candida read count for all samples

source_name: BMDMs

extract_protocol:
As described in Tucey, Verma et al Cell Metabolism 2018,doi:  10.1016/j.cmet.2018.03.019
As described in Tucey, Verma et al Cell Metabolism 2018,doi:  10.1016/j.cmet.2018.03.019

treatment_protocol: Infection of BMDMs with C. albicans (multiplicity of infection 6), and treatment with or without 10 mM crotonate

value: BMDMs

value: macrophage, bone marrow-derived

tag: time

value: 3 hour

value: infection with Candida albicans SC5314

value: crotonate


title: 3 hour, crotonate, rep2

growth_protocol: As described in Tucey, Verma et al Cell Metabolism 2018,doi:  10.1016/j.cmet.2018.03.019


title: 3 hour, crotonate, rep3


title: 3 hour, rep2

value: control


title: 3 hour, rep1


title: 1 hour, rep3

value: 1 hour


title: 1 hour, crotonate, rep3


title: Control, replicate 3, scRNAseq

description: 10 X genomics


title: F1, 100% ad lib, Control GP16.013

description:
F1, 100% ad lib, Control
generation, maternal diet, offspring diet
GP16.013

value: Carotid artery

value: endothelial cells


title: 1 hour, rep2


title: 1 hour, rep1


title: Transgenic, Barley, rep2

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

data_processing:
NGSQC toolkit used for QC.
Alignment and mapping of reads was performed using STAR (Dobin et al., 2013; https://github.com/alexdobin/STAR) and Trinity platform (genome-guided) (Bowtie2) (Hass et al., 2013; https://github.com/trinityrnaseq/trinityrnaseq).
Abundance estimation was calculated  using RSEM (RNA-Seq by Expectation-Maximization) method (Li and Dewey, 2011) and differential gene expression analysis was  performed using DESeq2 (Mi et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Assembly: MorexV3_pseudomolecules_assembly, INSDC Assembly GCA_904849725.1 (https://www.ebi.ac.uk/ena/browser/view/GCA_904849725.1)
Supplementary files format and content: tab-delimited text files having Trinity genes/transcripts
Supplementary files format and content: tab-delimited text files having COUNT matrix for each Sample
Supplementary files format and content: tab-delimited text files having TMM.EXPR matrix for each Sample

organism: Hordeum vulgare

source_name: Leaves

growth_protocol: Seeds of barley (Hordeum vulgare L.) Cv. Golden promise were germinated in a mixture of soil and soilrite (1:1) under controlled conditions in greenhouse- 18/16◦C (day/night) temperature and 16-hour photoperiod. Two-week-old plants were exposed to heat shock at 42◦C for 30 minutes and leaf samples were harvested at every time point and snap freezed in liquid nitrogen for RNA isolation.

extract_protocol:
Leaves five-week old non-transformed wild type (WT) and HvHSFA2e overexpression transgenic plants were used to extract the total RNA with RNeasy® plant mini kit (74904; Qiagen) as per the manufacturer’s instructions. During the total RNA extraction, RQ1 RNase-free DNase (M6101; Promega Corporation) was used to remove the genomic DNA. The RNA concentration was quantified by NanoDrop microvolume UV-Vis spectrophotometers (ND-ONE-W; Thermo Fisher Scientific), and total RNA (5µg) was separated on 1.2 % formaldehyde gel to determine concentration and integrity.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Transgenic lines and WT plants were grown in above-described conditions, two-week old plants were subjected to 40°C for 4hrs to assess the thermotolerance.

value: Leaves

tag: cultivar

value: Golden Promise

value: HvHSFA2e overexpression

value: Heat stress at 42 C for 30 minutes


title: Transgenic, Barley, rep1


title: Wild type, Barley, rep2

value: Wild type


title: Wild type, Barley, rep1


title: biol WT2

value: cortex

value: WT

value: male


title: Lung_fibroblasts from three mice

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

country: Japan

institute: Hamamatsu University School of Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz

source_name: Lung

extract_protocol:
Lung tissues were minced and digested with protease solution. Live cells were stained with antibodies for lineage cells (CD31, CD45, E-cadherin, LYVE-1, CD146, and TER119) and the lineage-negative cells were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Lung

value: Primary

value: Fibroblast

value: wild type

value: 12 weeks


title: 3 hour, rep3

value: BMDMs

value: macrophage, bone marrow-derived

value: 3 hour

value: infection with Candida albicans SC5314

value: control


title: C4-2_Dox_Ctrl_1

city: New Orleans

first: Yan

last: Dong

address: 1700 Tulane Ave

institute: Tulane University

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using bowtie. Gene expression was calculated by using RSEM.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: C4-2 and VCaP cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent. 2 ug of total RNA was used for the construction of sequencing libraries.
Poly-A selected unstranded RNA-seq libraries of C4-2 cells were constructed by Novogene Co, and Poly-A selected stranded RNA-seq libraries of VCaP tumors were constructed by the BGI.

