title: SAP 14

city: shanghai

first: li

last: zhang

state: shanghai

address: pujian road 160

department: Renji Hospital stem cell centre

institute: li zhang

description: SAP 14

data_processing:
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R, http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html) was utilized for differential expression analysis.
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: liver

extract_protocol:
Liver were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: strain

value: Balb/c

value: 6 week

value: wild type

tag: treatment

value: caerulein


title: X611608168

status: Public on Apr 06 2022

type: SRA

city: New York

first: Christian

last: Forst

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: tab-delimited  file using log2-transformed CPM values for each sample

molecule: total RNA

organism: Mustela putorius furo

source_name: whole blood

extract_protocol:
RNA was extracted from ferret blood using the Mouse RiboPure-Blood RNA Isolation Kit (Ambion)
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer-supplied protocol. Libraries were sequenced 100 bp paired-end to a depth of approximately 40 million host genome reads on Illumina HiSeq 2500 instruments.

treatment_protocol: Adult ferrets were infected intranasally with the A/California/07/2009 virus at a dose of 106 plaque-forming units (PFU). The animals were monitored daily for the severity of clinical disease using weight loss.

tag: Sex

value: Female

tag: age

value: Adult

tag: ferret id

tag: day

tag: infection agent

tag: viral load

tag: rel. weight


title: FMB_3013_D5

data_processing:
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: normalized.log2CPM.tsv (tab-delimited  file using log2-transformed CPM values for each sample)

value: Male

tag: ferretid

tag: infectionagent

tag: viralload

tag: relweight

tag: tissue

value: whole blood


title: 14Rik #1 total-RNA

city: Boston

first: Hanneke

last: Vlaming

state: MA

address: 45 Shattuck St

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: 14Rik #1 total-RNA

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences plus spliced versions of these inserts as called by STAR. STAR v2.7.0 was run on replicates 2-4 using flags --outSJfilterOverhangMin 10 4 4 4 --peOverlapNbasesMin 10 --peOverlapMMp 0.08 --alignEndsType EndToEnd --outFilterMismatchNmax 5 --scoreDelOpen -10 --scoreInsOpen -10. The detected splice junctions were filtered down to only junctions on the + strand with >10 read counts and >25% of the maximum counts for other junctions detected in the same insert. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: mESCs were cultured in KO-DMEM media (Gibco) supplemented with 15% KO Serum replacement (Gibco), GlutaMAX, penicillin-streptomycin, non-essential amino acids, beta-mercaptoethanol, 1000 U/ml LIF (Cell Guidance Systems), 1µM MEK inhibitor (PD0325901; Stemgent), and 3µM GSK3 inhibitor (CHIR99021; Stemgent). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol:
For total-RNA, >5M library-containing cells was pelleted and resuspended in Trizol (Ambion). RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer that annealed 287nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).

tag: cell line

value: F121-9 wt mESCs

tag: library integration location

value: 4930461G14Rik TSS + 102 (CAST allele)

tag: assay

value: RNA-based INSERT-seq

tag: condition

value: Untreated


title: SAP 13

country: China

description: SAP 13

tag: strain

tag: genotype

tag: treatment


title: FMB_3026_D2

tag: Sex

tag: age


title: gDNA corresponding to run-on-RNA #2

description: gDNA corresponding to run-on-RNA #2

library_source: genomic

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)


title: SAP 12

description: SAP 12


title: FMB_3034_D8

tag: day


title: SAP 11

description: SAP 11


title: FMB_3025_D3


title: run-on-RNA #2

description: run-on-RNA #2

extract_protocol:
For nascent RNA, library-containing cells were permeabilized and run on mostly as described (Reimer et al, 2021), but with a few changes. For permeabilization, buffers W and P were supplemented with 1 mM EGTA, and buffer F was supplemented with 1 mM EDTA. Cells were resuspended in 500 µL Buffer W, 10 mL Buffer P was added, and this was incubated on a Nutator for 1 minutes, then 6 minutes on ice. Cells were washed once with 10mL buffer W, before being resuspended in Buffer F. Run-on was performed on 30M permeabilized cells, and in the 2X run-on reaction mix MgCl2 was present at 10 mM, SUPERase-In at 0.4 U/µL and (biotin-)rNTPs are at 50 µM each. Run-on was performed at 37°C for 15 minutes, and Biotin-11-C/UTP (Perkin-Elmer) were mixed with regular rGTP and rATP (New England BioLabs). After RNA isolation using the Total RNA Purification Kit (Norgen Biotek Corp), biotinylated RNAs were immediately bound to Streptavidin M-280 magnetic beads (ThermoFisher) and binding and washing was done as described.
First, nascent RNA still bound to magnetic beads was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 that annealed 221nt downstream of the variable regions. cDNA from nascent RNA was removed from the beads with heat and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 19 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: 14Rik #1 gDNA

description: 14Rik #1 gDNA

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
In a first round of PCR, the 14Rik lincRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.


title: FMB_3014_D3


title: SAP 15

description: SAP 15


title: FMB_3036_D5


title: run-on-RNA #1

description: run-on-RNA #1


title: SAP 10

description: SAP 10


title: Control 8

description: Con 8

value: control


title: total-RNA #4

description: total-RNA #4

extract_protocol:
For total-RNA, >5M library-containing cells was pelleted and resuspended in Trizol (Ambion). RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: FMB_3004_D1


title: FMB_3031_D8


title: FMB_3036_D1


title: FMB_3013_D3


title: FMB_3032_D2


title: FMB_3008_D5


title: Control 7

description: Con 7


title: FMB_3029_D5


title: FMB_3005_D5


title: Control 6

description: Con 6


title: heart failure atient group (GH) [H4-BA]

city: shijiazhuang

first: xitian

last: hu

address: No.9 Fangbei Road, Shijiazhaung City 050000, Hebei Province, China

department: Department of Cardiovasology

institute: Shijiazhuang People’s Hospital

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

organism: Homo sapiens

source_name: heart failure atient group (GH)

extract_protocol:
HiSeq LncRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protacal

value: blood

tag: subject status

value: heart failure atient


title: FMB_3021_D1


title: FMB_3004_D2


title: gDNA corresponding to run-on-RNA #1 and total-RNA #4


title: heart failure atient group (GH) [H3-BA]


title: Control 5

description: Con 5

value: liver

value: Balb/c


title: FMB_3021_D5


title: Cardiac fibrosis patient group (GC) [C5-BA]

source_name: Cardiac fibrosis patient group (GC)

value: Cardiac fibrosis patient


title: FMB_3025_D5


title: FMB_3030_D2


title: Control 4

description: Con 4

value: 6 week

value: wild type


title: Control 3

description: Con 3


title: FMB_3022_D3

value: Adult


title: heart failure atient group (GH) [H5-BA]


title: Cardiac fibrosis patient group (GC) [C4-BA]


title: FMB_3036_D8

value: Male


title: FMB_3006_D1

value: whole blood


title: FMB_3004_D8


title: healthy controls group (GD) [D3-BA]

source_name: healthy controls group (GD)

value: healthy controls


title: FMB_3024_D3


title: FMB_3002_D3


title: healthy controls group (GD) [D2-BA]


title: S2 mouse, WT

city: Berlin

first: Valerie

last: Begay

address: Robert-Rössle-Str. 10

country: Germany

institute: Max Delbrück Center

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Reads were mapped to mm9 and hetGla2 respectively, using STAR version 2.5.3a
Raw reads were generated using htseq-count version 0.10.0
RNA differential gene expression was performed with DESeq2
Genome_build: hetGla2/hetGla_Female_1.0 and mm9
Supplementary_files_format_and_content: Normalized counts for mouse and naked mole rat samples

source_name: spleen

extract_protocol:
Spleens were dissected and fast frozen on dry-ice. Total RNA was extracted from 3 biological replicates per group using RNeasy extraction kit from Qiagen. RNA was sequenced on the Illumina HiSeq2500 platform according to the manufacturer's instruction at Macrogen (Korea)
Illumina TruSeq stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; library type: Illumina-transcriptome, library: TruSeq stranded mRNA, read length: Illumina 100bp PE

treatment_protocol: None. Heathly naked mole-rats kept under normal housing conditions (29°C, 50-60% humidity) and healthy mice kept at about 22°C under 55% humidity, 12h light/dark cycle.

