title: RNAseq NSCs Smchd1 WT rep2 batch2


title: RNAseq NSCs Smchd1 MD43 rep4 batch2

status: Public on May 08 2021

type: SRA

city: Melbourne

first: Andres

last: Tapia del Fierro

state: Victoria

address: 1G Royal Parade

department: EDD

country: Australia

institute: WEHI

library_source: transcriptomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were analysed using limma v3.40.6
Data were normalized for read depth and log2-transformed RPKM counts were corrected for batch effects using limma's removeBatchEffect function
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed RPKM counts normalized by sequencing depth for all genes and corrected for batch effects by using technical replicates. Transcript isoforms were merged.

molecule: polyA RNA

organism: Mus musculus

source_name: Neural stem cells

growth_protocol: NSCs derived and cultured for less than 10 passages as described in Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z

extract_protocol:
100ng total RNA from lysed NSCs used for library prep
mRNA TruSeq library prep kit

tag: strain

value: FVB/NJ

tag: cell type

value: Neural stem cells

tag: genotype

tag: Sex

value: female

tag: cell line number


title: RNAseq NSCs Smchd1 WT rep5 batch2


title: RNAseq NSCs Smchd1 MD43 rep5 batch2


title: RNAseq NSCs Smchd1GFP WT rep2 batch3


title: RNAseq NSCs Smchd1 MD43 rep1 batch1


title: RNAseq NSCs Smchd1 WT rep2 batch1


title: RNAseq NSCs Smchd1GFP MD43 rep1 batch1


title: RNAseq NSCs Smchd1 MD43 rep2 batch2


title: RNAseq NSCs Smchd1GFP WT rep3 batch1


title: RNAseq NSCs Smchd1GFP MD43 rep3 batch1


title: RNAseq NSCs Smchd1 WT rep1 batch1


title: RNAseq NSCs Smchd1GFP WT rep1 batch1


title: RNAseq NSCs Smchd1 MD43 rep3 batch1


title: RNAseq NSCs Smchd1 MD43 rep2 batch1


title: RNAseq NSCs Smchd1GFP WT rep2 batch1


title: PSM 8 somites female WT rep2

description:
Dissected from embryo 1813.7
PSM_RNAseq_8_somites_counts.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using hisat2 v2.0.5 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and log2-transformed RPKM counts were calculated for each gene using Seqmonk's RNAseq pipeline.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed RPKM counts normalized by sequencing depth for all genes. Transcript isoforms were merged, and libraries are opposing strand-specific.

source_name: NSCs

extract_protocol:
100ng total RNA from snap-frozen dissected tissue used for library prep
stranded mRNA TruSeq library prep kit

tag: tissue

value: tailbud containing pre-somitic mesoderm


title: H3K27me3 ChIP WCE WT rep1

description: H3K27me3_ChIPseq_counts_2.5kb_around_peaks.txt

library_source: genomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and counts per million values calculated using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed read counts normalized by library size within bins created ±2.5kb centered on a list of peaks determined using SeqMonk's MACS-like functionality for each genotype separately. The peak lists were then merged and probes closer than 1kb were merged together. Biological replicates were merged before peak calculation.

molecule: genomic DNA

extract_protocol:
Lysates were extracted from Mnase-digested nuclei and H3K27me3-DNA complexes were isolated with antibody, then purified with Zymo ChIP DNA clean and concentrator kit
Libraries were prepared with Illumina TruSeq DNA sample preparation kit following manufacturer's instructions

tag: antibody

tag: cell line name


title: PSM 8 somites female MommeD43 rep3

description:
Dissected from embryo 1807.4
PSM_RNAseq_8_somites_counts.txt


title: PSM 8 somites male MommeD43 rep1

description:
Dissected from embryo 1805.5
PSM_RNAseq_8_somites_counts.txt

value: male


title: H3K27me3 ChIP MommeD43 rep3

value: anti-H3K27me3 (Cell Signalling technologies C36B11)


title: H3K27me3 ChIP MommeD43 rep2


title: H3K27me3 ChIP WCE MommeD43 rep1


title: PSM 8 somites male WT rep1

description:
Dissected from embryo 1805.4 (#mother.#embryo)
PSM_RNAseq_8_somites_counts.txt


title: PSM 8 somites female MommeD43 rep2

description:
Dissected from embryo 1791.6
PSM_RNAseq_8_somites_counts.txt


title: RNAseq NSCs Smchd1 WT rep4 batch2


title: RNAseq NSCs Smchd1GFP MD43 rep2 batch1


title: RNAseq NSCs Smchd1 WT rep3 batch1


title: H3K27me3 ChIP WT rep3


title: H3K27me3 ChIP WT rep2


title: Smchd1-GFP ChIP WCE WT rep1

description: Smchd1-GFP_ChIPseq_counts_5kb_around_known_Smchd1_peaks.txt

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation using bcl2fastq conversion software v2.15.0.4
Alignment to GRCm38.p6 reference genome using Bowtie2 v2.3.4.1 with default parameters  after trimming adapters with Trim Galore! v0.4.4
Data were normalized for read depth and counts per million values calculated using Seqmonk.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-separated txt file containing log2-transformed read counts normalized by library size within bins created on previously published Smchd1 binding sites ±5kb (Jansz et al., Nature Structural Molecular Biology 2018 DOI:10.1038/s41594-018-0111-z). Biological replicates were merged.

extract_protocol:
Lysates were extracted from Mnase-digested nuclei and SMCHD1-DNA complexes were isolated with antibody, then purified with Zymo ChIP DNA clean and concentrator kit
Libraries were prepared with Illumina TruSeq DNA sample preparation kit following manufacturer's instructions


title: H3K27me3 ChIP WT rep1


title: Smchd1-GFP ChIP MommeD43 rep3

value: anti-GFP (Invitrogen A11122)


title: Smchd1-GFP ChIP WT rep3


title: Smchd1-GFP ChIP MommeD43 rep1


title: Smchd1-GFP ChIP WT rep2


title: PSM 8 somites female WT rep3

description:
Dissected from embryo 1823.7
PSM_RNAseq_8_somites_counts.txt


title: Smchd1-GFP ChIP WT rep1


title: Smchd1-GFP ChIP WCE MommeD43 rep1


title: Smchd1-GFP ChIP MommeD43 rep2


title: H3K27me3 ChIP MommeD43 rep1


title: Lig4Ku70K_D2_ZFN_Rep3

city: Stanford

first: Marie

last: Le Bouteiller

state: CA

address: 269 campus drive

department: Radiation Oncology

country: USA

institute: Stanford University

data_processing:
Library strategy: JoinT-seq
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm10 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: v-Abl pro B cells

growth_protocol: v-Abl pro-B cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 15% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Nextseq sequencing

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h, nucleofection of Cas9:c-Myc gRNA or doxycycline-inducing treatment (2µg/ml) was added to some of the samples

tag: clone

tag: cell cylce status

tag: treatment protocol

value: STI + doxycycline-induced ZFN-Eb expression

tag: target locus

value: Eb

tag: illumina sequencing

value: Nextseq

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

value: JoinT-seq

tag: figure displaying results for this library


title: Lig4Ku70K_D2_ZFN_Rep2


title: Lig4Ku70K_D2_ZFN_Rep1


title: Lig4Ku70_D2_ZFN_Rep3


title: Ku70_B1_RAG_Rep1

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm10 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

value: Emu-Bcl2, Ku70-/-

value: STI

value: LAM-HTGTS


title: Ku70_B1_RAG_Rep2


title: Lig4_B1_RAG_Rep2

value: Emu-Bcl2, Lig4-/-


title: Lig4_B1_RAG_Rep3


title: Lig4_B1_RAG_Rep1


title: Ku70_B1_RAG_Rep3


title: WT_B_RAG_Rep3

value: B


title: WT_B_RAG_Rep2


title: WT_B_RAG_Rep1


title: Lig4Ku70_D2_ZFN_Rep1


title: Lig4Ku70K_D1_ZFN_Rep3


title: Lig4Ku70_D2_ZFN_Rep2


title: Lig4Ku70K_D1_ZFN_Rep2


title: Lig4Ku70_D1_ZFN_Rep2


title: Lig4Ku70K_D1_ZFN_Rep1


title: Lig4Ku70_D1_ZFN_Rep3


title: Lig4L_D_ZFN_Rep3

value: Emu-Bcl2, Lig4-/- +Lig4

value: D


title: Lig4Ku70_D1_ZFN_Rep1


title: Lig4L_D_ZFN_Rep2


title: Lig4_D_ZFN_Rep3


title: Rep2_RNA_Cre_S6

status: Public on May 09 2021

first: Gerald

last: Tiu

state: California

address: 279 Campus Dr., Beckman Center B309

description: rRNA depleted total RNA

data_processing:
For analysis pre-processing, UMI-tools63 was used to extract sample barcodes and UMIs. Reads were demultiplexed, sample barcodes were removed, and reads were quality filtered (fastq_quality_filter -Q33 -q 20 -p 70) using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The 3’ adapter sequence CTGTAGGCACCATCAAT was removed using cutadapt64, and the 5’ end of each read was then removed using fastx_trimmer from FASTX-Toolkit. Raw files included have been preprocessed up to this point.
To remove reads that aligned to rRNA, tRNA, and snRNAs, reads were first aligned to these sequences using bowtie265 (bowtie2 parameters: -L 18) and subsequently discarded. Filtered reads that did not align to rRNA/tRNA/snRNAs were then aligned using bowtie2 (bowtie2 parameters: --norc -L 18) to an GRCm38/mm10 transcriptome reference derived from UCSC/GENCODE VM20 knownCanonical annotations filtered for high confidence transcripts that contain at least one of the following: a Uniprot ID, a RefSeq ID, or an Entrez ID.
PCR duplicates were then removed using UMI-tools. (Note 9 base UMI is in description of each read in FASTQ files)
Ribosome protected fragments (RPFs) were then parsed for uniquely aligned reads, separated into read length groups, and ribosome A site positions were determined by offsetting the distance of the 5’ end of each read to canonical start sites in each length group and adding 4 nucleotides62. RNA-Seq reads were also parsed for uniquely aligned reads and were assigned to the center of each read. RPFs and RNA-Seq reads were then counted using the transcriptome annotations detailed above.
Reads aligning to the CDS (with the first 15 codons and last 5 codons removed) were used for RPF libraries, and reads aligning to the entire transcript were used for RNA-Seq libraries.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Counts aligning to CDS (with the first 15 codons and last 5 codons removed) for ribosome protected fragments; counts aligning to entire transcript for RNA-Seq

molecule: total RNA

source_name: E10.5 mouse forelimbs

growth_protocol: Embryos were harvested at E10.5 from Prx1Cre x Rps6lox/lox;Trp53+/- mice

