title: AB/Tub larvae, 4.10 uM TPP GBT, Rep 1

description:
Library name: Sample 22
TPP_GBT_EC20_A

value: 20 Whole larvae

value: AB/Tub


title: Fetal liver, control 3

status: Public on Dec 04 2025

type: SRA

city: Corvallis

first: Daniella

last: Hasan

state: OR

address: Withycombe Hall

department: Animal and Rangeland Sciences

country: USA

institute: Oregon State University

description: Library name: Fetal_Liver_C3

library_source: transcriptomic

data_processing:
Trimmed using fastp
rRNA removal using SortMeRNA
Aligned using STAR
Quantified using Salmon
Assembly: Cavia porcellus Broad/cavPor3 (Feb 2008)
Supplementary files format and content: Fetal_and_Maternal_Liver_Data.xlsx; proceced maternal and fetal data provided on separate sheets

molecule: total RNA

organism: Cavia porcellus

source_name: Fetal liver

extract_protocol:
TRIzol-chloroform separation followed by purification with the Qiagen Rneasy Mini Kit
Libraries were prepared from high-quality RNA (RIN > 7.7) using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following the manufacturer's protocol and sequenced as 100 bp single-end reads on an Illumina NextSeq 2000.

tag: tissue

value: Fetal liver

tag: treatment

value: Vehicle


title: 180min_10mM_BR4

city: Berkeley

first: Allison

last: Gaudinier

state: CA

address: 54 Mulford Hall, Blackman Lab, University of California, Berkeley

institute: UC Berkeley

description: Library name: 180min_10mM_BR4

data_processing:
Read quality was assessed with FastQC before and after trimming and filtering reads by quality with reaper. Mapping to the reference genome (TAIR v10) was done with bowtie 2 (--time -p3 -k 10 --sensitive-local --no-unal). The alignment file was further processed with samtools to remove reads with low mapping quality or multi-aligned reads (samtools view -h -q 30 <sam file input> | grep -v "XS:i:" | samtools sort - -o <bam file output>). Annotation and read count of the aligned reads was done with ht-seq (-f sam --stranded yes --mode intersection-strict --idattr gene_id --type gene) using the GTF file matching the Arabidopsis TAIR v10 genome version.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: text file, read counts

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: roots

extract_protocol:
BrAD-seq Streptavidin bead mRNA isolation
BrAD-seq DGE

value: roots

tag: ecotype

value: 10mM KNO3

tag: batch


title: AB/Tub larvae, 4.10 uM TPP GBT, Rep 2

city: Saskatoon

first: Morgan

middle: W

last: Kirzinger

state: Saskatchewan

address: 110 Gymnasium Place

country: Canada

institute: National Research Council Canada

description:
Library name: Sample 23
TPP_GBT_EC20_B

data_processing:
raw sequence files were trimmed for adapter seqeunce/low quality sequences using cutadapt
trimmed reads were aligned to the GRCz11 reference genome using STAR (default parameters)
raw read per gene counts from STAR were formatted into a matrix and imported into DESeq2 for differential gene expression analysis and pair wise comparison - results were filtered using p-value = 0.05
corrected, normalized DEseq2 data tables were input directly into BMDexpress
Assembly: GRCz11
Supplementary files format and content: BMDExpress_TPP_ZET.tsv
Supplementary files format and content: BMDExpress_TPP_GBT.tsv

organism: Danio rerio

source_name: 20 Whole larvae

growth_protocol: For ZET assays, 6 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substance were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, where they were removed and flash frozen prior to RNA extraction.

extract_protocol:
Total RNA was extracted from each sample of 20 larvae using the Norgen BioTek Corp Total RNA Purification kit (Norgen Cat#17200, Thorold, ON, Canada) with the optional RNase-Free DNase I kit (Norgen Cat#25710, Thorold, ON, Canada).
Sequencing libraries were prepared using the Illumina Truseq Stranded mRNA kit using 1ug of total RNA.

treatment_protocol: Prior to treatment, GBT larvae were reared in nursery baskets on a recirculating system. At 72 hpf larvae were placed in 96-well plates in HEPES buffered E3 medium and 10X concentrations of test substance were added. Plates were sealed and incubated at 28 degrees C until 120 hpf, where they were removed and flash frozen prior to RNA extraction.

tag: genotype

tag: age

value: 72-120 hours post-fertilization


title: Maternal liver, control 3

description: Library name: Maternal_Liver_C3

source_name: Maternal liver

value: Maternal liver


title: 180min_1mM_BR4

description: Library name: 180min_1mM_BR4

value: 1mM KNO3


title: TCRβ CD8αα+ Ly49+ 1

city: Singapore

first: Lukasz

last: Wojciech

address: 5 Science Drive 2 Blk MD4

country: Singapore

institute: Nus

description:
Library name: TCRB CD8alphaalpha+ Ly49+ 1
TCRβ CD8αα Ly49 .txt

data_processing:
The raw reads were aligned using MiXCR
VDJtool was used to analyse TCR repertoires
Assembly: mm10
Supplementary files format and content: Tab-deliminated file include raw counts of TCR for each population
Library strategy: TCR-seq

organism: Mus musculus

source_name: small intestine

extract_protocol:
total RNA was extracted from sorted TCRβ CD8αα+ Ly49+, TCRβ+ CD8αα+ Bmp7+, TCRβ+ CD8αα+ DN IEL. using RNAeasy isolation KIT
Synthesis of TCR libraries was performed using reverse transcriptase reaction employing template-switching primers with the sequence TAAGAGACAGCAACTACTACTGCrGrGrGr

treatment_protocol: Adoptive transfer of T cell into Rag -/- lymphopenic host

value: small intestine

tag: cell line

value: IEL

tag: cell type

value: intraepithelial T lymphocyte

value: WT

value: SPF mouse


title: AB/Tub larvae, Carrier Control 0.5% TPP GBT, Rep 3

description:
Library name: Sample 21
TPP_GBT_CC20_C


title: cSCC_P2_850K

type: genomic

city: Kunming

first: Li

last: He

state: Yunnan

address: No. 295 Xichang Road

country: China

institute: First Affiliated Hospital of Kunming Medical University

hyb_protocol: DNA after bisulfite transformation was detected by using the Infinium Metallation- EPIC BeadChip Kit (illumina), and whether the CpG site was methylated was determined by genotyping results. DNA extraction, sample pretreatment and Illumina Infinium MethylationEPIC BeadChip detection were performed by Novogene Bioinformatic Technology Co., Ltd (Beijing, China).

scan_protocol: not provided

data_processing:
The data (IDAT files) were mainly analyzed using the R package “ChAMP”. The β values (range, 0-1) was used to represent the DNA methylation level, which were calculated from the intensity ratio of the methylated signals to the total (methylated and unmethylated) signals for each site. Then the methylation levels were compared between the samples of normal, AK and SCC. A CpG site with |Δβ| > 0.05 and P value < 0.05 was considered as a DMP. P value < 0.05 and the mean |Δβ| of the region > 0.05 was defined as a DMR. DMRs called from different methods (ProbeLasso, DMRcate, Bumphunter) were combined together and filtered to width shorter than 5kb. Promoters were defined as regions within TSS ± 1kb regions. DMRs overlap with promoters were defined as promoter-DMR and others overlapped with gene regions but not promoter were genebody-DMR.
The β values (range, 0-1) was used to represent the DNA methylation level, which were calculated from the intensity ratio of the methylated signals to the total (methylated and unmethylated) signals for each site.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: skin

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using a genomic DNA extraction kit (Tiangen, Beijing, China). DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen, USA) and the integrity was analyzed in a 1.3% agarose gel. The EZ DNA Metrology Kit (Zymo Research,CA, USA) was used to transform genomic DNA into bisulfite to keep the methylated cytosine unchanged and the unmethylated cytosine into uracil.

value: skin

value: cSCC


title: Normal_P5_850K

value: Normal


title: AB/Tub larvae, Carrier Control 0.5% TPP GBT, Rep 2

description:
Library name: Sample 20
TPP_GBT_CC20_B

value: 20 Whole larvae


title: Maternal liver, control 2

description: Library name: Maternal_Liver_C2


title: Maternal liver, treated 2

description: Library name: Maternal_Liver_T2

value: Dimethyl Fumarate


title: Fetal liver, control 1

description: Library name: Fetal_Liver_C1

value: Fetal liver


title: 90min_10mM_BR4

description: Library name: 90min_10mM_BR4


title: 90min_1mM_BR4

description: Library name: 90min_1mM_BR4


title: AB/Tub larvae, Carrier Control 0.5% TPP GBT, Rep 1

description:
Library name: Sample 19
TPP_GBT_CC20_A

value: AB/Tub


title: cSCC_P5_850K


title: AB/Tub larvae, 0.000227 uM TPP ZET, Rep 3

description:
Library name: Sample 18
TPP_ZET_10m4_C

value: 6-120 hours post-fertilization


title: Normal_P4_850K


title: 180min_1mM_BR3

description: Library name: 180min_1mM_BR3

value: roots


title: 90min_10mM_BR3

description: Library name: 90min_10mM_BR3

value: 10mM KNO3


title: Normal_P9_850K


title: Maternal liver, control 1

description: Library name: Maternal_Liver_C1

value: Maternal liver

value: Vehicle


title: 90min_1mM_BR3

description: Library name: 90min_1mM_BR3

value: 1mM KNO3


title: TCRβ CD8αα+ Ly49+ 3

description:
Library name: TCRB CD8alphaalpha+ Ly49+ 3
TCRβ CD8αα Ly49 .txt

value: small intestine

value: IEL


title: AK_P9_850K

value: AK


title: HP_CK_7_2,seeds,Day 7

city: Hohhot

first: yumei

last: Feng

address: No. 120, Ulanqab East Road, Saihan District

institute: Institute of Grassland Research, Chinese Academy of Agricultural Sciences

description:
Library name: Sample 17
Column name in raw_counts.txt: HP_CK_7_2

data_processing:
Raw data (raw reads) of fastq format were processed using Trimmomatic
clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity (vesion: 2.4) with paired-end
The function of the unigenes was annotated by alignment of the unigenes with the NCBI non-redundant (NR),Swiss-Prot, and so on.
use the eXpress software to calculate the expression level of Unigene (FPKM)
DEGs between different groups were identified using DESeq2 software to calculate the fold of difference, to test the significance of difference.
Hierarchical cluster analysis of DEGs was performed using R (v3.2.0)
GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution
R (v 3.2.0) was used to draw the column diagram and bubble diagram of the significant enrichment term.
Assembly: H and HP
Supplementary files format and content: processed data files were FPKM. txt for each Sample
Supplementary files format and content: processed data files were raw-counts.txt for each Sample

organism: Leymus chinensis

source_name: seeds

growth_protocol: L. chinensis seeds were sequentially disinfected in 5 % sodium hypochlorite and 75 % alcohol for 3 min, followed by rinsing quartic with sterile water.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol.
libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: The de-hulled and hulled seeds (50 seeds per sample) were soaked in sterile water for 12 h, respectively.