value: spleen

value: male

tag: age (months)


title: S3 mouse, WT


title: S1 mouse, WT


title: SAP 29

tag: disease state

value: severe acute pancreatitis


title: FMB_3032_D1

tag: ferretid

tag: infectionagent


title: healthy controls group (GD) [D1-BA]


title: FMB_3033_D5

tag: viralload

tag: relweight


title: FMB_3025_D8

tag: tissue


title: FMB_3029_D3


title: SAP 28


title: FMB_3011_D2


title: Cardiac fibrosis patient group (GC) [C1-BA]


title: heart failure patient group (GH), 3

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: miRNA.count.txt

source_name: heart failure patient group (GH)

extract_protocol:
HiSeq miRNA-Seq
RNA libraries were prepared for sequencing using standard illumina protacal

value: heart failure patient


title: FMB_3031_D2


title: Cardiac fibrosis patient group (GC), 3


title: FMB_3034_D2


title: FMB_3006_D8


title: SAP 26


title: FMB_3010_D5


title: FMB_3036_D3


title: SAP 25


title: FMB_3008_D8


title: Cardiac fibrosis patient group (GC), 2


title: SAP 27


title: SAP 24


title: FMB_3007_D8


title: FMB_3005_D1


title: FMB_3022_D1


title: heart failure patient group (GH), 2


title: FMB_3015_D1


title: healthy controls group (GD), 3


title: Cardiac fibrosis patient group (GC), 1


title: SAP 22


title: FMB_3013_D1


title: FMB_3001_D2


title: SAP 21


title: FMB_3010_D1


title: healthy controls group (GD), 2


title: heart failure patient group (GH), 1


title: FMB_3006_D5


title: AP 19

value: acute pancreatitis


title: FMB_4053_control

value: Control


title: FMB_4054_control


title: healthy controls group (GD), 1

value: blood


title: FMB_4052_control


title: AP 18


title: PC9_short_washout_3 [RNA-seq]

city: Cambridge

first: Paul

middle: D

last: Smith

address: AstraZeneca CRUK Cambridge Institute, Robinson Way

country: United Kingdom

institute: AstraZeneca

data_processing:
Fastq files were aligned using HISAT2 (v2.1.0)
Counts were quanitied using Salmon (v0.8.2) using Ensembl v79 annotations.
tximport was used to generate gene level count data using option countsFromAbundance = "lengthScaledTPM" and a log2 transcripts per kilobase million, log2(TPM +0.01), abundance matrix.
Genome_build: hg38
Supplementary_files_format_and_content: Count matricies.

source_name: Cell Line

growth_protocol: NCI-H1975 human NSCLC adenocarcinoma cells were obtained from American Type Culture Center (ATCC) and were grown in RPMI 1640, supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin-Streptomycin. All cells were maintained and propagated as monolayer cultures at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) and RNA extracted using the Qiacube HT according to manufacturer’s instructions, and RNA concentration quantified using the Qubit fluorometer.
Illumina mRNA TruSeq library was used for library preparation.
RNA-seq was sequenced on 9 lanes of Illumina HiSeq4000 with paired end 150bp reads by the CRUK Genomics Core Facility.

treatment_protocol: The NSCLC EGFR mutant cell lines (PC9, NCI-H1975, HCC827, and HCC2935) were treated with 500 nM osimertinib for 21 days (osimertinib DTPs). Cells were either harvested immediately or washed 2x with PBS and then replaced with drug-free media for a further 24 hrs. (short washout), or for a longer time-point (long washout) until exponential cell proliferation resumed (PC9: 7 days; NCI-H1975: 3 days; HCC827: 4 days; HCC2935: 10 days) and then harvested. In parallel, parental cell lines were grown in drug-free media for 21 days then treated with 500 nM osimertinib for 24 hrs. (osimertinib acute) or vehicle DMSO control for 24 hrs. (DMSO control).   Experiment was done using biological triplicates. There are 60 total RNA-seq samples.

tag: cell line

value: osimertinib DTPs short washout 24 hrs.


title: AP 16

value: liver


title: AP 17

value: Balb/c


title: FMB_3025_d5


title: PC9_short_washout_1 [RNA-seq]


title: PC9_short_washout_2 [RNA-seq]


title: FMB_3021_d5


title: AP 15


title: FMB_3022_d3


title: FMB_3004_d2


title: FMB_3021_d1


title: FMB_3027_D2


title: PC9_osi_DTP_3 [RNA-seq]

value: osimertinib DTPs 3w.


title: AP 13

value: 6 week


title: FMB_3035_D3


title: PC9_osi_DTP_2 [RNA-seq]


title: PC9_osi_DTP_1 [RNA-seq]


title: AP 12

value: wild type


title: FMB_3013_D8

value: Adult

value: no sample


title: AP 11


title: PC9_osi_acute_3 [RNA-seq]

value: osimertinib acute 24 hrs.


title: FMB_4051_control

value: Male

value: whole blood


title: FMB_3004_D3


title: FMB_3032_d1


title: FMB_3015_D3


title: Con 10

value: healthy control


title: FMB_3031_D1


title: PC9_osi_acute_2 [RNA-seq]


title: FMB_3009_D8


title: FMB_3014_D5


title: FMB_3012_D1


title: FMB_3033_D8


title: Con 9


title: PC9_osi_acute_1 [RNA-seq]


title: PC9_long_washout_7d_3 [RNA-seq]

value: osimertinib DTPs long washout 7 days


title: PC9_long_washout_7d_2 [RNA-seq]


title: FMB_3024_D5


title: Con 7


title: FMB_3007_D2


title: FMB_3005_D3


title: Con 6


title: FMB_3023_D5


title: FMB_3023_D2


title: FMB_3033_D3


title: PC9_DMSO_3 [RNA-seq]

value: DMSO


title: Con 5


title: PC9_long_washout_7d_1 [RNA-seq]


title: Con 3


title: PC9_DMSO_2 [RNA-seq]


title: FMB_3001_D3


title: FMB_3011_D5


title: FMB_3001_D5


title: PC9_DMSO_1 [RNA-seq]


title: Con 8


title: Con 1


title: FMB_3035_D2


title: HCC827_short_washout_3 [RNA-seq]


title: FMB_3021_D2


title: FMB_3008_D2


title: FMB_3029_D1


title: HCC827_short_washout_2 [RNA-seq]


title: FMB_3007_D3


title: FMB_3030_D8


title: S12 at R+3

city: Yerevan

first: Arsen

last: Arakelyan

state: Yerevan

address: 7 Hasratyan St.

department: Bioinformatics

country: Armenia

institute: Institute of Molecular Biology NAS RA

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for demultiplexing and basecalling.
The 3′ adaptor sequences were removed, and reads with the trimmed length <18 bp were discarded using Cutadapt v2.7. Read quality control was performed with FastQC v0.11.9 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Trimmed and filtered reads were mapped with bowtie (v1.1.1) to the reference genome (GRCh38.p12)
RUVSeq (Risso et al., 2014) was used to correct for batch effects and other unwanted variations.  Differentially expressed genes were then identified with edgeR (Robinson et al., 2010). Genes with false discovery rate adjusted p-value (FDR) less than 0.05 and log2 fold change greater than 1 were considered significantly differentially expressed genes.
Assembly: GRCh38.p12
Supplementary files format and content: comma-separated matrix table with CPM counts for every gene and every sample produced with RUVSeq

source_name: peripheral blood sEVs

extract_protocol:
sEVs were isolated from peripheral blood (PB) samples of using the ExoQuick Plasma preparation and sEV precipitation kit (Cat # EXOQ5TM, System Biosciences, CA, USA). Samples were subsequently centrifuged at 10,000 rpm for 5 minutes, incubated with the exosome precipitation solution and refrigerated at 4ºC for 30 minutes. After centrifugation at 1,500 x g for 30 minutes at 4ºC, a beige-colored pellet was dissolved in sterile 1xPBS.
Total RNA from sEVs was isolated using miRNeasy kit following manufacturer's protocol (Cat#217084, Qiagen). RNA sample quality was assessed by NanoDrop and Agilent 2100 BioAnalyzer. Samples with RNA integrity number (RIN) above 7, OD260/280: 2, and OD260/230 ≥ 2 were used. In addition, RNA degradation and contamination were monitored on 1% agarose gels before RNA-Seq. RNA quality was assessed using an Agilent TapeStation (Agilent, Palo Alto, CA, USA), and RNA concentration was quantified by Qubit 4.0 spectrophotometer. The library for small RNA sequencing was prepared using the Smarter smRNA-seq kit for Illumina (Takara Bio Inc., USA). The quantity and quality of amplified libraries were evaluated using Qubit (Invitrogen, Carlsbad, CA, USA) and Agilent TapeStation high sensitivity D1000 Screen Tape. Small RNA-seq libraries were sequenced using single-end 75 base pairs (SE75) sequencing chemistry on NextSeq 500 instruments following the manufacturer's protocols (Illumina).

value: peripheral blood sEVs

tag: time point


title: HCC827_short_washout_1 [RNA-seq]


title: S31 at L-10


title: FMB_3026_D5


title: S31 at R+3


title: HCC827_osi_DTP_3 [RNA-seq]


title: FMB_3034_D3


title: S30 at R+3


title: FMB_3022_D5


title: FMB_3006_D3


title: FMB_3002_D2


title: HCC827_osi_DTP_2 [RNA-seq]


title: S12 at L-10


title: FMB_3010_D2


title: S30 at L-10


title: FMB_3028_D8


title: FMB_3032_D3


title: S39 at R+3


title: FMB_3012_D3


title: HCC827_osi_acute_2 [RNA-seq]


title: HCC827_osi_DTP_1 [RNA-seq]


title: FMB_3003_D5


title: S34 at R+3


title: FMB_3010_D3

value: poor monolayer


title: FMB_3031_D3


title: FMB_3021_D3


title: FMB_3025_D1


title: HCC827_osi_acute_3 [RNA-seq]


title: S34 at L-10


title: HUVECs - VEGF+VP_3

city: Shanghai

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap(v1.0.8) according  to  the gene expression indifferent  samples.  Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by bonferroni.
Genome_build: hg38
Supplementary_files_format_and_content: text files include read statistics (total read number, adapter read number, etc)  for each Sample.
Supplementary_files_format_and_content: tab-delimited text files include raw counts and FPKM values for each Sample.