extract_protocol:
Limb pairs from each embryo were lysed via vigorous pipetting and 30 minute incubation at 4oC in 215 μL buffer A (25 mM Tris-HCl pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 8% glycerol, 1% Triton X-100, 100 μg/ml CHX (Sigma-Aldrich, C7698-1G), 20 U/ml Turbo DNAse (Thermo Fisher, AM2238), and Complete Protease Inhibitor EDTA-free (Sigma-Aldrich, 11836170001). Lysates were cleared via sequential centrifugation at 1,300g, 5 min and 10,000g, 10 min at 4oC. For RNA input for RNA-Seq, 70 μL of lysate was diluted in 55 μL of water and stored at -80oC in 375 μL of TRIzol LS (Thermo Fisher, 10296010). For ribosome profiling, 120 μL of cleared lysate was treated with 0.5 μg RNase A (Thermo Fisher, AM2271) and 300 U RNase T1 (Thermo Fisher, EN0541) for 30 min, RT with gentle rocking. The reaction was stopped by the addition of 100 U SUPERase RNase Inhibitor (Thermo Fisher, AM2694). Ribosomes were enriched by adding 110 μL lysate onto 900 μL sucrose cushion buffer (1 M sucrose in buffer A containing 20 U/mL SUPERase RNase Inhibitor), and centrifuging in a TLA 120.2 rotor (Beckman) 70,000 rpm, 4 h, 4 °C. The ribosome pellet containing the ribosome footprinted Ribo-Seq library was resuspended in 500 μL TRIzol.
Library preparation was adapted from previous protocols59,61 and the ARTseq Ribosome Profiling Kit manual (Epicentre, Illumina). In summary, total RNA and ribosome footprints were extracted using the Direct-zol Micro Kit (Zymo, R2060) with in-column DNase I treatment. To have an adequate amount of RNA for subsequent steps, pairs of samples of the same genotype were pooled to generate a single replicate sample, brought up to 90 μL with water, and precipitated with 150 μL isopropanol overnight -80oC after addition of 10 μL 3 M NaOAc pH 5.5 and 1.5 μL 15 mg/mL GlycoBlue Coprecipitant (Thermo Fisher, AM9515). The samples were then centrifuged at 21,000g, 30 min, 4oC, supernatant was removed, and the RNA pellet was washed 500 μL cold 75% ethanol. Pellets were dried for 10 min, RT and resuspended in 15 μL nuclease free water. After extraction and precipitation, both ribosome footprinting and total RNA samples were depleted of rRNA using the Ribo-Zero Gold rRNA Removal Kit (H/M/R) (Illumina, catalog no. MRZG126) with the modification that the 50oC incubation was not performed for the ribosome footprinting samples. The samples were then column purified (RNA Clean & Concentrator 5, Zymo Research, catalog no. R1016) with the modifications that 2 volumes of RNA Binding Buffer and 4.5 volumes of ethanol were added to ribosome footprinting samples to purify small RNAs and 1 volume of RNA Binding Buffer and 1 volume of ethanol was added to total RNA samples to isolate RNA > 200 nt. Total RNA samples were then fragmented by partial alkaline hydrolysis. The samples were diluted to 100 μL with 5 mM Tris-HCl, pH 7.5 and incubated with 100 μL 2x alkaline fragmentation buffer (100 mM Na2CO3 pH 9.2, 2 mM EDTA) for 20 minutes at 95oC. The reaction was neutralized with 440 μL STOP Buffer (70 μL 3 M NaOAc pH 5.5, 2 μL Glycoblue, and 370 μL nuclease free water) and isopropanol precipitated overnight at -80oC.   Ribosome protected fragments and total RNA samples were then size selected by running the samples out on a 15% TBE-Urea polyacrylamide gel. Ribosome protected fragments were size selected between 28-nt and 34-nt as marked by RNA oligonucleotides oNTI199 and oNTI265, respectively62. Total RNA samples were size selected between 34-70 nt as marked by a 10 bp DNA ladder (Invitrogen, catalog no. 10821015). Gel slices were crushed and extracted at room temperature overnight in 400 μL RNA extraction buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.25% SDS) and isopropanol precipitated. Samples were then 3’dephosphorylated by denaturing at 65oC for 5 min and incubating with T4 PNK (NEB, catalog no. M0201S) in a 10 μL reaction (7 μL precipitated RNA, 1 μL 10x T4 PNK Buffer, 1 μL SUPERase Inhibitor, 1 μL 10 U/μL T4 PNK) at 37oC for 1 hour. The reaction was stopped through heat inactivation at 65oC for 20 min. To ligate adaptor, samples were then incubated with 0.5 μL of 50 μM Universal miRNA Cloning Linker (NEB, catalog no. S1315S) and denatured at 65oC for 5 min. The denatured sample was then incubated with 1 μL T4 RNA Ligase 2, truncated KQ (NEB, M0373S), 1 μL 10x buffer, 6 μL 50% PEG 8000, and 1.5 μL water for 4.5 h at 25oC. Free adaptor was then removed by addition of 1 μL 10 U/μL 5’-Deadenylase (NEB, M0331S). 1 μL 10 U/μL RecJ Exonuclease (Lucigen/Epicentre, RJ411250). and 1 μL 20 U/μL SUPERase Inhibitor. Samples were then purified using Zymo RNA Clean & Concentrator-5 columns using the protocol above to preserve small RNAs (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol).    To perform reverse transcription, 10 μL sample was incubated with 2 μL of 1.25 μM RT primer (see table) and denatured at 65oC for 5 min. Reverse transcription (RT) was performed with primers containing sample barcodes and unique molecular identifiers. RT was performed with SuperScript III (Thermo Fisher, 18080-044) in a 20 μL reaction (48oC, 40 min). RNA was then hydrolyzed by adding 2.2 μL of 1N NaOH and incubating for 20 min at 98oC. Samples were then purified using Zymo RNA Clean & Concentrator-5 columns (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol). RT products were size selected and gel extracted from 10% TBE Urea polyacrylamide gels as described above instead that DNA extraction buffer was used for overnight extraction (300 mM NaCl, 10 mM Tris-HCl pH 8, 1 mM EDTA, 0.1% SDS). Eluate was then isopropanol precipitated overnight at -80oC overnight. Samples were then circularized with CircLigase (Illumina, CL4115K) in a 20 μL reaction (15 μL cDNA, 2 μL 10x CircLigase Buffer, 1 μL 1 mM ATP, 1 μL MnCl2, 1 μL CircLigase) for 12 hours at 60oC and subsequently purified by Zymo RNA Clean & Concentrator 5 columns (100 μL sample, 200 μL RNA binding buffer, 450 μL 100% ethanol) and eluted with 12 μL 10 mM Tris-HCl pH 8. 1 μL of library was used for PCR amplification with Phusion High-Fidelity DNA Polymerase (Thermo Fisher, catalog no. F530S) (98oC 30s, 98oC 10s, 65oC 10s, 72oC 5s) for 9-10 cycles (see table for primers). PCR product was PAGE purified from native 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated for > 2 h at -80oC. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid (PAN) Facility. Libraries were sequenced by the Stanford Functional Genomics Facility (SFGF) on the Illumina NextSeq 500 (1x75nt).
Ribosome profiling, RNA-Seq

tag: genotype simplified

value: Rps6 het; Trp53 WT

tag: replicate

value: Replicate 2


title: Lig4_D_ZFN_Rep2


title: Lig4_D_ZFN_Rep1


title: Ku70_B1_Cas9_Rep3

value: STI + nucleofection Cas9:c-Myc gRNA

value: c-Myc


title: Ku70_B1_Cas9_Rep2


title: Lig4_B1_Cas9_Rep3


title: Ku70_B1_Cas9_Rep1


title: Lig4_B1_Cas9_Rep2


title: Lig4L_D_ZFN_Rep1


title: WT_B_Cas9_Rep2


title: Lig4_B1_Cas9_Rep1


title: WT_B_Cas9_Rep1


title: WT_B_Cas9_Rep3


title: sno/SPA-lncRNA KD chRNA 1

city: Birmingham

first: Monika

last: Sledziowska

address: School of Biosciences, University of Birmingham, Edgbaston B15 2TT

country: United Kingdom

institute: University of Birmingham

description: chRNA

data_processing:
Data quality control was performed with FastQC v0.11.530, and aligned with STAR v2.5.3a31 to the human genome (GRCh38.p10, Gencode comprehensive annotation).
RNA-seq reads were aligned with parameters; --outSAMtype BAM SortedByCoordinate.
The counts per gene were calculated with LiBiNorm v2.432, in HTseq-count33 compatible mode with parameters; --htseq-compatible --order pos, --stranded no, --type gene, --idattr gene_name.
Count per million normalised bigwig files were constructed using deeptools34 bamcompare with parameters; --binSize 15, --normalizeUsing CPM. Once raw counts were extracted the data was analysed in R (version 4.0.5).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Induced pluripotent stem cells

growth_protocol: Induced pluripotent stem cells were grown on Matrigel(Corning) with StemFlex(Gibco) and passaged when 70-80% confluent.

extract_protocol:
chRNa was obtained through fractionation, extracted with Trizol and cleaned using RNeasy kit (Qiagen), total RNA was extracted using Trizol and cleaned using RNeasy kit (Qiagen)
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: KDs were achieved using deigner GapmeRs (Qiagen)

tag: cell type

value: Induced pluripotent stem cells

value: sno/SPA-lncRNA KD


title: sno-lncRNA KD chRNA 2

description: chRNA

tag: genotype

value: sno-lncRNA KD


title: Sample47_NIV, CDC Kendall, 96 hr, Replicate 3 [NIV-K-96-3]

city: Brandon

first: James

middle: Raymond

last: Tucker

state: MB

address: 2701 Grand Valley Rd.

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Fastq files for each sample were evaluated on an individual basis using FastQC v0.11.5 software via visual graphic inspection. Raw data (raw reads) of fastq format were firstly processed through Trimmomatic v0.36 software. In this step, clean data (clean reads) were obtained by removing reads containing Illumina adapters, low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly (publicly available Morex genome assembly, IBSC_v2 (International Barley Sequencing Consortium) release of the barley reference genome (Mascher et al. 2017) was accessed through Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben. Paired-end clean reads were aligned to the reference genome using HISAT2 v2.0.4 software.
Software package StringTie was utilized to approximate the gene expression levels in each sample from the BAM files. StringTie -merge procedure was used to input and combine lists of transcripts aligned to reference gene annotation list and newly assembled genes/ transcripts. After the HC genes and new assembled genes/transcripts were merged, the expression and coverage at all these annotations were estimated. Coverage was converted to raw reads counts by a python script within StringTie package. In order to annotate those newly assembled genes by StringTie, the protein sequences were extracted in fasta format from the genome reference using gene coordinates by a peal script. The protein fasta files were searched against a local NCBI nr database by blastp program.
Differential expression analysis was performed using the EdgeR package. Generalized linear models were applied both as: i) Pairwise single-factor contrasts or ii) additive model design (3 factor model with interaction) via Likelihood Ratio Test (LRT). EdgeR provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by EdgeR were assigned as differentially expressed.
Genome_build: 160404_barley_pseudomolecules_masked.fasta
Supplementary_files_format_and_content: Data is provided in .xls file containing  transcript per million mapped reads (TPM) values for each gene and sample.

