title: Human NK, MEF2C RNP, donor 159

city: Los Angeles

first: Joey

last: Li

address: 615 Charles E. Young Dr S

institute: UCLA

data_processing:
Bulk RNA-seq fastq files were first checked for quality using FastQC, then trimmed to remove low-quality reads and adaptors using Trimmomatic(version 0.40). The parameters used were SLIDINGWINDOW:4:20 MINLEN:40 LEADING:3 TRAILING:3. Then, reads were aligned to either the reference mouse genome (mm10) or the reference human genome (hg38) with STAR (version 2.7.11). STAR was run with default parameters and the –quantMode geneCounts parameter to generate ReadsPerGene.out.tab files, which are tab-delimited files with the raw number of reads mapped to each gene. The unstranded reads (column 2 of ReadsPerGene.out.tab) were combined into one counts matrix using Excel. Using DESeq2 (version 1.24.0) with default parameters, differential expression analysis was performed, and the counts matrix was normalized. All genes were filtered for significantly differentially expressed genes by p < 0.05. Only genes with counts per million (CPM) > 40 were used for differential expression analysis.
Assembly: hg38, mm10
Supplementary files format and content: Raw counts per gene

source_name: NK cell

extract_protocol:
RNA was isolated from purified NK cells using the Quick-RNA Micro-prep kit (Zymo).
Ribosomal RNA was depleted from samples using the QIAseq FastSelect -rRNA HMR kit (Qiagen). RNA libraries were prepared according to manufacturer instructions using the Stranded Total RNA Prep kit (Illumina, 20040525). Libraries were barcoded using the IDT for Illumina RNA UD Indexes Set A (Illumina, 20040553) and PCR-amplified libraries were cleaned up using Ampure XP beads (Beckman Coulter). Library quality and concentration were assessed by HSD1000 tape on 2200 Tapestation (Agilent) and Qubit 2.0 Fluorometer, and barcoded libraries were pooled to equimolar ratios for sequencing. Sequencing was performed on a NovaSeq 6000 system (Illumina).

value: NK cell

value: MEF2C KO

value: MEF2C RNP


title: Pembro_20

status: Public on Mar 11 2024

type: SRA

city: Seoul

first: Sung Wan

last: Kang

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan Medical Center

library_source: transcriptomic

data_processing:
Trimmomatic v0.38 was utilized to remove adapter sequences and trim bases with subpar quality before analysis.
The refined reads were aligned to the Homo sapiens (GRCh38) genome using HISAT v2.1.0, based on the HISAT and Bowtie2 implementations.
The aligned data, in SAM file format, were sorted and indexed using SAMtools v1.9.
StringTie v2.1.3b was employed for the assembly and quantification of transcripts after alignment.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Total RNA was isolated from the tumor tissues of SKOV-3 Luc xenograft in Hu-mice treated with either PBS or pembrolizumab. The isolation was performed using the mirVana miRNA isolation kit (Thermo Fisher Scientific).
A library was prepared with 100 ng of total RNA for each sample using the TruSeq RNA Access library prep kit (Illumina).

tag: tissue

value: Tumor

tag: cell line

tag: cell type

value: Cancer cells

tag: treatment

value: Pembrolizumab


title: R1-NHP-57_KP1

city: STANFORD

first: Katja

last: Pekrun

state: CA

address: 269 Campus Drive

department: Pediatrics & Genetics

country: USA

institute: Stanford School of Medicine

library_source: genomic

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the Mmul_1 build of the rhesus macaque genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: Mmul_1
Supplementary files format and content: Bedgraph

molecule: genomic DNA

organism: Macaca mulatta

source_name: liver

extract_protocol:
Macaques were euthanized 3.5 months after rAAV injection and liver tissue from 4 lobes was flash-frozen. Frozen liver tissue was pulverized on dry ice and aliquoted. Equal amounts of pulverized liver tissue from each lobe were combined and ~100 mg of this pool were homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 6 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. After passing nuclei through a 0.45um cell strainer quantitation was performed after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Total gDNA was extracted using a QIAamp DNA Mini kit (Qiagen) including RNAse treatment. The protocol for Illumina DNA prep was followed as per manufacturer’s instructions with 100ng of DNA as input, 30min tagmentation and 8 cycles of PCR. The same indexed primers as for Cut&Tag were used for PCR amplification.
Illumina DNA prep kit. Sequencing was performed with Illumina NovaSeq 6000, 150 cycles total per lane (2 lanes total), 2x75 paired-end reads, depth of >15M reads per sample.

treatment_protocol: Rhesus macaques were intravenously infused with rAAV packaged using different capsids. The rAAV vector expressed CpG depleted, codon-optimized huFIX under control of a liver-specific promoter.

value: liver


title: Human NK, MEF2C RNP, donor 161

middle: Han Tang

molecule: total RNA

tag: genotype


title: Epi2

type: RNA

city: Shanghai

first: yujuan

last: jin

address: Yueyang Road 320#

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

hyb_protocol: Each slide was hybridized with 1.65mg Cy3-labeled cRNA using Gene Expression Kit (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions.

scan_protocol: After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US) following the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution = 5 mm, PMT 100%, 16 bits.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). GSEA was performed following the developer’s protocol (http://www.broad.mit.edu/gsea/).

organism: Mus musculus

source_name: non-NE small cell lung cancer

label_protocol: Total RNAs were amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

extract_protocol: Total RNAs from the Mes and Epi cell lines were extracted by TRIzol reagent (Life Technologies) according to the manufacturer’s instruction.

treatment_protocol: no treatment

value: Epi cell line

tag: genetic backgroud

value: RbL/L, Trp53L/L


title: Mes5

value: Mes cell line


title: Epi5


title: Mes2


title: ESC, short read, heavy polyribosome (5+ ribosomes), rep1

city: San Francisco

first: Julie

last: Zikherman

address: 513 Parnassus Ave

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, San Francisco

data_processing:
Long read FASTQs: Bonito v0.0.1 (basecalling) and Mandalorion v4.0.0 (high confidence consensus sequence definition and transcriptome assembly)
Long read data analysis: SQANTI3 v5.1.1 (transcriptome QC and filtering) and IsoAnnot Lite v.2.7.3 (transcriptome annotation)
Short read data analysis: STAR v2.7.8a (mapping to the genome and to the transcriptome), Salmon v1.9.0 (alignment to the transcriptome) and tappAS v1.0.7 (differential and functional analyses)
Supplementary files format and content: Supplementary_tables.xlsx, contains: short read and long read library/mapping stats, transcriptome feature annotations and raw counts, differential isoform usage analysis results, alternative splicing analysis results and motif analysis results.
Supplementary files format and content: LR_transcriptome.gtf: de novo transcriptome from the long read libraries, made and filtered with Mandalorion and SQANTI3.

extract_protocol:
BIOO Scientific qRNA
BIOO qRNA seq v2  Library Preparation Kit  -- strand-specific, read1 is antiSense to input RNA
Frac-seq

value: embryonic stem cell (ESC)

value: control

tag: fraction

value: heavy polyribosome (5+ ribosomes)

tag: riborna depletion

value: poly A+

tag: pcr


title: Epi3


title: Mes3


title: Human NK, MEF2C RNP, donor 162


title: ChIPseq_ESC_CTCF_input_BPTFko_rep2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig

source_name: embryonic stem cells

extract_protocol:
DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 5 PCR amplification cycles for inputs.

value: embryonic stem cells

value: BPTF knock-out

tag: antibody


title: R1-NHP-42_KP1


title: R1-NHP-55_LK


title: Epi1


title: Mes1


title: Human NK, MEF2C RNP, donor 170


title: ESC, short read, monosome, rep3

value: monosome


title: ChIPseq_ESC_CTCF_input_BPTFko_rep1


title: ESC, short read, monosome, rep2


title: Mes4


title: Human NK, TRAC, donor 159

value: NK cell

value: Control

value: TRAC RNP


title: ChIPseq_ESC_CTCF_input_wt_rep2

value: wild-type


title: R1-NHP-04_LK


title: ChIPseq_ESC_CTCF_IP_wt_rep3

value: CTCF


title: Human NK, TRAC, donor 161


title: ESC, short read, cytosol, rep3

value: cytosol


title: R1-NHP-02_LK

value: liver


title: ChIPseq_ESC_CTCF_IP_BPTFko_rep2


title: ChIPseq_ESC_CTCF_input_wt_rep1


title: ESC, short read, monosome, rep1


title: Human NK, TRAC, donor 162


title: R2-NHP-57-N-H3K9me3

data_processing:
Reads were trimmed with Trimmomatic-0.39 program for classical Illumina adapters. Aligned using Bowtie2 version 2.2.5 (https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.5/) with options: --local --very-sensitive-local --nounal --no-mixed --no-discordant --phred33 -I 10 -X 700; mapping was performed using the mm10 build of the mouse genome, merged with viral genome sequence (gAAV).
PCR duplicates were eliminated with “MarkDuplicates” command of Picard version 2.23 (https://broadinstitute.github.io/picard/index.html).
Tracks were made as bedgraph files of normalized counts, using deeptools 3.3 (https://deeptools.readthedocs.io/en/develop/content/list_of_tools.html) bamCoverage with options: --binSize 1, --normalizeUsing CPM; track plots were made with R package Gviz 4.1. Coverage was calculated as SUM[(normalized count*(end-start position+1))/gAAV size] for each dataset. Importantly, ITR regions were removed from the calculation, as their coverage is overrepresented in all samples, perhaps due to recognition of ITRs from ssDNA.
Assembly: Mmul_1
Supplementary files format and content: Bedgraph

extract_protocol:
Macaques were euthanized 3.5 months after rAAV injection and liver tissue from 4 lobes was flash-frozen. Frozen liver tissue was pulverized on dry ice and aliquoted. Equal amounts of pulverized liver tissue from each lobe were combined and ~100 mg of this pool were homogenized in RINO 1.5-ml Screw-Cap tubes filled with stainless steel beads and 1mL of NE buffer using a bead homogenizer (Next Advance Bullet Blender Storm - BBY24M) at speed 8 for 6 minutes. The homogenate was transferred into to a 50mL tube with 12mL of NE buffer and incubated on ice for 10 min. Nuclei were pelleted by a 5 min centrifugation at 600g, the supernatant was decanted, and the pellet was resuspended in 1mL of NE buffer. After passing nuclei through a 0.45um cell strainer quantitation was performed after Trypan Blue staining using an automated cell counter (Countess, Thermo Fisher) and diluted accordingly. 1e5 nuclei per target protein were used for Cut&Tag.
Nuclei were mixed with activated Concanavalin A beads. After successive incubations with primary antibody (overnight) and secondary antibody (for 30 min) in antibody and Digitonin150 buffer respectively, the beads were washed with Digitonin150 buffer and resuspended in Digitonin300 buffer with 2.5uL of pA(G)-Tn5 for 1 hr and washed with the same buffer. Incubations were performed at room temperature in low-retention PCR strip tubes (Epicypher). Tagmentation was performed for 1 hr at 37C in Tagmentation buffer that provides MgCl2. Beads were washed with TAPS buffer and DNA material was released by adding SDS Release Buffer and incubating at 58C for 1hr. Quenching of SDS was performed by adding SDS Quench buffer and PCR was performed directly on this material. Universal P5 and indexed P7 primer solutions were used (see Supplemental Table 3 for sequences), and 17 cycles of PCR were performed. Clean-up was performed with AMPure beads, eluted in 15uL 0.1x TE buffer. Qubit and Bioanalyzer were used to verify library qualities before pooling samples for sequencing. The barcoded libraries were mixed to achieve equimolar representation aiming for a 10nM final concentration.
Cut & Tag. Sequencing of the same library was performed twice (R1, R2), once with Illumina HiSeq 4000 and once with Illumina NovaSeq SP100, 150 cycles total per lane, 2x75 paired-end reads, depth of >15M reads per sample.