source_name: cell line

extract_protocol:
Total RNA was extracted from the treated-HUVECs using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Cells were  homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3mL chloroform/isoamyl alcohol (24:1). The mix was shackedvigorously for 15s, and then centrifugedat 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phasewhere RNA remained was transferredinto a new tube withequal volume of supernatant of isopropyl alcohol,then centrifugedat 13,600rpm for 20 minutes at 4°C.After deserting the supernatant,the RNA pellet was washed twice with 1 mL75% ethanol,then the mix was centrifuged at 13,600rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

tag: cell type

value: HUVEC

value: VEGF+Verteporfin treated


title: HCC827_long_washout_96h_3 [RNA-seq]

value: osimertinib DTPs long washout 96 hrs.


title: S39 at L-10


title: HCC827_osi_acute_1 [RNA-seq]


title: FMB_3007_D1


title: HCC827_long_washout_96h_2 [RNA-seq]


title: FMB_3009_D1


title: HCC827_long_washout_96h_1 [RNA-seq]


title: FMB_3015_D5


title: HCC827_DMSO_3 [RNA-seq]


title: H3K27Ac_H1975_osi_DTP_AZD5153_combo_2

data_processing:
Fastq files were aligned using bwa mem (version 0.7.17)
Bams were deduplicated using biobambam v2.0.87 (bamsormadup) and narrowPeaks were called using MACS2 (v2.2.6)
Consensus peaks were geneted by opening a 500bp windown around each peak summit and a set of non-overlapping regions was determined using the maximal scoring peaks using BEDOPS v2.4.
Consensus peak counts were dtermined using featureCounts (v2.0.0) under the consensus peak regions and filtered by requring a maximum log2 counter per million >-2 in any experimental group.
Peaks were annotated ot the nearest gene using ChIPseeker (v1.29.1)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells pellets were sent to Active Motif to perform the ChIP-seq assay using their standard protocol. Briefly, chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.
An aliquot of chromatin (30 µg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ul of antibody against H3K27ac (Active Motif cat# 39133, lot# 16119013). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (qPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out qPCR for each primer pair using Input DNA. lllumina sequencing libraries were prepared from the ChIP and input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: H1975 EGFR mutant NSCLC cells were treated with 500 nM of osimertinib for 24 days (osimertinib DTPs) or treated with 500 nM of osimertinib for 21 days followed by 150 nM of AZD5153 for 3 days (osimertinib DTP AZD5153 sequential combination). In parallel, H1975 cells were grown in drug-free media for 21 days then treated with DMSO control for 3 days (DMSO control). The experiment was done using biological triplicates.  Including the Input control there were 10 ChIP-seq samples. Cells (10 million) were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.

value: osimertinib DTPs + AZD5153

tag: ip


title: HUVECs - VEGF+VP_1


title: HUVECs - VEGF_3

value: VEGF treated


title: H3K27Ac_H1975_osi_DTP_3

value: osimertinib DTPs


title: H3K27Ac_H1975_osi_DTP_2


title: HUVECs - VEGF_2


title: H3K27Ac_H1975_osi_DTP_AZD5153_combo_3


title: HCC827_DMSO_1 [RNA-seq]


title: FMB_3023_D3


title: HUVECs - VEGF_1


title: FMB_3003_D2


title: HCC827_DMSO_2 [RNA-seq]


title: FMB_3016_D8


title: H3K27Ac_H1975_osi_DTP_AZD5153_combo_1


title: HUVECs - VEGF+VP_2


title: H3K27Ac_H1975_osi_DTP_1


title: co-culture 2

city: Cleveland

first: Kuan-Hui

middle: Ethan

last: Chen

state: MS

address: 1003 W Sunflower Rd

institute: Delta State University

data_processing:
RNAseq was analyzed using the Hisat2 (v2.2.0)/Stringtie (v2.1.3) pipeline
Assembly: mm9
Supplementary files format and content: gtf files include FPKM values for each Sample

source_name: mouse 4T1 cell line

growth_protocol: 4T1 cells were cultured using ultralow attachment plates in serum free RPMI1640 supplemented with 2% SM1 supplement, 20 ng/mL EGF, 20 ng/ml FGF and 4 μg/ml heparin for 7 days. At day 7, CSC spheroids, greater than 40 μm, were enriched and collected using a 40 μm cell strainer

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

treatment_protocol: Eight-week-old female Balb/c mice were injected with syngeneic 4T1 tumor cells into the mammary fat pad and housed for 28 days. At day 28, spleens were collected and gently mashed through a cell strainer with 5 mL serum-free RPMI 1640. Red blood cells in this cell suspension were removed using ACK lysis buffer. Cell suspensions were then pelleted as splenocytes. These in vivo tumor-activated splenocytes were then either incubated in Dulbecco's phosphate buffered saline (DPBS) or were reinforcedly activated using anti-CD3/CD28 dynabeads in the presence of IL2. These splenocytes (tumor primed or tumor primed plus reinforced activation) were pipetted to generate an even single cell suspension and then co-cultured with CSC spheroids

tag: strain

value: Balb c/J

tag: tissue type

value: breast

value: cancer stem cell spheres

value: co-culture with reinforced activation of tumor antigen primed splenocytes


title: co-culture 1

tag: treatment

value: co-culture with tumor antigen primed splenocytes


title: HCC2935_short_washout_3 [RNA-seq]

value: osimertinib DTPs short washout 24 hrs.


title: H3K27Ac_H1975_DMSO_3


title: FMB_3031_D5

tag: Sex

value: Male

tag: age

value: Adult

value: whole blood


title: HCC2935_short_washout_2 [RNA-seq]


title: control

value: no co-culture


title: H3K27Ac_H1975_DMSO_2

value: DMSO


title: FMB_3024_D8

tag: day


title: Triple cross-biol-rep4__RNAseq

first: Johannes

middle: C.

last: van der Mijn

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

data_processing:
Differential expression of genes was determined by the DESeq package (version 1.32, Bioconductor) in R.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: kidney

extract_protocol:
Pieces of organ tissue were snap-frozen in liquid nitrogen; microdissected kidney cortex pieces were stored in RNAlater; Total RNA was extracted from four kidney cortices of four mice from each of the four cohorts using RNeasy spin columns (#74134, Qiagen). All samples passed the RNA quality control that was performed with a Bioanalyzer 2100 prior to further processing. The complete transcriptomes were sequenced using an Illumina HiSeq2000 Sequencer with 51bp single-end reads and 4 samples per lane as previously described
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After weaning for 2 weeks all mice were aged and sacrificed by cervical dislocation after 10 months weeks to harvest the organs.

tag: genotype

value: GGT-TTA / GGT-HIF1A_M3 / BPS-TRE-CAS9n

tag: diet

value: regular chow


title: HCC2935_short_washout_1 [RNA-seq]


title: FMB_3012_D2

tag: ferretid


title: HCC2935_osi_DTP_3 [RNA-seq]

value: osimertinib DTPs 3w.


title: H3K27Ac_H1975_DMSO_1


title: Triple cross-biol-rep3__RNAseq


title: FMB_3030_D1

tag: infectionagent


title: Triple cross-biol-rep2__RNAseq


title: HCC2935_osi_DTP_2 [RNA-seq]


title: FMB_3010_D8

tag: viralload


title: H1975_pooled_input-1

value: Input


title: H1975_osi_DTP_AZD5153_combo-3 [ATAC-seq]

data_processing:
Fastq files were aligned using bwa mem (version 0.7.17), mitochondrial reads were removed, and alignments were sorted (samtools v1.9), deduplicated (biobambam v2.0.87 bamsormadup), and tn5-shifted (deeptools v3.4 alignmentSieve)
Fragments smaller than 100 base pairs were extracted to generate a nucleosome free (NF) alignment bam file used for narrowPeak calling MACS2 (v2.2.6).
Consensus peaks were geneted by opening a 500bp window around each peak summit and a set of non-overlapping regions was determined using the maximal scoring peaks using BEDOPS v2.4.
Consensus peak counts were dtermined using featureCounts (v2.0.0) under the consensus peak regions and filtered by requring a maximum log2 counter per million >-2 in any experimental group.
Peaks were annotated ot the nearest gene using ChIPseeker (v1.29.1)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig; narrowPeak

growth_protocol: PC-9, NCI-H1975, HCC827, II-18, HCC4006, HCC2279, and HCC2935 human NSCLC adenocarcinoma cells were obtained from American Type Culture Center (ATCC) and were grown in RPMI 1640, supplemented with 10% FBS, 2 mM L-glutamine, and 1% Penicillin-Streptomycin. All cells were maintained and propagated as monolayer cultures at 37°C in a humidified 5% CO2 incubator.