organism: Hordeum vulgare

source_name: CDC Kendall_NIV strain_96 hr_grain

growth_protocol: Seeds of Norman and CDC Kendall barley genotypes were placed in pots of dimension of 20 × 30 cm (top diameter × height) in growth chamber conditions (28°C, 16 h L: 8h D photoperiod) at Brandon Research and Development Centre (BDRC), Brandon, Manitoba, Canada. Cones were filled with Pro-Mix Mycorrhizae growing medium (Premier Horticulture Inc. Quakertown, PA, USA). The experiment consisted of three replications for both the control and three Fusarium treatments (3ADON, 15ADON and NIV chemotypes) for each of the two genotypes tested. Starting at the fourth week post-seeding, plants were fertilized with 20 g l-1 of (20-20-20 NPK) and every two weeks thereafter.

extract_protocol:
Seeds were pulverized in liquid nitrogen using a mortar and pestle, and total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, Canada) following the manufacturer’s protocol. Three biological replicates of Norman and CDC Kendall at 72 h and 96 h time-points, were subjected to RNA-seq analysis. The RNA quality and concentration were verified using a NanoDrop 1000 spectrophotometer (ThermoFisher Scientific, Canada) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Canada) prior to sequencing.
Sequencing libraries were generated using Illumina first-strand TruSeq® mRNA Prep Kit following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using oligo (dT)-attached magnetic beads. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: Norman and CDC Kendall were submitted to Fusarium treatment (3ADON, 15ADON and NIV chemotypes), which involved spraying spikes with  5 x 104 macroconidia l-1. Spike samples were collected at the time-points 72 h and 96 h post-inoculated along with control plants. All samples collected were immediately submerged in liquid nitrogen and stored at -80 °C until further processing.

value: CDC Kendall

tag: treatment

value: NIV strain

tag: time point

value: 96 hr

value: grain


title: sno/SPA-lncRNA KD chRNA 2

description: chRNA


title: Sample46_NIV, Norman, 72 hr, Replicate 3 [NIV-N-72-3]

source_name: Norman_NIV strain_72 hr_grain

value: Norman

value: 72 hr

tag: tissue


title: sno/SPA-lncRNA KD total RNA 2

description: total RNA


title: negative control total RNA 2

description: total RNA

value: negative control


title: sno/SPA-lncRNA KD total RNA 1

description: total RNA


title: negative control total RNA 1

description: total RNA


title: sno-lncRNA KD chRNA 1

description: chRNA


title: Sample48_NIV, Norman, 96 hr, Replicate 3 [NIV-N-96-3]

source_name: Norman_NIV strain_96 hr_grain


title: Sample44_NIV, Norman, 96 hr, Replicate 2 [NIV-N-96-2]


title: SPA-lncRNA KD chRNA 2

description: chRNA

value: SPA-lncRNA KD


title: SPA-lncRNA KD chRNA 1

description: chRNA


title: Sample43_NIV, CDC Kendall, 96 hr, Replicate 2 [NIV-K-96-2]


title: Sample40_NIV, CDC Kendall, 96 hr, Replicate 1 [NIV-K-96-1]


title: Sample42_NIV, CDC Kendall, 72 hr, Replicate 2 [NIV-K-72-2]

source_name: CDC Kendall_NIV strain_72 hr_grain


title: Sample41_NIV, Norman, 72 hr, Replicate 2 [NIV-N-72-2]


title: negative control chRNA 2

description: chRNA


title: Sample39_NIV, Norman, 96 hr, Replicate 1 [NIV-N-96-1]


title: negative control chRNA 1

description: chRNA


title: Sample45_NIV, CDC Kendall, 72 hr, Replicate 3 [NIV-K-72-3]


title: 20180926-3-SXS

city: fuzhou

first: XUEQUN

last: HU

state: fujian province

address: 134 East Street, Gulou District, Fuzhou

country: China

institute: Clinical Medical College of Fujian Provincial Hospital, Fujian Medical University,

description: microRNA

data_processing:
Illumina NextSep 500 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt 1.14, then mapped to human NCBI genome build 36 whole genome using bowtie.
Counts per million reads reads(CPM) were calculated.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample ...

source_name: plasma

extract_protocol:
Venous blood samples (5 ml) were drawn from the experimental group and the control group, and immediately centrifuged at 4℃ for 10 min. The plasma was then collected and frozen at -80℃.Total RNA was isolated using TRIzol LS Reagent (Invitrogen,Carlsbat,CA,USA) according to the manufacturer’s instructions. The concentration and purity of RNA were measured by NanoDrop ND-1000(NanoDrop Technologies,USA).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Rapid SR Cluster Kit (#GD-402-4001, Illumina)

value: plasma

tag: diagnosis

value: Normal control


title: Sample38_NIV, CDC Kendall, 72 hr, Replicate 1 [NIV-K-72-1]


title: 20180928-1-ZYQ

description: microRNA


title: 20180930-1-TXZ

description: microRNA


title: Sample36_3ADON, Norman, 72 hr, Replicate 3 [3-N-72-3]

source_name: Norman_3ADON strain_72 hr_grain

value: 3ADON strain


title: Sample35_3ADON, CDC Kendall, 72 hr, Replicate 3 [3-K-72-3]

source_name: CDC Kendall_3ADON strain_72 hr_grain


title: 20180926-4-LBL

description: microRNA

value: Human with familial hypertrophic cardiomyopathy

value: MYBPC3 gene mutations


title: MLF

description: microRNA


title: CQH

description: microRNA


title: NK cells_YTHDF2_Input_WT_rep2

city: duarte

first: Shoubao

last: Ma

address: 1500 East Duarte Road

institute: City of Hope

description:
40094_NK2-RIP-input_S4_L999
processed data file: RIP_NK.peak_result.txt

data_processing:
Sequencing reads were mapped to the mouse genome using HISAT2 (Version: v101)
Mapped reads of IP and input libraries were provided for R package exomePeak
The m6A binding motif was analyzed by HOMER.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker
Peak calling results with IP and input libraries were generated by R package RIPSeeker
Called peaks were annotated by intersection with gene and transcript architecture using ChIPpeakAnno
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample, peak text files

source_name: NK cells_YTHDF2_Input_WT

growth_protocol: Purified splenic NK cells were expanded by IL-2 (1000 U/ml, National Cancer Institute, Cat No. Bulk Ro 23-6019).) in vitro for 7 days.

extract_protocol:
For m6A-seq, total RNA was isolated by TRIzol reagent (Thermo Fisher Scientific) from fifty million IL-2 expanded NK cells. Polyadenylated RNA was further enriched from total RNA by using Dynabeads® mRNA Purification Kit (Invitrogen). mRNA samples were fragmented into ~100-nucleotide-long fragments with RNA fragmentation reagents (Invitrogen). Fragmented mRNA (5 μg mRNA) was used for m6A immunoprecipitation (m6A-IP) using an m6A antibody (Synaptic, 202003) following the standard protocol of the Magna MeRIP m6A Kit (Merck Millipore). For Ythdf2 RIP-seq, fifty million IL-2-expanded NK cells were harvested and washed twice with cold PBS, and the cell pellet was lysed with two volumes of lysis buffer [10 mM HEPES pH 7.6, 150 mM KCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 Protease Inhibitor cocktail (Thermo Fisher Scientific), and 400 U/mL SUPERase-In RNase Inhibitor (Thermo Fisher Scientific)]. The lysate was incubated on ice for 5 min and centrifuged for 15 min to clear the lysate. One-tenth volume of cell lysate was saved as input. The rest of the cell lysate was incubated with 5 μg anti-YTHDF2 (MBL, Cat No. RN123PW) that was pre-coupled with Protein A magnetic beads (Invitrogen, Cat: 10001D) at 4℃ for 2h with gentle rotation. Afterward, the beads were washed five times with 1 ml ice-cold washing buffer (50 mM HEPES pH 7.6, 200 mM NaCl, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, and 200 U/mL RNase inhibitor). Immunoprecipitated samples were subjected to Proteinase K digestion in wash buffer supplemented with 1% SDS and 2 mg/mL Proteinase K (Thermo Fisher Scientific) incubated with shaking at 1200 rpm at 55℃ for 1 h. Total RNA was extracted from both input and immunoprecipitated RNA by adding 5 volumes of TRIzol reagent, followed by Direct-zol RNA Miniprep (Zymo Research).
For m6A-seq,RNA was enriched through RNA Clean & Concentration- 5 (Zymo Research) for library generation with a KAPA RNA HyperPrep Kit (Roche). Sequencing was performed at the City of Hope Genomics Facility on an Illumina HiSeq2500 machine with single read 50 bp mode. For Ythdf2 RIP-seq, cDNA library generation was produced with a KAPA RNA HyperPrep Kit (Roche) and sequenced on Illumina HiSeq2500 platform.

treatment_protocol: NK cells were purified from from Ythdf2 WT and Ythdf2 ∆NK  mice

tag: strain background

tag: genotype/variation

value: Ythdf2 {delta}NK

value: splenic NK cells

value: mouse immune cells


title: Sample34_3ADON, CDC Kendall, 96 hr, Replicate 3 [3-K-96-3]

source_name: CDC Kendall_3ADON strain_96 hr_grain


title: NK cells_YTHDF2_Input_WT_rep1

description:
40093_NK1-RIP-input_S3_L999
processed data file: RIP_NK.peak_result.txt


title: NK cells_YTHDF2_IP_WT_rep1

description:
40091_NK1-RIP_S1_L999
processed data file: RIP_NK.peak_result.txt

source_name: NK cells_YTHDF2_IP_WT

value: WT

tag: antibody

value: YTHDF2 (MBL, Cat No. RN123PW)


title: NK cells_YTHDF2_IP_WT_rep2

description:
40092_NK2-RIP_S2_L999
processed data file: RIP_NK.peak_result.txt


title: Sample31_3ADON, Norman, 96 hr, Replicate 2 [3-N-96-2]

source_name: Norman_3ADON strain_96 hr_grain


title: Sample29_3ADON, Norman, 72 hr, Replicate 2 [3-N-72-2]


title: NK cells_m6A_Input_cKO_rep2

description:
40076_mNK-KO2-input_S10_L999
processed data file: m6A_Input_genes_fpkm_expression.txt

source_name: NK cells_m6A_Input_cKO


title: Sample28_3ADON, CDC Kendall, 72 hr, Replicate 1 [3-K-72-1]

value: CDC Kendall


title: Sample27_3ADON, Norman, 72 hr, Replicate 1 [3-N-72-1]


title: NK cells_m6A_Input_cKO_rep3

description:
40078_mNK-KO3-input_S12_L999
processed data file: m6A_Input_genes_fpkm_expression.txt


title: Sample26_3ADON, Norman, 96 hr, Replicate 1 [3-N-96-1]

value: 96 hr


title: NK cells_m6A_Input_cKO_rep1

description:
40074_mNK-KO1-input_S8_L999
processed data file: m6A_Input_genes_fpkm_expression.txt


title: NK cells_m6A_IP_cKO_rep3

description:
40077_mNK-WT3-input_S11_L999
processed data file: m6A_KO_IPVSKO_input_peak.txt

source_name: NK cells_m6A_IP_cKO

value: m6A (Synaptic, 202003)


title: Sample37_NIV, Norman, 72 hr, Replicate 1 [NIV-N-72-1]

value: Norman

value: NIV strain

value: grain


title: Sample25_3ADON, CDC Kendall, 96 hr, Replicate 1 [3-K-96-1]


