title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat control 3

city: Leeds

first: Timothy

middle: James

last: Mottram

address: Faculty of Biological Sciences

country: United Kingdom

institute: University of Leeds

description: neg biol rep 3

data_processing:
Raw reads were subjected to adaptor trimming and low-quality reads removal using Trimmomatic v0.39 [1] with parameters (ILLUMINACLIP:2:30:10 and SLIDINGWINDOW:4:20). Quality filtered, and adapter trimmed reads were aligned to the GQ994935.1 (GenBank) assembly of the human gammaherpesvirus genome using BWA mem v0.7.17 [2] with default parameters. Peaks were called against matched background biotinylation control libraries at q<0.01 using MACS2 [3] under the option of -nomodel and -nolambda with -effective genome size and -shift size set to 1.3 x 105 and length of RNA fragments (150bp), respectively. Peaks were annotated using the prebed function in the RBPInper R package [4] based on GQ994935 annotation
Assembly: GQ994935.1
Supplementary files format and content: merged_counts contains read counts of KSHV viral genes across samples

molecule: nuclear RNA

source_name: TREx-BCBL1 Rta

growth_protocol: TREx-BCBL1-RTA cells, a gift from Professor JU Jung (University of Southern California), a B-cell lymphoma cell line latently infected KSHV engineered to contain a doxycycline-inducible myc-RTA were cultured in RPMI 1640 with glutamine (Gibco), supplemented with 1% P/S (Gibco), 10% FBS (Gibco) and 100 µg/ml hygromycin B (ThermoFisher). Briefly, 5x106 TREx-BCBL1-RTA cells were seeded onto a 100mm cell culture dish pre-treated with poly-L-lysine and left to settle for 3 hours prior to reactivation.

extract_protocol:
After 24 hours of lytic replication, cells were fixed with DSP (0.5 mg/mL) for 45 minutes at room temperature, washed three times with 20 mM Tris in PBS (pH 7.5), then permeabilised with 0.25% Triton in PBS for 15 minutes at room temperature. Cells were washed twice, followed by the addition of 6 mL of diluted probe mixture (25 nM DIG-labelled NEAT1 oligonucleotides in buffer (2xSSC buffer, 10% formamide, 10% dextran sulphate)). A control condition was included, in which 6 mL of buffer was added to cells with the absence of the probes. The cell culture plates were incubated at 37 °C overnight in a humidified chamber.  Samples were washed before being blocked, then incubated in purified HyPro protein (2.7 ng/mL) before washing again. Biotin-phenol and hydrogen peroxide were introduced to the cells for 1 minute followed by immediate quenching. Cells were lysed in high-SDS RIPA lysis buffer before scraping into a 1.5 mL microcentrifuge tube for further lysis. Samples were sonicated for 7 cycles of 30 seconds ON/ 30 seconds OFF, incubated at 37 °C for 30 minutes, then incubated in proteinase K. RNA was extracted from the lysates using TRIzol LS (Invitrogen) as per the manufacturers protocol and 5% from each sample were retained for inputs. MyOne streptavidin C1 pulldowns were performed on the remaining 95% of samples and final purified biotinylated RNA was extracted via the TRIzol LS extraction method coupled with the RNA clean and concentrator kit (Zymo Research).
Library construction was carried out as per Novogene RNA seq protocol

treatment_protocol: Virus lytic replication in TREx-BCBL1-RTA cells was induced via addition of 2 µg/ml doxycycline hyclate (Sigma-Aldrich). Cells were harvested after 24hours

value: TREx-BCBL1 Rta

value: B cell

value: WT

value: doxcycline induced lytic reactivation


title: Human periosteal cell replicate 3, scRNA-seq

status: Public on Nov 04 2024

type: SRA

city: Houston

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v 6.1.2. (https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/running-pipelines/cr-choosing-a-pipeline)
Assembly: GRCh38
Supplementary files format and content: tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: Periosteum