title: Human NK, TRAC, donor 170


title: ESC, short read, cytosol, rep2


title: R2-NHP-57-N-H3K4me3


title: ESC, short read, cytosol, rep1


title: R2-NHP-57-N-H3K27me3


title: HEK293_LARP4 eCLIP,  size-matched input, rep 2

city: La Jolla

first: Gene

last: Yeo

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

institute: UCSD

description: eCLIP size matched input replicate 2

data_processing:
Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0). Args: --random-seed 1 --bc-pattern NNNNNNNNNN
Reads were then trimmed with cutadapt (1.14). Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Reads were then trimmed again with cutadapt (1.14) to remove double-ligation events. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18  -a Ril19.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
Trimmed and filtered reads were then mapped with STAR (2.7.6a) against a repeat element database (RepBase 18.05). Args: --runThreadN 16 \  --genomeDir human_repbase \  --readFilesIn path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 30 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Unmapped reads filtered of repeat elements were then mapped with STAR (2.7.6a) against a human genome (hg19). Args: --runThreadN 16 \  --genomeDir genomedir \  --readFilesIn /path/to/read1 \  --outFileNamePrefix out_prefix \  --outReadsUnmapped Fastx \  --outSAMtype BAM   Unsorted \  --outSAMattributes All \  --outSAMunmapped Within \  --outSAMattrRGline ID:foo \  --outFilterType BySJout \  --outFilterMultimapNmax 1 \  --outFilterMultimapScoreRange 1 \  --outFilterScoreMin 10 \  --alignEndsType EndToEnd
Aligned reads were sorted with samtools (1.6)
Sorted reads were collapsed with umi_tools (1.0.0). Args: --random-seed 1 --method unique
BAM files were used to identify peak clusters with Clipper (1.2.2). Args: --species (hg19) --bam path/to/input.bam --timeout 3600000 --maxgenes 1000000 --save-pickle --outfile path/to/output.bam
Peak clusters were normalized using BAM files for IP against BAM files for INPUT with peaksnormalize.pl (overlap_peakfi_with_bam_PE.pl), included in eclip 0.1.5+.
Overlapping normalized peak regions were merged with compress_l2foldenrpeakfi_for_replicate_overlapping_bedformat.pl, included within eclip-0.1.5+
Normalized peak (compressed.bed) files were ranked by entropy score (make_informationcontent_from_peaks.pl included within the merge_peaks pipeline) and used as inputs to IDR (2.0.2) to determine reproducible peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Hek293_WT_P_rep_1.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.bed and Hek293_WT_P_rep_2.umi.r1.fq.genome-mappedSoSo.rmDupSo.peakClusters.normed.compressed.bed contain size matched input normalized eCLIP peaks from rep1 and rep2
Supplementary_files_format_and_content: LARP4_hek_WT.bed contains reproducible total eCLIP peaks across replicates (IDR peaks)
Supplementary_files_format_and_content: BigWig files contain RPM-normalized read densities

source_name: HEK293_LARP4 eCLIP,  size-matched input

growth_protocol: HEK293 cells were maintained in DMEM  supplemented with 10% FBS, at 37o C with 10% CO2. Cells were maintained at a density %30-%70

extract_protocol:
Each Biological replicate of HEK 293 cells (~20 million)  were treated with 400mJ of UV using the Hoefer UVC500 UV Crosslinker, harvested in ice cold PBS and pelleted by centrifugation. Cell pellets were flash frozen in liquid nitrogen and stored in -80 degrees until ready to IP with LARP4 antibody bound Dynabeads. Subsequent protocol was followed exactly as detailed in Van Nostrand et al 2016. Sequencing was performed on Illumina Hiseq 4000 single end reads and data processed through Dr. Yeo's eCLIP pipeline.
Libraries were constructed as per the eCLIP protocol using Illumina 50x forward and 70x reverse primers.
eCLIP

treatment_protocol: HEK 293 cells (~20 million) were UV cross-linked (254 nm; 400 mJ/cm2) and processed through the eCLIP protocol as previously described (van Nostrand et al, 2016). LARP4 antibody employed for immunoprecipitation was Bethyl, A303-900A.

tag: eclip antibody

tag: molecule

value: RNA size matched input

tag: inline barcode1


title: G3M,CT_like,D3,noDOX_rep2

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

data_processing:
Adaptor sequences and low-quality base calls were trimmed using fastp with default parameters.
Trimmed reads were aligned to the Human reference genome (GRCh38) using STAR v2.7.7a in paired-end mode with default parameters
Gene level counts were generated using FeatureCounts from Subread v2.0.
Assembly: GRCh38.p13
Supplementary files format and content: comma-separated csv file include TPM value of each sample

source_name: cell line

extract_protocol:
Total RNA was extracted from cultured cells using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Library for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit.

value: cell line

value: trophoblast cell

value: knock in

value: TSCM


title: R1-NHP-13_KP1


title: ChIPseq_ESC_CTCF_IP_wt_rep2


title: ChIPseq_ESC_CTCF_IP_BPTFko_rep1


title: G3M,CT_like,D3,DOX_rep2


title: HEK293_LARP4 eCLIP,  size-matched input, rep 1

description: eCLIP size matched input replicate 1


title: R2-NHP-57-N-H3K27ac


title: G3M,CT_like,D3,noDOX_rep1


title: ChIPseq_ESC_CTCF_IP_wt_rep1


title: R2-NHP-55-N-H3K9me3


title: RNAseq_ESC_bptf_ko_C_2

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: csv, count table

extract_protocol:
RNA was extracted with Qiagen Rneasy Mini Kit following manufacture's instruction.. Potential contaminating genomic DNA was removed using Invitrogen DNA-free removal kit, following manufacture's instructions.
Sequencing libraries were prepared from 100ng of purified total RNA using TruSeq stranded mRNA Library Prep (Illumina).

value: bptf knock-out


title: HEK293_LARP4 eCLIP, rep 2

description:
eCLIP IP replicate 2
LARP4_hek_WT.bed

source_name: HEK293_LARP4 eCLIP

value: LARP4 (Bethyl, A303-900A)

value: RNA IP


title: G3M,CT_like,D3,DOX_rep1


title: R2-NHP-55-N-H3K4me3


title: G3M,CT_like,D2,noDOX_rep2


title: RNAseq_ESC_wt_C_2

value: embryonic stem cells


title: R2-NHP-55-N-H3K27me3


title: RNAseq_ESC_wt_C_1


title: G3M,CT_like,D2,noDOX_rep1


title: HEK293_LARP4 eCLIP, rep 1

description:
eCLIP IP replicate 1
LARP4_hek_WT.bed


title: R2-NHP-55-N-H3K27ac


title: recovCVS606

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

data_processing:
FastQ files were analyzed using the Illumina Dragen® (Dynamic Read Analysis for Genomics) Bio-IT platform v 3.9.5 (Edico Genome, Illumina San Diego) on the Illumina cloud providing predesigned analysis pipelines.
Runs were prepared and quality checked using Fast Q toolkit pipeline (v1.0.0.) with a minimum length of 32 bp adapter trimming using the TRUESEQ HT/LT adapters sequence (Illumina San Diego, USA). Settings were: trimming strength: 4 and a quality score < 10 to trim bases at 5’ and 3’ sites prior to mapping.
Paired read FastQ files were then mapped using a Hash table generated by DRAGEN Reference builder (v.3.10.4) based on the mouse genome (GRCm38.p6.genome.fa). Fragments with a minimum read quality of at least 20 and a minimum read coverage of at least 5, as well as a maximum coverage of 99.9%, were considered for analysis. Deduplication, sorting, and alignment mapping to reference genome was performed using the DRAGEN Germline pipeline (version v3.2.8).
Outputs of sequence alignment/mapped Bam files were merged per condition using SamTools  and analyzed using the R package MeDIP (Settings were: extend: 300; paired: TRUE; shift: 0; uniq: 0.001, window size: 100) (Lienhard et al, 2014).
Assembly: GRCm38.p6.genome.fa
Supplementary files format and content: Dragen (TM) germline pipeline bam file (bam)
Supplementary files format and content: corresponding Dragen (TM) germline pipeline bam.bai file (bam.bai)

growth_protocol: C57/Bl6 male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.

extract_protocol:
Qiagen, Dneasy Blood & tissue Kit
500 ng of DNA were shared by ultrasound to an average length of 200 nt (Bioruptor® Pico; Diagenode SA, Seraing, Belgium). DNA was then processed in two steps and subsequently analyzed by Next-Generation Sequencing. Sample complexity was reduced by enrichment of DNA fragments with methylated cytosines using the EpiXplore™ Methylated DNA Enrichment Kit (Takara Bio Inc., Japan).  NEB Ultra-II Library kit (NewEngland BioLabs® Inc.) was used according to manufacturer's instructions. Libraries were paired-end sequenced on the NextSeq550™ instrument with automated FastQ raw data analyses (Illumina, San Diego, USA).