title: NK cells_m6A_IP_cKO_rep1

description:
40073_mNK-WT1-input_S7_L999
processed data file: m6A_KO_IPVSKO_input_peak.txt


title: Sample24_15ADON, Norman, 72 hr, Replicate 3 [15-N-72-3]

source_name: Norman_15ADON strain_72 hr_grain

value: 15ADON strain

value: 72 hr


title: NK cells_m6A_IP_cKO_rep2

description:
40075_mNK-WT2-input_S9_L999
processed data file: m6A_KO_IPVSKO_input_peak.txt


title: Sample33_3ADON, Norman, 96 hr, Replicate 3 [3-N-96-3]


title: Sample32_3ADON, CDC Kendall, 96 hr, Replicate 2 [3-K-96-2]


title: Sample30_3ADON, CDC Kendall, 72 hr, Replicate 2 [3-K-72-2]


title: NK cells_m6A_Input_WT_rep2

description:
40070_KO2-meRIP_S4_L999
processed data file: m6A_Input_genes_fpkm_expression.txt

source_name: NK cells_m6A_Input_WT

value: Ythdf2 WT


title: NK cells_m6A_Input_WT_rep3

description:
40072_KO3-meRIP_S6_L999
processed data file: m6A_Input_genes_fpkm_expression.txt


title: Sample22_15ADON, CDC Kendall, 96 hr, Replicate 3 [15-K-96-3]

source_name: CDC Kendall_15ADON strain_96 hr_grain


title: Sample21_15ADON, Norman, 96 hr, Replicate 3 [15-N-96-3]

source_name: Norman_15ADON strain_96 hr_grain


title: NK cells_m6A_IP_WT_rep3

description:
40071_WT3-meRIP_S5_L999
processed data file: m6A_WT_IPVSWT_input_peak.txt

source_name: NK cells_m6A_IP_WT


title: Sample17_15ADON, CDC Kendall, 72 hr, Replicate 2 [15-K-72-2]

source_name: CDC Kendall_15ADON strain_72 hr_grain


title: Sample19_15ADON, CDC Kendall, 96 hr, Replicate 2 [15-K-96-2]


title: NK cells_m6A_IP_WT_rep2

description:
40069_WT2-meRIP_S3_L999
processed data file: m6A_WT_IPVSWT_input_peak.txt


title: Sample20_15ADON, Norman, 96 hr, Replicate 2 [15-N-96-2]


title: NK cells_m6A_IP_WT_rep1

description:
40067_WT1-meRIP_S1_L999
processed data file: m6A_WT_IPVSWT_input_peak.txt


title: Sample18_15ADON, Norman, 72 hr, Replicate 2 [15-N-72-2]


title: Sample23_15ADON, CDC Kendall, 72 hr, Replicate 3 [15-K-72-3]


title: Sample15_15ADON, Norman, 72 hr, Replicate 1 [15-N-72-1]


title: Sample14_15ADON, CDC Kendall, 96 hr, Replicate 1 [15-K-96-1]


title: Sample13_15ADON, Norman, 96 hr, Replicate 1 [15-N-96-1]


title: Sample12_MOCK, CDC Kendall, 72 hr, Replicate 3 [M-K-72-3]

source_name: CDC Kendall_MOCK control_72 hr_grain

value: MOCK control


title: Sample11_MOCK, Norman, 72 hr, Replicate 3 [M-N-72-3]

source_name: Norman_MOCK control_72 hr_grain


title: Sample10_MOCK, Norman, 96 hr, Replicate 3 [M-N-96-3]

source_name: Norman_MOCK control_96 hr_grain


title: NK cells_m6A_Input_WT_rep1

description:
40068_KO1-meRIP_S2_L999
processed data file: m6A_Input_genes_fpkm_expression.txt


title: Sample9_MOCK, CDC Kendall, 96 hr, Replicate 3 [M-K-96-3]

source_name: CDC Kendall_MOCK control_96 hr_grain


title: Sample7_MOCK, CDC Kendall, 96 hr, Replicate 2 [M-K-96-2]


title: Sample6_MOCK, CDC Kendall, 72 hr, Replicate 2 [M-K-72-2]


title: Sample5_MOCK, Norman, 72 hr, Replicate 2 [M-N-72-2]


title: Sample4_MOCK, Norman, 96 hr, Replicate 1 [M-N-96-1]


title: Sample3_MOCK, CDC Kendall, 96 hr, Replicate 1 [M-K-96-1]


title: Sample2_MOCK, CDC Kendall, 72 hr, Replicate 1 [M-K-72-1]


title: Sample1_MOCK, Norman, 72 hr, Replicate 1 [M-N-72-1]


title: Sample8_MOCK, Norman, 96 hr, Replicate 2 [M-N-96-2]


title: C27IgE3

city: Nishinomiya

first: Kazufumi

last: Matsushita

state: Hyogo pref.

address: 1-1 Mukogawacho

department: Immunology

country: Japan

institute: Hyogo College of Medicine

description: Bone-marrow cells cultured with IL-3 for 7 weeks.

data_processing:
Illumina Casava v1.8 software used for basecalling.
Read quality was checked for each sample using FastQC v0.11.5
High-quality reads were aligned to mm10 reference genome using STAR v2.5.2a
Aligned reads were counted using HTSeq v0.6.1 with parameter -m union and FPKM were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene FPKM for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone-marrow-derived cultureed mast cells (BMCMCs)

growth_protocol: BMCMCs were generated from BM cells derived from CC, C57BL/6J or BALB/cJ mice. BM cells were cultured in DMEM containing 10% FBS and 10 ng/mL mouse IL-3 (at 37℃) for 7 weeks.

extract_protocol:
Total RNAs were extracted from BMCMCs using Rneasy Micro kit (Quiagen, Venlo, The Netherlands).
Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer. According to demand of customer, we have NEB library and strand specific library to choose.

treatment_protocol: BMCMCs were sensitized with anti-DNP IgE (1 μg/mL) overnight at 37℃, then were left untreated or stimulated with DNP-HSA (20 ng/mL) in DMEM containing 10% FBS and 10 ng/mL mouse IL-3 for 1 hour at 37℃.

value: Bone-marrow cells

tag: agent

tag: strain

tag: protocol

value: IgE-sensitization followed by DNP-HAS stimulation for 1h.


title: C27IgE2


title: C27none1

value: IgE-sensitization only


title: C27none3


title: C27none2


title: B6none3


title: C27IgE1


title: Lig4L_C_RAG_Rep2

source_name: v-Abl pro B cells

value: Emu-Bcl2, Lig4-/- +Lig4

tag: clone

value: C

tag: cell cylce status

tag: treatment protocol

value: STI

tag: target locus

tag: illumina sequencing

value: Miseq

tag: number of raw reads used for normalization

value: LAM-HTGTS


title: B6none2

tag: cell type


title: LNPMA_3

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 50ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing, followed by quantile normalization, comBat batch effect correction and statistical analysis with limma - Bioconductor package in R

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: Cells were extracted from skins, lesions and lymph nodes after enzymatic digestion with Collagenase IV (Sigma Aldrich).

extract_protocol: Trizol+RNeasy+Minelute

treatment_protocol: Cell-sorting were performed from cell suspensions of various organs to purified NKp46+ cells. Cells were maintained in medium containing RPMI + 10% fetal calf serum.

value: draining lymp nodes from control mice without skin lesions

tag: amount in (µg)

value: FVB/N

tag: rin number


title: NaiveSkin_1

tag: tissue

value: skin from mice without any skin treatment


title: B6none4


title: Lig4L_C_RAG_Rep1

tag: genotype

tag: pipeline used for the analysis

tag: figure displaying results for this library


title: TumorSkin_1

value: skin from mice with cancerous lesions


title: B6none1


title: Lig4L_C_RAG_Rep3


title: PMASkin_2

value: skin from mice without lesions


title: Tumor_3

value: cancerous lesions


title: PapillomaSkin_3

value: skin from mice with pre-cancerous lesions


title: TumorSkin_2


title: LNPMA_2


title: LNTumor_1

value: draining lymp nodes from mice with cancerous lesions


title: LNTumor_2

value: draining lymp nodes from mice with tumor


title: PapillomaSkin_1


title: TumorSkin_3


title: Papilloma_2

value: pre-cancerous lesions


title: LNPMA_1


title: PapillomaSkin_2


title: Tumor_2


title: B6IgE4

value: Bone-marrow cells

value: IgE-sensitization followed by DNP-HAS stimulation for 1h.


title: Papilloma_1


title: LNPapilloma_3

value: draining lymp nodes from mice with papillloma


title: LNPapilloma_2

value: draining lymp nodes from mice with pre-cancerous lesions


title: LNPapilloma_1


title: LNTumor_3


title: PMASkin_1


title: Tumor_1


title: Lig4Ku70K_C1_RAG_Rep3

value: STI


title: Sample16_15ADON, CDC Kendall, 72 hr, Replicate 1 [15-K-72-1]

value: CDC Kendall

tag: treatment

value: 15ADON strain

tag: time point

value: 72 hr

value: grain


title: B6IgE3

tag: agent

tag: strain


title: B6IgE1

tag: protocol


title: B6IgE2


title: Lig4Ku70_C1_RAG_Rep3

tag: clone

tag: cell cylce status

value: Miseq

value: LAM-HTGTS


title: Lig4Ku70K_C1_RAG_Rep1

tag: treatment protocol

tag: target locus


title: ZB318_cycling

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
reads were quantified for specific loci using samtools version 1.8
wig files were produced using RseqQ package
Genome_build: mm9_AJ851868ins
Supplementary_files_format_and_content: wig files contain peak information for samples

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making Groseq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318).

treatment_protocol: G1-arrested cells were treated with STI-571 (3µM) for 96h

tag: illumina sequencing

value: Nextseq

value: Rad21 degron, RAG2-/-, Emu-Bcl2, IgH JH4 barcode, Igk cer/sis +/-

value: No treatment


title: ZB318_G1


title: 11-L-045-C-stroma-Pt

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterine Cervix

extract_protocol:
Total RNA was isolated from all cervical stroma samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA concentration and quality were analyzed using Nanodrop 2000 spectrophotometer (#ND-2000; Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer® (Agilent, Santa Clara, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.

treatment_protocol: Placentitis was induced in five mares at approximately 290d of gestation (placentitis group), four mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group), and the remaining three mares were maintained until approximately 330 d of gestation (prepartum group). For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.

value: Cervical stroma

tag: group

value: Prepartum


title: JET-wt-Input

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: input DNA

data_processing:
Reads were mapped to the human reference genome GRCh38.d1.vd1 containing the HTLV-1 sequence (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files) using NovoAlign (V3.04.06). with bowtie2 (v2.2.5) with default settings (Langmead and Salzberg, 2012).
Peak detection was performed using the model-based analysis of the ChIP-seq data (MACS version 2.1.1.20160309). Histone modification peaks were defined by significant enrichment of each signal over input-DNA peaks at a P cutoff value of 10−5.
Genome_build: GRCh38.d1.vd1 + HTLV-1 sequence (NC_001436.1 Human T-lymphotropic virus 1, complete genome)

organism:
Homo sapiens
Human T-cell leukemia virus type I

source_name: Jurkat cell line

growth_protocol: PBMCs were cocultured with radiated 729B-HTLV-1 cells in RPMI with IL-2 and medium was changed every week. After three weeks live cells were counted and p19 in the medium was measured by ELISA every week to monitor infection and immortalization of PBMCs by HTLV-1. Immortalized PBMCs were cultured for 4-5 months and stored at -80°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 3000 following the manufacturer's protocols.