value: seeds

value: seeds cells

value: HP

value: sterile water

value: 7 day


title: AB/Tub larvae, 0.00227 uM TPP ZET, Rep 3

description:
Library name: Sample 15
TPP_ZET_10m3_C

value: 20 Whole larvae


title: Normal_P8_850K

value: skin

value: Normal


title: AB/Tub larvae, 0.000227 uM TPP ZET, Rep 1

description:
Library name: Sample 16
TPP_ZET_10m4_A

value: AB/Tub

value: 6-120 hours post-fertilization


title: Fetal liver, control 2

description: Library name: Fetal_Liver_C2

value: Fetal liver


title: 45min_10mM_BR3

description: Library name: 45min_10mM_BR3

value: roots

value: 10mM KNO3


title: HP_CK_7_3,seeds,Day 7

description:
Library name: Sample 18
Column name in raw_counts.txt: HP_CK_7_3


title: HP_CK_7_1,seeds,Day 7

description:
Library name: Sample 16
Column name in raw_counts.txt: HP_CK_7_1


title: AB/Tub larvae, 0.000227 uM TPP ZET, Rep 2

description:
Library name: Sample 17
TPP_ZET_10m4_B


title: 45min_1mM_BR3

description: Library name: 45min_1mM_BR3

value: 1mM KNO3


title: AK_P8_850K


title: AB/Tub larvae, 0.00227 uM TPP ZET, Rep 2

description:
Library name: Sample 14
TPP_ZET_10m3_B


title: HP_CK_2_3,seeds,Day 2

description:
Library name: Sample 15
Column name in raw_counts.txt: HP_CK_2_3

value: 2 day


title: AB/Tub larvae, 0.00227 uM TPP ZET, Rep 1

description:
Library name: Sample 13
TPP_ZET_10m3_A


title: 15min_10mM_BR3

description: Library name: 15min_10mM_BR3


title: HP_CK_2_2,seeds,Day 2

description:
Library name: Sample 14
Column name in raw_counts.txt: HP_CK_2_2


title: 15min_1mM_BR3

description: Library name: 15min_1mM_BR3


title: AK_P7_850K


title: Normal_P7_850K


title: AB/Tub larvae, 0.0227 uM TPP ZET, Rep 3

description:
Library name: Sample 12
TPP_ZET_10m2_C


title: 0min_1mM_BR3

description: Library name: 0min_1mM_BR3


title: AB/Tub larvae, 0.0227 uM TPP ZET, Rep 2

description:
Library name: Sample 11
TPP_ZET_10m2_B


title: 45min_10mM_BR4

description: Library name: 45min_10mM_BR4


title: HP_CK_0_2,seeds,Day 0

description:
Library name: Sample 11
Column name in raw_counts.txt: HP_CK_0_2

value: 0 day


title: HP_CK_0_3,seeds,Day 0

description:
Library name: Sample 12
Column name in raw_counts.txt: HP_CK_0_3


title: AB/Tub larvae, 0.0227 uM TPP ZET, Rep 1

description:
Library name: Sample 10
TPP_ZET_10m2_A


title: AK_P6_850K

value: AK


title: Normal_P6_850K


title: Normal_P3_850K


title: Normal 3,scRNAseq

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

description:
10x Genomics
N3

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (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

source_name: colon

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagents were added
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cell suspension 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: colon

value: Intestinal tissue single cell suspension

value: Tumor cells,Stromal cells,Immune cells

value: water

tag: disease state

value: normal


title: H_CK_7_3,seeds,Day 7

description:
Library name: Sample 9
Column name in raw_counts.txt: H_CK_7_3

value: seeds

value: seeds cells

value: H

value: sterile water

value: 7 day


title: 45min_1mM_BR4

description: Library name: 45min_1mM_BR4


title: 0min_1mM_BR4

description: Library name: 0min_1mM_BR4


title: AB/Tub larvae, 2.27 uM TPP ZET, Rep 3

description:
Library name: Sample 6
TPP_ZET_EC20_C

value: 20 Whole larvae

value: AB/Tub

value: 6-120 hours post-fertilization


title: H_CK_7_1,seeds,Day 7

description:
Library name: Sample 7
Column name in raw_counts.txt: H_CK_7_1


title: Normal_P2_850K

value: skin

value: Normal


title: AB/Tub larvae, 0.227 uM TPP ZET, Rep 3

description:
Library name: Sample 9
TPP_ZET_10m1_C


title: AB/Tub larvae, 2.27 uM TPP ZET, Rep 2

description:
Library name: Sample 5
TPP_ZET_EC20_B


title: 15min_10mM_BR4

description: Library name: 15min_10mM_BR4

value: roots

value: 10mM KNO3


title: AB/Tub larvae, 0.227 uM TPP ZET, Rep 2

description:
Library name: Sample 8
TPP_ZET_10m1_B


title: cSCC_P3_850K

value: cSCC


title: cSCC_P4_850K


title: AB/Tub larvae, 0.227 uM TPP ZET, Rep 1

description:
Library name: Sample 7
TPP_ZET_10m1_A


title: H_CK_2_3,seeds,Day 2

description:
Library name: Sample 6
Column name in raw_counts.txt: H_CK_2_3

value: 2 day


title: 180min_10mM_BR2

description: Library name: 180min_10mM_BR2


title: AB/Tub larvae, 2.27 uM TPP ZET, Rep 1

description:
Library name: Sample 4
TPP_ZET_EC20_A


title: HP_CK_2_1,seeds,Day 2

description:
Library name: Sample 13
Column name in raw_counts.txt: HP_CK_2_1

value: HP


title: AK_P10_850K

value: AK


title: HP_CK_0_1,seeds,Day 0

description:
Library name: Sample 10
Column name in raw_counts.txt: HP_CK_0_1

value: 0 day


title: 180min_1mM_BR2

description: Library name: 180min_1mM_BR2

value: 1mM KNO3


title: AB/Tub larvae, Carrier Control 0.5% TPP ZET, Rep 3

description:
Library name: Sample 3
TPP_ZET_CC20_C


title: 15min_1mM_BR4

description: Library name: 15min_1mM_BR4


title: H_CK_7_2,seeds,Day 7

description:
Library name: Sample 8
Column name in raw_counts.txt: H_CK_7_2

value: seeds

value: seeds cells


title: 90min_10mM_BR2

description: Library name: 90min_10mM_BR2


title: Normal_P1_850K


title: H_CK_2_1,seeds,Day 2

description:
Library name: Sample 4
Column name in raw_counts.txt: H_CK_2_1

value: H

value: sterile water


title: AB/Tub larvae, Carrier Control 0.5% TPP ZET, Rep 2

description:
Library name: Sample 2
TPP_ZET_CC20_B

value: 20 Whole larvae


title: Normal_P10_850K


title: H_CK_0_3,seeds,Day 0

description:
Library name: Sample 3
Column name in raw_counts.txt: H_CK_0_3


title: cSCC_P1_850K


title: AB/Tub larvae, Carrier Control 0.5% TPP ZET, Rep 1

description:
Library name: Sample 1
TPP_ZET_CC20_A

value: AB/Tub


title: 90min_1mM_BR2

description: Library name: 90min_1mM_BR2


title: 180min_10mM_BR3

description: Library name: 180min_10mM_BR3


title: H_CK_0_2,seeds,Day 0

description:
Library name: Sample 2
Column name in raw_counts.txt: H_CK_0_2


title: H_CK_2_2,seeds,Day 2

description:
Library name: Sample 5
Column name in raw_counts.txt: H_CK_2_2


title: Formalehyde treated, FA3

city: Kayseri

first: Saffet

last: Teber

address: Erciyes Üniversitesi Ziraat Fakültesi Köşk Mahallesi Fuat Sezgin Caddesi No:12 Melikgazi/KAYSERİ

country: Turkey

institute: Erciyes University

description: Library name: R8

data_processing:
miRDeep2 package
Assembly: GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts

organism: Gallus gallus

source_name: embryo liver

extract_protocol:
Total RNA was extracted from liver tissues utilizing an RNA extraction kit (Nu-cleogene, Istanbul, Türkiye) following with the manufacturer's instructions.
Small RNA libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) in accordance with the manufacturer's instructions.

value: embryo liver

value: Formalehyde treated


title: H_CK_0_1,seeds,Day 0

description:
Library name: Sample 1
Column name in raw_counts.txt: H_CK_0_1


title: 45min_10mM_BR2

description: Library name: 45min_10mM_BR2


title: Formalehyde treated, FA2

description: Library name: R7


title: A. castellanii infected with Δ4G APMV, time 8 h, biological rep 2 (RIBO-seq)

city: Boston

first: Amy

middle: Si-Ying

last: Lee

state: MA

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Library name: RIBO-18A

library_source: other

data_processing:
cutadapt v4.6 was used to trim read elements added during library construction (5’ GGG-rich trinucleotide, 3’ adapter sequence, and 3’-end poly-A sequence).
Trimmed reads were then aligned to A. castellanii rRNA sequences using STAR v2.7.9a
Reads not mapping to rRNA sequences were then aligned to the APMV genome (NC_014649) and A. castellanii nuclear (NW_004457733.1) and mitochondrial genomes (NC_001637.1) accounting for intron/exon gene-structure annotations
Assembly: NC_014649, NW_004457733.1, NC_001637.1
Supplementary files format and content: xlsx, TPM for each gene

molecule: other

organism: Acanthamoeba castellanii

source_name: Trophozoite

growth_protocol: Acanthamoeba castellanii str. Neff (ATCC, 30010) were maintained at 28°C in PYG (20 g L-1 peptone, 2 g L-1 yeast extract, 9 g L-1 glucose, 4 mM MgSO4, 0.4 mM CaCl, 50 µM Fe(NH4)2(SO4)2, 2.5 mM Na2HPO4, 2.5 mM KH2PO4, 4 mM sodium citrate) supplemented with 1% penicillin-streptomycin (Gibco, 15140122). Cells were subcultured at 2–3-day intervals to maintain the cells in trophozoite stage.

extract_protocol:
Cell pellets were lysed on ice using lysis buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 20 U ml-1 RQ1 DNAse (Promega, M6101), 0.1% NP-40, 100 µg mL-1 cycloheximide) and triturated through a 21-gauge needle five times.
Preparation of RIBO-seq libraries was carried out by TB-SEQ, Inc. Lysates were digested with RNase I for 45 min at room temp. Digestion was stopped with SuperaseIN and monosomes purified by size exclusion chromatography on MicroSpin S-400 HR columns (GE Healthcare). Size selection of footprints with length 25-33 nt was performed by electrophoresis on 15% TBE-urea gels. Illumina ready RIBO-seq libraries were prepared using a SMARTer smRNA-seq kit (TakaraBio). Library concentrations were measured by qubit fluorometer and their quality assessed on an Agilent 2100 bioanalyzer. RIBO-seq libraries were sequenced on an Illumina Novaseq 6000 sequencer, single read, 1x50 cycles. Preparation of matching RNA-seq libraries was carried out by TB-SEQ, Inc. Total RNA was purified from an aliquot of cell lysate and polyA mRNA prepared using a NEBNext polyA mRNA magnetic isolation module following manufacturer instructions. mRNA fragmentation was conducted for 20 min at 94°C  to generate RNA fragments of sizes similar to those of the ribosome footprints. SMARTer smRNA-seq kit (TakaraBio) was used to generate Illumina ready RNA-seq libraries. Library concentrations were measured by qubit fluorometer and their quality assessed on an Agilent 2100 bioanalyzer. RNA-seq libraries were sequenced on an Illumina Novaseq 6000 sequencer, single read, 1x50 cycles.

treatment_protocol: Lysates for in vitro translation assays were generated from infected and mock-infected Acanthamoeba castellanii. All cells were cultured in 150 cm2 flasks in complete PYG until ~90% confluency was reached. Cells were then inoculated with mutant and WT Mimivirus at MOI = 5. At 1 hpi the inoculum was removed and cells were washed three times with PYG. At 8 hpi, 10 mL of ice-cold amoeba salt solution (4 mM MgSO4, 0.4 mM CaCl, 50 µM Fe(NH4)2(SO4)2, 2.5 mM Na2HPO4, 2.5 mM KH2PO4, 4 mM sodium citrate) supplemented with 9 g L-1 of glucose and 100 µg mL-1 of cycloheximide was added to each flask. Cells were then harvested by scraping, pelleted by low-speed centrifugation, washed once in amoeba salt solution, and flash-frozen in LiNi.