extract_protocol:
To isolate human periosteal cells, the periosteum tissues were carefully removed from undamaged surgical site during fracture reparing procedure. Collected periosteum were transferred to MEM-alpha medium containing 10% FBS, and the overlying fascia and muscle were carefully removed. The tissues were fragmented with a scalpel into small pieces and washed with phosphate buffered saline (PBS), and then resuspended in pre-warmed PBS containing 2% FBS and 5mg/mL Collagenase type I and incubated at 37℃ for 1 hour. Samples were washed and resuspended in PBS containing 2% FBS, 5mg/mL type I Collagenase, and 2mg/mL Dispase, and incubated at 37℃ for 1 hour. The dissociated periosteal cells were washed with PBS, filtered with a 70um and then 40um strainer, and resuspended at 1x10^7cells/mL. Isolated cells were FACS-sorted based on CD45, CD31, CD235a, and DAPI staining. Trypan blue stain was used to assess cell viability and number. Cells were then sorted in 10% FBS with MEM-alpha media.
Libraries were constructed using the Chromium Single Cell 3' v3.1 (10x genomics, PN-11000121) Reagent Kit, according to the manufacturer's protocol. Amplified cDNA and final libraries were evaluated on an Agilent BioAnalyzer using a High Sensitivity DNA Kit (Agilent Technologies).

tag: tissue

value: Periosteum

tag: cell type

value: Periosteal cells


title: prostate epithelial cells, C_rep3

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

library_source: transcriptomic

data_processing:
Raw FASTQ files from murine RNA-Seq were subject to a quality check with FastQC (v0.11.5).
Adapters and low-quality read ends were trimmed using Trimmomatic (v0.36, reads shorter than 35 nt were discarded.
The pre-processed reads were mapped to the reference mouse genome (Ensembl GRCm38) using gene annotation (Ensembl v91) with STAR.
Gene quantification was performed on uniquely mapped reads only, with featureCounts (v1.5.2).
Assembly: GRCm38
Supplementary files format and content: featureCount gene counts TSV

molecule: polyA RNA

organism: Mus musculus

source_name: prostate

extract_protocol:
Briefly, single cell suspension of mouse prostate tissue of wild type, L-gp130peKI/KI, PtenpeΔ/Δ and PtenpeΔ/Δ;L-gp130peKI/KI mice was done and magnetic cell separation (MagniSort technology, Thermo Fisher) was performed for EpCAM positive fraction using anti-mouse CD326 (EpCAM) Biotin antibody (13-5791-82, eBioscience). For higher RNA output, three wild type and three L-gp130peKI/KI mouse prostates, respectively, were pooled to generate one sample. Per genotype n≥5 samples were analyzed by RNA-Seq. RNA isolation was performed using TriReagent (T9424-100ML, Sigma-Aldrich) and ReliaPrep RNA Tissue Miniprep System (Z6111, Promega) according to the manufacturer’s instructions.
Library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, New England Biolabs) according to manufacturer’s instructions in combination with a poly(A) mRNA magnetic isolation module (E7490) and multiplex oligos for Illumina (E7600). Libraries were amplified with 11 PCR cycles and the library size was analyzed by Agilent Tape Station (G2938-90014, Agilent Technologies).

value: prostate

tag: genotype

value: L-gp130peKI/KI (C)


title: Day14_timeseries_replicate3

city: Heidelberg

first: Elias

last: Böhl

address: Im Neuenheimer Feld 580

department: Divison of Epigenetics

country: Germany

institute: German Cancer Research Center (DKFZ)

library_source: genomic

data_processing:
Reads were trimmed using Trimmomatic  and mapped with BSMAP  version 2.9. The assembly of Cricetulus_griseus CHOK1GS_HDv1.108 was used as genome reference. Duplicate reads were removed using the Picard tool (http://broadinstitute.github.io/picard).
Methylation ratios were determined using a Python script (methratio.py) that is distributed with the BSMAP package. For all further analysis, only CpGs covered by at least five reads were considered.
Assembly: Cricetulus_griseus CHOK1GS_HDv1.108
Supplementary files format and content: BED files containing CpGs with information about coverage (_cov) and methylation ratios (_ratio)

molecule: genomic DNA

organism: Cricetulus griseus

source_name: Ovary

extract_protocol:
Genomic DNA was extracted using the PureLink Genomic DNA Isolation Minikit kit (Invitrogen), including RNAase treatment following the manufacturer's instructions
Libraries for whole-genome bisulfite sequencing (WGBS) were prepared using the VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, Catalog #ND608).