treatment_protocol: The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief,  the  Cvs protocoll consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days. the first cohort was analysed immediately after the stress protocoll, a recovery cohor was analysed 3 month later. Age matched unstressed animals were used as control pe cohort.

tag: Sex

value: male

value: recovery

value: CVS


title: recovCVS608


title: G3M,CT_like,D2,DOX_rep2


title: RNAseq_ESC_tip5_ko_B_2

value: tip5 knock-out


title: G3M,CT_like,D2,DOX_rep1


title: R2-NHP-42-N-H3K9me3


title: recovCVS598


title: RNAseq_ESC_wt_B_1

value: wild-type


title: R2-NHP-42-N-H3K4me3


title: RNAseq_ESC_tip5_ko_B_1


title: R2-NHP-42-N-H3K27me3


title: G3M,CT_like,D1,noDOX_rep2


title: recovCtrl652r

value: Ctrl


title: RNAseq_ESC_wstf_ko_A_2

value: wstf knock-out


title: G3M,CT_like,D1,DOX_rep2


title: recovCtrl651

value: liver


title: R2-NHP-13-N-H3K9me3


title: G3M,CT_like,D1,noDOX_rep1


title: R2-NHP-42-N-H3K27ac


title: G3M,CT_like,D1,DOX_rep1


title: acuteCVS270

value: acute


title: RNAseq_ESC_bptf_ko_C_1


title: RNAseq_ESC_wstf_ko_A_1


title: acuteCVS269


title: R2-NHP-13-N-H3K27me3


title: G3M,CT_like,D0_rep2

value: cell line

value: pluripotent stem cell

value: EPSCM


title: G3M,CT_like,D0_rep1

value: knock in


title: acuteCVS268


title: R2-NHP-13-N-H3K4me3


title: RNAseq_ESC_rsf1_ko_A_1

value: rsf1 knock-out


title: RNAseq_ESC_wt_B_2


title: RNAseq_ESC_rsf1_ko_A_2


title: recovCtrl533


title: RNAseq_ESC_wt_A_2


title: R2-NHP-13-N-H3K27ac


title: G3M/S6G,LOW_rep2

value: trophoblast cell

value: TSCM


title: RNAseq_ESC_wt_A_1

value: embryonic stem cells


title: R2-NHP-04-N-H3K9me3


title: acuteCVS267

value: male


title: acuteCVS266


title: G3M/S6G,LOW_rep1


title: acuteCtrl300


title: R2-NHP-04-N-H3K4me3


title: G3M/S6G,HIGH_rep2


title: acuteCtrl299


title: R2-NHP-04-N-H3K27me3


title: Aire_KO_PolII_ChIP_rep1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Low-quality reads were removed using Sickle.
Reads were aligned to mm10 by bowtie2 (v2.3.4.3) with the single-end mode.
Non-uniquely mapped and mitochondrial DNA reads were removed using a combination of SAMtools functions.
PCR duplicates were removed using Picard (‘MarkDuplicates’, v2.8.0).
Bigwig files were generated using deepTools (‘bamCoverage’, v3.0.2).
Assembly: mm10
Supplementary files format and content: *.bw: bigwig files

source_name: Thymus

extract_protocol:
Cells were cross-linked with 1% formaldehyde and then lysed for 10 min on ice in RadioImmunoPrecipitation Assay (RIPA) buffer supplemented with complete protease inhibitor cocktail (Roche). Chromatin was fragmented using Covaris for 15 min (duty cycle 2%, intensity 3, cycle/burst 200) and the sheared material was cleared by a 10-min centrifugation at 13,000 rpm at 4 °C. The cleared material was immunoprecipitated overnight at 4 °C with Pol II Ab conjugated to magnetic Protein-G beads (Life Technologies, Dynabeads), followed by extensive washing of the beads with ice-cold RIPA, high-salt RIPA, LiCl. Chromatin was eluted from the beads, treated with 1µg DNase-free RNase (Roche) for 30 min at 37°C and then treated with Proteinase K (Roche) for 2 hrs at 37°C.
Chromatin was reverse cross-linked by incubating at 65°C overnight. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and then subject to sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification. DNA was PCR amplified for 15 cycles. Libraries were size-selected for 200–500-bp fragments with SPRI beads.

treatment_protocol: mTECs were isolated by collagenase and dispase digestion, CD45+ cells depletion using magnetic beads, fluorescent antibodies staining, and flow sorting.

value: Thymus

value: mTEChi

tag: chip antibody

value: RNA-PolII (MMS-128P, Covance)

value: Aire-KO

tag: age

value: 4-6 weeks old

value: Female

tag: strain


title: acuteCtrl289

tag: tissue

value: liver

value: Ctrl


title: R2-NHP-04-N-H3K27ac


title: G3M,SP6KO,CT_like_rep2

value: cell line

tag: cell line

value: knock out


title: acuteCtrl284

tag: cell type

value: acute


title: G3M,CON,CT_like_rep2

value: knock in

tag: treatment


title: acuteCtrl283

tag: genotype


title: R2-NHP-02-N-H3K27me3


title: R2-NHP-02-N-H3K9me3


title: NPC, long read, light polyribosome (2-4 ribosomes), rep2

extract_protocol:
R2C2
BIOO qRNA seq v2  Library Preparation Kit  -- strand-specific, read1 is antiSense to input RNA
Frac-seq

value: neural progenitor cell (NPC)

value: dual-SMAD inhibition

value: light polyribosome (2-4 ribosomes)

value: poly A+


title: R2-NHP-02-N-H3K27ac


title: NPC, long read, light polyribosome (2-4 ribosomes), rep1


title: G3M,CON,CT_like_rep1

value: trophoblast cell

value: TSCM


title: DMC6 (old MYCN T58A) [DMEM.1]

city: Uppsala

first: Finn

last: Hallböök

address: Dag Hammarskjölds v 20

department: Dept Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
Quality check and alignment of the data was done with nf-core/rnaseq pipeline (version 3.4) by adjusting the alignment parameter (--alignEndsProtrude 100 ConcordantPair).
The first 10bp was clipped to avoid biased base composition.
To extract fragment counts, featurecounts (version 2.0.0) (Liao, Smyth, and Shi 2014) was used with minimum mapping quality of 20, and requiring both pairs to be properly aligned on the same chromosome.
Differential expression analysis was done by edgeR (Robinson, McCarthy, and Smyth 2009). Significant differential expressed genes were selected by 1) FDR by the Benjamini and Hochberg method <= 0.05 and 2) |log2 fold-change| >= 1.
For GO/Pathway enrichment analysis, clusterProfiler (version 4.0.6) (Yu et al. 2012) was used. GO gene set enrichment analysis was done by gseGO and at least 10 genes were required to be included in the GO term to be visualized. KEGG gene set enrichment analysis was done by gseKEGG.
Assembly: Galgal6, added transgenes "human MYCN" (Ensembl ID: ENST00000281043.4), "eGFP"
Supplementary files format and content: normalized gene counts using TMM values with every gene and every sample

organism: Gallus gallus

source_name: Retina

growth_protocol: For MYCN-overexpressing cell lines, the cells were kept in suspension in RPMI 1640 medium supplemented with 10%FBS, 1% MEM-NEAA and 1% Pen/Strep. The medium was changed twice a week.

extract_protocol:
The central region of E14 chicken retina was dissected and dissociated with 1X Trypsin EDTA. The total RNA was extracted with Qiagen Rneasy Micro Kit (Qiagen, #74004). The RIN value and RNA concentration was measured by TapeStation and 1µg of total RNA was sent for library construction.
MYCN-overexpressing cells were taken and dissociated by vibration and pipetting. The total RNA was extracted with Qiagen Rneasy Micro Kit (Qiagen, #74004). The RIN value and RNA concentration was measured by TapeStation and 1µg of total RNA was sent for library construction.
The library was prepared using the TruSeq stranded mRNA library preparation kit with polyA selection (Illumina Inc.).

value: Retina

value: Primary cells

value: Retinoblastoma cells

value: White Leghorn

value: MYCN T58A overexpression

tag: in ovo_mycn_electroporation

value: At E3.5

value: > 200 days in culture


title: DMC5 (old MYCN T58A) [RPMI.2]


title: NPC, long read, heavy polyribosome (5+ ribosomes), rep2

tag: fraction

value: heavy polyribosome (5+ ribosomes)


title: pat1 mutant exposed to Congo Red 2 hours_3

city: Madrid

first: Raul

last: Garcia

state: Madrid

address: Plaza Ramon y Cajal s/n

department: Microbiologia y Parasitologia

country: Spain

institute: Universidad Complutense de Madrid

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scanner were analyzed using RMA (Robust Multichip Average) algorithm from Bioconductor software

label: biotin

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: Following affymetrix labelling instructions

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown for 2 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the NucleoSpin RNA kit (Macherey-Nagel, Dueren, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown with Congo Red for 2 hours

tag: genetic background


title: Aire_KO_PolII_ChIP_rep2

value: Thymus

value: mTEChi

value: RNA-PolII (MMS-128P, Covance)

value: Aire-KO

value: 4-6 weeks old

value: Female


title: pat1 mutant exposed to Congo Red 2 hours_2


title: pat1 mutant exposed to Congo Red 2 hours_1


title: pat1 mutant 2 hours_3


title: NPC, long read, heavy polyribosome (5+ ribosomes), rep1

value: neural progenitor cell (NPC)

value: dual-SMAD inhibition

tag: riborna depletion

value: poly A+

tag: pcr


title: pat1 mutant 2 hours_2


title: G3MS6G,HA_rep1

data_processing:
Trimmed paired-end reads were mapped to a mouse GRCh38 genome reference genome with bowtie2.
Duplicate reads were removed using picard. Only uniquely reads>1000 cells will be remained.
Peaks were called uing macs2 2.2.7.1 with nolambda、nomedel and broad.
Bigwig files were generated using the Deeptools.
BamCoverage，reads were normalized to 1000000.
Assembly: GRCh38
Supplementary files format and content: bigWig, broadPeak
Supplementary files format and content: Fragments data contains fragment position