tag: strain

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite

value: Δ4G APMV infection 8 h


title: 15min_10mM_BR2

description: Library name: 15min_10mM_BR2

value: roots

value: 10mM KNO3


title: ChIP-Seq for H3K27ac landscape in doxorubicin-resistant MDA-MB-231

city: Lodz

first: Magdalena

middle: Alicja

last: Strachowska

address: Pomorska 141/143

country: Poland

institute: University of Lodz

description: Library name: ACMD

library_source: genomic

data_processing:
In silico stage of the study was initiated by analyzing the results obtained by the ChIP-Seq method using the UseGalaxy platform (RRID:SCR_006281). After removing the adapters, the quality of the obtained reads was checked. Then the reads were mapped to the human hg19 genome using the Bowtie 2 tool.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: For the first five passages, the MDA-MB-231 triple-negative breast cancer line was cultured in L15 medium with supplementation of 15% FBS, penicillin-streptomycin antibiotics (sequentially 50 U/mL and 50 µg/mL) without CO2 (as recommended by the manufacturer Sigma-Aldrich). Then, over the next two weeks, the cells were adapted to DMEM medium with 10% bovine serum FBS, including the antibiotics penicillin-streptomycin (successively 50 U/mL and 50 µg/mL) and cultured in an atmosphere of 5% CO2.

extract_protocol:
The chromatin immunoprecipitation (ChIP) method was performed according to the published protocol included in the publication by Wisnik et al.. MDA-MB-231 wild-type and doxorubicin-resistant cell lines were seeded at a density of 10 million cells per 150 mm diameter dish. After 24 hours, the cells were fixed with 1% formaldehyde, and after a 10-minute incubation, the process was arrested with 125 mM glycine and cell were rinsed 3-times with cold PBS. After incubation with appropriate buffers containing PIC and PMSF inhibitors, cells were resuspended in lysis buffers. Isolated chromatin was sonicated using a Diagenode Bioruptor sonicator, followed by centrifugation for 10 min at 10,000 rpm at 4°C. Conjugated antibodies with magnetic beads were added to the prepared samples. After a 24-hour incubation at 4°C, the immunoprecipitated chromatin was rinsed in purification buffers, which was followed by an overnight desquamation process at 65°C. DNA was isolated by phenol:chloroform:isoamyl (PCI) alcohol extraction. H3K4me3 was immunoprecipitated with anti-H3K4me3 antibody (CST C42D8 - Rabbit mAb #9751, RRID:AB_2616028) and H3K27ac was immunoprecipitated with anti-H3K27ac antibody (Cell Signaling Technology Cat# 4353, RRID:AB_10545273) as previously described (doi: 10.1016/j.biopha.2023.115798).
For ChIP-Seq targeting histone modifications such as histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) the library for sequencing was prepared with MGIEasy Cell-free DNA Library Prep Set and sequenced on DNBSEQ-G400 using DNBSEQ-G400RS High-throughput Sequencing Kit from MGI at the Department of Clinical Genetics, University of Medical Sciences, Lodz, Poland.

treatment_protocol: Doxorubicin at a concentration of 1 µM was added to proliferating MDA-MB-231 cells. Cells were treated with selected anthracycline for 48 h every 4 weeks for a total number of 6 cycles in single doses, bearing in mind recovery of the cells to a normal proliferative process. Then, after 48 hours, the drug was removed from the culture, and the cells were cultured in DMEM medium without the addition of doxorubicin until the next treatment cycle.

value: doxorubicin-resistant MDA-MB-231


title: Formalehyde treated, FA1

description: Library name: R5


title: 15min_1mM_BR2

description: Library name: 15min_1mM_BR2


title: A. castellanii infected with Δ4G APMV, time 8 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-17A


title: 0min_1mM_BR2

description: Library name: 0min_1mM_BR2


title: A. castellanii infected with Δ4G APMV, time 4 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-15A

value: Δ4G APMV infection 4 h


title: Control 3, C3, non-treated

description: Library name: C4

value: Control, non-treated


title: No.2753-1-1-1-1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on MGISEQ-2000 platform in a 28+100 or 100+100 base paired-end mode.
Generated reads were input into the cellranger count pipeline (10x Genomics) for alignment to the human genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: GRCh38
Supplementary files format and content: raw_feature.h5: HDF5 format files including raw counts data for each gene and cell barcode combination

source_name: peripheral blood

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits User Guide.

value: peripheral blood

value: COVID-19 non-ventilator weaning group

value: Neutrophil


title: No.2708-1-1-1

value: COVID-19 ventilator weaning group


title: A. castellanii infected with Δ4G APMV, time 4 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-16A


title: Control 2, C2, non-treated

description: Library name: C2


title: 180min_10mM_BR1

description: Library name: 180min_10mM_BR1


title: A. castellanii infected with Δ4E APMV, time 8 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-14C

value: Δ4E APMV infection 8 h


title: ChIP Pld6 KO, P21, input

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: Library name: ChIP_Sc_Pld6-KO_input

data_processing:
The adapter and low-quality sequences were removed by Trim_Galore!. The trimmed sequences were mapped onto the mm10 reference genome by Hisat2, and duplicated read pairs were discared using samtools.
Assembly: mm10
Supplementary files format and content: bigwig files for mapping intensity

source_name: spermatocytes

extract_protocol:
Chromatin was prepared by MNase treatment. Chromatin immunoprecipitation was conducted against anti-H3K9me3 antibody (MABI0308, Monoclonal Research Institute) or anti-H3K4me3 antibody (07-473, Merck) for 2 hours at 4 °C.
ChIP-seq libraries were made by NEBNext Ultra DNA Library Prep Kit for Illumina.

treatment_protocol: EPCAM-positive spermatogonia were purified by FACS from testes of mice at postnatal day 7, and leptoten and zygoten stages of spermatogonia were purified by FACS from testes of mice at postnatal day 21.

value: spermatocytes

value: Pld6 KO

value: FACS-purified from testes at P21


title: No.2706-1-1-1-1


title: A. castellanii infected with Δ4E APMV, time 8 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-13A


title: 180min_1mM_BR1

description: Library name: 180min_1mM_BR1

value: 1mM KNO3


title: Control 1, C1, non-treated

description: Library name: C1

value: embryo liver


title: No.2765-1-1-1


title: 45min_1mM_BR2

description: Library name: 45min_1mM_BR2


title: 90min_10mM_BR1

description: Library name: 90min_10mM_BR1


title: No.2646-3-1-3-1, HTO-derived cDNA

description: Hashtag-derived oligonucleotide (HTO)

data_processing:
Sequencing was performed on MGISEQ-2000 platform in a 100+100 base paired-end mode.
Generated reads were input into the cellranger count pipeline (10x Genomics) for alignment to the human genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: GRCh38
Supplementary files format and content: 2646-3-1-1-1_raw_feature.h5: HDF5 format files including raw counts data for each gene (or feature) and cell barcode combination
Supplementary files format and content: feature_reference.csv: comma-delimited text file including feature-name, ID of Totalseq (BioLegend) and sequence of each hashtag
Supplementary files format and content: Hashtag-condition.xlsx: microsoft Excel file including condition information for each hashtag

molecule: protein

value: Healthy


title: ChIP-Seq for H3K4me3 landscape in doxorubicin-resistant MDA-MB-231

description: Library name: MEMD


title: ChIP Pld6 KO, P21, H3K9me3 (MABI0308)

description: Library name: ChIP_Sc_Pld6-KO_K9


title: No.3116-1-2-2


title: No.2646-3-1-1-1, mRNA-derived cDNA

description: poly A RNA


title: 90min_1mM_BR1

description: Library name: 90min_1mM_BR1


title: ChIP Pld6 KO, P21, H3K4me3 (07-473)

description: Library name: ChIP_Sc_Pld6-KO_K4


title: A. castellanii infected with Δ4E APMV, time 4 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-12A

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite

value: Δ4E APMV infection 4 h


title: A. castellanii infected with Δ4E APMV, time 4 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-11A


title: A. castellanii infected with Δ4A APMV, time 8 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-10A

value: Δ4A APMV infection 8 h


title: 45min_10mM_BR1

description: Library name: 45min_10mM_BR1

value: roots

value: 10mM KNO3


title: WT Late biol rep 4

city: Los Angeles

first: Sean

middle: P

last: Curran

address: University of Southern California

institute: University of Southern California

description:
Library name: Sample 7
Column name in gene_count: WTL_L4_4

data_processing:
Prepared by Novogene
Prepared by Novogene
Prepared by Novogene
Prepared by Novogene
Prepared by Novogene
Assembly: Prepared by Novogene
Supplementary files format and content: xls that includes the raw counts for each sample
Supplementary files format and content: xls that includes the fpkm values for each sample

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were synchronized overnight as L1s and then dropped on NGM+streptomycin plates with 25x OP50 until L4 and then collected.

extract_protocol:
Worms were then homogenized and had their RNA extracted using the Zymo Direct-zol RNA Miniprep Kit (Cat. #R2052)
Prepared by Novogene

value: whole animal

value: 50+ generations of late selection


title: WT Late biol rep 3

description:
Library name: Sample 6
Column name in gene_count: WTL_L4_3


title: A. castellanii infected with Δ4A APMV, time 8 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-9A


title: ChIP Dnmt3 KO, P21, input

description: Library name: ChIP_Sc_Dnmt3l-KO_input

value: Dnmt3l KO


title: WT Late biol rep 2

description:
Library name: Sample 5
Column name in gene_count: WTL_L4_2


title: ChIP Dnmt3l KO, P21, H3K9me3 (MABI0308)

description: Library name: ChIP_Sc_Dnmt3l-KO_K9


title: WT Late biol rep 1

description:
Library name: Sample 4
Column name in gene_count: WTL_L4_1


title: 15min_10mM_BR1

description: Library name: 15min_10mM_BR1


title: 15min_1mM_BR1

description: Library name: 15min_1mM_BR1


title: ChIP wild-type, P21, input

description: Library name: ChIP_Sc_WT_input

value: wild-type


title: WT biol rep 3

description:
Library name: Sample 3
Column name in gene_count: WT_L4_3

value: no selection


title: A. castellanii infected with Δ4A APMV, time 4 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-7A

value: Δ4A APMV infection 4 h


title: A. castellanii infected with WT APMV, time 8 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-6A

value: WT APMV infection 8 h


title: 0min_1mM_BR1

description: Library name: 0min_1mM_BR1


title: WT biol rep 2

description:
Library name: Sample 2
Column name in gene_count: WT_L4_2


title: ChIP wild-type, P21, H3K9me3 (MABI0308)

description: Library name: ChIP_Sc_WT_K9

value: spermatocytes

value: FACS-purified from testes at P21


title: AD_After_Drought

city: York

first: Isaac

middle: Joel

last: Reynolds

state: North Yorkshire

address: Department of Biology, University of York

department: Department of Biology

country: United Kingdom

institute: University of York (York)

description:
Library name: AD
after_CX in processed files

data_processing:
After sequencing, quality control was carried out using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw reads were then filtered by trimming low quality sequences (average Phred score < 20), trimming short length reads (<20bp) and clipping Illumina adapters. 8 bp from the 5’ end of each read was trimmed to avoid sequencing/ methylation biases. FastQC was also run post-trimming to verify adapter and poor-quality sequence removal.
Bismark was used to map reads to the Triticum aestivum reference genome assembly v1.0  (IWGSC RefSeq v1.0; GCA_900519105.1) using the standard Bismark workflow for Illumina samples. Alignment (bowtie2) was run at mostly default settings (parameters: ‘--score_min L,0,-0.4’) with slightly relaxed penalties to account for differences between the landraces and Chinese Spring.
Bismark (coverage2cytosine script) was used to produce the processed files from the .cov output. Coverage threshold was set at 3 reads.
Assembly: IWGSC V1.0 genome assembly (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies)
Supplementary files format and content: Processed data is provided in the genome-wide cytosine methylation format. This uses the headers <chromosome>  <position>  <strand>  <count methylated>  <count unmethylated>  <C-context> <trinucleotide context>.
Supplementary files format and content: Processed files are provided separately by cytosine context (CG, CHG, CHH).