tag: cell type

value: infected with HTLV-1 wt

tag: chip antibody

value: no antibody, input control


title: 12-L-061-C-stroma-Pt

tag: tissue


title: JET-p12-Input

description: input DNA

value: infected with HTLV-1p12stop


title: Lig4Ku70_C1_RAG_Rep2

tag: genotype

tag: number of raw reads used for normalization


title: JET-CTCF-K27

description: ChIP DNA

value: infected with HTLV-1-delta-CTCF

value: H3K36me3 (Cell Signaling, #4909)


title: Lig4Ku70K_C1_RAG_Rep2

value: STI

tag: pipeline used for the analysis

tag: figure displaying results for this library


title: JET-CTCF-K36

description: ChIP DNA

value: H3K27me3 (Cell Signaling, #9733)


title: JET-CTCF-Input

description: input DNA


title: JET-CTCF-K4

description: ChIP DNA

value: H3K4me3 (Cell Signaling, #9751)


title: Lig4Ku70_C1_RAG_Rep1


title: 10-H-034-C-stroma-Pt


title: JET-p12-K36

description: ChIP DNA


title: 9-L-056-C-stroma-Prg

value: Control


title: Lig4_C_RAG_Rep2

value: Emu-Bcl2, Lig4-/-

value: C


title: Lig4_C_RAG_Rep3

value: Miseq

value: LAM-HTGTS


title: 8-L60-C-stroma-Prg


title: JET-wt-K36

description: ChIP DNA


title: JET-wt-K27

description: ChIP DNA


title: JET-p12-K4

description: ChIP DNA


title: JET-wt-K4

description: ChIP DNA


title: Lig4Ku70K_A1_1_RAG_Rep3


title: PBMC-p12stop-input

description: input DNA

source_name: human peripheral blood mononuclear cell

value: HTLV-1p12stop immortalized PBMCs


title: PBMC-CTCF-input

description: input DNA

value: HTLV-1-delta-CTCF immortalized PBMCs


title: 6-K56-C-stroma-Prg

value: Cervical stroma


title: PBMC-wt-input

description: input DNA

value: HTLV-1 wt immortalized PBMCs


title: PBMC-CTCF-K36

description: ChIP DNA


title: 4-L63-C-stroma-Tx

value: Placentitis


title: Lig4Ku70K_A1_1_RAG_Rep2


title: JET-p12-K27

description: ChIP DNA


title: PBMC-p12stop-K36

description: ChIP DNA


title: Lig4Ku70K_A1_1_RAG_Rep1


title: PBMC-p12stop-K27

description: ChIP DNA


title: Lig4Ku70_A1_1_RAG_Rep3


title: PBMC-CTCF-H3K4

description: ChIP DNA


title: 3-L50-C-stroma-Tx


title: PBMC-p12stop-H3K4

description: ChIP DNA


title: PBMC-wt-K27

description: ChIP DNA


title: 7-L53-C-stroma-Prg


title: Lig4_C_RAG_Rep1


title: PBMC-wt-K36

description: ChIP DNA


title: PBMC-wt-K4

description: ChIP DNA


title: PBMCs from healthy controlHIP015

first: Aaron

middle: James

last: Wilk

address: 300 Pasteur Dr Bldg S131, Grant

data_processing:
mRNA reads in read 2 FASTQ files tagged with cell barcode and UMI from read 1 file with dropTag (dropEst)
Tagged reads aligned with STAR using GRCh37 reference that included the complete genome sequences for all SARS-CoV-2 strains sequenced from California before March 24, 2020
Count matrices built from BAM files using dropEst
scATAC reads were aligned and quantified using cellranger-atac software (10x Genomics, v1.2)
Genome_build: GRCh37 including the complete genome sequences for all SARS-CoV-2 strains sequenced from California before March 24, 2020
Supplementary_files_format_and_content: .rds files containing exonic, intronic, and spanning count matrices

source_name: Peripheral blood mononuclear cells

extract_protocol:
The single-cell ATAC sequencing was performed by using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics, PN-1000175) and following the Demonstrated Protocol (Nuclei Isolation for Single Cell ATAC Sequencing) provided by the 10x Genomics company. Briefly, cryopreserved PBMCs were thawed and 50,000-500,000 cells were aliquoted, washed with PBS and then lysed with 100 Œºl lysis buffer for 4 min. The lysed nuclei were centrifuged after washing with 1 ml washing buffer, and resuspended in Diluted Nuclei buffer. The nuclei concentration was then determined with TC20‚Ñ¢ Automated Cell Counter (Bio-rad, #1450102), and approximately 6,000 nuclei were used for Tn5 transposition, single nuclei barcoding and library preparation following the instructions in the kit.
Library preparation was performed with the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics, PN-1000175), according to the manufacturer protocol

value: cryopreserved PBMCs

tag: disease state

value: Healthy control


title: PBMC-CTCF-K27

description: ChIP DNA


title: 5-M74-C-stroma-Tx


title: Lig4Ku70_A1_1_RAG_Rep1


title: 1-K51-C-stroma-Tx


title: 12-L-061-C-Mucosa-Pt

extract_protocol:
Total RNA was isolated from all cervical mucosa samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA concentration and quality were analyzed using Nanodrop 2000 spectrophotometer (#ND-2000; Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer® (Agilent, Santa Clara, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.

value: Cervical Mucosa

value: Prepartum


title: PBMCs from healthy controlHIP045


title: Lig4_A1_b_RAG_Rep3

value: STI


title: Lig4Ku70_A1_1_RAG_Rep2


title: Lig4_A1_b_RAG_Rep2


title: 2-L48-C-stroma-Tx


title: PBMCs from healthy controlHIP043


title: 11-L-045-C-Mucosa-Pt


title: Lig4_A1_b_RAG_Rep1


title: PBMCs from healthy controlHIP023


title: 10-H-034-C-Mucosa-Pt


title: PBMCs from healthy controlEV08


title: Lig4L_A1_RAG_Rep3

value: Emu-Bcl2, Lig4-/- +Lig4


title: PBMCs from healthy controlHIP002


title: PBMCs from COVID-19 patient55650-0086

value: Patient with confirmed COVID-19


title: PBMCs from COVID-19 patient55650-0083


title: PBMCs from COVID-19 patient55650-0067


title: Lig4L_A1_RAG_Rep2


title: PBMCs from COVID-19 patient55650-0066d7


title: 9-L-056-C-Mucosa-Prg

value: Control


title: Lig4L_A1_RAG_Rep1


title: 8-L60-C-Mucosa-Prg


title: PBMCs from healthy controlHIP044


title: 7-L53-C-Mucosa-Prg


title: Lig4_A1_RAG_Rep3

value: Emu-Bcl2, Lig4-/-


title: PBMCs from COVID-19 patient28205-0564d0


title: PBMCs from COVID-19 patient55650-0066d0


title: 6-K56-C-Mucosa-Prg


title: Lig4_A1_RAG_Rep2


title: PBMCs from COVID-19 patient28205-0564d2


title: PBMCs from COVID-19 patient28205-0560


title: PBMCs from COVID-19 patient28205-0558


title: Lig4_A1_RAG_Rep1


title: PBMCs from COVID-19 patient28205-0557


title: PBMCs from COVID-19 patient28205-0555d2


title: PBMCs from COVID-19 patient28205-0559


title: 4-L63-C-Mucosa-Tx


title: 5-M74-C-Mucosa-Tx


title: PBMCs from COVID-19 patient28205-0555d0


title: Ku70_A1_RAG_Rep2

value: Emu-Bcl2, Ku70-/-


title: PBMCs from COVID-19 patient55650-0052


title: Ku70_A1_RAG_Rep1

value: Miseq


title: PBMCs from COVID-19 patient55650-0132d0


title: PBMCs from COVID-19 patient55650-0057


title: 2-L48-C-Mucosa-Tx


title: 1-K51-C-Mucosa-Tx


title: PBMCs from COVID-19 patient55650-0055


title: WT_A_RAG_Rep3

value: A

value: LAM-HTGTS


title: Neutrophils from healthy donor HIP002 WBNeut

description: WBNeut

source_name: Isolated peripheral neutrophils from whole blood

extract_protocol:
Immediately after Ficoll separation, 50,000 PBMCs were resuspended in RPMI + 10% FCS at a concentration of 75,000 cells/mL. 200 μL of this cell suspension (15,000 cells) was then loaded onto Seq-Well arrays pre-loaded with mRNA capture beads (ChemGenes). Following four washes with DPBS to remove serum, the arrays were sealed with a polycarbonate membrane (pore size of 0.01 µm) for 30 minutes at 37°C and then frozen at -80°C for no less than 24 hours and no more than 14 days to allow batching of samples processed at irregular hours. Next, arrays were thawed, cells lysed, transcripts hybridized to the mRNA capture beads, and beads recovered from the arrays and pooled for downstream processing.
Library preparation was performed with a Nextera XT DNA library preparation kit (Illumina FC-131-1096) with 1 ng of pooled library using dual-index primers. Tagmented and amplified libraries were again purified by Agencourt AMPure XP beads with a 0.6x volume wash followed by a 1.0x volume wash, and quality and concentration determined by Fragment Analysis. Libraries between 400-1000bp with no primer peaks were considered successful and pooled for sequencing. Sequencing was performed on a NovaSeq S2 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with read 1 beginning from a custom read 1 primer11 containing a 12bp cell barcode and an 8 bp unique molecular identifier (UMI), and with read 2 containing 50bp of mRNA sequence.

value: Un-cryopreserved neutrophils


title: SI_AsPA5

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: A. suum + PAC 5 SI

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sus Scrofa (ss11.1) using HISAT
DEG assessed using DeSeq2
Genome_build: ss11.1
Supplementary_files_format_and_content: excel file with count data for each sample.