treatment_protocol:
FAM3B-inducible-expressing C4-2 cells and the control cells were treated with 200 ng/ml doxycycline for 48 hours.
Control-shRNA- or FAM3B-shRNA-expressing VCaP cells were mixed with 50% matrigel and inoculated subcutaneously into male CB17 SCID mice at 6-7 weeks of age. Mice were castrated when tumors reached ~100 mm3. At the termination of the experiment, the mice were sacrificed, and tumors were collected for molecular analysis.

value: Prostate cancer cells

value: doxycycline (200 ng/ml)

value: 48 hours


title: C4-2_Dox_FAM3B_2

value: FAM3B inducible overexpression


title: C4-2_Dox_FAM3B_1


title: C4-2_Dox_Ctrl_2


title: 1 hour, crotonate, rep2

value: 1 hour

value: crotonate


title: 1 hour, crotonate, rep1


title: day 0  AS-374778-LR-45569

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

institute: German Cancer Research Center

description: day 0

data_processing:
Raw sequencing data was demultiplexed and fastq files were generated using using bcl2fastq software (Illumina, v2.20.0.422).
FASTQ files were mapped to the mouse reference genome using salmon (v0.7.2) and count matrices were constructed with tximport (v1.18.0)
Assembly: GRCm38
Supplementary files format and content: count matrices - CSV file includes raw counts for each sample
Supplementary files format and content: annotation sheets - CSV file inculding metadata for respective count matrix

source_name: cultured cells

extract_protocol:
Single cells were sorted directly into 96 well-plates containing 1 µl of lysis buffer per well, centrifuged and snap frozen in liquid nitrogen.
ScRNAseq libraries of tumour cell subpopulations and endothelial cells were constructed using a modified SMART-Seq2 protocol

value: cultured cells

value: breast cancer cells

value: day 0


title: day 0  AS-374784-LR-45569

description: day 0


title: day 0  AS-374782-LR-45569

description: day 0


title: day 0  AS-374786-LR-45569

description: day 0


title: day 0  AS-374788-LR-45569

description: day 0


title: day 0  AS-374780-LR-45569

description: day 0


title: day 0  AS-374776-LR-45569

description: day 0


title: day 0  AS-374774-LR-45569

description: day 0


title: day 0  AS-374768-LR-45569

description: day 0


title: day 0  AS-374766-LR-45569

description: day 0


title: day 0  AS-374764-LR-45569

description: day 0


title: day 0  AS-374760-LR-45569

description: day 0


title: day 0  AS-374758-LR-45569

description: day 0


title: HNES1_d0_rep_2, D0A-1

value: embryo-derived HNES1

value: embryo-derived naive hPSC

tag: biological replicate

value: N2B27 and 2uM XAV939


title: day 0  AS-374772-LR-45569

description: day 0


title: day 0  AS-374754-LR-45569

description: day 0


title: day 0  AS-374770-LR-45569

description: day 0


title: day 0  AS-374750-LR-45569

description: day 0


title: day 0  AS-374748-LR-45569

description: day 0


title: FBP1 OE MDA-MB231

first: Stefan

last: Wolfl

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

institute: Heidelberg University, Heidelberg, Germany

description:
SAMPLE 1
FBP1

hyb_protocol: standard Illumina protocol (Human-HT12-V4 Expression BeadChip)

scan_protocol: According to manufacturer with BeadArray Reader (Illumina).

data_processing: quantile normalization with all samples

source_name: MDA-MB231 cells

label_protocol: standard Illumina protocol

growth_protocol: MDA-MB231 cells were cultivated in DMEM with 10% FCS and pen/strep in the presence of 5% CO2 at 37° C .

extract_protocol: RNA extraction was done by triazole/chloroform follwoing established protocols (Sigma-Aldrich). RNA was extracted from 500.000 cells. RNA concentrations were adjusted to 100ng/µl. Quality control with Agilent 2100.

treatment_protocol: Cells were transfected with FBP1 expression vector or empty vector as control.