extract_protocol:
Cells were resuspended with 80 µl Antibody Buffer (mix 4 µL 0.5 M EDTA with 1 mL 0.01% Digitonin-Wash Buffer (Dig-Wash Buffer) supplemented with cocktail, 10 mM sodium butyrate and 0.05% Triton X-100) containing 0.4 µg primary antibody. The mixture was incubated at 4°C for 4 h in a rotator with 30 rpm. Cells were then washed twice with 180 µL Dig-Wash Buffer. The secondary antibody was incubated in the same buffer and condition except for the duration of 10 min. After washing with Dig-Wash Buffer twice, cells were suspended with 80 µl Dig-Wash Buffer (with 0.05% Triton-X, cocktail, and 10 mM sodium butyrate) containing 0.83 µM PAT-MEA/B at 4°C for 1 h. The free PAT-MEA/B were then dislodged with 180 µL Dig-Wash Buffer containing 0.05% Triton X-100 three times at 5 min each time. The reaction was activated by suspending the cells with 10 µL Reaction Buffer (10 mM TAPS-NaOH pH 8.3, 5 mM MgCl2, 10% DMF, 300 mM NaCl, 0.05% Triton-X, 0.01% Digtonin and supplemented with cocktail, 10 mM sodium butyrate), followed by gently flicking and incubating at 37°C for 1 h in the Eppendorf ThermoMixer with 300 rpm. The reaction was gently mixed once after 30 min incubation and stopped by the addition of 10 µl 40 mM EDTA followed by further incubation at 4°C for 10 min.
Samples were washed with 0.1% BSA/PBS and finally resuspended in 5 µl Lysis Buffer (0.1 mg/ml Proteinase K, 10 mM Tris-HCl PPH 8.5 and 0.05% SDS) and lysed at 55°C for 3 h in a PCR cycler. 1.8% Triton X-100 with 5 mM PMSF was added to the cell lysate and incubated at RT for 10 min to quench the proteinase K followed by incubation at 55°C for 5 min to quench SDS in the reaction. The DNA can be directly used for PCR amplification by adding 1 µL 25 µM i5 index primer, 1 µL 25 µM i7 index primer, 25 µl 2ⅹKAPA master mix and 17 µL 1 mM MgCl2 to the 6 µL cell lysate for total 50 µl amplification condition. The reaction is set up by incubation at 72°C for 5 min, 98°C for 45 s, 14-18 cycles of (98°C for 15 s, 63°C for 30 s, 72°C for 1 min), and finally 72°C extension for 5 min. After PCR, size selection was carried out by first 0.5ⅹ SPRI beads to remove > 1 kb fragments, and second 0.4ⅹ SPRI beads to the supernatant to obtain 200-1,000 bp fragments for sequencing. The libraries were sequenced with paired-end 150-bp reads on NovaSeq 6000 platform (Illumina).

value: cell line

value: trophoblast cell

value: knock in

value: HA

value: TSCM


title: G3M/S6G,HIGH_rep1


title: DMC4 (old MYCN T58A) [RPMI.1]

value: Retina

value: Primary cells

value: Retinoblastoma cells

value: White Leghorn

value: MYCN T58A overexpression

value: At E3.5


title: NPC, long read, monosome, rep2

value: monosome


title: R2-NHP-02-N-H3K4me3

value: liver


title: pat1 mutant 2 hours_1


title: G3M,CON,IgG

value: IgG


title: G3M,SP6KO,CT_like_rep1

value: knock out


title: DMC3 (old MYCN) [MYCN.2828]

value: MYCN overexpression

value: > 200 days in culture


title: NPC, long read, monosome, rep1

value: neural progenitor cell (NPC)

value: dual-SMAD inhibition

value: poly A+


title: G3M,SP6KO,H3K4me3_rep2

value: cell line

value: trophoblast cell


title: wild type exposed to Congo Red 2 hours_3


title: wild type exposed to Congo Red 2 hours_2


title: G3MS6G,HA_rep2

value: knock in

value: HA

value: TSCM


title: DMC2 (old MYCN) [MYCN.2826]

value: Retina

value: Primary cells

value: Retinoblastoma cells

value: White Leghorn


title: NPC, long read, cytosol, rep2

value: cytosol


title: G3M,SP6KO,H3K4me3_rep1


title: DMC1 (old MYCN) [MYCN.2825]

value: At E3.5


title: NPC, long read, cytosol, rep1


title: G3M,SP6KO,IgG

value: knock out

value: IgG


title: G3M,CON,H3K4me3_rep2


title: DMC10 (young MYCN) [DMC.10]

value: MYCN overexpression

value: < 4 weeks in culture


title: ESC, long read, light polyribosome (2-4 ribosomes), rep2

value: embryonic stem cell (ESC)

value: control

value: light polyribosome (2-4 ribosomes)


title: ESC, long read, light polyribosome (2-4 ribosomes), rep1

value: poly A+


title: G3M,CON,H3K4me3_rep1

value: cell line

value: trophoblast cell

value: knock in


title: G3M,SP6KO,H3K27me3_rep2

value: TSCM


title: wild type 2 hours_3


title: DMC8 (young MYCN) [DMC.8]

value: Retina

value: Primary cells


title: Control E14 chicken retina replicate 3 [E14.Retina.Rpt3]

value: Developing chicken retinal cell

value: White Leghorn

value: Normal

value: No

value: E14 dissection


title: G3M,SP6KO,H3K27me3_rep1

value: knock out


title: wild type 2 hours_1


title: ESC, long read, heavy polyribosome (5+ ribosomes), rep1

value: heavy polyribosome (5+ ribosomes)


title: G3M,CON,H3K27me3_rep2


title: Control E14 chicken retina replicate 2 [E14.Retina.Rpt2]


title: ESC, long read, monosome, rep2

value: embryonic stem cell (ESC)

value: monosome


title: G3M,CON,H3K27me3_rep1


title: Control E14 chicken retina replicate 1 [E14.Retina.Rpt1]


title: wild type exposed to Congo Red 2 hours_1


title: DMC9 (young MYCN) [DMC.9]

value: Retinoblastoma cells

value: MYCN overexpression

value: At E3.5

value: < 4 weeks in culture


title: 2-3 Hb9GFP_Ctrl_MN_D9_N2

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression in control EB on Day9 (ES~MNs)

hyb_protocol: 825 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4858A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software10.5.1 (Agilent) using default parameters (protocol GE1-105_D08 and Grid: 028005_D_F_20110711) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: control ES~MNs on day 9

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Whole EBs were dissociated into single cells on day 5

extract_protocol: Total RNA isolation by Trizol, DNase treated by TURBO DNA-free Kit (Life Technology), and checked with Bioanalyzer 2100 (Agilent) for RIN > 9.

treatment_protocol: To get the time series samples from ES cell to MNs, RA/Shh were applied from day 2 to day 5 during spinal MN differention. After EB dissociation, GDNF were applied until sampling.

value: dissociated MNs

tag: gender

value: male


title: WT_PBS_mTEC and WT_Spermidine_mTEC, Cite-Seq Hashtag data

description:
4 samples (2  WT_PBS_mTEC and 2 WT_Spermidine_mTEC) were hashed together into a single 10X scRNA-seq run
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz

library_source: other

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics) and  bcl2fastq Conversion (Illumina)
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-Seq

molecule: protein

extract_protocol:
mTECs were isolated by collagenase and dispase digestion, CD45+ cells depletion using magnetic beads, fluorescent antibodies staining, and flow sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v3 chemistry

value: Thymus

value: mTEChi and post-Aire mTEClo

value: WT

value: Female

value: PBS ip injection or Spermidine ip injection

tag: library type

value: HTO

tag: hashid

value: WT_PBS_mTEC_scRNA_seq_rep1 (HT4-AAAGCATTCTTCACG), WT_PBS_mTEC_scRNA_seq_rep2 (HT5-CTTTGTCTTTGTGAG), WT_Spermidine_mTEC_scRNA_seq_rep1 (HT2-GGTCGAGAGCATTCA), WT_Spermidine_mTEC_scRNA_seq_rep2 (HT3-CTTGCCGCATGTCAT)


title: ESC, long read, cytosol, rep2

value: control

value: cytosol

value: poly A+


title: enasidenib (2)

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

institute: Health Research Institute of Asturias (ISPA)

data_processing:
The generated libraries were normalized and combined in equimolecular concentrations for optimal generation of DNA clusters.
Pair-end sequencing (2x100 pb) of the libraries were performed on the NovaSeq 6000  (Illumina Inc.) with a read quality of 90%>Q30
All sequencing data files were evaluated using the fastQC software (v.0.11.9) for quality control
Adapters and poor quality paired-end reads were removed using fasp (v.0.20.1)
Preprocessed reads were pseudo-aligned to the GRCh38 human genome
Preprocessed reads were quantified at the transcript-level using the mapping-based mode of the Salmon package (v.1.3.0)
Analyses of gene expression data were performed using R statistical software (v.4.0.2)
Transcript-level information was summarized at the gene-level for both exploratory and differential analyses using the tximport package (v.1.16.1)
The matrix of raw counts was rlog (regularized logarithm) transformed according to the DESeq2 package (v.1.28.1)
Non-expressed genes (< 2 counts across all conditions) were discarded
Differential gene expression analyses were performed using the negative binomial generalized linear model fitting implemented in DESeq2
Assembly: GRCh38 human genome
Supplementary files format and content: tab-delimited text files include Illumina statistics
Supplementary files format and content: .xlsx file include matrix of counts

source_name: chondrosarcoma cell line

growth_protocol: T-CDS17#1 chondrosarcoma cell line were growth in high glucose DMEM suplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNA was extracted using EurX Universal RNA purification Kit (EurX). > 1 ug of total RNA (concentration >50 ng/ul) was used for the construction of sequencing libraries
Stranded library for RNA-seq was generated with TrueSeq mRNA Library Prep (Illumina Inc.) following manufacturer´s protocols

treatment_protocol: T-CDS17#1 chondrosarcoma cell line was treated with 20 uM of enasidenib and DMSO (control) for 48 h

value: chondrosarcoma cell line

value: chondrosarcoma cells

value: IDH2 mutant

value: ENASIDENIB 20 uM

tag: time


title: 2-4 Hb9GFP_LitchiKO_MN_D9_N2

description: Gene expression in Litchi knockout EB on Day9 (ES~MNs)

source_name: Litchi knockout ES~MNs on day 9


title: WT_PBS_mTEC and WT_Spermidine_mTEC, Cite-Seq RNA data

tag: Sex

value: GEX


title: ESC, long read, cytosol, rep1

value: embryonic stem cell (ESC)


title: ESC, long read, heavy polyribosome (5+ ribosomes), rep2

value: heavy polyribosome (5+ ribosomes)


title: enasidenib (1)