organism: Triticum aestivum

source_name: Leaves

growth_protocol: Seeds fo the 14 wheat landraces were sown in Levington Advance Seed & Modular F2S compost mixed with Aggregate Industries Garside Sands 16/30 sand (80:20 ratio). The pots were treated with CaLypso insecticide (Bayer CropScience Ltd., 0.083ml mixed with 100ml water, applied to each litre of compost) and grown under long day (16/8h, 20°C/14°C) glasshouse conditions.

extract_protocol:
Each DNA extraction consisted in 6cm of leaf tissue. BD tissue was collected upon the wheat seedlings reaching GS13 whilst the AD tissue was collected at the end of the drought period (13 days after GS13, 10 days draught stress+3 days recovery). Tissue was collected individually for each sample, and immediately immersed in liquid nitrogen to prevent nucleic acid degradation. Tissue samples were stored at -80°c for later processing. Genomic DNA was extracted from <100 mg of individual leaf tissue samples using the the Wizard HMW DNA Extraction Kit (Promega, WI, USA) according to the manufacturer’s protocol, including an RNAse treatment. DNA was initially measured using NanoDrop ND-1000 Spectrophotometer (Thermo-Fisher Scientific, MA, USA) and a Qubit 4 Fluorometer (Life Technologies, CA, USA) whilst the quality was assessed by running 2 μl of sample on an Agilent Technology Tapestation (Agilent Technologies, CA, USA) and only keeping samples with DIN>7. Replicates (4 plants) were pooled into 1 sample per landrace per treatment at equimolar proportions. Each pool was pooled again (7 landraces) per treatment in equimolar proportiopns.
The library was constructed as thus: After the addition of lambda DNA negative control, DNA samples were fragmented into 200-400bp using Covaris S220. DNA fragments were repaired, dA tailed, and ligated to sequencing adaptors with all methylated cytosines. DNA fragments were bisulfite treated with the EZ DNA Methylation Gold Kit (Zymo Research). After the treatment, Cytosines without methylation changed to U (after PCR amplification to T), while Cytosines with methylation remained unchanged. The library was then subject to size selection and PCR amplification.

treatment_protocol: Four plants of each accession were watered normally to maintain soil moisture, until they reached GS13 (Zadok’s growth scale) whereby stress was applied by withholding water for a ten-day period. Normal watering then resumed for three-days to serve as a recovery period. The negative control consisted in four replicates of each accession growing at the same time but not being exposed to drought stress. Plants were harvested 13 days after GS13.

value: Leaves

value: Pool contains DNA from 7 landraces after drought (YoGI_007=CIMMYT collection accession identifier BW 19498; YoGI_021=CIMMYT collection accession identifier CWI 6075; YoGI_026=CIMMYT collection accession identifier CWI 6118; YoGI_047=CIMMYT collection accession identifier CWI 13432; YoGI_059=CIMMYT collection accession identifier CWI 15005; YoGI_145=Watkins collection accession identifier 1190224; YoGI_261=Watkins collection accession identifier 1190705)

value: drought


title: A. castellanii infected with WT APMV, time 4 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-4A

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite

value: WT APMV infection 4 h


title: WT biol rep 1

description:
Library name: Sample 1
Column name in gene_count: WT_L4_1


title: ChIP wild-type, P21, H3K4me3 (07-473)

description: Library name: ChIP_Sc_WT_K4


title: scRNA-seq-MGA271

city: Cincinnati

first: Richard

last: Lu

state: Ohio

institute: CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER

description:
Library name: S3
10x Genomics

data_processing:
Single-cell RNA sequencing (scRNA-seq) raw data were aligned to the human reference genome (GRCh38). The raw count matrix and BAM files were generated using Cell Ranger v9.0. Nuclear fraction scores were computed using the nuclear_fraction_annotation function in the DropletQC package, and cells with low nuclear fraction values were excluded. The raw count matrix was subsequently converted into a Seurat object using the Seurat v5.0 package. High-quality cells were defined as those expressing more than 500 and fewer than 7,500 genes, containing more than 3,000 unique molecular identifiers (UMIs), and exhibiting a mitochondrial transcript ratio below 15%. Data normalization was performed using the NormalizeData function, followed by principal component analysis (PCA) on the scaled expression matrix of the top 2,000 variable features identified by the FindVariableFeatures function. Batch effects were corrected using the Harmony package. Cell clustering and Uniform Manifold Approximation and Projection (UMAP) were performed using the top 25 Harmony components.
Assembly: hg38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: pbmc

extract_protocol:
Single-cell RNA sequencing was performed using the sorted CAR-T cells and control T cells (GFP⁺) cells on day 12 of culture. After sorting, dead cells were removed using a Dead Cell Removal kit (Miltenyi Biotec, #130-090-101). The cells were then resuspended using PBS with 0.04% BSA.
The scRNA-Seq assay was performed according to the manufacturer’s instructions (Chromium GEM-X Single Cell 3' Reagent Kits v4 (Dual Index), 10x Genomics). Briefly cells were resuspended in the reverse transcription master mix and loaded together with partitioning oil and gel beads into the chip to generate a gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every GEM was reverse transcribed into cDNA, adding an Illumina TruSeq R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The cell barcoded molecules were then cleaned up with Silane DynaBeads and amplified using 11 PCR cycles.  Next, full-length, barcoded cDNA was enzymatically fragmented, sized-selected, adapter-ligated, and amplified for library construction. During the library construction, P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added. Samples were pooled and run on the NovaSeq X Plus sequencer using one lane of the 10B flow cell using the following sequencing parameters: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.

value: pbmc

value: T cell


title: scRNA-seq-Hu8H9

description:
Library name: S4
10x Genomics


title: MDA-MB-468-olaparib-rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
Library name: MB468_olaparib_rep2_S17_R1_001.fastq.gz
MDA-MB-468-olaparib-rep2

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using tophat.
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig - Browser Tracks showing normalized count for visualization on IGV or UCSC geneome browser

source_name: Breast

growth_protocol: T-47D were maintained in RPMI media (Sigma-Aldrich, R8758) supplemented with 2 mM Glutamax, 10% fetal bovine serum (FBS; Sigma-Aldrich, F0926) and 1% penicillin/streptomycin (P/S). MDA-MB-468 cells were maintained in alpha-MEM (Sigma-Aldrich, M8042) supplemented with 10% FBS, 0.1 mM HEPES, 1% non-essential amino acids, 2 mM glutamine, 1% sodium pyruvate, 1 mg/mL insulin, 1 ng/mL hydrocortisone, 12.5 ng/mL epidermal growth factor and 1% P/S.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions.
The NEBNext Ultra II Directional RNA Library Prep (NEB, E7765L) in conjunction with Poly(A) mRNA Magnetic Isolation Module kit (NEB, E7490L) was then used to prepare libraries according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with DMSO or Olaparib 20 micromolar for 6 hours.

value: Breast

value: epithelial breast cancer

value: wt

value: Olaparib


title: Mock-infected A. castellanii, time 0, biological rep 2 (RIBO-seq)

description: Library name: RIBO-2A

value: Mock-infection


title: ChIP Pld6 KO, P7, H3K9me3 (MABI0308)

description: Library name: ChIP_Sg_Pld6-KO_K9

source_name: spermatogonia

value: spermatogonia

value: Pld6 KO

value: FACS-purified from testes at P7


title: ChIP Pld6 KO, P7, H3K4me3 (07-473)

description: Library name: ChIP_Sg_Pld6-KO_K4


title: 45min_1mM_BR1

description: Library name: 45min_1mM_BR1

value: roots

value: 1mM KNO3


title: MDA-MB-468-olaparib-rep1

description:
Library name: MB468_olaparib_rep1_S14_R1_001.fastq.gz
MDA-MB-468-olaparib-rep1


title: A. castellanii infected with WT APMV, time 4 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-3A


title: MDA-MB-468-ctrl-rep2

description:
Library name: MB468_ctrl_rep2_S16_R1_001.fastq.gz
MDA-MB-468-ctrl-rep2

value: Control


title: ChIP Dnmt3l KO, P21, H3K4me3 (07-473)

description: Library name: ChIP_Sc_Dnmt3l-KO_K4

value: spermatocytes

value: Dnmt3l KO

value: FACS-purified from testes at P21


title: Mock-infected A. castellanii, time 0, biological rep 1 (RIBO-seq)

description: Library name: RIBO-1A

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite


title: ChIP Dnmt3 KO, P7, input

description: Library name: ChIP_Sg_Dnmt3l-KO_input


title: A. castellanii infected with Δ4G APMV, time 8 h, biological rep 2 (RNA-seq)

description: Library name: RNA-18A

value: Δ4G APMV infection 8 h


title: ChIP Dnmt3l KO, P7, H3K9me3 (MABI0308)

description: Library name: ChIP_Sg_Dnmt3l-KO_K9


title: A. castellanii infected with Δ4A APMV, time 4 h, biological rep 2 (RIBO-seq)

description: Library name: RIBO-8A

value: Δ4A APMV infection 4 h


title: T-47D-olaparib-rep2

description:
Library name: T47D_olaparib_rep2_S5_R1_001.fastq.gz
T-47D-olaparib-rep2

value: Breast

value: epithelial breast cancer


title: BD_Before_Drought

description:
Library name: BD
before_CX in processed files

value: Leaves

value: Pool contains DNA from 7 landraces before drought (YoGI_007=CIMMYT collection accession identifier BW 19498; YoGI_021=CIMMYT collection accession identifier CWI 6075; YoGI_026=CIMMYT collection accession identifier CWI 6118; YoGI_047=CIMMYT collection accession identifier CWI 13432; YoGI_059=CIMMYT collection accession identifier CWI 15005; YoGI_145=Watkins collection accession identifier 1190224; YoGI_261=Watkins collection accession identifier 1190705)


title: iPSCs, UPF1 knockdown, rep3

city: Chicago

first: Evangelos

last: Kiskinis

state: IL

address: 303 E. Superior Street

department: Neurology

institute: Northwestern University Feinberg School of Medicine

description: Library name: IPS_UPF3

data_processing:
Raw reads were trimmed using cutadapt (v3.4) to remove Illumina universal adapter sequences (-a AGATCGGAAGAGC), trailing N bases (--trim-n), and bases with Phred score < 10 (-q 10,10), as well as any reads that were too short after trimming (-m 25). Trimmed reads were aligned to Gencode V38 (GRCh38.p13) using STAR (v.2.7.5a). The following flags were used during alignment: --twopassMode Basic, --outSAMstrandField intronMotif, --outFilterIntronMotifs RemoveNoncanonical, --alignEndsType EndToEnd, as well as the “ENCODE options” flags provided by the STAR manual. Gene-level counts were quantified using featureCounts (v2.0.1).
Assembly: hg38 (GRCh38.p13, Gencode V38 gene annotations)
Supplementary files format and content: tab-delimited text file includes gene-level counts for each sample