treatment_protocol: The NSCLC EGFR mutant cell lines (PC9, NCI-H1975, HCC827, and HCC2935) were treated with 500 nM of osimertinib for 24 days (osimertinib DTPs) or treated with 500 nM of osimertinib for 21 days followed by 150 nM of AZD5153 for 3 days (osimertinib DTP AZD5153 sequential combination). In parallel, parental cell lines were grown in drug-free media for 21 days then treated with vehicle DMSO control for 3 days (DMSO control). As an additional control, PC9 and H1975 cell lines were grown in drug-free media for 21 days then treated with 150 nM of AZD5153 for 3 days (AZD5153 monotherapy). Experiment was done using biological triplicates.  There are 42 total ATAC-seq samples. Cells (100,000) were harvested and frozen in culture media containing FBS and 10% DMSO.

value: osimertinib DTPs + AZD5153


title: Triple cross-biol-rep1__RNAseq


title: HCC2935_osi_DTP_1 [RNA-seq]


title: FMB_3028_D5

tag: relweight


title: FMB_3021_D8

tag: tissue


title: WT-biol-rep3__RNAseq (control)

value: wild type


title: H1975_osi_DTP_AZD5153_combo-2 [ATAC-seq]

tag: cell line


title: HCC2935_osi_acute_3 [RNA-seq]

value: osimertinib acute 24 hrs.


title: FMB_3012_D5


title: H1975_AZD5153_3 [ATAC-seq]


title: WT-biol-rep2__RNAseq (control)


title: H1975_osi_DTP_AZD5153_combo-1 [ATAC-seq]


title: H1975_AZD5153_2 [ATAC-seq]


title: HCC2935_osi_acute_2 [RNA-seq]


title: WT-biol-rep1__RNAseq (control)


title: FMB_3025_D2


title: FMB_3015_D8


title: HCC2935_osi_acute_1 [RNA-seq]


title: HCC2935_long_washout_10d_3 [RNA-seq]

value: osimertinib DTPs long washout 10 days


title: FMB_3016_D5


title: FMB_3032_D5


title: H1975_AZD5153_1 [ATAC-seq]


title: 415s012848: sponge138_2

city: Zürich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: D-HEST

country: Switzerland

institute: ETH Zürich

data_processing:
We removed sequencing adapter and quality-trimmed all short reads from the 3’end using FLEXBAR 2.5.3 and a Phred score cutoff >10.
All reads longer than 18bp were retained and rRNA reads were subtracted in silico using bowtie2 and an index of the complete repeating rRNA unit (BK000964.3).
We used the STAR aligner 2.4.2a4 to map against the mouse genome (EnsEMBL 79 genome + annotations).
We performed differential gene expression analysis using the Cuffdiff 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: sponge_geneFPKM.csv contains a gene-level normalized expression matrix (FPKM)

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
RNA was isolated using miRVana isolation kit (Life Technologies)
50nt paired-end protocol (Illumina)

value: Mir-138 sponge

value: adult

value: male

value: hippocampus


title: 415s012847: sponge138_1


title: HCC2935_long_washout_10d_2 [RNA-seq]


title: H1975_Osi_DTP-2 [ATAC-seq]

value: osimertinib DTPs


title: HCC2935_DMSO_2 [RNA-seq]


title: FMB_3035_D8

value: Male

value: Adult


title: HCC2935_long_washout_10d_1 [RNA-seq]


title: H1975_Osi_DTP-3 [ATAC-seq]


title: FMB_3023_D8

value: whole blood


title: 415s012846: ctrl_3

value: flox


title: FMB_3023_D1


title: H1975_Osi_DTP-1 [ATAC-seq]


title: 415s012845: ctrl_2


title: 415s012849: sponge138_3


title: H1975_DMSO-3 [ATAC-seq]

value: DMSO


title: 415s012844: ctrl_1


title: H1975_short_washout_2 [RNA-seq]

value: osimertinib DTPs short washout 24 hrs.


title: Sample_3_neuron_shDcPS-2set_1_S15

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Base calling was done by sequencing vendor using Illumina software
Raw fastq files were filtered for quality and trimmed using FASTP software v0.12.2
Filtered fastq files were aligned with transcript-annotated mouse genome index (grcm38_tran) using HISAT2 v2.2.0
Sam files were converted to bam, sorted, and indexed using samtools v1.3.1
Alignments were deduplicated using picard
Gene-level counts were produced using R/Rsubread function featureCounts using the GRCm38.102.gtf downloaded from Ensembl
Differential expression analysis was performed using R/DESeq2.  Normalized counts were exported from the DESeq2 data object.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts

source_name: Mouse primary neuronal cell cultures from E13 wild-type mice transfected with DcpS shRNA

growth_protocol: Neuron cultures were grown in Neurobasal medium (Gibco 1097077) with sodium pyruvate, 2 mM GlutaMax (Gibco 35050-061), penicillin/streptomycin (Cellgro 30-001-C1) and B27 supplement (Gibco 17504).

extract_protocol:
Total cellular RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary neuronal cells

tag: transfected

value: DcpS shRNA


title: FMB_3035_D1

extract_protocol:
RNA was extracted from ferret blood using the Mouse RiboPure-Blood RNA Isolation Kit (Ambion)
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer-supplied protocol. Libraries were sequenced 100 bp paired-end to a depth of approximately 40 million host genome reads on Illumina HiSeq 2500 instruments.


title: FMB_3028_D1


title: H1975_short_washout_3 [RNA-seq]


title: HCC2935_osi_DTP_AZD5153_combo-3 [ATAC-seq]

value: osimertinib DTPs + AZD5153


title: FMB_3009_D3

value: poor monolayer


title: FMB_3008_D1


title: Sample_2_neuron_conset_2_S16

source_name: Mouse primary neuronal cell cultures from E13 wild-type mice transfected with control shRNA

tag: cell type

value: Control shRNA


title: H1975_short_washout_1 [RNA-seq]


title: HCC2935_DMSO_3 [RNA-seq]


title: HCC2935_osi_DTP_AZD5153_combo-2 [ATAC-seq]


title: HCC2935_DMSO_1 [RNA-seq]


title: H1975_DMSO-1 [ATAC-seq]


title: Sample_1_neuron_conset_1_S13


title: H1975_osi_DTP_3 [RNA-seq]

value: osimertinib DTPs 3w.


title: H1975_DMSO-2 [ATAC-seq]


title: Tissue-resident NK cells recipient group 3 [NK30]

first: Marta

last: Requesens Rueda

address: 149, 13th Street

description:
NK30
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

data_processing:
Samples were quasi-mapped to GRCm38 (mm10) using Salmon with the "gcBias" and "seqBias" options.
Samples were collapsed down to gene-level abundance estimates using the "EnsDb.Mmusculus.v79" annotation package.
The results table was restricted to genes with minimum 10 total counts across the dataset, and mitochondrial, pseudo- and ribosomal genes were removed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: DESeq2.normalized.xlsx

source_name: CD49a+ NK cells

growth_protocol: NK cells are sorted from different tissues and skin grafts.

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

tag: mouse genotype

value: Recipient skin

value: CD49a+ NK cells


title: FMB_3026_D3


title: HCC2935_osi_DTP_AZD5153_combo-1 [ATAC-seq]


title: Sample_4_neuron_shDcPS-2set_2_S18

tag: strain


title: H1975_osi_DTP_2 [RNA-seq]


title: FMB_3008_D3


title: HCC2935_DTP-2 [ATAC-seq]


title: H1975_osi_DTP_1 [RNA-seq]


title: HCC2935_DTP-3 [ATAC-seq]


title: Tissue-resident NK cells recipient group 2 [NK29]

description:
NK29
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3022_D2


title: FMB_3002_D5


title: H1975_osi_acute_2 [RNA-seq]

value: osimertinib acute 24 hrs.


title: HCC2935_DTP-1 [ATAC-seq]


title: HCC2935_DMSO-3 [ATAC-seq]


title: Tissue-resident NK cells recipient group 1 [NK28]

description:
NK28
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: HCC2935_DMSO-2 [ATAC-seq]


title: FMB_3026_D8


title: HCC2935_DMSO-1 [ATAC-seq]


title: CD49a+ NK cells donor skin day 10 group 3 [NK27]

description:
NK27
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Donor skin


title: FMB_3013_D2


title: FMB_3026_D1


title: H1975_osi_acute_1 [RNA-seq]


title: CD49a+ NK cells donor skin day 10 group 1 [NK25]

description:
NK25
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3014_D2


title: conventional NK cells donor skin day 10 group 3 [NK24]

description:
NK24
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

source_name: CD49b+ NK cells

value: CD49b+ NK cells


title: H1975_osi_acute_3 [RNA-seq]


title: H1975_long_washout_72h_1 [RNA-seq]

value: osimertinib DTPs long washout 72 hrs.