title: TSks-3

city: Lanzhou

first: jinqiang

last: huang

address: Yintanlu Stress

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include counts, FPKM values, TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: skin tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA/miRNA libraries were prepared for sequencing using standard Illumina protocols

value: skin tissues

value: wild-type

tag: infection

value: IHNV


title: TSks-2


title: control (3)

value: DMSO


title: 2-1 Hb9GFP_Ctrl_MN_D7_N2

description: Gene expression in control EB on Day7 (ES~MNs)

source_name: control ES~MNs on day 7

tag: strain

value: dissociated MNs

value: male


title: EO-PE rep4

first: Wen-Long

last: Zhao

address: Guangyuan road 145#

institute: The International Peace Maternity and Child Health Hospital

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: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Placenta from early-onset preeclampsia mice

extract_protocol:
Placetnas on pregnant 17.5 days were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Placenta

tag: devolopmental stage

value: Placenta at pregnant 17.5 days


title: EO-PE rep3


title: EO-PE rep2


title: control (2)

tag: cell line

tag: cell type


title: TSks-1

tag: genotype


title: ESC, long read, monosome, rep1

tag: treatment

value: control

value: monosome


title: enasidenib (3)

value: chondrosarcoma cell line


title: 293T cells, RAD51AP1

city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

institute: Westlake University

data_processing:
The gene annotation (GTF format) of CHM13 is generated with parameters: gffread chm13.draft_v1.1.gene_annotation.v4.gff3 -o chm13.draft_v1.1.gene_annotation.v4.gtf
The STAR reference of human CHM13 genome assembly v1.1 is built with parameters: STAR --runThreadN 8 --runMode genomeGenerate --genomeDir hsa_chm13v1.1_genanno_v4 --genomeFastaFiles chm13.draft_v1.1.fasta --sjdbGTFfile chm13.draft_v1.1.gene_annotation.v4.gtf --sjdbOverhang 150
The BLAST database of human ribosomal DNA is built with parameters: makeblastdb -in Hsa_rDNA_Kim.fa -dbtype nucl -out HsaKimrDNA -parse_seqids
RNA-seq reads are aligned to the pre-built human CHM13 v1.1 using STAR version 2.7.6a with the following parameters: STAR --runMode alignReads --genomeLoad NoSharedMemory --runThreadN 8 --readFilesCommand gunzip -c --genomeDir [dir_of_hsa_CHM13v1.1] --readFilesIn [read1.fq.gz] [read2.fq.gz] --chimOutJunctionFormat 1 --outReadsUnmapped Fastx --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --twopassMode Basic --outFileNamePrefix [outdir_bam] --sjdbOverhang 150 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS --outSAMunmapped Within --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 50000000000 --outFilterMultimapNmax 50
Gene count data is generated using featureCounts version 2.0.2 with the following parameters: featureCounts -T 8 -p -t exon -g gene_id -a [location_of_hsa_CHM13v1.1_gtf] -o [output_featurecounts.txt] [star_align_output_sorted.bam]
The unaligned reads are converted to FASTA format and the reads shorter than 18nt are excluded using seqkit version 2.1.0: seqkit fq2fa -j 16 [unmapped_reads] | seqkit seq -m 18 -o [unmapped_reads_filtered.fa]
The unaligned sequences are aligned with human ribosomal DNA sequence (KY962518.1) using BLAST 2.11.0+ with following parameters: blastn -db [path_of_blastdb_HsaKimrDNA] -query [unmapped_reads_filtered.fa] -outfmt '6 qseqid sseqid pident length slen qlen mismatch gapopen qstart qend sstart send evalue bitscore' -out [blast_results_table]
The BLAST data are filtered, only results in 45S region are kept. These results were splitted into bins of 1nt.
Assembly: human CHM13 v1.1, and the reference sequence of human ribosomal DNA is extracted from NCBI (GenBank: KY962518.1).
Supplementary files format and content: TXT (readpergene table generated from STAR)
Supplementary files format and content: TXT (featurecounts table generated from featurecounts)
Supplementary files format and content: TXT (10nt binned blast results)

source_name: Kidney

growth_protocol: 293T Cells were cultured at 37 °C with 5% CO2 in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
Protein associated RNAs were released by proteinase K and were extracted by phenol/chloroform.
RNAs were purified by phenol/chloroform and all of the RNAs were used for the construciton of sequencing libraries.

treatment_protocol: Cells were cultured 14 h in DMEM medium supplemented with 100 μM 6-SG.

value: Kidney

value: fetal kidney cells

value: RAD51AP1 expression

value: PAR-Clip by streptavidin resin and Flag resin


title: 293T cells, Mock

value: WT


title: wild type 2 hours_2


title: 2-2 Hb9GFP_LitchiKO_MN_D7_N2

description: Gene expression in Litchi knockout EB on Day7 (ES~MNs)

source_name: Litchi knockout ES~MNs on day 7


title: CSks-3


title: control (1)

value: chondrosarcoma cells

value: IDH2 mutant


title: EO-PE rep1


title: LO-PE rep4

source_name: Placenta from later-onset preeclampsia mice


title: 1-2 Hb9GFP_LitchiKO_MN_D7_N1


title: 1-3 Hb9GFP_Ctrl_MN_D9_N1


title: 1-4 Hb9GFP_LitchiKO_MN_D9_N1


title: CSks-2

value: skin tissues

value: wild-type


title: 1-1 Hb9GFP_Ctrl_MN_D7_N1


title: SMF_ESC_BPTFko_rep3

data_processing:
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were trimmed using Trimmomatic v0.32 (24695404) in paired-end mode using the ILLUMINACLIP option. Trimmed reads were mapped to the mm10 mouse genome using the qAlign function from the QuasR package v_1.36.0 with parameters for bisulfite data.
Supplementary files format and content: DNA methylation was quantified for all Cs using qMeth and then separated into Cs in the CpG or GpC context, removing GCG and CCG sequence contexts as these cannot be distinguished between endogenous methylation and SMF methylation. Plots of SMF data are of 1 − GpC methylation to visualize the footprint.
Library strategy: Single-molecule footprinting

extract_protocol:
DNA was extracted using phenol:chloroform and further extracted with chloroform.
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) .

value: embryonic stem cells

value: BPTF knock-out


title: LO-PE rep3


title: SMF_ESC_BPTFko_rep2


title: Human_colon_cryopreserved

city: Barcelona

first: Laura

last: Jiménez-Gracia

address: c/ Baldiri Reixac, 4  Barcelona Science Park - Tower I

institute: Centre Nacional d'Anàlisi Genòmic (CNAG)

description:
xj1wbujr_xv3enf58
10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10; GRCh38

source_name: Colon

extract_protocol: The Next GEM Single Cell 3’ Reagent Kits v3.1 (PN-  1000268, 10X Genomics) were used to prepare cDNA sequencing libraries, following the  manufacturer's instructions. Briefly, after GEM-RT clean up, cDNA was amplified for 11  cycles and then subjected to quality control and quantification using an Agilent Bioanalyzer  High Sensitivity chip (Agilent Technologies). The Dual Index Kit TT Set A (PN-1000215, 10X  Genomics) was used for indexing cDNA libraries by PCR. The size distribution and  concentration of 3' cDNA libraries were verified again on an Agilent Bioanalyzer High  Sensitivity chip (Agilent Technologies). The cDNA libraries were sequenced on an Illumina  NovaSeq 6000 using the following sequencing conditions: 28 bp (Read 1) + 8 bp (i7 index) +  0 bp (i5 index) + 89 bp (Read 2) to generate approximately 40,000 read pairs per cell.

value: Colon

tag: type

value: cryopreserved


title: Human_colon_fixed

description:
vy7zj9cf_acmeyhd6
10x Genomics

value: fixed


title: CSks-1

value: control


title: LO-PE rep2

value: Placenta

value: Placenta at pregnant 17.5 days


title: B.abortus, ∆mucR, exponential growth (fast5)

city: Amherst

first: Maxwell

middle: B

last: Campbell

address: 240 Thatcher Way

department: Molecular and Cellular Biology

institute: UMass Amherst

description: R10.4.1 pores

data_processing:
Samples were de-multiplexed, and unique molecular identifiers (UMIs) were added during PCR steps removed using Je
The clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC011916.1) using bwa and sorted with samtools.
Duplicate transposon reads removed by Je and indexed with samtools.
Genome positions are assigned to the 5′ position of transposon insertions using bedtools genomecov.
bedtools map is used to count either the total number of transposon insertions per gene using the bedtools map -o sum argument or the unique number of insertions using the bedtools map -o count argument
Assembly: NCBI Reference Sequence: NC011916.1
Supplementary files format and content: tab delimited text files include raw total or unique insertion counts for each gene.

organism: Brucella abortus 2308

source_name: bacteria

growth_protocol: Transposon mutagenesis libraries were thawed and recovered in PYE or PYE + %0.2 Xylose overnight at saturating concentrations to minimize growth during recovery. Only for dnaK-NI library, overnights were recovered in saturating Xylose concentrations (%0.2), and treatment and T24 control conditions were grown in minimal Xylose concentrations. (%0.002)

extract_protocol:
Following overnight growth, 1 ml of saturated culture from each Tn library was pelleted at 8000xg for 2 minutes. Genomic DNA was extracted by Monarch Genomics DNA Preparation Kit (NEB) according to the manufacturer’s protocol.
The sequencing libraries for Next-generation sequencing were prepared using a customized three-step PCR protocol. Genomic DNA input was normalized to a concentration of 100 ng/μl. The initial transposon junction amplification (PCR1) was carried out using an arbitrary PCR amplification method. This step utilized a forward primer designed to align with one end of the transposon and three reverse arbitrary primers. The PCR1 process employed a 2-step cycling protocol with annealing temperatures set at 42°C and 58°C, and number of cycles at 6 and 15, respectively.  Subsequently, the second PCR step (PCR2) involved the addition of 16S adapters for Illumina indexing, along with unique molecular identifiers (UMI), and amplification of the library for 36 cycles. Post-PCR2 cleanup was performed using Aline PCRClean DX magnetic beads. The final PCR step (PCR3) incorporated NexteraXT indexing in accordance with the manufacturer's protocol. Post-indexed library (PCR3) cleanup was carried out using Aline PCRClean DX magnetic beads.