value: Ovary

tag: cell line

value: Chinese hamster ovary (CHO) cells


title: Day14_timeseries_replicate1


title: CAGE EGFP KD rep1 #1

city: Tokyo

first: Masaru

last: Ariura

address: Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio university

data_processing:
CLASH : Adapter sequences were removed using Cutadapt v4.0, low-quality reads were removed, and duplicate reads collapsed using SeqKit v2.3.1. Four random nucleotides at both ends were removed from the obtained reads using Cutadapt v4.0, and reads between 23-30 nt were extracted and re-collapsed using the ‘make_comp_fasta.pl’ script from Hyb v0.0. To remove non-chimeric RNAs, reads were mapped to the gene reference using Hisat2 v2.2.1 with the parameters ‘--known-splicesite-infile known_splicing_sites.txt –rna-strandness F -k 2000’ and sense mapped reads were removed. Then, piRNAs were mapped to the chimeric reads using Bowtie v1.0.0 with the parameters ‘-a -v 0’, and only reads with full-length piRNAs at the 5' or 3' end and with the remaining read greater than 15 bp were selected. Selected reads were mapped to the gene reference using Bowtie2 v2.2.5 with the parameters ‘-a’ and sense mapping reads were extracted. To map spliced reads, unmapped reads were mapped to the gene reference using Hisat2 v2.2.1 with the parameters ‘--known-splicesite-infile known_splicing_sites.txt –rna-strandness F -k 2000’. To remove re-ligations of the same RNA, if the piRNA and the rest of the RNA mapped to the same gene, it was excluded from further analysis. Reads in which the piRNA or target sequence was dominated by more than 90% of a given base were also excluded. Gibbs free energy (ΔG) between the piRNA and target RNA was calculated using RNAplex from the ViennaRNA package v2.4.18 with the parameter ‘--temp=26’.
CAGE : Adapters, N-containing reads and reads shorter than 100 nt were removed using Cutadapt v4.0. The remaining reads were mapped to the dm6 genome using STAR v2.7.10b with the parameters ‘--outSAMattributes All --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped None --alignSplicedMateMapLmin 30 --alignMatesGapMax 200000 --outFilterMultimapNmax 20 --alignIntronMax 20000’, and bed files were generated using Samtools v1.651 and Bedtools v2.30.0 as follows: ‘samtools view -f 0x2 -bS -uq 20 | samtools sort -m 4G -n - | bedtools bamtobed -mate1 -bedpe -i stdin’. Input CAGE tag starting sites (CTSSs) were generated by R. CAGEr v2.4.0 was used to detect OSC TSSs. TSSs were clustered using ‘clusterCTSS(threshold = 0.1, thresholdIsTpm = TRUE, nrPassThreshold = 0.1, method = "distclu", maxDist = 20, removeSingletons = TRUE, keepSingletonsAbove = 5)’ from EGFP KD and Piwi KD samples. TE-mapped TSSs were removed, and annotations were obtained using Bedtools intersect v2.30.0. The coverage of each sample was calculated using Bedtools intersect v2.30.0. Only TSSs present in the 5’UTR and <100 bp upstream of the dm6 TSS were considered as a TSS for that gene.