title: conventional NK cells donor skin day 10 group 2 [NK23]

description:
NK23
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3032_D8

source_name: whole blood

value: Male

value: Adult


title: H1975_long_washout_72h_3 [RNA-seq]


title: HCC827_osi_DTP_AZD5153_combo_3 [ATAC-seq]


title: Spleen NK cells group 3 [NK21]

description:
NK21
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Spleen


title: H1975_DMSO_2 [RNA-seq]

value: DMSO


title: FMB_3034_D1

value: whole blood


title: H1975_DMSO_3 [RNA-seq]


title: H1975_DMSO_1 [RNA-seq]


title: CD49a+ NK cells donor skin day 10 group 2 [NK26]

description:
NK26
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3027_D3


title: HCC827_DTP-3 [ATAC-seq]

value: osimertinib DTPs


title: Spleen NK cells group 2 [NK20]

description:
NK20
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3029_D2


title: H1975_long_washout_72h_2 [RNA-seq]


title: FMB_3028_D3


title: HCC827_DTP-2 [ATAC-seq]


title: Spleen NK cells group 1 [NK19]

description:
NK19
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: conventional NK cells donor skin day 10 group 1 [NK22]

description:
NK22
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: Peripheral blood NK cells group 3 [NK18]

description:
NK18
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Peripheral blood


title: HCC827_osi_DTP_AZD5153_combo_1 [ATAC-seq]

value: osimertinib DTPs + AZD5153


title: Peripheral blood NK cells group 2 [NK17]

description:
NK17
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: HCC827_DTP-1 [ATAC-seq]


title: FMB_3007_D5


title: FMB_3036_D2


title: HCC827_DMSO-3 [ATAC-seq]


title: HCC827_DMSO-2 [ATAC-seq]


title: Peripheral blood NK cells group 1 [NK16]

description:
NK16
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: FMB_3027_D5


title: 77CR_Control

first: Xintao

last: Qiu

address: 440 brookline ave

institute: Dana Faber Cancer Institute

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to hg19 using STAR
For fpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of FPKM table

source_name: CRPC PDX

extract_protocol:
RNA was extracted from subcutaneous control pretreatment PDX tumors using STAT-60 (Fisher Scientific, cat # NC9489785)
RNA from the control and SPT-treated PDX tumors for analysis of SPT effects was sent to Novogene for RNA library prep and mRNA Sequencing (Illumina HiSeq Platform, PE150.)

treatment_protocol: Testosterone cypionate (Roadrunner Pharmacy) was administered intramuscularly every two weeks (10  uL of 100 mg/ml); control animals received an injection of 10 uL sesame oil.

value: CRPC pdx

value: control


title: 96CR_Control


title: 77CR_HighT

value: SPT


title: 73CR_Control


title: FMB_3024_D2

data_processing:
Paired-end reads were aligned to ferret genome Ensembl version 1.0.80 using tophat (version v2.0.13)
Following read alignment, featureCounts (v1.4.6) was used to quantify the mRNA expression levels based on Ensembl gene model.
mRNAs with more than 5 reads in at least 1 sample were considered expressed and hence retained for further analysis, otherwise removed.
The mRNA read counts data was normalized using trimmed mean of M-values normalization (TMM) method of the edgeR package (Robinson et al., 2010. PMCID: PMC2796818) to adjust for sequencing library size difference.
Genome_build: ferret genome Ensembl version 1.0.80
Supplementary_files_format_and_content: normalized.log2CPM.tsv (tab-delimited  file using log2-transformed CPM values for each sample)


title: 73CR_HighT


title: 96CR_HighT


title: PC9_osi_DTP_AZD5153_combo-3 [ATAC-seq]


title: Tissue-resident NK cells recipient group 2 [NK14]

description:
NK14
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Recipient skin


title: FMB_3004_D5


title: HCC827_osi_DTP_AZD5153_combo_2 [ATAC-seq]


title: PC9_osi_DTP_AZD5153_combo-2 [ATAC-seq]


title: 35CR_HighT


title: HCC827_DMSO-1 [ATAC-seq]


title: CD49a+ NK cells donor skin day 20 group 3 [NK12]

description:
NK12
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: CD49a+ NK cells


title: 35CR_Control


title: PC9_osi_DTP_AZD5153_combo-1 [ATAC-seq]


title: iUB

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

data_processing:
Sequencing and making Fastq files by illumina HiSeq X Ten. Read length: Read1:26, Index read 1(i7):8, Read2:98.
Cell Ranger v2.0.0 software was used to perform alignment and gene and UMI counting each cell.
Assembly: GRCm38_93
Supplementary files format and content: tab-delimited text files and comma-separated value files

source_name: ES cell-derived ureteric buds

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: ES

value: Wild type


title: Tissue-resident NK cells recipient group 3 [NK15]

description:
NK15
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: iNP

source_name: ES cell-derived nephron progenitors


title: iSP

source_name: ES cell-derived stromal progenitors


title: CD49a+ NK cells donor skin day 20 group 2 [NK11]

description:
NK11
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Donor skin


title: PC9_AZD5153_3 [ATAC-seq]


title: 167CR_HighT


title: LPS+BHB 3

description: All.counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: BMDMs

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDMs

value: Balb/c

value: 6 week

value: wild type

value: LPS plus BHB


title: PC9_AZD5153_2 [ATAC-seq]


title: CD49a+ NK cells donor skin day 20 group 1 [NK10]

description:
NK10
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: 167CR_Control


title: 147CR_Control


title: conventional NK cells donor skin day 20 group 1 [NK07]

description:
NK07
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: CD49b+ NK cells


title: PC9_osi_DTP-2 [ATAC-seq]

value: osimertinib DTPs


title: PC9_osi_DTP-3 [ATAC-seq]


title: conventional NK cells donor skin day 20 group 2 [NK08]

description:
NK08
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: LPS+BHB 1

description: All.counts.txt


title: LPS+BHB 2

description: All.counts.txt


title: 136CR_HighT


title: Tissue-resident NK cells recipient group 1 [NK13]

description:
NK13
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: LPS 3

description: All.counts.txt

value: LPS


title: PC9_osi_DTP-1 [ATAC-seq]


title: Spleen NK cells group 3 [NK06]

description:
NK06
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Spleen


title: Spleen NK cells group 2 [NK05]

description:
NK05
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: conventional NK cells donor skin day 20 group 3 [NK09]

description:
NK09
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: PC9_DMSO-3 [ATAC-seq]

value: DMSO


title: 147CR_HighT

value: CRPC pdx


title: LPS 2

description: All.counts.txt


title: 136CR_Control

value: control


title: LPS 1

description: All.counts.txt


title: Con 3

description: All.counts.txt


title: PC9_DMSO-1 [ATAC-seq]


title: PC9_DMSO-2 [ATAC-seq]


title: Peripheral blood NK cells group 3 [NK03]

description:
NK03
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx

value: Peripheral blood


title: Con 1

description: All.counts.txt


title: Spleen NK cells group 1 [NK04]

description:
NK04
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: Peripheral blood NK cells group 1 [NK01]

description:
NK01
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: Con 2

description: All.counts.txt


title: 105CR_Control


title: Peripheral blood NK cells group 2 [NK02]

description:
NK02
smartRNA-Seq
processed data file: DESeq2.normalized.xlsx


title: PC9_AZD5153_1 [ATAC-seq]


title: K27ac96CR

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced on the Illumina platform at the Dana-Farber Cancer Institute.

tag: chip antibody

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: JMJ4-OE_GFP_ChIPSeq_Input rep3

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

data_processing:
Illumina Casava1.7 software used for basecalling.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to Tomato reference genome (version SL3.0) using the BWA program.
Peaks were called using MACS2 software with the following setting: MACS2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B –SPMR --broad --broad-cutoff 0.05.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: bigwig files were generated using MACS2 software.

organism: Solanum lycopersicum

source_name: Ailsa Craig

growth_protocol: Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.

extract_protocol:
Tomato leaves of 8-week-old plants.were collected, immediately cross-linked in 1% formaldehyde for chromatin isolation and Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated 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 Genome Analyzer following the manufacturer's protocols.

tag: cultivar

value: Ailsa Craig

tag: age

value: leaves

value: none (input)


title: HOX96CR

tag: treatment

value: Santa Cruz Biotechnology


title: HOX73CR


title: AR96CR

value: AR


title: AR73CR


title: K27ac77CR


title: 105CR_HighT

value: SPT


title: K27ac96CR_T


title: JMJ4-OE_GFP_ChIPSeq_Input rep1


title: Control [7044M63]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
7044M63_GT17-14738_ACAGTG_S4
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt

data_processing:
Paired-end 25bp reads were mapped to the UCSC transcriptome by Bowtie, allowing up to two mismatches, and expression levels of all UCSC genes were estimated by RSEM with default parameters.
Genome_build: not provided
Supplementary_files_format_and_content: Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt: Tab-delimited count matrix.