treatment_protocol:
Control condition: Libraries were back diluted to OD 0.008 into 7 ml of PYE or PYE+0.002% xylose and grown overnight until they reached saturation at OD ∼1.6.
Heat stress: Libraries diluted to OD of 1 and heat-stressed at low, medium, or high (37, 42, 43.8◦C, respectively) for 45 minutes in a Biorad Thermocycler. After 45 minutes, cells diluted back to a final OD of 0.008 in 7 ml media for 24-hour growth.
Oxidative stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (0.025mM, 0.05mM, 0.1mM) level hydrogen peroxide. Cells were grown for 24 hours in these chronic stress conditions.
L-canavanine stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (25ug/ml, 50ug/ml, 100ug/ml) levels of L-canavanine. Cells were grown for 24 hours in these chronic stress conditions.

value: delta-mucR

tag: development stage

value: exponential

value: bacteria


title: SMF_ESC_BPTFko_rep1

source_name: embryonic stem cells


title: B.abortus, ccrM overexpression, exponential growth (fast5)

description: R10.4.1 pores

value: CcrM OE


title: SMF_ESC_wt_rep3


title: SMF_ESC_wt_rep2


title: Human_PBMC_fixed

description:
r7nri3n5_f7z94ntj
10x Genomics

source_name: PBMC

value: PBMC


title: Control rep2

source_name: Placenta from control mice


title: B.abortus, ∆lon, exponential growth (fast5)

description: R10.4.1 pores

value: delta-lon


title: Human_colon_fresh

description:
drqqjzym_3c2ryvzv
10x Genomics

value: fresh


title: Human_PBMC_fresh

description:
d9dyw64v_o4ypmvlg
10x Genomics


title: SMF_ESC_wt_rep1


title: Control rep1


title: PAV-104-8

status: Public on Mar 10 2024

first: Li

last: Du

address: 360 Spear St

institute: Vitalant Research Institute

data_processing:
The raw RNA sequencing data were aligned to the human genome (GRCh38) using STAR (version 2.7.3a).
Assembly: human genome (GRCh38)
Supplementary files format and content: txt file includes counts for each sample

source_name: Donor 8 tracheobronchial tissue was obtained at the time of lung transplant

growth_protocol: The tissue was washed and placed in DMEM with 0.1% protease and antibiotics overnight at 4ºC. The next day, the solution was agitated, and the remaining tissue was removed. Cell pellets were treated with 0.05% trypsin-EDTA, then filtered through a cell strainer. Cells were plated onto 6mm/0.4mm Transwell ALI insert (Corning, 3470) after treatment with FNC coating mixture (Athena Enzyme Systems, 0407). 10% FBS in DMEM and ALI media were added in equal volumes to each basal compartment and cultures were incubated at 37ºC with 5% CO2. The next day, the media was removed and both compartments were washed with PBS and antibiotics. ALI media was then added to each basal compartment and changed every three days for at least 28 days until differentiated airways were ready for use .

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
RNA libraries were constructed and sequencing was performed by Novogene or Seqpal using their mRNA sequencing protocol

treatment_protocol: For infection of primary AECs in ALI culture, cells were pretreated with PAV-104 in the basal compartment for one hour. SARS-CoV-2 (diluted in ALI-culture medium, MOI=0.1) was added to the apical chamber of inserts (250 μl) and the basal compartment (500 μl). Then the cultures were incubated for 2 hours at 37ºC (5% CO2) to enable virus entry. Subsequently, the cells were washed and fresh ALI medium (500 μl) containing PAV-104 was added into the basal compartment. Cells were incubated at 37ºC (5% CO2) and harvested for analysis at 36 hours post-infection.

value: Donor 8 primary airway epithelial cells

value: primary cells

value: PAV-104 treatment


title: PAV-104-7

source_name: Donor 7 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 7 primary airway epithelial cells


title: PAV-104-6

source_name: Donor 6 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 6 primary airway epithelial cells


title: DMSO-8

value: Donor 8 tracheobronchial tissue was obtained at the time of lung transplant

value: DMSO


title: PAV-104+SARS-CoV-2 infection-5

source_name: Donor 5 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 5 primary airway epithelial cells

value: PAV-104 treatment and SARS-CoV-2 infection


title: PAV-104+SARS-CoV-2 infection-4

source_name: Donor 4 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 4 primary airway epithelial cells


title: DMSO-6

value: Donor 6 tracheobronchial tissue was obtained at the time of lung transplant


title: PAV-104+SARS-CoV-2 infection-3

source_name: Donor 3 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 3 primary airway epithelial cells


title: DMSO-7

value: Donor 7 tracheobronchial tissue was obtained at the time of lung transplant


title: PAV-104+SARS-CoV-2 infection-2

source_name: Donor 2 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 2 primary airway epithelial cells


title: LO-PE rep1

value: Placenta

value: Placenta at pregnant 17.5 days


title: SARS-CoV-2 infection-4

value: Donor 4 tracheobronchial tissue was obtained at the time of lung transplant

value: SARS-CoV-2 infection


title: SARS-CoV-2 infection-5

value: Donor 5 tracheobronchial tissue was obtained at the time of lung transplant

value: primary cells


title: SARS-CoV-2 infection-3

value: Donor 3 tracheobronchial tissue was obtained at the time of lung transplant


title: SARS-CoV-2 infection-2

value: Donor 2 tracheobronchial tissue was obtained at the time of lung transplant


title: SARS-CoV-2 infection-1

source_name: Donor 1 tracheobronchial tissue was obtained at the time of lung transplant

value: Donor 1 primary airway epithelial cells


title: DMSO-5

value: DMSO


title: DMSO-4


title: DMSO-2


title: DMSO-3


title: EBV biol rep 4

city: Oklahoma City

first: Patrick

middle: M

last: Gaffney

state: OK

address: 825 NE 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

description: EBV RNA

data_processing:
Oligo-barcode associations and barcode counting. Paired oligo-barcode associations were determined in the four sequenced mpra∆orf plasmid control libraries using analysis scripts (e.g. MPRAmatch.wdl) and the pipeline designed by Dr. Ryan Tewhey (https://github.com/tewhey-lab/MPRA_oligo_barcode_pipeline) Pairs with alignment score error rates of greater than 5% were discarded. Only barcodes that uniquely mapped to one oligo were used for downstream analysis. Oligo-barcode pairs from the four libraries were then merged together for a total of 66,949 (99.87%) oligos captured and 145M total oligo-barcode pairs in the initial oligo-barcode pools.  Barcode read counting for each oligo-barcode pair was determined in each of the four plasmid control replicates and six transfected EBV B cell line replicates using the MPRAcount.wdl script. Reads were totaled across all barcodes associated with each oligo.
Expression modulating sequence (emSeq) and allele-specific expression modulating variant (emVar) identification.  EmSeq and emVar discovery utilized Dr Ryan Tewhey’s MPRA count analysis pipeline (https://github.com/tewhey-lab/MPRAmodel).  Oligo counts were normalized by DESeq2  and modeled as a negative binomial distribution to obtain estimates of variance in oligo counts across all samples. EmSeqs – defined as sequences with regulatory activity that modulate GFP reporter gene expression – were determined for the plasmid controls and library replicates and tested for significant expression differences in GFP reporter gene expression using a Wald’s test .  A fold change (FC) difference of 1.5 between the plasmid controls and EBV library replicates and an FDR<0.05 were required for significance.  EmSeqs were then assessed for allele-specific transactivation potential (emVars) by comparing log2 ratios of the reference versus alternate alleles using a Student’s t-test . A FC=1.25 between the two alleles and an FDR<0.05 were required for significance.  For the 320 multiallelic variants, the reference allele was compared to each alternate allele separately.
Assembly: hg38
Supplementary files format and content: Combined_oligo_counts.txt is a text file that contains the summed read counts for all barcodes assigned to an oligo in each EBV and plasmid control sample (EBV biological reps 1-6 and plasmid control biological reps 3-6).
Supplementary files format and content: Combined.merged.parsed.txt is a text file that contains CIGAR and error data on each unique barcode-oligo combination from the Barcode tag libraries 1-4.

source_name: EBV cell line

extract_protocol:
EBV B cells were cultured in RPMI medium supplemented with 15% FBS, 100U/mL penicillin, 100µg/mL streptomycin, and 2mM L-glutamine at 37°C, 5% CO2.  Cells were seeded at 5x10^5 cells-per-mL 36 hours before transfection.  Cells were collected and split into six transfections with 100 million cells and 100µg mpra:gfp plasmid library per replicate. Transfection was performed with the Neon transfection system in 100µL tips containing 10 million cells per tip with 3 pulses of 1200V and 20ms each. After transfection, cells were cultured with RPMI supplemented with 15% FBS and without antibiotics for 24 hours. Cells were then collected and lysed in RLT buffer (Qiagen Midi RNeasy 75144) by passing through 18-gauge needles. Cell lysate was stored in -80°C until RNA purification.
MPRA was performed as described previously (PMID: 27259153; 33712590) with minor modifications.  First, oligo-barcode libraries were constructed by 28X parallel PCR reactions to add 20bp random barcodes to the synthesized 180bp oligos.  Mpra∆orf libraries were assembled using Gibson Assemble Master Mix (NEB E2611L).  The GFP amplicon containing a minimal promoter, GFP open reading frame, and partial 3’UTR was amplified from the pGL4.23:minP GFP plasmid and inserted into purified mpra∆orf plasmids by Gibson Assembly. Constructed mpra:gfp libraries were transformed into NEB 10-b E. coli (NEBC3020K) by electroporation and expanded in 5L LB media supplemented with 100µg/mL carbenicillin at 37°C, shaking for 16 hours.  The mpra:gfp plasmid libraries were purified using the Qiagen Plasmid Plus Giga Kit.
MPRA Library Complexity Validation. The fragment containing the oligo-barcode combination was amplified from mpra∆orf plasmids and attached to Illumina sequencing adapters with the Illumina TruSeq Universal Adapter and unique P7 index primers. Libraries were sequenced using 2x150 PE reads on the Illumina Novaseq platform.   Sequencing Library Preparations. Total cell lysis was thawed on ice and lysed again by passing 5-10 times through 18-gauge needles. GFP mRNA extraction, pull down, and cDNA synthesis was performed as previously described 6,14.  Plasmid libraries and cDNA samples were amplified, and Illumina sequencing adaptors were added using the Illumina TruSeq Universal Adapter and TruSeq_Index primer (NEB E7335S).  Libraries were sequenced using the Illumina NovaSeq targeting 400 million reads per sample.