Iso-seq : Nanostat v1.6.0 and Nanoplot v1.40.2 were used for quality control of the reads. The raw PacBio Iso-seq data was analyzed using the IsoSeq3 v3.8.1 pipeline (https://github.com/PacificBiosciences/IsoSeq). First, circular consensus sequences (CCS) were generated using CCS v6.4.0 (https://github.com/PacificBiosciences/ccs) with the parameter ‘-all’. Primers were removed using Lima v2.6.0 (https://github.com/PacificBiosciences/barcoding) with the parameters ‘--isoseq --dump-clips’ and poly-A containing reads were selected using ‘isoseq3 refine –require-polya’, to obtain full-length non-chimeric (FLNC) sequences. Then, ‘isoseq cluster –use-qvs’ was used to generate high quality isoforms with an accuracy of >99%. The generated isoforms were mapped to dm6 or TEs using Minimap2 v2.2256 with the parameters ‘-ax splice -uf --secondary=no -C5’, and collapsed using the ‘collapse_isoform_by_sam.py’ script with parameters ‘--dun-merge-5-shorter --gen_mol_count’ and the ‘get_abundance_post_collapse.py’ script from cDNA_Cupcake v29.0.0 (https://github.com/Magdoll/cDNA_Cupcake). 5’ degraded isoforms were removed using the ‘filter_away_subset.py’ script and expression counts were obtained using the ‘demux_isoseq_with_genome.py’ script from cDNA_Cupcake v29.0.0. Finally, the isoforms were annotated using the ‘sqanti3_qc.py’ script from SQANTI3 v5.1.
PacBio-DNAseq : For haplotype-resolved assemblies, the reads were assembled using Hifiasm v0.17.3 in Hi-C integration mode with the parameters ‘-t 28 --primary -D 10’. Hi-C data (SRR12655953, SRR12655954) was extracted from the Gene Expression Omnibus (GEO) database (accession code GSE158082)53. Assembly completeness was calculated with BUSCO v3.2.1 using diptera_odb10, and further assessed by Quast v5.2.0 (reference: dm6 full genome) to check the quality of the assemblies.
piRNA-seq : Adapter sequences were removed using Cutadapt v4.0 and collapsed using SeqKit v2.3.1. Four random nucleotides at both ends were removed using Cutadapt and reads with sizes between 23-30 nt were extracted for downstream analysis. The CPM of each piRNA was calculated and piRNAs with fewer than 1 CPM or 3 counts were discarded. Poly-A repeat sequences were also removed.
ChIP-seq : Adapters were removed using Cutadapt v4.0, and reads shorter than 50 nt were discarded. The remaining ChIP-seq reads were mapped to the dm6 genome using Bowtie2 v2.2.5 with default parameters. Uniquely mapping reads were extracted and used for further analysis. ChIP/input bigWigs were generated using the bamCompare function from Deeptools with the parameters ‘--binsize=10 --minMappingQuality 15 --normaliseUsing CPM –operation log2’. For Luciferase plasmid mapping, Adapter-trimmed reads were mapped to the pMT promoter and FLuc or NLuc regions of the plasmid. Read coverage was calculated as (1000000 * count / total reads in adapter trimmed reads). The NLuc / FLuc value was calculated.
Assembly: dm6
Supplementary files format and content: CLASH : clash_raw.csv.gz contains piRNA and target pairing. This files contains all possible pairings. clash_collapse.csv.gz contains collapsed pairings.
Supplementary files format and content: CAGE : CAGE_bw.zip contains TSS region and intensity bigwig. CAGE_matrix.zip contains each TSS’s intensity.
Supplementary files format and content: Iso-seq : isoforms.zip contains SQANTI3 output files.
Supplementary files format and content: PacBio-DNAseq : assembled_genome.zip contains assembled haploid genome sequence. Flam.zip contains flam and 20A sequence.
Supplementary files format and content: piRNA-seq : piRNA_CPM_GEO.zip contains each piRNA’s expression levels.
Supplementary files format and content: ChIP-seq : The bigwig file is the result of mapping to the genome. The bedgraph file is the result of mapping to Luciferase plasmid.