source_name: Human whole heart

extract_protocol:
RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico assay (Agilent Technologies). Libraries were constructed using the SMARTer Stranded Total RNA-Seq Kit v2-Pico (Takara), according to the manufacturer’s protocol. Libraries were pooled and sequenced 75 bp single-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2.5 reagents (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Whole heart

tag: diagnosis

value: Healthy


title: K27ac73CR_T


title: K27ac77CR_T


title: K27ac73CR


title: Heart failure [7-0201HD]

description:
7-0201HD_GT17-14744_AGTTCC_S1
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt

value: Heart failure


title: JMJ4-OE_GFP_ChIPSeq_IP rep3

value: GFP (ab290, Abcam)


title: K27ac35CR_T


title: JMJ4-OE_GFP_ChIPSeq_IP rep2


title: JMJ4-OE_GFP_ChIPSeq_IP rep1


title: K27ac167CR_T


title: K27ac35CR


title: JMJ4-OE_GFP_ChIPSeq_Input rep2


title: Control [4-083LV3]

description:
4-083LV3_GT17-14743_AGTCAA_S10
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: Control [6-086LV]

description:
6-086LV_GT17-14737_TGACCA_S6
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: K27ac147CR_T


title: Heart failure [4-070LV11]

description:
4-070LV11_GT17-14740_CAGATC_S7
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: K27ac167CR


title: Control [4-062LV19]

description:
4-062LV19_GT17-14736_CGATGT_S9
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: 1520_M_KO_fast

city: St. Louis

first: Brian

last: Finck

address: 660 Euclid Ave

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Liver

extract_protocol: oligo-dT

tag: diet

value: Fasted

tag: genotype


title: 2165_M_KO_fast


title: 1025_M_KO_fast


title: 2043_M_KO_fast


title: K27ac147CR


title: Heart failure [3-149LV]

description:
3-149LV_GT17-14741_ACTTGA_S3
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: HF1

type: RNA

city: Frankfurt am Main

first: Xinlai

last: Cheng

state: Hessen

address: Max-von-Laue-Strasse 15. R. 3.652

department: Chemical Biology

institute: Goethe Frankfurt University. BMLS

hyb_protocol: No modifications were made to the recommended manufacturer's protocol for BeadChips.

scan_protocol: Standard protocol for a BeadArray Reader.

data_processing: The data were obtained from Beadstudio Software and transferred to R Software. The data were quantile-normalized across all hybridizations on BeadArrays.

label: Biotin

source_name: Human Foreskin Fibroblasts

label_protocol: The Illumina Totalprep RNA Amplification Kit was used to synthesize cDNA as well as to amplify biotinylated cRNA.

growth_protocol:
HFF: Cells were culturted in standard DMEM medium enriched with FCS 10% and with Penicillin/Streptomycin added. The cells were cultured for at least 40 passages.
hiPSCs: Cells were culturted in Essential8 medium and Penicillin/Streptomycin. Cells were passaged when 60% confluence was achieved, including a ROCK inhibitor (10µM) in the culture medium for 24 hours after passaging.

extract_protocol: Total RNA was extracted and purified by means of the Guanadine thyocyanate-phenol-chloroform extraction method using QIAzol Lysis Reagent.

treatment_protocol:
CSKML: Cells were transfected with Sox2, Klf4, c-Myc and Lin28 using Lipofectamine 3000  as transfection reagent (Life Technologies), then cultured in DMEM/F12 GlutaMAX knockout medium containing 1% N2, 2% B27 and 100 ng/mL bFGF for 7 days in the presence of O4I4 5 µM. Essential®8 medium was used after 10 days.
OSKML: Cells were transfected with Oct4, Sox2, Klf4, c-Myc, and Lin28 using Lipofectamine 3000  as transfection reagent (Life Technologies), then cultured in DMEM/F12 GlutaMAX knockout medium containing 1% N2, 2% B27 and 100 ng/mL bFGF for 7 days. Essential®8 medium was used after 10 days.
SKML: Cells were transfected with Sox2, Klf4, c-Myc, and Lin28 using Lipofectamine 3000  as transfection reagent (Life Technologies), then cultured in DMEM/F12 GlutaMAX knockout medium containing 1% N2, 2% B27 and 100 ng/mL bFGF for 7 days. Essential®8 medium was used after 10 days.
O4I3/4: Cells were cultured in DMEM with FBS 10% and Penicillin/Streptomycin 1% for 2 days in the presence of O4I3 0.25 µM and O4I4 5 µM.

value: Somatic cells


title: O4I3/4


title: SKML


title: iPSCs ctrl1

source_name: Non-treated hiPSCs

value: Fully reprogrammed cells


title: OSKML

value: Somatic cells being reprogrammed


title: iPSCs ctrl2


title: K27ac136CR_T

value: CRPC pdx


title: HF2


title: 2044_M_KO_fast


title: Control [6-038LV14]

description:
6-038LV14_GT17-14739_GCCAAT_S2
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: CSKML3

source_name: CSKML-treated hiPSCs


title: CSKML2


title: Heart failure [2-048LV]

description:
2-048LV_GT17-14745_ATGTCA_S5
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: K27ac136CR

value: control


title: Heart failure [2-044LV]

description:
2-044LV_GT17-14742_CTTGTA_S8
Milena_Furtado_011718_HEART FAILURE_vs_CONTROL-FINAL-counts.txt


title: S5 NMR

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Reads were mapped to mm9 and hetGla2 respectively, using STAR version 2.5.3a
Raw reads were generated using htseq-count version 0.10.0
RNA differential gene expression was performed with DESeq2
Genome_build: hetGla2/hetGla_Female_1.0 and mm9
Supplementary_files_format_and_content: Normalized counts for mouse and naked mole rat samples

organism: Heterocephalus glaber

source_name: spleen

extract_protocol:
Spleens were dissected and fast frozen on dry-ice. Total RNA was extracted from 3 biological replicates per group using RNeasy extraction kit from Qiagen. RNA was sequenced on the Illumina HiSeq2500 platform according to the manufacturer's instruction at Macrogen (Korea)
Illumina TruSeq stranded mRNA LT Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; library type: Illumina-transcriptome, library: TruSeq stranded mRNA, read length: Illumina 100bp PE

value: african naked mole-rat

value: spleen

tag: spleen size

value: enlarged

tag: Sex

value: male

tag: age (months)


title: S4 NMR

tag: tissue

value: female


title: K27ac_96CR

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: Diagenode


title: 1928_M_KO_fast


title: 967_M_KO_fed

value: Fed


title: 1888_M_KO_fed


title: 2166_M_KO_fed


title: CSKML1

tag: cell type


title: K27ac105CR


title: HOX77CR

value: Santa Cruz Biotechnology


title: K27ac_81CR


title: K27ac_78CR


title: S3 NMR

value: small


title: S2 NMR


title: 2042_M_KO_fed


title: K27ac105CR_T

value: SPT


title: K27ac_70CR


title: HOX167CR


title: S1 NMR


title: K27ac_167CR


title: 1927_M_KO_fed


title: HOX147CR


title: K27ac_147CR


title: H3K27ac ChIP-seq in NRVMs at pH 7.4 treated with A485

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

institute: University of Oxford

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome (Bowtie2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads using Picard
Reference normalization by scaling read counts to mapped Drosophila reads (dm6) in IP and input samples
Genome_build: rn6
Supplementary_files_format_and_content: Peak calling and annotation using Homer v4.11

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: Primary neonatal rat ventricular myocytes were isolated from P1/P2 hearts of 1-2 day old Sprague-Dawley rats by enzymatic digestion, and a ‘pre-plating’ step was introduced to reduce fibroblasts in the myocyte-containing supernatant. Cells were plated onto fibronectin-coated TC culture dishes and cultured in M2 medium (80% DMEM medium containing 24 mM NaHCO3 and 20% M199 medium with 26mM NaHCO3) and incubated in a 5% CO2 atmosphere.  Initially, medium was supplemented with 10% horse serum, 5% newborn calf serum and penicillin/streptomycin mixture. Next day, cells were serum-starved, followed by incubation in either 3.05 mM (pH 6.4) or 24.4 mM (pH 7.4) NaHCO3 with addition of 0.05% DMSO, or 24.4mM NaHCO3 plus 3µM A485 (p300 inhibitor) for 48 h.

extract_protocol:
Cells were washed with PBS and fixed in 1% FA for 10 minutes. Cells were sonicated to give fragments of 200-300bp, then pooled with fixed, sonicated Drosophila S2 cells at a ratio of 4:1 rat:Drosophila, followed by IP.
DNA libraries were made using the NEBnext Ultra II DNA library preparation kit for Illumina (Cat no. E7645).

treatment_protocol: See sample table

value: Sprague-Dawley

value: Serum-starved cells were incubated in 24.4 mM NaHCO3 with addition of 3 µM A485 (p300 inhibitor) for 48 h


title: ChIP-seq input for H3K27ac in NRVMs at pH 7.4 treated with A485

value: Neonatal rat ventricular myocytes (NRVMs)


title: S6 NMR


title: HOX136CR


title: 1521_M_fl/fl_fast

value: Fasted

value: Control


title: ChIP-seq input for H3K27ac in NRVMs at pH 6.4

value: Serum-starved cells were incubated in 3.05 mM NaHCO3 with addition of 0.05% DMSO for 48 h


title: 2312_M_fl/fl_fast


title: HOX105CR

value: CRPC pdx

value: control


title: H3K27ac ChIP-seq in NRVMs at pH 6.4


title: K27ac_105CR


title: 1023_M_fl/fl_fast


title: FOX96CR

value: Abcam


title: ChIP-seq input for H3K27ac in NRVMs at pH 7.4

value: Serum-starved cells were incubated in 24.4 mM NaHCO3 with addition of 0.05% DMSO for 48 h


title: FOX_96CR


title: HOX35CR


title: FOX_81CR


title: 1024_M_fl/fl_fast


title: 1519_M_KO_fed


title: H3K27ac ChIP-seq in NRVMs at pH 7.4


title: FOX73CR


title: K27ac_136CR


title: 1667_M_fl/fl_fast


title: FOX_70CR


title: FOX35CR


title: WT_3

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Sequences were trimmed in order to remove adaptors and low quality bases
Trimmed reads were mapped in to the zebrafish genome GRCz11 using STAR software v.2.5.4b (Dobin et al., 2013) and gene expression was measured from the mapped reads by using built-in STAR module (--quantMode GeneCounts).
Genome_build: GRCz11 - release 92 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for annotations for each Sample

organism: Danio rerio

source_name: Endodermal cells

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols and staged according to Kimmel (Kimmel et al., 1995).