value: EBV cell line


title: EBV biol rep 5

description: EBV RNA


title: B.abortus, wild-type, exponential growth (fast5)

description: R10.4.1 pores

value: wild-type

value: exponential

value: bacteria


title: EBV biol rep 3

description: EBV RNA


title: EBV biol rep 6

description: EBV RNA


title: Human_colon_fixed_cryopreserved

description:
o5p4sf2u_vwljz9k4
10x Genomics

value: Colon

value: fixed cryopreserved


title: EBV biol rep 1

description: EBV RNA


title: EBV biol rep 2

description: EBV RNA


title: Gastric, 11th tumor organoid, patient no.17

city: Beijing

first: Ye-guang

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
The raw FASTQ data were aligned to the human genome reference (GRCh38) using the Burrows-Wheeler Aligner (BWA) algorithm with default parameters of BWA-MEM
Duplicate reads were marked and removed using Picard, and local realignment around indels was performed to enhance variant calling accuracy
Base quality scores were recalibrated using BQSR (Base Quality Score Recalibration) to correct systematic errors
Variant calling was conducted using Mutect, and the called variants were subsequently filtered based on criteria such as read depth, mapping quality, allele frequency, and functional impact and SNV annotation was performed using ANNOVAR
Assembly: hg38
Supplementary files format and content: vcf file of all mutations
Library strategy: Whole exosome sequencing

source_name: Gastric tumor organoids

extract_protocol:
Total DNA from tissues and cultured organoids was extracted using TIANamp Genomic DNA Kit (DP304, TIANGEN).
DNA-sequencing libraries were prepared using NEB Next Ultra DNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s instruction. Then, the DNA libraries were sequenced using Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

tag: subject

value: patient no.17

value: Gastric tumor organoids

tag: sample id


title: Gastric, 22th tumor organoid, patient no.17


title: PAV-104+SARS-CoV-2 infection-1

value: Donor 1 tracheobronchial tissue was obtained at the time of lung transplant

value: PAV-104 treatment and SARS-CoV-2 infection


title: K562 cells, Control, rep1

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Snakemake pipeline (https://github.com/snakemake-workflows/rna-seq-star-deseq2) was used to process the bulk RNA-seq sample
Cutadapt v3.4 was used to trim adapters from reads, STAR was used to align the spliced transcripts to the reference genome (GRCh37 assembly release 75) and quantify the read counts per gene.
DESeq2 was used to perform differential expression analysis. P-values were corrected by the BH procedure for FDR control.
Assembly: GRCh37 assembly release 75
Supplementary files format and content: tab-delimited files with raw counts of gene expression from all samples
Supplementary files format and content: tab-delimited files with differential gene expression test results from DESeq2

growth_protocol: K562 cells were cultured in RPMI 1640 + L-Glutamine (Gibco), 10% fetal bovine serum (Biowest), and 1% Penicillin-Streptomycin (Gibco). Cell density and culture conditions were maintained according to the ENCODE Cell Culture Guidelines.

extract_protocol:
RNA was isolated using ISOLATE II RNA Mini Kit (BIO-52073)
sequencing libraries were made with the Invitrogen Collibri Stranded RNA Library Preparation kit (A39003024)

treatment_protocol: To generate the UCE-KO cell clones, the gRNA sequences designed to target UCE regions were cloned into the dual-CRISPR-Cas9-U6-H1 (pBP48) plasmid containing the gRNA scaffold and Cas9 sequence. K562 cells were transfected with the plasmids containing the respective pairs of guide RNAs and then selected for successful transfection using puromycin. Single clones of cells were picked and verified using PCR and Sanger sequencing.

value: erythroleukemia

value: WT


title: K562 cells, Control, rep2


title: K562 cells, PAX6_Tarzan Knockout, rep1

value: PAX6_Tarzan Knockout


title: Gastric, 4th tumor organoid, patient no.17


title: K562 cells, PBX3_Claudia Knockout, rep1

value: PBX3_Claudia Knockout


title: K562 cells, PBX3_Claudia Knockout, rep2


title: Gastric, Adjacent normal, patient no.17

source_name: Gastric adjacent normal

value: Gastric adjacent normal


title: Gastric, Tumor tissue, patient no.17

source_name: Gastric tumor tissues

value: Gastric tumor tissues


title: Skin Black 3

city: Dunedin

first: Donna

last: Bond

address: 270 Great King Street

department: Department of Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Raw reads were trimmed using Trim Galore! (v0.6.10) to remove adapters and low-quality base calls (Phred score < 20)
Trimmed reads were mapped to the possum reference genome (GCA_011100635.1) using HISAT2 (v2.2.1) with the following parameters: hisat2 -p 8 --dta --rna-strandness R
Any amplicon contamination from the opposing strand (from a previous experiment) was detected and removed using grep
Aligned RNA-sequencing reads were assembled using StringTie (v2.2.0) with the following annotation-guided assembly parameters: stringtie -p 8 -G --rf -A -C
Assembly: Trichosurus vulpecula (GCA_011100635.1)
Supplementary files format and content: For each sample, a StringTie generated GTF file containing the aligned and assembled transcripts is supplied. This includes the abundance (transcripts per million, TPM) of each transcript as determined by StringTie

organism: Trichosurus vulpecula

source_name: Skin

extract_protocol:
Total RNA was extracted from tissue samples (~50 mg) stored in RNAlater using TRIzol Reagent (Invitrogen) following the manufacturer’s guidelines. RNA samples were treated to remove any contaminating DNA using the Turbo DNA-free kit (Invitrogen) according to the protocol.
250 ng of DNase-treated RNA was used to construct poly(A) enriched, strand-specific RNA sequencing libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Poly(A) mRNA Magnetic Isolation Module (1/2 of the standard reaction volume) (NEB)

value: Skin

tag: tiisue source

value: Ear punch

tag: coat colour

value: Black

value: Female

tag: developmental stage

value: Adult


title: Skin Black 2


title: Skin Black 1


title: Gastric, Adjacent normal, patient no.16

value: patient no.16


title: Gastric, Tumor tissue, patient no.16


title: Gastric, 12th tumor organoid, patient no.13

value: patient no.13


title: DMSO-1

city: San Francisco

value: Donor 1 primary airway epithelial cells

value: primary cells

value: DMSO


title: Skin Grey 3

value: Grey


title: Gastric, Adjacent normal, patient no.13


title: Gastric, 22th tumor organoid, patient no.12

value: patient no.12

value: Gastric tumor organoids


title: Skin Grey 2


title: K562 cells, PAX6_Tarzan Knockout, rep2

value: erythroleukemia

value: PAX6_Tarzan Knockout


title: Gastric, 11th tumor organoid, patient no.12


title: Gastric, Tumor tissue, patient no.13


title: Skin Grey 1


title: Gastric, Tumor tissue, patient no.10

value: patient no.10


title: Gastric, 21th tumor organoid, patient no.10


title: Barcode tag library 4

description:
Plasmid for barcode and oligo association
mpra∆orf plasmid

organism: synthetic construct

source_name: other

value: other


title: Gastric, Adjacent normal, patient no.12

value: Gastric adjacent normal


title: Gastric, Adjacent normal, patient no.10


title: Gastric, 18th tumor organoid, patient no.16


title: Gastric, 11th tumor organoid, patient no.10


title: Barcode tag library 3


title: Gastric, 33th tumor organoid, patient no.9

value: patient no.9


title: Gastric, 9th tumor organoid, patient no.9


title: Gastric, Tumor tissue, patient no.12

value: Gastric tumor tissues


title: Gastric, 24th tumor organoid, patient no.9


title: Root_P_3

city: 杭州

first: Fei

last: Wang

state: 浙江

address: 紫金港校区

institute: 浙江大学

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: rap-db (http://rapdb.dna.affrc.go.jp/download/irgsp1.html)
Supplementary files format and content: tab-delimited text files include FPKM values,  log2FoldChange, padj and gene information for each Sample ...

organism: Oryza sativa Japonica Group

source_name: Root

extract_protocol:
Roots sample were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Nipponbare

value: Root

value: P deficiency


title: Root_P_2


title: Gastric, Adjacent normal, patient no.9


title: Plasmid control biol rep 6

description:
Plasmid control DNA
mpra:gfp plasmid


title: Barcode tag library 1


title: Plasmid control biol rep 5

description:
Plasmid control DNA
mpra:gfp plasmid


title: Gastric, Tumor tissue, patient no.5

value: patient no.5


title: Gastric, 5th tumor organoid, patient no.5


title: Root_N_3

value: N deficiency


title: KRASG12D transforms murine B-Cell 2

city: Houston

first: Xiaoping

last: Sun

state: Texas

address: 2130 Westholcombe Blvd, LSP12.3014

department: Laboratory Medicine

institute: UT MD Anderson Cancer Center

hyb_protocol: The fragmented and labeled sscDNA (3.8 µg) was then hybridized to Affymetrix Mouse Gene Array 2.0 ST at 45ºC for 16h and subsequently washed and stained using Affymetrix proprietary reagents in the GeneChip Fluidics Station 450 (FS450).

scan_protocol: Array scanning was performed in the GeneChip Scanner 3000 7G (Affymetrix) at UT MD Anderson Cancer Center DNA Core Facility.

data_processing:
RMA expression value derived from Expression Console software
CEL files generated after the Mouse Gene 2.0 ST GeneChip scanning were uploaded onto the Expression Console software for analysis with RMA algorithm (Affymetrix). Standard expression microarray analysis consists of normalizing the signal intensity distributions of all probe features on all arrays. A probe feature is a location on the array that contains many copies of the same 25-mer DNA sequence. Normalizing these distributions enables comparison of probe signal between groups. Next, the signal intensities for all probes in a probe set that defines a gene or exon are aggregated into a single value for each array or sample. The aggregate signal value is used to compare gene-level or exon-level expression changes between sample groups or conditions. Raw Affy data contains about twenty probes for the same RNA target. Half of these are "mismatch spots", which do not precisely match the target sequence. These can theoretically measure the amount of nonspecific binding for a given target. Robust Multi-array Average (RMA) [9] is a normalization approach that does not take advantage of these mismatch spots, but still must summarize the perfect matches through median polish.

source_name: KRASG12D transforms murine B-Cell

label_protocol: One hundred nanograms (100ng) of Total RNA was used to process the samples for Whole Transcriptome Expression Analysis with the WT Plus assay (Affymetrix). Samples were reversed transcribed to generate amplified, fragmented and biotinylated sense-strand cDNA, according to manufacturer’s standard protocol.