organism: Sus scrofa

source_name: Small intestine tissue

growth_protocol: Pigs (aged 10 weeks) were infected with 5000 A. summ eggs or left as controls, and killed 14 days post-infection. Dietary treatments were for 28 days, 14 days pre- and 14 days post-infection

extract_protocol:
Tissue was collected at euthanasia. Total RNA was extracted using miRNAeasy kits (Qiagen).
Standard Illumina

value: Small intestine tissue

tag: breed

value: Danish Landrace x yorkshire

tag: infection

value: infected with A. suum

tag: diet

value: supplemented with 1 % PAC


title: WT_A_RAG_Rep2

tag: clone


title: PBMCs from HIP002

description: PBMC

value: Un-cryopreserved PBMCs

value: Healthy control


title: PBMCs from COVID-19 patient Imm_077_PBMC


title: SI_AsPA4

description: A. suum + PAC 4 SI


title: PBMCs from COVID-19 patient28205-0556

value: cryopreserved PBMCs


title: Ku70_A1_RAG_Rep3

tag: cell cylce status

value: STI


title: 3-L50-C-Mucosa-Tx

value: Cervical Mucosa

value: Placentitis


title: RBC-lysed whole blood from COVID-19 patient Imm_077_ACK

source_name: RBC-lysed whole blood leukocytes

value: Un-cryopreserved RBC-lysed whole blood leukocytes

value: Patient with confirmed COVID-19


title: SI_AsPA3

description: A. suum + PAC 3 SI


title: PBMCs from COVID-19 patient Imm_061


title: PBMCs from COVID-19 patient Imm_060


title: PBMCs from COVID-19 patient Imm_059


title: WT_A_RAG_Rep1

tag: treatment protocol


title: PBMCs from COVID-19 patient Imm_058


title: PBMCs from COVID-19 patient Imm_057


title: Lig4L_C_Cas9_Rep3

value: Emu-Bcl2, Lig4-/- +Lig4

value: C

value: STI + nucleofection Cas9:c-Myc gRNA

tag: target locus

value: c-Myc

value: JoinT-seq


title: SI_AsPA2

description: A. suum + PAC 2 SI

value: Small intestine tissue


title: SI_As6

description: A. suum 6 SI

value: Danish Landrace x yorkshire

value: control


title: Lig4Ku70K_C1_Cas9_Rep3

tag: illumina sequencing

value: Miseq


title: Lig4L_C_Cas9_Rep1


title: PBMCs from COVID-19 patient Imm_056

value: Un-cryopreserved PBMCs


title: SI_AsPA1

description: A. suum + PAC 1 SI

value: infected with A. suum

value: supplemented with 1 % PAC


title: PBMCs from COVID-19 patient Imm_006_PBMC


title: SI_As5

description: A. suum 5 SI


title: SI_As4

description: A. suum 4 SI


title: SI_As3

description: A. suum 3 SI


title: PBMCs from COVID-19 patient Imm_003_PBMC


title: Lig4Ku70K_C1_Cas9_Rep2


title: Lig4Ku70K_C1_Cas9_Rep1


title: T6121

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

description: Experimental Control group: Mice treated with IgG2a isotype control

data_processing:
RNA degradation was examined by SCISSOR (shape changes in selecting sample outliers in RNA-seq) which uses unsupervised screening of a range of structural alterations in RNA-seq data.
Benjamini-Hochberg procedure was used to control false discovery rate (FDR) for adjusted P value.
Transcript-level abundance was imported into gene-level abundance with the R package tximport.
Genes with low expression were identified and filtered out from further analysis using filterByExpr function of the edgeR package in R software.
Voom transformation function was applied to normalize log2-cpm values using mean-variance trend in the limma software package.
ClaNC was used to create classifier genes that characterize the groups of interest for heatmap and tables.
Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.8 was used for pathway analysis.
Immune infiltration estimations based on bulk gene expression data from RNA-seq was plotted using TIMER2.0.
Genome_build: GRCm38

source_name: Tumor - breast cancer

growth_protocol: E0771 cells were thawed from a 0.5 million cell aliquot stored in -80, plated and passed the same time for every injection. Each mouse received 250,000 cells in 25% matrigel in 1 syringe.

extract_protocol:
RNA was extracted from tumor tissue using RNeasy mini kit (QIAGEN, Germantown, MD). The integrity of RNA was assessed using Agilent Bioanalyzer and samples with RIN >5.0 were used.
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kits (non-directional) for Illumina, following manufacturer protocols. mRNA was enriched using oligo-dT beads.

treatment_protocol: Female mice were fed  high fat diet (HFD, D12492i – 60% kcal derived from fat from  Research Diets Inc., New Brunswick, NJ) from age 8 -26 weeks of age. E0771-luciferase cells (gift from Korkaya, Augusta University) were injected orthotopically into 4th mammary gland (250K in 25% matrigel). Three days after cell injection, IgG2a or anti-PD-1 intraperitoneal (IP) injections occured every 3 days until sacrifice at 21 days.

tag: cell syngeneic orthotopic transplant

value: E0771-luciferase cells

tag: mouse strain

tag: treatment

value: IgG2a (BE0089,BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: Lig4L_C_Cas9_Rep2


title: Lig4Ku70_C1_Cas9_Rep3


title: T6122


title: Lig4Ku70_C1_Cas9_Rep2


title: T6118

description: Experimental Treatment group: Mice treated with immune checkpoint inhibitor drug anti-PD-1.

value: Anti-PD-1 (BE0146, BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: RBC-lysed whole blood from COVID-19 patient Imm_003_ACK

tag: cell type

value: Un-cryopreserved RBC-lysed whole blood leukocytes


title: T6120


title: RBC-lysed whole blood from COVID-19 patient Imm_037_ACK

value: Patient with confirmed COVID-19


title: SI_As1

description: A. suum 1 SI

tag: tissue


title: SI_As2

description: A. suum 2 SI


title: RBC-lysed whole blood from healthy control HIP046_ACK

value: Healthy control


title: Lig4Ku70_C1_Cas9_Rep1

tag: genotype

tag: number of raw reads used for normalization


title: PBMCs from COVID-19 patient Imm_037_PBMC


title: RBC-lysed whole blood from healthy control HIP022_ACK


title: SI_PA6

description: PAC 6 SI

value: uninfected


title: PBMCs from healthy control HIP015_PBMC_2


title: Lig4_C_Cas9_Rep3

value: Emu-Bcl2, Lig4-/-

value: C

value: STI + nucleofection Cas9:c-Myc gRNA

tag: pipeline used for the analysis

tag: figure displaying results for this library


title: SI_PA5

description: PAC 5 SI

value: Small intestine tissue

tag: breed


title: RBC-lysed whole blood from COVID-19 patient Imm_006_ACK

tag: disease state


title: HEK293T-control-STAMP 24h low rep1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw reads were trimmed using cutadapt (v1.14) using the following parameters -O 5 -f  fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -o data.fastqTr.fq -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT data.fastq.gz
Trimmed reads were mapped to and filtered of repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType  EndToEnd  --genomeDir  repbase  --genomeLoad  NoSharedMemory  --outBAMcompression  10  --outFileNamePrefix  data  --outFilterMultimapNmax  10  --outFilterMultimapScoreRange  1  --outFilterScoreMin  10  --outFilterType  BySJout  --outReadsUnmapped  Fastx  --outSAMattrRGline  ID:foo  --outSAMattributes  All  --outSAMmode  Full  --outSAMtype  BAM  Unsorted  --outSAMunmapped  Within  --outStd  Log  --readFilesIn data.fastqTr.fq  --runMode  alignReads  --runThreadN  8
Reads unmapped to repeat elements were mapped to the human genome with STAR using the same parameters as the previous step, using an hg19 index in place of the repeat element index
Subread featureCounts (-a gencode.v19.annotation.gtf -s 2 -p -o counts.txt data.bam) was used to count features using human annotations (Gencode v19)
Edits were called using SAILOR (http://github.com/yeolab/sailor) using default parameters and dbSNP (v147) to remove known SNPs.
bigwig files were generated from filtered BAM files (intermediates from SAILOR), using the following commands from BedTools (v2.27.1). :     bedtools genomecov -split -strand - -g hg19.chrom.sizes -bg -ibam fwd.bam > fwd.bg  bedtools sort -I fwd.bg > fwd.sorted.bg   bedGraphToBigWig fwd.sorted.bg hg19.chrom.sizes fwd.sorted.bw    bedtools genomecov -split -strand + -g hg19.chrom.sizes -bg -ibam rev.bam > rev.bg  bedtools sort -I rev.bg > rev.sorted.bg   bedGraphToBigWig rev.sorted.bg hg19.chrom.sizes rev.sorted.bw
Genome_build: hg19

growth_protocol: All stable STAMP HEK293T cell lines were generated using human lenti-X HEK293T cells (HEK293XT, Takara Bio) which are derived from transformed female human embryonic kidney tissue. Cells were maintained in DMEM (4.5 g/L D-glucose) supplemented with 10% FBS (Gibco) at 37o C with 5% CO2. Cells were periodically passaged once at 70-90% confluency by dissociating with TrypLE Express Enzyme (Gibco) at a ratio of 1:10.

extract_protocol:
Trizol extraction (Fisher) and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol
Illumina TruSeq stranded mRNA or total RNA

treatment_protocol: For STAMP fusion protein expression STAMP stable HEK293T cells were induced with 50ng/ml (low) or 1ug/ml (high) doxycycline in DMEM for 24-72 hours, followed by Trizol extraction and Direct-zol miniprep (Zymo Research) column purification in accordance with manufacturer protocol.  Uninduced cells of the same genetic background were used as negative controls. For mTOR perturbation experiments, cells were treated with 100nM Torin-1 or 100nM insulin alongside 1ug/ml doxycycline induction and harvested for RNA after 72 hours 37C incubation.

tag: cell line


title: Lig4_C_Cas9_Rep2

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina Miseq or Nextseq sequencing

tag: clone

value: c-Myc

value: JoinT-seq


title: T6115


title: SI_PA4

description: PAC 4 SI

value: Danish Landrace x yorkshire

tag: infection

tag: diet


title: RBC-lysed whole blood from healthy control HIP015_ACK


title: Lig4_C_Cas9_Rep1

tag: cell cylce status

tag: treatment protocol

tag: target locus

value: Miseq


title: SI_PA3

description: PAC 3 SI


title: WT_A_cycling_Cas9_Rep3

value: A

value: cycling

value: nucleofection Cas9:c-Myc gRNA

tag: illumina sequencing


title: RBC-lysed whole blood from healthy control HIP002_ACK


title: SI_PA2

description: PAC 2 SI

value: supplemented with 1 % PAC


title: PBMCs from healthy control HIP002_PBMC_2

value: Un-cryopreserved PBMCs


title: T6117

tag: cell syngeneic orthotopic transplant

value: E0771-luciferase cells

tag: mouse strain

tag: treatment

value: Anti-PD-1 (BE0146, BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: T6109


title: T6112


title: WT_A_cycling_Cas9_Rep2

tag: genotype


title: SI_PA1

description: PAC 1 SI

tag: tissue


title: T6116

value: IgG2a (BE0089,BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: T6100


title: SI_Con6

description: Control 6 SI

value: uninfected

value: control


title: RBC-lysed whole blood from COVID-19 patient ED_139_ACK

tag: cell type

value: Un-cryopreserved RBC-lysed whole blood leukocytes

value: Patient with confirmed COVID-19


title: PBMCs from COVID-19 patient ED_139_PBMC


title: WT_A_cycling_Cas9_Rep1

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

tag: figure displaying results for this library


title: SI_Con5

description: Control 5 SI

value: Small intestine tissue

tag: breed


title: T6098


title: RBC-lysed whole blood from COVID-19 patient ED_132_ACK

tag: disease state


title: WT_A_b_Cas9_Rep3

tag: clone

value: STI + nucleofection Cas9:c-Myc gRNA

value: c-Myc


title: WT_A_b_Cas9_Rep2

value: JoinT-seq


title: PBMCs from COVID-19 patient ED_085_PBMC


title: SI_Con4

description: Control 4 SI

value: Danish Landrace x yorkshire

tag: infection

tag: diet


title: T6097


title: T6114


title: T6099


title: WT_A_b_Cas9_Rep1

value: A

tag: cell cylce status

tag: treatment protocol

value: Miseq


title: SI_Con3

description: Control 3 SI


title: PBMCs from COVID-19 patient ED_084_PBMC


title: RBC-lysed whole blood from COVID-19 patient ED_084_ACK


title: Lig4Ku70K_A1_1_Cas9_Rep2

tag: target locus

tag: illumina sequencing


title: SI_Con2

description: Control 2 SI


title: T6094

tag: cell syngeneic orthotopic transplant

tag: mouse strain


title: HEK293T-RBFOX2- STAMP 24h low rep1

tag: cell line


title: SI_Con1

description: Control 1 SI

tag: tissue


title: A6199

description: Experimental Control group: Mice treated with IgG2a isotype control (LEAN)

source_name: Tumor adjacent adipose Mammary Fat Pad

extract_protocol:
RNA was extracted from tumor adjacent adipose tissue using a kit specific for lipid rich tissue (Norgen Biotek, Ontario, Canada). The integrity of RNA was assessed using Agilent Bioanalyzer and samples with RIN >5.0 were used.
Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kits (non-directional) for Illumina, following manufacturer protocols. mRNA was enriched using oligo-dT beads.