extract_protocol:
EECs were isolated by dissecting the gut from about 200 transgenic neurod1ΔUCE/ΔUCE or wild-type Tg(pax6b:GFP)ulg515 larvae at 4 dpf, taking care of not including pancreatic tissue.  Cell dissociation was performed by incubation in HBSS 1x supplemented with 100 U/ml collagenase IV and 0.3 U/ml Dispase (Life Technologies) for 10 minutes. Cells were washed in HBSS (Mg2+ and Ca2+ free) containing 1% BSA and GFP-expressing EECs were selected by FACS purification using FACS Aria II.  This procedure allows us to obtain between 1000 to 2000 isolated GFP+ cells.    Endodermal sox17-dsred+ cells were isolated by dissecting the trunk from about 150 double transgenic Tg(hsp70l:eGFP-2A-ARP/Ascl) or wild-type Tg(sox17:dsred) larvae at 52 dpf, heat-shocked at 38 and 48hpf, taking care of not including pancreatic tissue. Cell dissociation was performed by incubation in TrypLE select 1X (Gibco) for 8 minutes. Cells were washed in HBSS (Mg2+ and Ca2+ free) containing 1% BSA and dsred+ EECs were selected by FACS purifications using FACS Aria II.  This procedure allow us to obtain between 2000 to 4000 isolated dsred+ cells.
Each FACS-sorted cells sample was directly pelleted by centrifugation and resuspended in 3.5 µl of reaction buffer, lysed by freezing in liquid nitrogen and stored at -80°C according the Smart-seq2 protocol [49]. cDNA was synthesised and amplified by a 13 cycles PCR reaction. Quality of cDNA was verified by 2100 High Sensitivity DNA assay (Agilent technologies). 1 ng cDNA was used for preparing each cDNA library using Nextera-XT kit (Illumina) and sequenced on Hi-seq 2000 to obtain around 20 million of reads (75 base single-end).

treatment_protocol: The following zebrafish transgenic and mutant lines were used: Tg(pax6b:GFP)ulg515 (Delporte et al., 2008b), Tg(sox17:dsred) (Field et al, 2003), neurod1 ulg052

value: AB

value: Endoderm

value: Wild type

tag: transgene

value: heat-shock


title: 2384_M_fl/fl_fast


title: FOX167CR


title: FOX_167CR


title: WT_2

tag: strain


title: FOX147CR

tag: chip antibody


title: 970_M_fl/fl_fed

value: Fed


title: FOX_147CR

tag: chip antibody vendor


title: WT_1


title: neurod1delECD_3


title: FOX_136CR

tag: chip antibody cat.#


title: FOX77CR

tag: chip antibody lot/batch#


title: 1665_M_fl/fl_fed


title: FOX136CR


title: FOX105CR


title: neurod1delECD_2


title: FOX_105CR


title: 969_M_fl/fl_fed


title: FOX_78CR


title: 1929_M_fl/fl_fed


title: neurod1delECD_1


title: AR_96CR

value: AR

value: Santa Cruz Biotechnology


title: AR96CR_T

value: SPT


title: 2313_M_fl/fl_fed


title: neurod1delUCE_3


title: MG_LPS

city: Beijing

first: Minmin

last: Luo

address: 7 Science Park Road, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

description: Microglia in vivo - LPS (scRNAseq) - SMART-SEQ2

data_processing:
Illumina Casava used for base calling.
For 10x Chromium scRNA-seq, reads were aligned to mm10 reference genome with cellranger (v6.0.1) using "cellranger count" and all groups were aggregated using "cellranger aggr" commands with default parameters.
For Smart-seq2 scRNA-seq, we built a custom mm10 genome where the sequence and annotation of a transgene encoding mScarlet was added; read were aligned to this custom reference genome using STAR (v2.7.8a from snakemake-wrapper) with the following parameters --outFilterMultimapNmax 1 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNmax 6. umi_tools was used for preprocessing of barcoded reads and counting of umis per gene per cell. featureCounts from the subread package (v1.6.3) was used for gene assignment.
For bulk RNA-seq, reads were aligned to mm10 using Salmon (v1.6.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with raw/estimated counts for every gene in every sample

source_name: Brain

extract_protocol:
For scRNAseq datasets (in vivo), single cell suspension of microglia is obtained by a modified version of mechanical dissociation protocol as described in Bennett et al. Briefly, mice were perfused and brains were harvested and dounced. Microglia were enriched by Percoll density gradient centrifugation. For RNAseq datasets (in vitro), microglia were extracted from neonatal mouse by magnetic activated cell sorting (MACS) with Cd11b-beads and cultured
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For scRNAseq datasets (in vivo), mouse in the MG_S/MG_L/MG_P group was administered with saline/lipopolysaccharide/poly(i:c) i.p. 6 hours before microglia were harvested. Mice from the MG_AAV groups were injected with AAV variant AAV-MG.1.1 or AAV-MG.1.2 via stereotaxic surgery 2 weeks before microglia were harvested. For RNAseq datasets (in vitro), primary microglia were harvested from prenatal mice and cultured in TIC medium (Bohlen et al., 2017). treatment protocols were applied non-treated (homeostatic state), or treated with 200ng/ml LPS (reactive state), 20ng/ml IL4 (alternatively activation state), and AAV-MG.WPP.

value: Brain

value: microglia


title: neurod1delUCE_2


title: AR_81CR

city: Boston


title: AR73CR_T


title: AR_78CR


title: AR77CR


title: MG_AAV_1.2

description: Microglia in vivo - AAV transduction MG1.2 (scRNAseq) - SMART-SEQ2


title: AR_70CR


title: neurod1delUCE_1


title: 1890_M_fl/fl_fed


title: AR35CR_T


title: AR_167CR


title: neurod1_3


title: MG_AAV_1.1

description: Microglia in vivo - AAV transduction MG1.1 (scRNAseq) - SMART-SEQ2


title: MG_P

description: Microglia in vivo - Poly(i:c) (scRNAseq reference dataset) - 10x Chromium


title: neurod1_4


title: AR167CR_T


title: neurod1_2


title: MG_L

description: Microglia in vivo - LPS (scRNAseq reference dataset) - 10x Chromium


title: AR_147CR


title: AR35CR


title: AR_136CR


title: neurod1_1


title: AR77CR_T


title: MG_S

description: Microglia in vivo - Saline (scRNAseq reference dataset) - 10x Chromium


title: AR_105CR


title: AR167CR


title: ascl1a_3


title: AR147CR


title: AR147CR_T


title: LysICO54

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: Peritoneal macrophages

growth_protocol: Eight-week old IKKβF/F and IKKβΔMye were intraperitoneally injected with 1 mL of 3% thioglycollate solution 3 days prior to the peritoneal macrophage collection.  The peritoneal macrophages were then collected from abdominal cavity and seeded to twelve-well plate.

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophages were allowed to attach to cell culture plates for 4 hours and then treated with lenti-spike or lenti-control for 24 hours

value: Peritoneal macrophages (In vitro cultured)

value: IKKBeta delta_Mye

value: Lenti-Spike

tag: treatment duration

value: 24 hr


title: LysICO52


title: LysICO53


title: AR136CR

value: CRPC pdx

value: control


title: LysICO55


title: ascl1a_1

tag: age


title: mutant_neurod1delUCE_2

source_name: Enteroendocrine cells (EECs)

value: Enteroendocrine cells

value: 4 dpf

tag: treatment


title: AR136CR_T

source_name: CRPC PDX


title: ascl1a_2

value: AB

value: Endoderm


title: mutant_neurod1delUCE_4


title: AR105CR


title: mutant_neurod1delUCE_3


title: LysICO45

value: Lenti-Control


title: LysICO51


title: AR105CR_T


title: LysICO43


title: GS115 Sample-E

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

description:
GS115
Wild Type

data_processing:
demultiplexing and base call to fastq conversion using illumina’s bcl2fastq v2.19.0.316
Adapter trimming using fastp 0.19.6
Read alignment to reference GCA_900235035.1_ASM90023503v1 using bowtie2
Counts per gene were obtained using featureCounts v1.6.4
Differential expression analysis was performed using DESeq2.
Genome_build: GCA_900235035.1_ASM90023503v1
Supplementary_files_format_and_content: read counts per gene in excel file

organism: Komagataella pastoris

source_name: Cells cultured in YPA supplemented with 650uM His for 24 hrs

growth_protocol: cells cultured in YPA or YPA+650 uM His for 24 hours

extract_protocol:
RNeasy Mini Kit Qiagen
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare the library after depleting rRNA from the total RNA  using RiboMinus™ Transcriptome Isolation Kit, bacteria.