growth_protocol: All cells were grown in Minimum Essential Medium. Alpha 1x supplemented with 20% FBS and 10ng/ml IL-7.

extract_protocol: Total RNA was isolated from KRASG12D-transformed cells and vector-transduced control cells using the TRI reagent (Ambion, Grand Island, NY). During RNA precipitation, 20 µg of linear polyacrylamide (Ambion) was added to isopropanol (Sigma-Aldrich). Precipitated RNA was gently washed once with n-butanol (Sigma-Aldrich) and twice with 70% alcohol; the air-dried RNA pellets were then dissolved in diethylpyrocarbonate-treated water (Fisher Scientific).

value: B-Cell Progenitors

tag: genotype/variation

value: vector-transduced


title: Vector transduced murine B cells 1

source_name: Vector transduced murine B cells


title: KRASG12D transforms murine B-Cell 3


title: Vector transduced murine B cells 3


title: Vector transduced murine B cells 2


title: Barcode tag library 2


title: IEL Tbet&Tgfbr2-KO Hic1 OE CD69+CD103+ rep2

city: Changsha

first: Liwen

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

data_processing:
Original image data file from Illumina is transformed to sequenced reads (Raw reads) by CASAVA base recognition
Raw reads of FASTQ format were firstly processed through the Fastp (0.19.5) to obtain the clean reads
The paired-end clean reads were aligned to the reference genome (mm39) using the Bowtie 2(2.4.1)
FeatureCounts(Subread 2.0.6) was used to count the read numbers mapped of each gene. And then raw counts of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Small Intestine Intraepithelial lymphocytes

growth_protocol: WT, Tbet-/-Tgfbr2-/-, and Tbet-/-Tgfbr2-/- Hic1 over-expression P14 Naive CD8 T cells were adoptively transferred into C57BL/6 recipient mice followed by LCMV-Arm infection. Around 22 days later, all recipient mice were sacrificed and the lymphoctes were isolated from spleen and small intestine.

extract_protocol:
Donor P14 T cells were FACS sorted based on CD8, CD45.1 and CD45.2. RNA was extracted from sorted cells using the Quick-RNA™ MiniPrep, according to manufacturer’s instructions (Zymo Research).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: All recepients mice were infectied with LCMV-Arm by i.p.

tag: time

value: Day 22

value: Tbet-/-Tgfbr2-/- Hic1 OE

value: day 22 after LCMV-Arm infection


title: Gastric, Tumor tissue, patient no.9


title: Plasmid control biol rep 3

description:
Plasmid control DNA
mpra:gfp plasmid


title: Root_N_2


title: IEL Tbet&Tgfbr2-KO Hic1 OE CD69+CD103+ rep1

value: Small Intestine Intraepithelial lymphocytes

tag: strain


title: Gastric, 10th tumor organoid, patient no.4

value: patient no.4

tag: tissue

value: Gastric tumor organoids


title: IEL Tbet&Tgfbr2-KO CD69+CD103+ rep3


title: Plasmid control biol rep 4

description:
Plasmid control DNA
mpra:gfp plasmid

value: other


title: Gastric, Adjacent normal, patient no.5

value: Gastric adjacent normal


title: P7 Zmiz1 KO cortex #3

city: new orleans

first: Rajan

last: K C

state: LA

address: 6602 Freret St

department: Cell and Molecular Biology

institute: Tulane University

data_processing:
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Assembly: mm10
Supplementary files format and content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: Cortex

extract_protocol:
Total RNA was extracted from Wildtype and Zmiz1KO P7 cortex using GeneJET RNA Purification Kit (Thermo Fisher Scientific, K0732).
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 1 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).

treatment_protocol: Zmiz1f/f as wildtype and Zmiz1f/f;Emx1Cre as Zmiz1-knockout P7 cortices were used to isolate progenitors cells.

value: Cortex

value: Zmiz1 knockout


title: Root_CK_3

description:
Root_NvsRoot_CK_deg
Root_PvsRoot_CK_deg

value: Nipponbare

value: CK


title: IEL Tbet&Tgfbr2-KO CD69+CD103+ rep2


title: P7 Zmiz1 KO cortex #2


title: Gastric, Adjacent normal, patient no.4


title: Root_CK_2

description:
Root_NvsRoot_CK_deg
Root_PvsRoot_CK_deg

value: Root


title: Root_CK_1

description:
Root_NvsRoot_CK_deg
Root_PvsRoot_CK_deg


title: P7 Zmiz1 KO cortex #1


title: Root_N_1


title: KRASG12D transforms murine B-Cell 1


title: spaQ, light, polysomal RNA, rep3

first: Mei-Chun

last: Cheng

address: No. 1, Roosevelt Rd

institute: National Taiwan University

data_processing:
The constructed library was quality checked by Agilent 2100 Bioanalyzer (Waldbroon, Germany)
The constructed library was sequenced on Illumina NovaSeq 6000 platform
The quality of raw reads (FASTQ) was initially checked using bcl2fastp (Illumina) (v2.20).
The checked raw reads were aligned to the Arabidopsis genome using HISAT2 calling Bowtie2 (v2.1.0)
FeatureCounts (subread v2.0.1) was used to generate counts of reads mapped to annotated Arabidopsis genes.
The raw reads in each batch were analyzed by the StringTie (StringTir v2.1.4) and DEseq (DEseq v1.39.0).
Enrichment analysis (Gene Ontology) was implemented using the Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.8.
Assembly: TAIR10.1
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: (We have only one processed file for each sample)

organism: Arabidopsis thaliana

source_name: the whole plant

extract_protocol:
Polysomal RNA was isolated as describe in Liu et al., 20121. The 500 μL of ground sample powders were resuspended by 500 μL of polysome extraction buffer (200 mM Tris-HCl, pH 8.0, 50 mM KCl, 25 mM MgCl2, 50 µg/mL cycloheximide, 100 µg/mL heparin, 2% PTE, 10% DOC, 400 U/mL RNasin) and centrifuged at 12,000 xg at 4℃ for 10 minutes. The supernatants were filtered and loaded to 11 mL of sucrose gradient (12.5% to 60%) and then were ultracentrifuged at 210,000 xg at 4℃ for 3.5 h. The OD254 of gradients were detected by UV detector to illustrate the pattern of ribosomal RNA profiling. PL% is the percentage of the polysomal RNA relative to the sum NP and PL RNA. After the centrifugation, the NP and PL fractions were collected and extracted with PCI, precipitated by LiCl, and resuspended with Ultra-Pure water. The total RNAs were extracted by the pine tree method (Chang et al., 1993).
TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to generate mRNA sequencing library according to the manufacturer’s instructions.

treatment_protocol: The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days before treated for 4 hours of white light. The 4 d-old dark-grown seedlings were further treated with (L) or without (D) white light before sampling.

value: the whole plant

value: spaQ

value: light


title: P7 Wildtype cortex #2

value: Wildtype


title: LepRpos_Membrane_rep8

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
Detailed pipeline description and parametrization is available at https://gitlab.com/hssgenomics/pipelines/-/tree/master/RNAseq . Briefly, Read quality was assessed and adaptors trimmed using FASTP. Reads were then mapped to thehuman genome (hg38) and reads in exons were counted against Gencode with STAR2.6 Aligner. Differential gene expression analysis was performed in R using edgeR. Genes with low expression levels (<3 counts per million in at least one group) were filtered from all downstream analyses. Differential expression was estimated using quasi-likelihood framework. Benhamini-Hochberg false discovery rate (FDR) procedure was used to correct for multiple testing. Genes with an FDR-corrected pvalue less than 0.05 were considered differentially expressed. Downstream analyses were performed in R using a visualization platform built with Shiny developed by bioinformaticians at the David Z. Rosensweig Genomics Research Center at HSS
Assembly: hg38
Supplementary files format and content: countMatrix.tsv – TAB-separate gene count matrix
Supplementary files format and content: edgeR_DEGs_2022-06-30.xlsx – an excel table with the results of EdgeR differential expression analysis and data transformations

source_name: Fibrous Tissue

extract_protocol: Bone or fibrous tissue obtained from patients undergoing primary joint arthropalsty or revision arthropalsty due to aseptic loosening, respectively, were subjected to both mechnical and enzymatic digestion. Single cells were otbtained, stained for Flow cytometry antibodies and FACS was conducted to sort the desired cell types. RNA sample were prepared using the RNAeasy Plust Micro Kit Cat no 74034. cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced on NovaSeq 6000 sequencer

value: Fibrous Tissue

value: LepR pos


title: P7 Wildtype cortex #3


title: LepRpos_Membrane_rep9


title: spaQ, light, polysomal RNA, rep2


title: IEL WT CD69+CD103+ rep2

value: Day 22

value: wild type

value: day 22 after LCMV-Arm infection


title: spaQ, light, total RNA, rep3


title: P7 Wildtype cortex #1


title: spaQ, light, polysomal RNA, rep1


title: LepRpos_Membrane_rep7


title: PMMA500-3

first: lu

last: huan

address: 866 Yuhangtang Road

institute: Zhejiang University medical center

data_processing:
Illumina Casava1.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore-0.6.5, then mapped to mm10 whole genome using hisat2-2.2.1 with default parameters
sam files were transformed to bam files and filtered with samtools to get unique properly paired reads.
featureCounts v2.0.1 were used to get raw gene counts.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: long-term hematopoietic stem cells

growth_protocol: Stemspan medium with SCF (100 ng/ml) and TPO (100 ng/ml) on rounded-bottom 96-wells plate

extract_protocol:
Total RNA was isolated with Trizol
First-strand cDNA synthesis  and cDNA libraries were constructed using the NEBNext Ultra TM  II RNA Library Prep  Kit  (New  England  Biolabs).
cDNA  quality  was  determined  on  Agilent  2100   BioAnalyzer  (Agilent  Technologies),  and  then  sequenced  on  NovaSeq  6000  device   (Illumina) to obtain pair-end 150 bp reads.

treatment_protocol: Co-cultured with different polymer spheres (1 μg/ml)  for 72 h and then 10000  long-term HSCs (Lin-Sca1+c-Kit+CD150+CD48-) were sorted by FACS.

tag: marker

value: PMMA spheres with 500 nm diameter


title: LepRpos_Membrane_rep6


title: IEL WT CD69+CD103+ rep1

value: Small Intestine Intraepithelial lymphocytes


title: spaQ, light, total RNA, rep2


title: PMMA500-2


title: LepRpos_Membrane_rep5