value: Mammary fat pad adipose adjacent to E0771-luciferase breast cancer (tumor adjacent tissue)

tag: lean or obese

value: Lean (low fat diet, LFD, 10% kcal from fat)

tag: treatment


title: PBMCs from COVID-19 patient ED_082_PBMC

tag: cell type

value: Un-cryopreserved PBMCs


title: Lig4Ku70K_A1_1_Cas9_Rep1

tag: genotype

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

tag: figure displaying results for this library


title: RBC-lysed whole blood from COVID-19 patient ED_082_ACK

tag: disease state


title: A6156


title: Lig4Ku70K_A1_1_Cas9_Rep3

tag: clone


title: T6096

value: E0771-luciferase cells


title: Lig4Ku70_A1_1_Cas9_Rep3

tag: cell cylce status


title: SMA220A

city: Boston

first: Kathryn

last: Swoboda

state: MA

address: 185 Cambridge St.

department: Neurology

institute: Massachusetts General Hospital

data_processing:
RNA sequencing FASTA files were trimmed and quality checked using FastQC.
RNA-sequencing reads were then mapped to the hg38 human genome, which had been annotated with exons and introns
Counts for each gene were generated using the package STAR
. Package DESeq2 was used for all differential expression at default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Matrix count file with raw gene counts for each sample

source_name: WholeBlood_SMA-2 CN

extract_protocol:
RNA was extracted using the PAXgene Blood RNA kit (Qiagen, Hilden, Germany; 762164)
RNA-sequencing libraries were prepared from 250 ng of DNase-treated total RNA using the TruSeq Stranded mRNA kit (Illumina)

value: Whole Blood

tag: age (years)

tag: smn2 copy number

value: spinal muscular atrophy


title: A6133

value: IgG2a (BE0089,BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: SMA214


title: A6132

description: Experimental Treatment group: Mice treated with immune checkpoint inhibitor drug anti-PD-1. (LEAN)

value: Anti-PD-1 (BE0146, BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: Lig4Ku70_A1_1_Cas9_Rep2

data_processing:
Library strategy: JoinT-seq
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm10 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

tag: treatment protocol

tag: target locus

tag: illumina sequencing


title: Lig4Ku70_A1_1_Cas9_Rep1


title: SMA-187-7month


title: Neutrophils from healthy donor HIP002 CPTNeut

description: CPTNeut

source_name: Isolated peripheral neutrophils from CPT pellet

value: Un-cryopreserved neutrophils

value: Healthy control


title: A6131

tag: cell syngeneic orthotopic transplant

tag: mouse strain


title: Lig4_A1_c_Cas9_Rep3

value: Emu-Bcl2, Lig4-/-


title: SMA176A

tag: tissue


title: RBC-lysed whole blood from healthy donor HIP002 ACK

description: ACK

value: Un-cryopreserved RBC-lysed whole blood leukocytes


title: A6130

tag: lean or obese

tag: treatment


title: Ctrl476

source_name: WholeBlood _Healthy

value: healthy control


title: SMA244A


title: Lig4_A1_c_Cas9_Rep1

tag: genotype

value: STI + nucleofection Cas9:c-Myc gRNA

value: c-Myc

value: JoinT-seq


title: PBMCs from COVID-19 patient 570_PBMC

tag: cell type

value: Patient with confirmed COVID-19


title: A6127

value: Mammary fat pad adipose adjacent to E0771-luciferase breast cancer (tumor adjacent tissue)


title: Lig4_A1_c_Cas9_Rep2

value: Miseq

tag: number of raw reads used for normalization

tag: pipeline used for the analysis


title: Lig4_A1_cycling_Cas9_Rep2

value: cycling

value: nucleofection Cas9:c-Myc gRNA

tag: figure displaying results for this library


title: Ctrl445B

value: Whole Blood

tag: disease state


title: Ctrl-430-7month


title: RBC-lysed whole blood from COVID-19 patient ED_080_ACK


title: Lig4_A1_cycling_Cas9_Rep3

tag: clone

tag: cell cylce status


title: RBC-lysed whole blood from COVID-19 patient 569_ACK


title: PBMCs from COVID-19 patient 568_PBMC

value: Un-cryopreserved PBMCs


title: A6126

value: Lean (low fat diet, LFD, 10% kcal from fat)


title: Lig4_A1_cycling_Cas9_Rep1


title: Ctrl-252-6month

tag: age (years)

tag: smn2 copy number


title: Lig4L_A1_Cas9_Rep3

value: Emu-Bcl2, Lig4-/- +Lig4

tag: treatment protocol

tag: target locus


title: RBC-lysed whole blood from COVID-19 patient 568_ACK


title: A6115

description: Experimental Control group: Mice treated with IgG2a isotype control (OBESE)

tag: cell syngeneic orthotopic transplant

value: Obese (high fat diet, HFD, 60% kcal from fat)

value: IgG2a (BE0089,BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: PBMCs from COVID-19 patient 566


title: SNU719 small fraction sequencing, replicate 3

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: SNU719 cells

data_processing:
Alignment using bowtie2
Genome_build: hg38
Supplementary_files_format_and_content: counts, tsv

source_name: Cell line

extract_protocol:
TRIzol
Illumina TruSeq Small RNA Library Prep Kit

tag: cell line

value: Gastric adenocarcinoma

tag: virus

value: EBV+

tag: molecule subtype

value: small RNA


title: A6114

tag: mouse strain

tag: lean or obese

tag: treatment


title: PBMCs from COVID-19 patient 565

tag: cell type


title: Lig4L_A1_Cas9_Rep2

tag: genotype

value: STI + nucleofection Cas9:c-Myc gRNA

tag: illumina sequencing

tag: number of raw reads used for normalization

tag: pipeline used for the analysis


title: SNU719 small fraction sequencing, replicate 2

description: SNU719 cells


title: PBMCs from COVID-19 patient 569_PBMC

tag: disease state


title: A6129


title: A6109

description: Experimental Treatment group: Mice treated with immune checkpoint inhibitor drug anti-PD-1. (OBESE)

value: Anti-PD-1 (BE0146, BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: Lig4L_A1_Cas9_Rep1

tag: clone

tag: cell cylce status

value: c-Myc

value: JoinT-seq

tag: figure displaying results for this library


title: SNU719 small fraction sequencing, replicate 1

description: SNU719 cells


title: PBMCs from COVID-19 patient 564_B

value: Patient with confirmed COVID-19


title: Ctrl307B

tag: tissue

tag: age (years)

tag: smn2 copy number

value: healthy control


title: PBMCs from COVID-19 patient 564_A


title: A6108

tag: cell syngeneic orthotopic transplant

value: Mammary fat pad adipose adjacent to E0771-luciferase breast cancer (tumor adjacent tissue)


title: A6125


title: Akata small fraction sequencing, replicate 3

description: Akata cells

tag: cell line

value: Akata

value: B-Cell lymphoma cell line

tag: virus

tag: molecule subtype


title: Lig4_A1_b_Cas9_Rep2

value: Emu-Bcl2, Lig4-/-

tag: treatment protocol

tag: target locus

value: Miseq


title: PBMCs from COVID-19 patient 563

tag: cell type

value: Un-cryopreserved PBMCs


title: Lig4_A1_b_Cas9_Rep1

tag: genotype

tag: illumina sequencing


title: A6105

tag: mouse strain

tag: lean or obese

value: Obese (high fat diet, HFD, 60% kcal from fat)

tag: treatment


title: A6107

value: IgG2a (BE0089,BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: Akata small fraction sequencing, replicate 2

description: Akata cells


title: PBMCs from COVID-19 patient 562

tag: disease state


title: Ku70_A1_Cas9_Rep3

data_processing:
Library strategy: JoinT-seq / LAM-HTGTS / HTGTS-Rep-ReOther: Join
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm10 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify rejoining events and then combined to translocations using JoinT
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

value: Emu-Bcl2, Ku70-/-

tag: clone

tag: cell cylce status

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

value: JoinT-seq / LAM-HTGTS / HTGTS-Rep-Rejoin

tag: figure displaying results for this library


title: Akata small fraction sequencing, replicate 1

description: Akata cells

tag: cell line

value: EBV+

value: small RNA


title: iTE_PD_D3

city: THUWAL

first: Samhan

middle: M.

last: Alsolami

address: Thuwal 23955

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
processed in sequentia platoform A.I.R
Supplementary_files_format_and_content: FPKM
Supplementary_files_format_and_content: TMM

source_name: TROPHECTODERM

growth_protocol: EPS has been cultured in N2B27 with LCDM on iMEF, then these are dissociated, MEF was removed by pasting these cells on gelatin for 30 minutes. These cells are then differentiated on laminin to TE with N2B27 medium with apprioprate trreatments

extract_protocol:
RNA was extracted using qiagen RNeasy kit and QC'ed with bioanalyzers before library preparations.
Directional library was preparation was prepaed
library was directional and pair-end sequencing was performed.

treatment_protocol: EPS were differentiated toward TE fate with PD0325901, A83-01, and BMP4 treatment combinations, for a period of three days.

value: human extended pluripotent stem (EPS) cells

tag: agent


title: A6103

tag: cell syngeneic orthotopic transplant

value: Anti-PD-1 (BE0146, BioXcell, West Lebanon, NH), IP, 200ug per mouse in 50ul)


title: iTE_PD_BMP_D3


title: A6101


title: iTE_PD_A83_D3


title: gTLE3 KO_1 enza

city: Amsterdam

first: Sander

last: Palit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
A differential analysis of TLE3KO vs Wildtype samples was done using DESeq2. The DESeq2 result were sorted on the DESeq2 statistic in decreasing order and used as input for GSEA.
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples

source_name: LNCaP

growth_protocol: Library-infected LNCaP cells were cultured in RPMI medium supplemented with 10% FBS, 1% penicillin/streptomycin.