organism: Drosophila melanogaster

growth_protocol: Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).

extract_protocol:
CLASH : 1e+8 OSCs were washed once with ice-cold PBS and then irradiated with 200 mJ/cm2 at 254 nm. Cells were pelleted and lysed in lysis buffer (20 mM HEPES-KOH pH 7.3, 150 mM NaCl, 1 mM EDTA, 1 mM DTT, 0.5% NP-40, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin). Lysates were centrifuged at 20,000 g for 10 min at 4˚C, and the supernatants treated with 1 U/μl RNase T1 (Roche) for 15 min at room temperature on a rotator. RNA-protein complexes were immunoprecipitated using 10 μg of anti-Piwi antibody (Saito et al., 2006) and 100 μl Dynabeads protein G (Invitrogen) for 2 h at 4˚C. Beads were washed three times with wash buffer (20 mM HEPES-KOH pH 7.3, 300 mM NaCl, 1 mM DTT, 0.05% NP-40, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin), and three times with high-salt wash buffer (20 mM HEPES-KOH pH 7.3, 500 mM NaCl, 1 mM DTT, 0.05% NP-40, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin). The beads were resuspended in 100 μl PNK buffer (1 × PNK buffer, 6,000 Ci/mmol 32P-γ-ATP (Perkin Elmer), 10 units T4 Polynucleotide kinase (NEB), 40 units RNasin (Promega)) and incubated for 30 min at 37˚C. Piwi-piRNA complexes were washed 5 times with PNK wash buffer (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 10 mM MgCl2). Piwi-bound, interacting RNA molecules were ligated overnight using 25 units of T4 RNA ligase 1 (NEB) in T4 RNA ligase buffer (1 × T4 RNA ligase buffer, 1 mM ATP, 15% PEG8000, 40 units RNasin (Promega)) at 16˚C. The ligation mixture was washed 5 times with PNK wash buffer. Piwi-piRNA/RNA complexes were eluted in 1 × LDS sample buffer (Life Technologies) for 10 min at 70°C and then resolved on a 4%–12% Bis-Tris NuPAGE gel (Life Technologies) in NuPAGE SDS MOPS running buffer (Life Technologies). The Piwi-piRNA/RNA complexes were transferred to a nitrocellulose blotting membrane (GE Healthcare) in a wet-transfer tank with NuPAGE transfer buffer (Life Technologies) containing 10% methanol for 100 min at 30 V. After excising the region of nitrocellulose containing Piwi-piRNA/RNA complexes, RNAs were released from the membrane using 10 μl of Proteinase K (Roche) in proteinase K buffer (50 mM Tris-HCl pH 7.5, 75 mM NaCl, 6.25 mM EDTA, 10% SDS) for 30 min at 55˚C. The RNA was extracted with phenol/chloroform/isoamyl alcohol, and then precipitated with ethanol and PelletPaint NF (Millipore). RNA pellets were washed with 70% ethanol and dissolved in Nuclease-Free Water.
CAGE & Iso-seq : Total RNA was extracted using Isogen II (Nippon Gene).
Pacbio-DNAseq : High molecular weight DNA was extracted using Blood & Cell Culture DNA kit (Qiagen).
piRNA-seq : 1e+8 OSCs were lysed in Lysis Buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5% NP-40, 1 mM EDTA, 1 mM DTT, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin, 40 U/ml RNasin (Promega)) and spun at 135,000 rpm for 15 min at 4°C. The supernatant was collected and cooled on ice. 10 μg of Anti-Piwi antibody (Saito et al., 2006) was immobilised on 50 μl of Dynabeads protein G (Invitrogen) and incubated with lysates for 2 h at 4°C. The supernatant was discarded and the beads washed three times with IP wash buffer (20 mM Tris-HCl pH 7.5, 300 mM NaCl, 0.05% NP-40, 1 mM DTT, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin) and three times with High salt buffer (20 mM Tris-HCl pH 7.5, 500 mM NaCl, 0.05% NP-40, 1 mM DTT, 2 μg/ml Pepstatin, 2 μg/ml Leupeptin, 0.5% Aprotinin). After washing, RNAs were extracted from the beads with acid phenol-chloroform and precipitated with ethanol. Purified RNAs were denatured in Gel Loading Buffer II (Invitrogen, AM8546G) for 5 min at 95°C, resolved on a denaturing 15% TBE polyacrylamide gel and sizes between 22-30 nt were excised.
ChIP-seq : ChIP was performed as described in the ultra-low-input native ChIP (ULI-NChIP) protocol (Brind’Amour et al., 2015) with minor modifications. Briefly, 5e+5 OSCs were lysed in 20 μl of Nuclei EZ lysis buffer (Sigma Aldrich, N3408). The chromatin was digested with 10 U/μl of MNase (NEB) at 37°C for 10 min and the reaction quenched with 100 mM EDTA. The digested chromatin was then diluted in IP buffer (20 mM Tris-HCl pH 7.5, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl, 1 x cOmplete Protease Inhibitor Cocktail (Roche)). An aliquot of chromatin (10 μl) was used as the input control. Chromatin was pre-cleared with 20 μl of 1:1 Dynabeads protein A (invitrogen) : Dynabeads protein G (invitrogen) and