tag: phenotype

value: Histidine auxotroph

tag: media conditions

value: YPA+650uM His


title: LysICO44

tag: genotype


title: GS115 Sample-F

description:
GS115
Wild Type


title: LysICO42


title: X33 Sample-D

description:
X33
Wild Type

source_name: Cells cultured in YPA for 24 hrs

value: Histidine prototroph

value: YPA


title: WTpax6b_3

value: Wild type


title: WTpax6b_2


title: X33 Sample-C

description:
X33
Wild Type


title: LysICO41


title: SJRHB013759_X15_barcode

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas Pl MS 324

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: barcode dialout PCR

data_processing:
Library strategy: tagged amplicon
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Orthotopic patient-derived xenograft

extract_protocol:
barcode dialout PCR
Tagged amplicon PCR of 10x gene expression libraries using primers targeted to the lineage barcode
Tagged amplicon PCR

value: xenograft

tag: protocol

value: Barcode dialout PCR


title: SJRHB013759_X14_barcode

description: barcode dialout PCR


title: WTpax6b_1


title: GS115 Sample-B

description:
GS115
Wild Type


title: fkh1Δfkh2-dsm rpd3Δ_rep1 (Total)

city: Los Angeles

first: Yiwei

last: He

state: CA

address: 1050 Childs Way RRI 203

department: Molecular Biology

institute: University of Southern California

description: Sample 23

data_processing:
Barcode-splitting: Sequenced reads were first processed using ea-utils which de-multiplexes the reads based on the specified barcode sequences.
Alignment: The raw sequencing reads were then aligned to the indexed genome of S288C from Saccharomyces Genome Database using bowtie2.
Data-cleaning: Filterred reads that were mapped to more than one region in the genome using samtools view. Reads were sorted by coordinates of the reference genome using samtools sort. PCR duplicates were removed using samtools rmdup
Binning: sequencing reads were binned over 50bp bins across the genome using coverageBed.
Assembly: R64
Supplementary files format and content: binned.bed files
Library strategy: BrdU-IP-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: 10–20 mL of cells were grown per sample to OD ~ 0.5 in YEPD at 23 °C

extract_protocol:
Cells were resuspend in 500 μL genomic lysis buffer and disrupted by bead-beating with FastPrep. Followed by PCI extractracion and ethanol precipitaion.
Samples were end-labeled using KAPA Hyper prep kit with unique barcoded adapters that are compatible with the subsequent library-amplification and sequencing primers for the Illumina sequencing platform.

treatment_protocol: Cells were arrested with α-factor (~5 nM ) and incubated for ~4 h at 23 °C then released in fresh YEPD containing 400 μg/mL BrdU, 200 μg/mL Pronase and 200 mM hydroxyurea. Harvested cells after 60/90min of incubation.

tag: antibody

value: fkh1{delta} fkh2-dsm rpd3{delta}

value: hydroxyurea


title: fkh1Δfkh2-dsm rpd3Δ_rep2 (Total)

description: Sample 24


title: LysICO22

value: Peritoneal macrophages (In vitro cultured)

value: IKKBetaF/F

value: Lenti-Spike

value: 24 hr


title: GS115 Sample-A

description:
GS115
Wild Type


title: SJRHB013758_X2_barcode

description: barcode dialout PCR


title: mutant_neurod1delUCE_1

value: Enteroendocrine cells

value: 4 dpf


title: LysICO25


title: SJRHB013757_X1_barcode

description: barcode dialout PCR


title: LysICO24


title: LysICO21


title: rpd3Δ_90min_rep1 (Total)

description: Sample 21


title: LysICO14


title: SJRHB049189_X1_barcode

description: barcode dialout PCR


title: SJRHB012_Z_barcode

description: barcode dialout PCR


title: fkh1Δfkh2-dsm_rep1 (Total)

description: Sample 19

value: fkh1{delta} fkh2-dsm


title: rpd3Δ_90min_rep2 (Total)

description: Sample 22


title: LysICO15

value: Lenti-Control


title: SJRHB012405_X1_barcode

description: barcode dialout PCR


title: SJRHB011_X_barcode

description: barcode dialout PCR


title: fkh1Δfkh2-dsm_rep2 (Total)

description: Sample 20


title: SJRHB013758_X1_barcode

description: barcode dialout PCR


title: LysICO11


title: WT_90min_rep1 (Total)

description: Sample 17

value: WT


title: WT_90min_rep2 (Total)

description: Sample 18


title: LysICO12


title: SJRHB012_Y_barcode

description: barcode dialout PCR


title: WT [HON082820_008]

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

description: wild-type mouse heart

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: quant_counts.txt: Tab-delimited text table.

source_name: WT

extract_protocol:
Maxwell® RSC simplyRNA Tissue Kit (Promega PN AS1340).
Universal Plus mRNA-Seq Library Preparation Kit with NuQuant (Tecan PN 0520-A01).
PolyA capture based library construction.

treatment_protocol: Hv1 gene knockout.

value: Heart


title: WT [HON082820_007]

description: wild-type mouse heart


title: LysICO13


title: LysICO23


title: gDNA corresponding to total-RNA #1

first: Hanneke

last: Vlaming

address: 45 Shattuck St

department: Department of Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: gDNA corresponding to total-RNA #1

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

source_name: Mouse embryonic stem cells

extract_protocol:
Genomic DNA was extracted from >6M cells using QuickExtract (Lucigen).
In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Samples were amplified for ~22 cycles total between the first and second PCR step, cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select.

tag: cell line

value: F121-9 mESCs with at the 129 allele of Pou5f1:mKate2  uaTSS +172, TagBFP2  Oct4 C terminus

tag: library integration location

value: Pou5f1 uaTSS + 157 (129 allele, upstream of mKate2 reporter)

tag: assay

value: RNA-based INSERT-seq

tag: condition

value: Untreated


title: SJRHB000026_X1_barcode

description: barcode dialout PCR

tag: tissue

value: xenograft

value: Barcode dialout PCR


title: total-RNA #1

description: total-RNA #1

data_processing:
Library strategy: targeted amplification
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences plus spliced versions of these inserts as called by STAR. STAR v2.7.0 was run on replicates 2-4 using flags --outSJfilterOverhangMin 10 4 4 4 --peOverlapNbasesMin 10 --peOverlapMMp 0.08 --alignEndsType EndToEnd --outFilterMismatchNmax 5 --scoreDelOpen -10 --scoreInsOpen -10. The detected splice junctions were filtered down to only junctions on the + strand with >10 read counts and >25% of the maximum counts for other junctions detected in the same insert. For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Genome_build: mm10
Supplementary_files_format_and_content: "sequences*.fa" are fasta files that contain all sequences that were mapped to by bowtie2 (after indexing it using bowtie2-build). One file has only the sequences originally desigend to be part of the library, the other file also contains spliced versions of inserts as detected by STAR using total-RNA replicates 2-4.
Supplementary_files_format_and_content: "HV20210611_normalized_*screens.txt" files are tab-delimited tables containing fully processed data. For RNA samples: RNA counts were normalized to gDNA counts and the median of randomized controls total counts was set to 1 for each sample. Splicing efficiencies by dividing the summed abundance of all spliced versions of an insert over the total abundance of that insert. For sort-seq, the distribution in unsorted cells was used to calculate the contribution of each bin and then  a weighted mean (sort-seq score) was calculated from the distribution of each insert over the bins.
Supplementary_files_format_and_content: "*idxstats.txt" files are tab-delimited tables containing the number of reads mapped to each insert (unspliced and spliced versions separately) in the library. First column is length of the sequence, second is counts (2 counts per read pair, so divide by 2), third column not used.
Supplementary_files_format_and_content: "mESC_F121-9.H3K4me3.ChIPseq.50bp.bins.bw" is a bigwig file with combined data from two H3K4me3 ChIP-seq replicates
Supplementary_files_format_and_content: "200421_mm10_mESC_TTseq_20m_DMSO_BJM_N2_F/R.bw" are bigwig file with combined data from two TT-seq replicates, + and - strand in separate files

extract_protocol:
For total-RNA, >5M library-containing cells was pelleted and resuspended in Trizol (Ambion). RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through 17-20 PCR cycles using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).


title: WT_rDNA20_rep2 (Total)

description: Sample 14

tag: strain

value: WT rDNA20

value: hydroxyurea


title: rpd3Δ_rDNA20_rep1 (Total)

description: Sample 15

value: rpd3{delta} rDNA20


title: SJRHB010927_X1_barcode

description: barcode dialout PCR


title: WT [HON082820_005]

description: wild-type mouse heart


title: SJRHB000026_X2_barcode

description: barcode dialout PCR


title: KO [HON082820_004]

description: Hv1 null mouse heart

source_name: KO

value: Hv1 null


title: WT_rDNA20_rep1 (Total)

description: Sample 13


title: KO [HON082820_003]

description: Hv1 null mouse heart