tag: transfection

value: FBP1 overexpression


title: day 0  AS-374746-LR-45569

description: day 0


title: day 0  AS-374742-LR-45569

description: day 0


title: day 0  AS-374756-LR-45569

description: day 0


title: day 0  AS-374752-LR-45569

description: day 0


title: day 0  AS-374740-LR-45569

description: day 0


title: day 0  AS-374744-LR-45569

description: day 0


title: day 0  AS-374738-LR-45569

description: day 0


title: day 0  AS-374734-LR-45569

description: day 0


title: day 0  AS-374728-LR-45569

description: day 0


title: day 0  AS-374732-LR-45569

description: day 0


title: day 0  AS-374736-LR-45569

description: day 0


title: cont2 empty vector MDA-MB231

description:
SAMPLE 3
control 2

value: control empty vector


title: day 0  AS-374722-LR-45569

description: day 0


title: day 0  AS-374724-LR-45569

description: day 0


title: day 0  AS-374762-LR-45569

description: day 0


title: cont1 wt MDA-MB231

description:
SAMPLE 2
control 1

value: control wt


title: day 0  AS-374720-LR-45569

description: day 0


title: day 0  AS-374716-LR-45569

description: day 0


title: day 0  AS-374726-LR-45569

description: day 0


title: day 0  AS-374714-LR-45569

description: day 0


title: day 0  AS-374712-LR-45569

description: day 0


title: day 0  AS-374718-LR-45569

description: day 0


title: day 0  AS-374708-LR-45569

description: day 0


title: day 0  AS-374700-LR-45569

description: day 0


title: day 0  AS-374702-LR-45569

description: day 0


title: day 0  AS-374706-LR-45569

description: day 0


title: day 0  AS-374698-LR-45569

description: day 0


title: day 0  AS-374704-LR-45569

description: day 0


title: day 0  AS-374696-LR-45569

description: day 0


title: day 3.5 - replicate 3 AS-374693-LR-45381

description: day 3.5 - replicate 3

source_name: lung

value: lung

value: endothelial cells

value: WT

value: 3.5 day post tumor cell injection


title: day 3.5 - replicate 3 AS-374691-LR-45381

description: day 3.5 - replicate 3


title: day 0  AS-374710-LR-45569

description: day 0


title: day 0  AS-374730-LR-45569

description: day 0


title: day 3.5 - replicate 3 AS-374683-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374685-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374689-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374687-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374679-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374681-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374675-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374677-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374671-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374669-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374667-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374663-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374661-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374665-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374659-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374655-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374657-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374651-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374647-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374645-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374641-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374649-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374643-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374639-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374637-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374633-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374631-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374629-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374627-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374623-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374625-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374615-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374673-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374617-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374619-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374621-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374611-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374605-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374613-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374603-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374653-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374607-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374609-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374599-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374601-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374597-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374635-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374589-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374591-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374593-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374595-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374583-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374579-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374581-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374577-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374587-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374585-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374575-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374573-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374569-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374571-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374567-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374565-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374563-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374561-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374555-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374547-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374553-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374557-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374545-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374549-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374551-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374543-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374539-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374537-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374535-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374531-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374541-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374529-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374533-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374525-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374515-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374517-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374521-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374523-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374511-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374509-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374513-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374519-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374507-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374503-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374505-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374559-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374501-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374491-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374499-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374497-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374493-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374489-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374483-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374485-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374481-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374479-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374527-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374487-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374473-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374477-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374469-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374467-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374471-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374457-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374463-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374461-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374459-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374455-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374453-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374495-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374449-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374447-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374445-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374441-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374437-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374475-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374423-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374427-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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title: day 3.5 - replicate 3 AS-374381-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374353-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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title: day 3.5 - replicate 3 AS-374295-LR-45381

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title: day 3.5 - replicate 3 AS-374291-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374289-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374273-LR-45381

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title: day 3.5 - replicate 3 AS-374261-LR-45381

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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374277-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374263-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374253-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374301-LR-45381

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title: day 3.5 - replicate 3 AS-374255-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374249-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374251-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374207-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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title: day 3.5 - replicate 3 AS-374201-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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title: day 3.5 - replicate 3 AS-374169-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374171-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374167-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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title: day 3.5 - replicate 3 AS-374139-LR-45381

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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374105-LR-45381

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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374027-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374023-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374031-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-374021-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-373993-LR-45381

description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


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description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-373975-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 2 AS-373922-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 3 AS-373927-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-373935-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 3 AS-373929-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 2 AS-373924-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 3 AS-373931-LR-45381

description: day 3.5 - replicate 3


title: day 3.5 - replicate 2 AS-373918-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373916-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373910-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373908-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373912-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373920-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373914-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373902-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373906-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373904-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373898-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373900-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373894-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373892-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373882-LR-45380

description: day 3.5 - replicate 2


title: day 3.5 - replicate 2 AS-373884-LR-45380

description: day 3.5 - replicate 2