source_name: Induced Pluripotent Stem Cells

extract_protocol:
Cells were harversted in 1mL TRIzol Reagent (Thermo Fisher Scientific) per 1-3 million cells. Samples were added with chloroform (0.2mL), mixed and centrifuged at 4°C for 15 minutes at 12,000xg after 3 minutes of resting at room temperature. The aqueous phase containing the RNA was transferred to a new tube and 5μg of RNase-free Glycogen (Thermo Fisher Scientific) have been added. 0.5mL of isopropanol was added to the aqueous phase, the solution was incubated for 25 minutes at room temperature and centrifuged for 10 minutes at 15,000xg at 4°C.
Samples were sent to Novogene for strand-specific polyA-purified library preparation and 150bp paired-end (PE150) sequencing

value: Induced Pluripotent Stem Cells


title: ChIP Dnmt3l KO, P7, H3K4me3 (07-473)

description: Library name: ChIP_Sg_Dnmt3l-KO_K4

value: spermatogonia


title: ChIP Pld6 KO, P7, input

description: Library name: ChIP_Sg_Pld6-KO_input

value: Pld6 KO

value: FACS-purified from testes at P7


title: ChIP wild-type, P7, input

description: Library name: ChIP_Sg_WT_input

value: wild-type


title: A. castellanii infected with Δ4G APMV, time 8 h, biological rep 1 (RNA-seq)

description: Library name: RNA-17A


title: iPSCs, UPF1 knockdown, rep2

description: Library name: IPS_UPF2


title: T-47D-ctrl-rep2

description:
Library name: T47D_ctrl_rep2_S4_R1_001.fastq.gz
T-47D-ctrl-rep2

value: wt

value: Control


title: A. castellanii infected with Δ4G APMV, time 4 h, biological rep 2 (RNA-seq)

description: Library name: RNA-16A

value: Δ4G APMV infection 4 h


title: scRNA-seq-376

description:
Library name: S2
10x Genomics

value: pbmc

value: T cell


title: ChIP wild-type, P7, H3K4me3 (07-473)

description: Library name: ChIP_Sg_WT_K4


title: iPSCs, scramble siRNA, rep3

description: Library name: IPS_SCR3

value: Scr


title: T-47D-ctrl-rep1

description:
Library name: T47D_ctrl_rep1_S1_R1_001.fastq.gz
T-47D-ctrl-rep1


title: iPSCs, scramble siRNA, rep2

description: Library name: IPS_SCR2


title: A. castellanii infected with WT APMV, time 8 h, biological rep 1 (RIBO-seq)

description: Library name: RIBO-5A

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite

value: WT APMV infection 8 h


title: iPSCs, UPF1 knockdown, rep1

description: Library name: IPS_UPF1


title: A. castellanii infected with Δ4G APMV, time 4 h, biological rep 1 (RNA-seq)

description: Library name: RNA-15A


title: WGBS Pld6-/- KO

description: Library name: sg_P7_Epcam_Pld6_KO_DNAme

data_processing:
The adapter and low-quality sequences were removed by Trim_Galore!. The trimmed sequences were mapped onto the mm10 reference genome using bismark. After de-duplication, methylation states were called for individual cytosines at CpG.
Assembly: mm10
Supplementary files format and content: tab separated file containing chromosome, position, methylation ratio (%), methylated calls, and unmethylated called.

extract_protocol:
DNA was extracted by phenol-chloroform extractio.
Genomic DNA was fragmented by sonication on Bioruptor for 15 cycles of high output for 30 seconds, then purified by Agencourt AMPure XP. After the bisulfite treatment as described previously (Ichiyanagi et al. 2011), the sequencing library was made using ACCEL-NGS methyl-seq library Kit (Swift Biosciences).

treatment_protocol: EPCAM-positive spermatogonia were purified by FACS from testes of mice at postnatal day 7.


title: scRNA-seq-Control T

description:
Library name: S1
10x Genomics


title: iPSCs, scramble siRNA, rep1

description: Library name: IPS_SCR1


title: A. castellanii infected with Δ4E APMV, time 8 h, biological rep 1 (RNA-seq)

description: Library name: RNA-13A

value: Δ4E APMV infection 8 h


title: miR137_3

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

description: Library name: miR137_3

data_processing:
Paired-end reads of poly(A) RNA-seq from control and cells harboring overexpression of miR-137 were aligned to human genome assembly version (GRCh38/hg38) using TopHat2 version 2.1.0 with default parameter in three replicates from independent experiments.
Differential expression gene analysis was carried out by Cuffdiff, FDR<0.05 was considered as significant changes of genes.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

source_name: brain

growth_protocol: The human neuroblastoma cell lines BE(2)-M17 were cultured in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (HyClone).

extract_protocol:
RNA was isolated from BE(2)-M17 cells harboring overexpression of miR-137 using TRIzol following manufacturer’s instructions (Invitrogen). An Agilent 2100 Bioanalyzer was used to determine the quality of RNA. Ribosomal RNA depletion was carried out with Ribo-zero rRNA Removal Kit (Illumina Inc., San Diego, CA).
Libraries were sequenced on an Illumina HiSeq platform (Admera Health, LLC, South Plainfield, NJ, USA) with a read length configuration of 150 PE for 80M total reads per sample (40M in each direction).

treatment_protocol: Cells were transfected with 100 pmol of a negative control siRNA or hsa-miR-137 mimics, using Lipofectamine 2000 (Invitrogen) following manufacturer’s instructions.

value: brain

value: neuroblast

value: has-miR-137 mimic treated


title: MDA-MB-468-ctrl-rep1

description:
Library name: MB468_ctrl_rep1_S13_R1_001.fastq.gz
MDA-MB-468-ctrl-rep1

value: Breast

value: epithelial breast cancer


title: miR137_2

description: Library name: miR137_2


title: A. castellanii infected with Δ4E APMV, time 8 h, biological rep 2 (RNA-seq)

description: Library name: RNA-14C


title: WGBS Pld6+/+ wild-type

description: Library name: sg_P7_Epcam_Pld6_WT_DNAme

value: spermatogonia

value: Pld6 WT

value: FACS-purified from testes at P7


title: T-47D-olaparib-rep1

description:
Library name: T47D_olaparib_rep1_S2_R1_001.fastq.gz
T-47D-olaparib-rep1

value: wt

value: Olaparib


title: A. castellanii infected with Δ4E APMV, time 4 h, biological rep 2 (RNA-seq)

description: Library name: RNA-12A

value: Δ4E APMV infection 4 h


title: miR137_1

description: Library name: miR137_1


title: Intestine, diet restriction, 20 weeks, rep4

city: Vienna

first: Christian

last: Schoefer

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description: Library name: Intestine_w20dr_rep4

data_processing:
Raw reads were trimmed using trimmomatic.
Then aligned to the killifish reference genome (Nfu_20140520) using STAR
Gene expression was quantified by counting uniquely aligned reads in exons using the featureCounts package in R.
Gene annotations were based on Ensembl release 108
Assembly: Nfu_20140520
Supplementary files format and content: csv file of read counts.

organism: Nothobranchius furzeri

source_name: Whole Intestine

growth_protocol: N. furzeri (strain GRZ) were kept under a 12 hour dark-light cycle at 28oC. Animals were fed a diet of nauplia larvae for newborns and Chironomus larvae for older stages and received ad libitum quantities.

extract_protocol:
Total RNA from snap-frozen tissues was extracted in TRI-Reagent (Sigma) using TissueLyser LT (Qiagen). Phase separation was performed in Phasemaker™ Tubes (Invitrogen) and RNA purification, including a DNase I digestion step, was accomplished using the ReliaPrep™ RNA Tissue Miniprep System (Promega). Enrichment of mRNA was performed via oligo dT-based mRNA isolation by using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB); libraries were prepared from 1 µg of isolated total RNA.
Libraries for RNASeq were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB) in combination with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set1) (NEB) according to the manufacturer’s instructions. Purification steps were performed using Beckman Coulter™ AMPure XP beads. Library quality was assessed using the 4200 TapeStation system (Agilent).

treatment_protocol: Intermittent fasting regimen: ad-libitum feeding interrupted by fasting every other day.

value: Whole Intestine

value: WT

value: diet restriction


title: A. castellanii infected with Δ4E APMV, time 4 h, biological rep 1 (RNA-seq)

description: Library name: RNA-11A

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite


title: Hu8H9-2

description: Library name: A10

data_processing:
RNA-seq reads in FASTQ format were subjected to quality control to determine the need for adapter trimming and removal of low-quality sequences using FastQC (v0.11.7), Trim Galore! (v0.4.2), and Cutadapt (v1.9.1). Trimmed reads were aligned to the human reference genome (hg38) using STAR (v2.6.1e). Duplicate reads were removed using Sambamba (v0.6.8). Gene-level expression was quantified by counting aligned reads corresponding to gene features defined in the NCBI RefSeq database, using featureCounts (v1.6.2) from the Rsubread package. Raw counts were normalized as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM  values for each Sample

extract_protocol:
Total RNA was extracted from sorted CAR-T cells and control T cells (GFP⁺), as well as untransduced T cells, on day 12 of culture using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit

value: pbmc

value: T cell


title: Hu8H9-1

description: Library name: A9


title: A. castellanii infected with Δ4A APMV, time 8 h, biological rep 2 (RNA-seq)

description: Library name: RNA-10A

value: Δ4A APMV infection 8 h


title: ChIP wild-type, P7, H3K9me3 (MABI0308)

description: Library name: ChIP_Sg_WT_K9

value: wild-type


title: Con-137_1

description: Library name: Con-137_1

value: brain

value: neuroblast

value: wildtype control


title: MGA271-2

description: Library name: A8


title: A. castellanii infected with Δ4A APMV, time 8 h, biological rep 1 (RNA-seq)

description: Library name: RNA-9A


title: Intestine, diet restriction, 20 weeks, rep3

description: Library name: Intestine_w20dr_rep3


title: RNA_GATA2_3

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

data_processing:
The analysis of RNA-seq data was performed using the nf-core/rnaseq (10.5281/zenodo.1400710) pipeline version 3.14.0.This pipeline performs quality control (QC) producing an extensive report, trimming, alignment and produces a gene expression matrix.FastQC/MultiQC was used to perform QC checking of sequencing data. After that, reads were aligned to the hg38 reference genome using STAR (23104886). Gene expression was quantified with rsem (21816040).After that, differentially expressed genes (DEGs) were identified from gene expression matrix generated by the pipeline using DESeq2 (25516281) R package (https://bioconductor.org/packages/DESeq2/) version 1.36.0. DEGs were considered as significant when the adjusted p-value was below 0.05 and the absolute of log2 fold change value was bigger than 0.5, and were used for the downstream analyis.
Assembly: hg38
Supplementary files format and content: Matrix of gene-level raw counts across all samples in tab separated format

source_name: Cord blood hematopoietic stem cells

growth_protocol: Cells were cultured on SFM StemPro-34 + 1%P/S + 1%Glu supplemented with early hematopoietic cytokines (100 ng/ml SCF , 100ng/ml FLT3L, 20ng/ml IL-3,  20ng/ml IL-6, 100ng/ml TPO

extract_protocol:
RNA was extracted using RNAqueous™-Micro Total RNA Isolation Kit
TBA

value: Cord blood hematopoietic stem cells


title: Con-137_2

description: Library name: Con-137_2


title: Con-137_3

description: Library name: Con-137_3


title: Intestine, diet restriction, 20 weeks, rep1

description: Library name: Intestine_w20dr_rep1


title: A. castellanii infected with Δ4A APMV, time 4 h, biological rep 1 (RNA-seq)