extract_protocol:
RNA extraction using Trizol
gNT_enza: GATCAGA
gTLE3 KO_1_enza: GTTTCGG
gTLE3 KO_2_enza: ATTCCTT

treatment_protocol: Library-infected LNCaP cells were cultured in RPMI medium supplemented with 10% FBS, 1% penicillin/streptomycin in the presence of 10 uM enzalutamide

value: prostate cancer

tag: genotype/variation

value: TLE3 KO

tag: tag


title: Ku70_A1_Cas9_Rep1

first: Marie

last: Le Bouteiller

address: 269 campus drive

tag: treatment protocol

value: STI + nucleofection Cas9:c-Myc gRNA

tag: target locus

value: c-Myc


title: Lig4_A1_b_Cas9_Rep3

tag: genotype

tag: illumina sequencing

value: JoinT-seq


title: iTE_PD_A83_BMP_D3

tag: cell type


title: Lig4_A1_Cas9_Rep3


title: A6104

value: Mammary fat pad adipose adjacent to E0771-luciferase breast cancer (tumor adjacent tissue)

tag: mouse strain

tag: lean or obese

tag: treatment


title: A6096


title: iTE_BMP_D3


title: A6098


title: A6097


title: iTE_A83_BMP_D3


title: gTLE3 KO_2 enza

tag: disease state


title: 5: siRNA control exp 3

type: mixed

city: Nanjing

first: Yan

last: Zeng

state: Jiangsu

address: XuanWu District, No.1 WeiGang

institute: Nanjing Agricultural University

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).   Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing:
BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.
Data processed by Bluefuse is absolute value.  Individual spots were inspected to correct for anormalities during microarray fabrication.

source_name: human cell line

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: 293T cells were grown under standard conditions

extract_protocol: 293T RNA was isolated using Trizol (Invitrogen)

treatment_protocol: 293T cells were transfected using Lipofectamine 2000 (Invitrogen)

tag: tissue

value: human 293T cells

value: Control

molecule: other

source_name: Reference DNA

value: synthetic DNA oligos corrresponding to human miRNAs


title: 6: siRNA Exp5 exp 3

value: Exp5 siRNA


title: WT_A_Cas9_Rep3

city: Stanford

institute: Stanford University

source_name: v-Abl pro B cells

tag: clone

value: A

tag: cell cylce status

value: Miseq

tag: number of raw reads used for normalization

tag: pipeline used for the analysis


title: Lig4_A1_Cas9_Rep1

value: Emu-Bcl2, Lig4-/-

value: JoinT-seq / LAM-HTGTS / HTGTS-Rep-Rejoin

tag: figure displaying results for this library


title: A6093

tag: cell syngeneic orthotopic transplant

value: Obese (high fat diet, HFD, 60% kcal from fat)


title: Ku70_A1_Cas9_Rep2

value: Emu-Bcl2, Ku70-/-


title: Lig4_A1_Cas9_Rep2


title: 3: siRNA control exp 2

tag: genotype/variation


title: In-vitro Leydig differentiation Day 14

city: Ann Arbor

first: Qianyi

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.13.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2a.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.13.
Gene expressoin matrix was generated using Drop-seq tools v1.13.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: Testis

growth_protocol: Testes were collected from adult C57BL/6 males, dissociated into a single cell suspension, and sorted for Sca1+/cKit- cells. Cells were plated into a 24 well, Matrigel-coated plates at a density of 100,000 cells/well in DMEM/F12 supplemented with 10% FBS and 1X Normocin. FACs sorted cells were initially recovered for 18 hours in DMEM+10%FBS and then the cells were expanded for 3 days in DMEM/F12 supplemented with 1X Normocin, 10 ng/ml PdgfAA, 10 ng/ml PdgfBB, 0.5 uM SAG, and 10 ng/ml Fgf2. After 3 days, the expansion media was replaced with differentiation media- DMEM/F12 supplemented with 1X Penicillin/streptomycin, 10 ng/ml PdgfAA, 10 ng/ml PdgfBB, 0.5 uM SAG, 10 ng/ml Fgf2, 5 mM LiCl2, and 10 uM DAPT.

extract_protocol:
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation.
A total of 600 pg of amplified cDNA per sample was used for a Nextera XT library preparation (Illumina).

tag: strain

tag: age

value: adult 8-12 weeks

value: testis

tag: culture day

value: Day 14


title: 4: siRNA Exp5 exp 2


title: WT_A_Cas9_Rep2

tag: genotype

tag: treatment protocol

value: STI + nucleofection Cas9:c-Myc gRNA

tag: target locus

tag: illumina sequencing


title: 2: siRNA Exp5 exp 1


title: In-vitro Leydig differentiation Day 7

value: Day 7


title: 17-postconception weeks-  fetal livers

city: Shenzhen

first: Hou

last: Xianliang

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: fetal livers

extract_protocol: For Spatial Transcriptomics-seq, the fetal liver cells were dissociated into single cells suspensions using Ficoll-Paque buffer (Sigma), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

value: liver

value: 17 weeks post-conception


title: WT_A_Cas9_Rep1

value: c-Myc


title: 1: siRNA control exp 1

value: human 293T cells

value: Control


title: 8-postconception weeks-  fetal livers

value: 8 weeks post-conception


title: In-vitro Leydig differentiation Day 4

value: Day 4


title: iTE_A83_D3

tag: cell type

value: human extended pluripotent stem (EPS) cells

tag: agent


title: PBMCs from COVID-19 patient ED_080_PBMC

source_name: Peripheral blood mononuclear cells

value: Un-cryopreserved PBMCs

tag: disease state

value: Patient with confirmed COVID-19


title: Bdkai2-1_KAR1_rep3

status: Public on May 07 2021

city: CRAWLEY

first: Mark

last: Waters

state: WA

address: 35 Stirling Hwy

department: School of Molecular Sciences

institute: The University of Western Australia

description:
Sample 30
2-14-26 vs. 6-18-30.xlsx
5-17-29 vs. 6-18-30.xlsx

data_processing:
Basecalls performed using Illumina Nextseq
Data was trimmed based on read length and quality. Minimum number of nucleotides in reads = 50, Software: CLC Genomics Workbench 11.0
CLC RNA-Seq analysis was carried out. Min. length fraction = 0.8, Min. similarity fraction = 0.8, Maximum number of mismatches allowed 2, Unspecific match limit = 10, Software: CLC Genomics Workbench Tool 11.0
Genome_build: Brachypodium distachyon strain Bd21 v3 27-MAR-2018, NC_016131, NC_016132, NC_016133, NC_016134, NC_016135, NC_011032
Supplementary_files_format_and_content: MS Excel, gene expressions
Supplementary_files_format_and_content: Text file, matrix table with RPKM values for every gene and every sample

organism: Brachypodium distachyon

growth_protocol: Seeds were soaked, de-glumed, and surface sterilized by treating with 70% ethanol for 30s, followed by 10% sodium hypochlorite for 3 min, followed by 4 rinses with sterile deionized water. Seeds were sown on a double layer of saturated, sterile 3MM Whatman paper and sealed in 100 mm square petri dishes. Pllates were incubated at 4 degC in the dark for 72 h. Seeds were then manually transferred to solid 0.5xMS medium (pH 5.9, no sucrose, 0.8% w/v agar) and incubated at 22 degC day, 16 degC night on a 16 h/8h day/night cycle, with broad-spectrum white light supplied at 120 µmol/m2/s, for a further 72 h. Approximately 10 seedlings per sample were transferred to 25 mL liquid 0.5xMS medium (pH 5.9) in a 250-mL conical flask, and shaken at 70 rpm under the same growth conditions, for a further 24 h to acclimatize the seedlings to growth in liquid.

extract_protocol:
Whole seedlings were recovered from flasks, shoot tissue dissected using microscissors and collected in a 2-mL microfuge tube. Tissue was immediately frozen in liquid nitrogen, and ground to a fine powder with a bead mill. RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich).
Paired-end libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturers' protocol.

treatment_protocol: Treatment solutions (acetone, KAR1, KAR2, rac-GR24) were added directly to the flasks by manual pipetting. Incubation and shaking continued for a further 4 h before seedlings were harvested. Treatments within a replicate were peformed in parallel.

tag: tissue

value: whole shoots

tag: treatment

value: 1 µM KAR1

tag: developmental stage

value: four-day-old seedlings


title: WT_KAR1_rep3

description:
Sample 26
1-13-25 vs. 2-14-26.xlsx
2-14-26 vs. 6-18-30.xlsx
2-14-26 vs. 10-22-34.xlsx

value: WT


title: Bdkai2-2_KAR1_rep3

description:
Sample 34
2-14-26 vs. 10-22-34.xlsx
9-21-33 vs. 10-22-34.xlsx


title: Bdkai2-2_mock_rep2

description:
Sample 21
1-13-25 vs. 9-21-33.xlsx
9-21-33 vs. 10-22-34.xlsx
9-21-33 vs. 11-23-35.xlsx
9-21-33 vs. 12-24-36.xlsx

value: mock


title: Bdkai2-1_KAR2_rep3

description:
Sample 31
3-15-27 vs. 7-19-31.xlsx
5-17-29 vs. 7-19-31.xlsx

value: 1 µM KAR2


title: Bdkai2-2_GR24_rep3

description:
Sample 36
4-16-28 vs. 12-24-36.xlsx
9-21-33 vs. 12-24-36.xlsx

value: 10 µM rac-GR24


title: Bdkai2-2_mock_rep3

description:
Sample 33
1-13-25 vs. 9-21-33.xlsx
9-21-33 vs. 10-22-34.xlsx
9-21-33 vs. 11-23-35.xlsx
9-21-33 vs. 12-24-36.xlsx


title: Bdkai2-1_GR24_rep3

description:
Sample 32
4-16-28 vs. 8-20-32.xlsx
5-17-29 vs. 8-20-32.xlsx


title: Bdkai2-2_KAR2_rep3

description:
Sample 35
3-15-27 vs. 11-23-35.xlsx
9-21-33 vs. 11-23-35.xlsx


title: Bdkai2-1_KAR2_rep2

description:
Sample 19
3-15-27 vs. 7-19-31.xlsx
5-17-29 vs. 7-19-31.xlsx


title: Bdkai2-2_KAR1_rep2

description:
Sample 22
2-14-26 vs. 10-22-34.xlsx
9-21-33 vs. 10-22-34.xlsx


title: Bdkai2-2_KAR2_rep2

description:
Sample 23
3-15-27 vs. 11-23-35.xlsx
9-21-33 vs. 11-23-35.xlsx


title: WT_mock_rep3

description:
Sample 25
1-13-25 vs. 2-14-26.xlsx
1-13-25 vs. 3-15-27.xlsx
1-13-25 vs. 4-16-28.xlsx
1-13-25 vs. 5-17-29.xlsx
1-13-25 vs. 9-21-33.xlsx


title: Bdkai2-1_GR24_rep2

description:
Sample 20
4-16-28 vs. 8-20-32.xlsx
5-17-29 vs. 8-20-32.xlsx


title: Bdkai2-1_mock_rep3

description:
Sample 29
1-13-25 vs. 5-17-29.xlsx
5-17-29 vs. 6-18-30.xlsx
5-17-29 vs. 7-19-31.xlsx
5-17-29 vs. 8-20-32.xlsx


title: WT_GR24_rep3

description:
Sample 28
1-13-25 vs. 4-16-28.xlsx
4-16-28 vs. 8-20-32.xlsx
4-16-28 vs. 12-24-36.xlsx