description: Library name: RNA-7A

value: Δ4A APMV infection 4 h


title: A. castellanii infected with Δ4A APMV, time 4 h, biological rep 2 (RNA-seq)

description: Library name: RNA-8A


title: Intestine, no diet, 20 weeks, rep4

description: Library name: Intestine_w20c_rep4


title: Intestine, no diet, 20 weeks, rep3

description: Library name: Intestine_w20c_rep3


title: Intestine, diet restriction, 20 weeks, rep2

description: Library name: Intestine_w20dr_rep2


title: MGA271-1

description: Library name: A7


title: 376-1

description: Library name: A5


title: A. castellanii infected with WT APMV, time 8 h, biological rep 2 (RNA-seq)

description: Library name: RNA-6A

value: WT APMV infection 8 h


title: Control T-2

description: Library name: A4


title: A. castellanii infected with WT APMV, time 8 h, biological rep 1 (RNA-seq)

description: Library name: RNA-5A


title: Control T-1

description: Library name: A3


title: Intestine, no diet, 20 weeks, rep2

description: Library name: Intestine_w20c_rep2


title: RNA_CTRL_2


title: Intestine, no diet, 20 weeks, rep1

description: Library name: Intestine_w20c_rep1


title: A. castellanii infected with WT APMV, time 4 h, biological rep 2 (RNA-seq)

description: Library name: RNA-4A

value: WT APMV infection 4 h


title: RNA_CTRL_1


title: A. castellanii infected with WT APMV, time 4 h, biological rep 1 (RNA-seq)

description: Library name: RNA-3A


title: Intestine, no diet, 10 weeks, rep4

description: Library name: Intestine_w10_rep4


title: 376-2

description: Library name: A6


title: Untransduced T-1

description: Library name: A1


title: Intestine, no diet, 10 weeks, rep2

description: Library name: Intestine_w10_rep2


title: RNA_GATA2_2


title: Mock-infected A. castellanii, time 0, biological rep 1 (RNA-seq)

description: Library name: RNA-1A

value: Mock-infection


title: mRNA Pld6-/- KO, biological replicate 4

description: Library name: sg_P7_Epcam_Pld6_KO4

data_processing:
The adapter and low-quality sequences were removed by Trim_Galore!. The trimmed sequences were mapped onto (1) the mm10 reference genome and (2) consensus sequences of mouse-specific retrotransposons. Reads that were mapped onto antisense strand of the retrotransposon consensus sequences were counted (because the reads are antisense to mRNA), and normalized by total reads that were mapped to the mouse genome.
Assembly: mm10
Supplementary files format and content: commaseparated file containing repName and RPM (reads per million genome-mapped reads)

extract_protocol:
RNA was extracted by isogen and DirectZol RNA kit.
polyA(+) RNAs were purified using NEBNext Poly(A) mRNA Magnetic Isolation Module, and mRNA-seq libralies were made using NEBNext Ultra II Directional mRNA library prep kit for illumina.

value: spermatogonia

value: Pld6 KO

value: FACS-purified from testes at P7


title: Intestine, no diet, 10 weeks, rep3

description: Library name: Intestine_w10_rep3

value: Whole Intestine

value: WT


title: eHAP iCas9, IR Day15, Replicate 1

city: Boulder

first: Nausica

last: Arnoult

state: CO

address: 1945 Colorado ave

department: MCDB

institute: University of Colorado Boulder

description:
Library name: IR_day15_rep1
Corresponds to IR_day15_rep1 column in combined count file
IR_day15_rep1_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv
IR_grna1_coupled_counts.tsv

data_processing:
Reads were trimmed to guide and barcode sequences with BBDuk v38.05 by trimming off surrounding context sequences. Those sequences were then mapped using HISAT2 v2.1.0 to the guide library to identify guide and barcode pairs. Python scripts (Python v3.6.3) were used to match reads from mapped files. In all cases where the guide1 sequence matched the barcode1 sequence (yielding coupled sequences), the barcodes were translated to guide pairs and all guide pairs were counted within each biological replicate.
Assembly: hg38
Supplementary files format and content: Individual replicate count files are tab-delimited text files containing the guide pair and the raw (non-normalized) number of observances
Supplementary files format and content: Combined replicate count files are tab-delimited text files containing the guide pair and a column for each sample that lists the raw number of observances in each sample. Irradiated cell data is separated into its own combined count file, and these irradiated day14 replicates (rep1 and rep2) correspond to the day0 rep1 and rep2 in the basal screen file.

source_name: eHAP iCas9-cl#6

growth_protocol: eHAP cells were fed Iscove's Modified Dulbecco's Medium (IMDM, brand) supplemented with 10% FCS, MEM non-essential amino acids, and penicillin/streptomycin and grown in 3% CO2 and 12% O2. 1 Billion eHAP iCas9-cl#6 cells were transduced with the DDRDKO library at an MOI of 0.15. and selected with Puromycin (1µg/mL) 500 million selected cells were seeded at 10 million per 15cm plates with 1µg/mL Doxycycline to induce Cas9 expression and in Blasticidin (1µg/mL) to maintain expression from the inducible-Cas9-integration locus. Cells were split every 3 days to prevent confluence. While passaging, all cells from each sample were collected and pooled to maintain library coverage. After 7 days, doxycycline was no longer supplemented and cells were passaged for another 7 days until collection. This comprised 12 PD for cells under standard growth conditions and 10 PD for irradiated conditions.

extract_protocol:
Genomic DNA was extracted from 500M cells per condition using a Quiagen Blood Maxi kit, per manufactururs protocol.
Extracted genomic DNA was used as template for a primary PCR amplification of the guide-harboring locus. This  amplicon was purified by gel extraction, concentrated, and used for a secondary PCR with illumina indexes unique to each sample.

treatment_protocol: Cells were either allowed to grow under standard growth conditions described above or were exposed to an LD20 dose of ionizing radiation 24 hours after each split (0.6 Gy, Faxitron Xray Cabinet). This allowed cells time to re-attach before irradiating. In the radiation samples, cells were split every three days, with the treatment occuring 24 hours after each split. These cells were grown for 15 days instead of the untreated cells' 14 and represented 10PD.

value: eHAP iCas9-cl#6

value: p53 null

value: 0.6Gy X-ray radiation

tag: time

value: Day 15


title: eHAP iCas9, IR Day15, Replicate 2

description:
Library name: IR_day15_rep2
Corresponds to IR_day15_rep2 column in combined count file
IR_day15_rep2_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv
IR_grna1_coupled_counts.tsv


title: mRNA Pld6-/- KO, biological replicate 3

description: Library name: sg_P7_Epcam_Pld6_KO3


title: RNA_GATA2_1


title: RDv16_uter

city: Minneapolis

first: David

last: Masopust

address: 2101 6th St. SE

institute: University of Minnesota

data_processing:
RNA sequencing (50-bp single-end) with the HiSeq 2500 Illumina was done at the University of Minnesota Genomics Center (UMGC). The sequences were processed with the Collection of Hierarchical UMII-RIS Pipelines (CHURP, v 0.2.2) developed by the Research Informatics Solutions (RIS) group at the Minnesota Supercomputing Institute. The reference implementation of the CHURP package is at: https://github.com/msi-ris/CHURP.git 64. For whole tissue cell lysates, 2x 50bp FastQ paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. For CM9-specific CD8 T cells, 2 x 50bp FastQ paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30 and headcrop 3. Quality control on raw sequence data for all samples was performed with FastQC.
Read mapping was performed via Hisat2 (v2.1.0) using the Macaca mulata genome (Mmul_10) as reference.
Assembly: Mmul_10
Supplementary files format and content: csv files contain raw read counts for each sample

organism: Macaca mulatta

source_name: uterus

extract_protocol:
For bulk RNA sequencing experiments, reproductive tract tissue was isolated directly into RNAlater (Qiagen). Tissue was homogenized in Trizol (Sigma-Aldrich) using a Tissuemiser homogenizer (Fisher Scientific), and RNA was extracted using a RNeasy mini kit as per the manufacturer’s instructions (QIAGEN). RNA integrity was assessed using capillary electrophoresis with the Agilent 2100 BioAnalyzer system (Agilent Technologies).
Sequencing libraries for CM9-specific CD8 T cells were prepared using the Clontech SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit. Libraries for whole tissue cell extracts were prepared using the TruSeq stranded mRNA library prep kit (Illumina).

value: uterus

value: all

tag: Sex

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: eHAP iCas9, Control Day14, Replicate 2

description:
Library name: day14_rep2
Corresponds to day14_rep2 column in combined count file
day14_rep2_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv

value: Day 14


title: Intestine, no diet, 10 weeks, rep1

description: Library name: Intestine_w10_rep1


title: mRNA Pld6-/- KO, biological replicate 2

description: Library name: sg_P7_Epcam_Pld6_KO2


title: RDv16_endo

source_name: endocervix

value: endocervix


title: eHAP iCas9, Control Day0, Replicate 2

description:
Library name: day0_rep2
Corresponds to day0_rep2 column in combined count file
day0_rep2_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv

value: Day 0


title: mRNA Pld6-/- KO, biological replicate 1

description: Library name: sg_P7_Epcam_Pld6_KO1

value: spermatogonia


title: BL_Med12KO_M_3

city: Fort Collins

first: Michelle

middle: M

last: Halstead

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

description: Library name: GNCO1434-Mutant-2991-E5

data_processing:
Raw reads were trimmed with Trim_Galore (v0.6.7) and aligned to the GRCm39 assembly with STAR (v2.7.10b). Low quality alignments (q < 5) were removed with SAMtools (v1.16) and raw counts for genes in the Ensembl (v108) annotation were calculated with HTSeq (v2.0.2) in mode “intersection-nonempty”.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw gene counts for each sample

source_name: Blastocyst

growth_protocol: For blastocyst (E3.5) collection, female mice older than 6 weeks were synchronized by 5 IU PMSG for 48 h, then injected with 5 IU hCG and mated with wild-type stud males of proven fertility. Uteri were collected from euthanized females 4 days post hCG and transferred to 1X DPBS supplemented with 0.1% BSA. Individual blastocysts were flushed from oviducts, washed to remove debris, and stored in 1X Lysis Buffer (Takara Bio) supplemented with RNase Inhibitor (Takara Bio).

extract_protocol:
Individual blastocysts were lysed and stored in lysis buffer at -80°C prior to library preparation. Each blastocyst was stored in 1X Lysis Buffer (Takara Bio) supplemented with RNase Inhibitor (Takara Bio): per embryo, 0.95 uL 10X Lysis Buffer, 10.5 uL nuclease-free water, 0.05 uL RNase Inhibitor.
For blastocysts, libraries were constructed from individual embryos with the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio).

value: Blastocyst

value: Maternal Med12 knockout

tag: developmental stage

tag: embryo sex

value: Male


title: BL_Med12KO_M_2

description: Library name: GNCO1434-Mutant-2991-E4

tag: tissue


title: mRNA Pld6-/- KO, biological replicate 5

description: Library name: sg_P7_Epcam_Pld6_KO5

value: Pld6 KO

tag: treatment

value: FACS-purified from testes at P7


title: RDv16_ecto

source_name: ectocervix

value: ectocervix


title: mRNA Pld6+/- heterozygous, biological replicate 3

description: Library name: sg_P7_Epcam_Pld6_het3


title: Untransduced T-2

description: Library name: A2

value: pbmc

value: T cell


title: mRNA Pld6+/- heterozygous, biological replicate 2

description: Library name: sg_P7_Epcam_Pld6_het2


title: RBc15_vag

source_name: vagina

value: vagina

value: no intravaginal challenge


title: BL_Med12KO_F_3

description: Library name: GNCO1434-Mutant-2991-E3

value: Female


title: BL_Med12KO_M_1

description: Library name: GNCO1434-Mutant-2991-E2


title: Mock-infected A. castellanii, time 0, biological rep 2 (RNA-seq)

description: Library name: RNA-2A

data_processing:
cutadapt v4.6 was used to trim read elements added during library construction (5’ GGG-rich trinucleotide, 3’ adapter sequence, and 3’-end poly-A sequence).
Trimmed reads were then aligned to A. castellanii rRNA sequences using STAR v2.7.9a
Reads not mapping to rRNA sequences were then aligned to the APMV genome (NC_014649) and A. castellanii nuclear (NW_004457733.1) and mitochondrial genomes (NC_001637.1) accounting for intron/exon gene-structure annotations
Assembly: NC_014649, NW_004457733.1, NC_001637.1
Supplementary files format and content: xlsx, TPM for each gene

source_name: Trophozoite

extract_protocol:
Cell pellets were lysed on ice using lysis buffer (20 mM Tris-HCl pH 7.4, 100 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 20 U ml-1 RQ1 DNAse (Promega, M6101), 0.1% NP-40, 100 µg mL-1 cycloheximide) and triturated through a 21-gauge needle five times.
Preparation of RIBO-seq libraries was carried out by TB-SEQ, Inc. Lysates were digested with RNase I for 45 min at room temp. Digestion was stopped with SuperaseIN and monosomes purified by size exclusion chromatography on MicroSpin S-400 HR columns (GE Healthcare). Size selection of footprints with length 25-33 nt was performed by electrophoresis on 15% TBE-urea gels. Illumina ready RIBO-seq libraries were prepared using a SMARTer smRNA-seq kit (TakaraBio). Library concentrations were measured by qubit fluorometer and their quality assessed on an Agilent 2100 bioanalyzer. RIBO-seq libraries were sequenced on an Illumina Novaseq 6000 sequencer, single read, 1x50 cycles. Preparation of matching RNA-seq libraries was carried out by TB-SEQ, Inc. Total RNA was purified from an aliquot of cell lysate and polyA mRNA prepared using a NEBNext polyA mRNA magnetic isolation module following manufacturer instructions. mRNA fragmentation was conducted for 20 min at 94°C  to generate RNA fragments of sizes similar to those of the ribosome footprints. SMARTer smRNA-seq kit (TakaraBio) was used to generate Illumina ready RNA-seq libraries. Library concentrations were measured by qubit fluorometer and their quality assessed on an Agilent 2100 bioanalyzer. RNA-seq libraries were sequenced on an Illumina Novaseq 6000 sequencer, single read, 1x50 cycles.

value: Acanthamoeba castellanii Str. Neff

value: Trophozoite

value: Mock-infection


title: eHAP iCas9, Control Day0, Replicate 1

description:
Library name: day0_rep1
Corresponds to day0_rep1 column in combined count file
day0_rep1_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv

value: eHAP iCas9-cl#6

value: p53 null


title: BL_Med12KO_F_4

description: Library name: GNCO1434-Mutant-712-E3


title: mRNA Pld6+/- heterozygous, biological replicate 1

description: Library name: sg_P7_Epcam_Pld6_het1

value: spermatogonia


title: BL_Med12KO_M_4

description: Library name: GNCO1434-Mutant-712-E2

value: Blastocyst


title: RBc15_endo

value: endocervix

value: all

value: female

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag


title: BL_Med12KO_F_1

description: Library name: GNCO1434-Mutant-2984-E1

value: Maternal Med12 knockout


title: BL_Med12KO_F_2

description: Library name: GNCO1434-Mutant-2991-E1


title: mRNA Pld6+/+ wild-type, biological replicate 3

description: Library name: sg_P7_Epcam_Pld6_WT3

value: Pld6 WT

value: FACS-purified from testes at P7


title: RBc15_ecto

value: ectocervix


title: mRNA Pld6+/+ wild-type, biological replicate 1

description: Library name: sg_P7_Epcam_Pld6_WT1


title: BL_WT_M_2

description: Library name: GNCO1434-Control-2989-E4

value: WT

value: Male


title: eHAP iCas9, Control Day14, Replicate 1

description:
Library name: day14_rep1
Corresponds to day14_rep1 column in combined count file
day14_rep1_grna1_coupled_counts.tsv
fullbasal_grna1_coupled_counts.tsv

value: Day 14


title: mRNA Dnmt3l-/- KO, biological replicate 3

description: Library name: sg_P7_Epcam_Dnmt3l_KO3

value: Dnmt3l KO


title: Sample-10 Day-7 sam-RNA

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

description: Library name: p22167-s050_RZm19-D7

data_processing:
Sequencing data was aligned to Mmul10 Ensembl release 100 using STAR 2.7.3a. Transcript abundance estimates were calculated using the STAR '--quantMode GeneCounts'.
Assembly: Mmul10 Ensembl release 100
Supplementary files format and content: Tab separated reads-per-gene table from STAR --quantMode, with Gene Symbols in first column and counts for Unstranded, Sense stranded and Anti-sense stranded interpretations of the alignments. Library prep was Unstranded

source_name: Bood

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific).
RNA quality was assessed using a TapeStation 4200 (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific). Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer's instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000

value: Bood

value: sam-RNA

value: Day 7


title: BL_WT_F_2

description: Library name: GNCO1434-Control-2989-E3

value: Female


title: Sample-9 Day-7 sam-RNA

description: Library name: p22167-s049_RPm19-D7


title: mRNA Dnmt3l-/- KO, biological replicate 2

description: Library name: sg_P7_Epcam_Dnmt3l_KO2

value: spermatogonia


title: BL_WT_M_1

description: Library name: GNCO1434-Control-2989-E2

value: Blastocyst


title: mRNA Dnmt3l-/- KO, biological replicate 1

description: Library name: sg_P7_Epcam_Dnmt3l_KO1


title: BL_WT_F_1

description: Library name: GNCO1434-Control-2989-E1


title: mRNA Dnmt3l+/- heterozygous, biological replicate 3

description: Library name: sg_P7_Epcam_Dnmt3l_het3


title: RBc15_uter

value: uterus

value: all

value: no intravaginal challenge


title: Sample-7 Day-7 sam-RNA

description: Library name: p22167-s047_RFg19-D7


title: mRNA Pld6+/+ wild-type, biological replicate 2

description: Library name: sg_P7_Epcam_Pld6_WT2


title: S15_KMS28_BM_D1_C

type: RNA

city: Salamanca

first: Ignacio

middle: J

last: Cardona-Benavides

address: Campus Miguel Unamuno

department: Hematology

institute: Centro de Investigación del Cáncer

description: Gene expression data from KMS28-BM (bone marrow) cell line

hyb_protocol: Hybridization  was performed on Thermo Fisher's Clariom S Human Array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Thermo Fisher (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Raw data were quantile normalized, background corrected and log2 transformed with the Robust Multi-array Average (RMA) algorithm using the oligo package (v.1.60) in R (v4.3.2).  BrainArray custom CDF files (version 25 Ensembl) at  gene level were used as reference.

label: biotin

source_name: KMS28-BM, CCND1 overexpression, replicate C

label_protocol: As per manufacturer's instructions (Thermo Fisher)

growth_protocol: KMS28-BM and KMS28-PE multiple myeloma cell lines were cultured in RPMI 1640 medium supplemented with 10-20% fetal bovine serum (FBS), while HEK293T cells were grown in 10% FBS-DMEM medium. Both media were supplemented with Penicillin/Streptomycin (Gibco Life Technologies).

extract_protocol: RNA extraction was performed using the AllPrep DNA/RNA Mini Kit (Qiagen).

treatment_protocol: Gene overexpression of cyclin D1 and cyclin D2 was achieved using plasmids designed by VectorBuilder™: pLV-EGFP-MSCV>hCCND1 [NM_053056.3] and pLV-EGFP-MSCV>hCCND2 [NM_001759.4], respectively.

value: CCND1 overexpression


title: Sample-6 Day-7 sam-RNA

description: Library name: p22167-s046_RAt19-D7


title: Old_comb sncRNA transfection, replicate 4

city: Salt Lake City

first: Qi

last: Chen

state: Utah

institute: university of utah

description: Library name: Old_4F

data_processing:
The data sequencing analyses were performed on the clean reads after data filtration. The mRNA library preparation, quality examination and RNA-seq processes were performed by Novogene.
RNA sequences were annotated using kallisto with Ensembl mouse cDNA annotation information (GRCm38)
Assembly: mm39 (for mouse)
Supplementary files format and content: tsv file include TPM values for each sample

source_name: V6.5 Mouse embronic stem cell

growth_protocol: V6.5 mESC were maintained in Knockout DMEM supplemented with 15% FBS), 2 mM GlutaMAX, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µM non-essential amino acids, 55 µM β-mercaptoethanol and 1,000 U/mL LIF.

extract_protocol:
For RNA-seq experiment, total RNA were extracted by Trizol (Invtrogen) and followed by Zymo RNA clean and concentrator-5 kit process to clean and concentrate.
For mRNA seq, the libraries were constructed by NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA Isolation kit following manufacture's protocols.

treatment_protocol: mESc were tranfected with vector or 200nM sncRNA mixture by Lipostem reagents.

value: V6.5 Mouse embronic stem cell

value: 200nM old_comb sncRNA mixture tranfection

value: 24 hours


title: S16_KMS28_BM_D2_A

source_name: KMS28-BM, CCND2 overexpression, replicate A

value: CCND2 overexpression


title: Sample-5 Day-7 LNP-RNA

description: Library name: p22167-s045_ROj19-D7

value: Male

value: LNP-RNA


title: Old_comb sncRNA transfection, replicate 3

description: Library name: Old_3F


title: S18_KMS28_BM_D2_C

source_name: KMS28-BM, CCND2 overexpression, replicate C


title: S17_KMS28_BM_D2_B

source_name: KMS28-BM, CCND2 overexpression, replicate B


title: S13_KMS28_BM_D1_A

source_name: KMS28-BM, CCND1 overexpression, replicate A


title: mRNA Dnmt3l+/- heterozygous, biological replicate 1

description: Library name: sg_P7_Epcam_Dnmt3l_het1

source_name: spermatogonia

value: FACS-purified from testes at P7


title: S14_KMS28_BM_D1_B

source_name: KMS28-BM, CCND1 overexpression, replicate B


title: Sample-8 Day-7 sam-RNA

description: Library name: p22167-s048_RKf19-D7

value: Bood


title: mRNA Dnmt3l+/+ wild-type, biological replicate 2

description: Library name: sg_P7_Epcam_Dnmt3l_WT2

value: Dnmt3l WT


title: Old_comb sncRNA transfection, replicate 2

description: Library name: Old_2F


title: Sample-4 Day-7 LNP-RNA

description: Library name: p22167-s044_RKn19-D7

value: Day 7


title: Old_comb sncRNA transfection, replicate 1

description: Library name: Old_1F


title: Sample-3 Day-7 LNP-RNA

description: Library name: p22167-s043_RKd19-D7


title: S11_KMS28_BM_CTRL_B

source_name: KMS28-BM, Control, replicate B

value: Control


title: mRNA Dnmt3l+/+ wild-type, biological replicate 1

description: Library name: sg_P7_Epcam_Dnmt3l_WT1

value: spermatogonia


title: mRNA Dnmt3l+/- heterozygous, biological replicate 2

description: Library name: sg_P7_Epcam_Dnmt3l_het2


title: Young_comb sncRNA transfection, replicate 4

description: Library name: Young_4F

value: 200nM young_comb sncRNA mixture transfection


title: S12_KMS28_BM_CTRL_C

source_name: KMS28-BM, Control, replicate C


title: Young (2 month old) C57BL/6 lung fibroblasts and epithelium

city: San Francisco

first: Nancy

last: Allen

address: 513 Parnassus Ave.

department: Medicine

institute: UCSF

description: Library name: Young_Sample

data_processing:
Data was processed with Cell Ranger.
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Lung

extract_protocol:
After euthanasia and cardiac perfusion with PBS, mouse lungs were tracheally insufflated with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lungs were incubated in digestion cocktail for 1 hour at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cell suspensions were blocked with mouse FcR blocking reagent (Miltenyl Biotec 130-092-575) for 15 minutes and then incubated with the appropriate fluorescently-conjugated antibodies in sorting buffer for 30 min at 4C. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and DRAQ7, respectively. The following antibodies were used for staining: anti-CD45 PE-Cy7, anti-CD31 PerCP, and anti-Epcam BV421. FACS was performed on a BD FACS Aria using FACSDiva Software.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

value: Lung

value: Fibroblasts and epithelium

value: Homeostasis


title: Sample-2 Day-7 LNP-RNA

description: Library name: p22167-s042_RKr19-D7


title: Aged (22 month old) C57BL/6 lung fibroblasts and epithelium

description: Library name: Aged_Sample


title: Sample-1 Day-7 LNP-RNA

description: Library name: p22167-s041_RCl19-D7


title: Sample-10 Day-4 sam-RNA

description: Library name: p22167-s040_RZm19-D4

value: sam-RNA

value: Day 4


title: Young_comb sncRNA transfection, replicate 3

description: Library name: Young_3F

value: V6.5 Mouse embronic stem cell


title: Young_comb sncRNA transfection, replicate 2

description: Library name: Young_2F

value: 200nM young_comb sncRNA mixture tranfection

value: 24 hours


title: S9_KMS28_PE_D2_C

description: Gene expression data from KMS28-PE (pleural exudade) cell line

source_name: KMS28-PE, CCND2 overexpression, replicate C

value: CCND2 overexpression


title: Sample-9 Day-4 sam-RNA

description: Library name: p22167-s039_RPm19-D4

value: Male


title: Young_comb sncRNA transfection, replicate 1

description: Library name: Young_1F


title: PDGFRA+ lung fibroblasts from Dermo1-cre/+;Tnfaip3f/f mouse 6622

description: Library name: 6622-D1cA20

data_processing:
For scRNA sequencing data was processed using Cell Ranger. For bulk RNA sequencing reads were aligned using HISAT and assembled with Stringtie software to the reference genome Mus musculus, UCSC version mm10
Assembly: mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual. For bulk RNA sequencing data raw counts per gene are listed per sample in comma-separated values (.csv) format.

extract_protocol:
Prior to sacrifice animals were anesthetized and injected retro-orbitally with 3ug of fluorescently labeled anti-mouse CD45 (clone 30-F11, BD563890) in 150 uL PBS. After 3 minutes of antibody circulation mice were euthanized with isofluorane. After cardiac perfusion with PBS, mouse lungs were tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was incubated in digestion cocktail for 1 hour at 37C with continuous shaking. The mixture was then washed with FACS buffer (2% FBS and 1% Penicillin-Streptomycin in DMEM) and passed through a 70 μm cell strainer. Cells were pelleted at 550xg for 5 minutes and then resuspended in red blood cell (RBC) lysis buffer for 2 minutes. After RBC lysis cells were passed through a 40 μm cell strainer. Cell suspensions were blocked with mouse FcR blocking reagent (Miltenyl Biotec 130-092-575) for 15 minutes and then incubated with the appropriate fluorescently-conjugated antibodies in sorting buffer for 30 min at 4C. After washing with FACS buffer cells were sorted. Doublets and dead cells were excluded based on forward and side scatter and DRAQ7 (CST #7406), respectively. The following antibodies were used for staining: anti-CD45 UVC (BD 564279), anti-CD31 BV711(BD 740680), anti-Epcam BV711 (Biolegend 118233), anti-Pdgfra APC (Fisher Scientific 50-112-9423). FACS was performed on a BD FACS Aria using FACSDiva Software.
For scRNA sequencing cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument.

value: Fibroblast


title: S6_KMS28_PE_D1_C

source_name: KMS28-PE, CCND1 overexpression, replicate C

value: CCND1 overexpression


title: Sample-8 Day-4 sam-RNA

description: Library name: p22167-s038_RKf19-D4

value: Bood


title: S7_KMS28_PE_D2_A

source_name: KMS28-PE, CCND2 overexpression, replicate A


title: S10_KMS28_BM_CTRL_A

source_name: KMS28-BM, Control, replicate A


title: Vector transfection, replicate 4

description: Library name: Cont_4F

value: Tranfection reagents treatment


title: Vector transfection, replicate 3

description: Library name: Cont_3F


title: Sample-7 Day-4 sam-RNA

description: Library name: p22167-s037_RFg19-D4


title: PDGFRA+ lung fibroblasts from Dermo1-cre/+;Tnfaip3f/f mouse 6492

description: Library name: 6492-D1cA20


title: S8_KMS28_PE_D2_B

source_name: KMS28-PE, CCND2 overexpression, replicate B


title: Sample-6 Day-4 sam-RNA

description: Library name: p22167-s036_RAt19-D4

source_name: Bood


title: S5_KMS28_PE_D1_B

source_name: KMS28-PE, CCND1 overexpression, replicate B


title: PDGFRA+ lung fibroblasts from Tnfaip3f/f mouse 6624

description: Library name: 6624-A20ctrl


title: Vector transfection, replicate 2

description: Library name: Cont_2F

source_name: V6.5 Mouse embronic stem cell


title: Δkmt6a, ChIP-seq input

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v.0.6.7 (parameters -- quality: 20, phread33, stringency: 1)
Trimmed sequence reads were mapped to Fusarium oxysporum f. sp. lycopersici (Fol) using Novoalign V3.09.00 (parameters -k -c 20)
For RNA-seq: Reads were counted per feature using Rsubread’s featureCounts v.1.6.0
For RNA-seq: Read counts were normalized by the “Median by-Ratio Normalization (MRN)” method from EBSeq
For ChIP-seq: Reads were normalized using bamCoverage deeptools v.3.5.1 (parameters --normalizeUsing RPGC --effectiveGenomeSize 56213053 --binSize 10 --extendReads 150 --smoothLength 150 –centerReads)
For ChIP-seq: Means of all replicates were calculated and combined to one output file by using WiggleTools 1.2.11
For ChIP-seq: Peaks from each mean file were called by using Homer v.4.11 (parameters -style histone -region -size 500 -minDist 1000 -C 0)
Assembly: UvA_Fol4287 (GCA_001703175.2)
Supplementary files format and content: An excel file includes a matrix of raw read count values for every sample (RNAseq_raw_counts.xls)
Supplementary files format and content: Peak file format from Homer contains all identified peaks for every genotype

organism: Fusarium oxysporum f. sp. lycopersici

source_name: Δkmt6a, ChIP-seq input

extract_protocol:
RNA-seq: isolation of total RNA using Trizol reagent according to the manufacturer's instructions. ChIP-seq: cross-linking, antibody hybridization, de-crosslinking and purification of gDNA as previously described (Janevska et al., 2018, Genetics 208: 153-171)
PolyA enrichment for RNA-seq (library preparation and sequencing at the University of Amsterdam, Netherlands), ChIP-seq library preparation and sequencing by CRG Barcelona (Spain)

value: Vegetative mycelium

value: none (input)


title: Sample-5 Day-4 LNP-RNA

description: Library name: p22167-s035_ROj19-D4

value: LNP-RNA


title: S1_KMS28_PE_CTRL_A

source_name: KMS28-PE, Control, replicate A

value: Control


title: S3_KMS28_PE_CTRL_C

source_name: KMS28-PE, Control, replicate C


title: PDGFRA+ lung fibroblasts from Tnfaip3f/f mouse 6488

description: Library name: 6488-A20ctrl

value: Lung


title: PDGFRA+ lung fibroblasts from Dermo1-cre/+;Tnfaip3f/f mouse 6621

description: Library name: 6621-D1cA20

value: Homeostasis


title: PDGFRA+ lung fibroblasts from Tnfaip3f/f mouse 6489

description: Library name: 6489-A20ctrl


title: Vector transfection, replicate 1

description: Library name: Cont_1F


title: Δash1, ChIP-seq input

source_name: Δash1, ChIP-seq input


title: Sample-3 Day-4 LNP-RNA

description: Library name: p22167-s033_RKd19-D4


title: S2_KMS28_PE_CTRL_B

source_name: KMS28-PE, Control, replicate B


title: 688M PDA cells, H3K36me2, shKdm8-2, hypoxia, replicate 1

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

institute: Rutgers Cancer Institute of New Jersey

description: Library name: Sample 23

data_processing:
ChIP-Seq reads that passed the QC process were aligned to a mm39 genome build using bowtie2 (v2.4.1). Bam files were filtered for reads mapped to blacklisted regions and duplicated reads. Peaks were called using MACS3 (v3.0.0a6) with mapped bam files (--nomodel --broad --nolambda --keep-dup all -p 0.01 -B --SPMR) and only reads with low false discovery rate (qValue > 5) were included in the analysis.
Assembly: mm39
Supplementary files format and content: BigWig

source_name: Pancreatic

growth_protocol: PDA 688M cells expressing the control or Kdm8-targeting shRNAs (shKdm8_1 and shKdm8_2) were maintained in DMEM media with 10% FBS and antibiotics in humidified 5% CO2 at 37C

extract_protocol:
Briefly, 2.5x10^7-1x10^8 688M cells were cultured for each ChIP. To crosslink, formaldehyde solution was directly added to cell culture media to a final concentration of 1% for 10 min, followed by quenching with 125 mM glycine solution. Fixed cells were rinsed twice in ice-cold PBS and lysed in ice-cold lysis buffer (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, with protease inhibitor cocktail). Lysates were transferred to a 1.5 ml TPX tube (Diagenode) and sonicated using Bioruptor (Diagenode) three times of 10 min (output level: high, interval: 0.5). An aliquot (50 μl) of the lysates was reserved for QC and input library. For immunoprecipitation, 4mg of ChIP-grade antibodies against H3K36me2 (ab9049, abcam) or H3K27me3 (ab192985, abcam) were added to the lysate (containing ~50μg of sheared gDNA) and rotated overnight at 4°C, followed by an incubation with 25 μl of Protein A Dynabeads (Life Technology) for 2 hours at 4°C. The beads were washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate) prior to elution and reverse crosslink through an incubation with 400 μl of digestion buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65°C for 2 hours with agitation every 30 min. Eluted DNA samples were purified by organic extraction and ethanol precipitation.
DNA libraries were prepared using KAPA Hyperprep Kit (Roche) and sequenced on the Illumina Nova-seq X platform.

treatment_protocol: PDA 688M cells were either cultured in normoxia (atmospheric O2) or hypoxia (<0.5% O2) for 48 hours prior to chromatin extraction.

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells

value: hypoxia


title: Sample-1 Day-4 LNP-RNA

description: Library name: p22167-s031_RCl19-D4

value: Day 4


title: WT, ChIP-seq input

source_name: WT, ChIP-seq input

value: WT


title: 688M PDA cells, H3K36me2, shKdm8-1, hypoxia, replicate 2

description: Library name: Sample 22