immunoprecipitated with antibody–bead complexes (1 μl of H3K9me3 antibody (abcam, ab8898) or 1 μl of H3K4me3 antibody (abcam, ab8580) in 10 μl of 1:1 protein A:protein G Dynabeads) overnight at 4°C. Immunopurified protein-DNA complexes were washed twice with 1 ml of Low salt buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 150 mM NaCl) and once with 1 ml of High salt buffer (20 mM Tris-HCl pH 7.5, 0.1% SDS, 1% Triton X-100, 2 mM EDTA and 500 mM NaCl). After washing, protein-DNA complexes were eluted in 30 μl of elution buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS). One hundred ng of RNAse A was added to the eluate and the mixture incubated for 30 min at 37°C, followed by 90 min at 65°C. Lastly, the DNA was purified using the QIAquick PCR purification Kit (Qiagen).
CLASH : The RNA was incubated with 10 units of T4 PNK (NEB) in 3′ end RNA dephosphorylation buffer (50 mM imidazole-HCl pH 6.0, 10 mM MgCl2, 5 mM DTT, 40 units RNasin (Promega)) for 30 min at 37˚C. Following dephosphorylation, the RNA was purified using SPRI select beads according to the manufacturer’s instructions. Dephosphorylated RNAs were ligated at their 3′ ends to a pre-adenylated DNA adaptor (AppNNNNTGGAATTCTCGGGTGCCAAGGddC) with 200 units of T4 RNA ligase 2 truncated KQ (NEB) in 3′ adaptor ligation buffer (1 ×T4 RNA ligase buffer, 15% PEG8000, 40 units RNasin (Promega)) overnight at 16˚C. 3′-ligation products were purified using SPRI select beads according to the manufacturer’s instructions. The 5’ ends of the RNAs were ligated to a 5′ RNA adaptor (GUUCAGAGUUCUACAGUCCGACGAUCNNNN) with 10 units of T4 RNA ligase 1 (NEB) in 5′ adaptor ligation buffer (1 ×T4 RNA ligase buffer, 1 mM ATP, 15% PEG8000, 40 units RNasin (Promega)) overnight at 16˚C. The RNA was subsequently purified using SPRI select beads according to the manufacturer’s instructions. Isolated RNA was reverse-transcribed using Superscript III Reverse Transcriptase (invitrogen) and the RT primer (GCCTTGGCACCCGAGAATTCCA), according to the manufacturer’s instructions. The cDNA was amplified using Illumina PR1 and RPI primers (TruSeq Small RNA kit) and the Q5 High-Fidelity DNA Polymerase (NEB), according to the manufacturer’s instructions. PCR products were separated on a 6% polyacrylamide gel in 1 × TBE buffer and the gel stained with SYBR Gold Nucleic Acid Gel Stain (Life Technology). Gel slices containing amplified libraries (180 to 200 bp) were excised and homogenized in 0.4 M NaCl, followed by an incubation overnight at 4˚C on a rotor. PCR products were precipitated with ethanol and PelletPaint NF (Millipore). Lastly, the DNA pellets were washed with 70% ethanol and dissolved in Nuclease-Free Water. Libraries were sequenced on an Illumina HiSeq platform.
CAGE : The 5 µg total RNAs from each replicate sample were reverse transcribed to cDNAs with random primers, and the capped RNA-cDNA hybrids were trapped by streptavidin beads. After the cap-trap, the single strand (ss)cDNAs were released from the beads and ligated to the Illumina Index containing a barcode identifier for each sample.
Iso-seq : Total RNA was sequenced on a PacBio Sequel HiFi platform (Pacific Biosciences) by Macrogen Japan.
Pacbio-DNAseq : The DNA was sequenced on a PacBio Sequel II HiFi platform (Pacific Biosciences) by Macrogen Japan.
piRNA-seq : Library construction were performed using the NEXTflex small RNA-seq kit v3 (PerkinElmer) or following method. One μl of a 3’ pre-adenylated adapter (20 pmol/μl) (AppNNNNTGGAATTCTCGGGTGCCAAGGddC) was added to 10.2 μl of purified RNA and incubated at 70°C for 2 min, followed by cooling to 4°C. The RNAs were then ligated to the adaptor at their 3′ ends in 3’ ligation buffer (2 μl of 10 x T4 RNA ligase buffer (no ATP) (NEB), 4.8 μl of 50% PEG8000 (NEB), 1 μl of RNasin (Promega), 1 μl of T4 RNA ligase 2 truncated KQ (NEB)) at 16°C overnight (>16 h). The RNA was purified using SPRIselect beads (Beckman Coulter), eluted with 16 μl of Nuclease-Free Water, and the 3’ adaptors degraded using deadenylase (NEB) and RecJf (NEB). After SPRIselect purification and elution with 8.2 μl of Nuclease-Free Water, the 5’ adaptor ligation buffer (2 μl 10 x T4 RNA ligase Buffer (no ATP) (NEB), 2 μl of 10 mM ATP (NEB), 4.8 μl of 50% PEG8000 (NEB), 1 μl of 5’ adaptor (20 pmol/μl) (GUUCAGAGUUCUACAGUCCGACGAUCNNNN), 1 μl of RNasin (Promega, N2111), 1 μl of T4 RNA ligase 1 (NEB, M0202L)) was added to the 3’ ligated RNAs and incubated at 16°C overnight (>16 h). After SPRIselect purification and elution with 10.2 μl of Nuclease-Free Water, 2 μl of 10 μM RT primer (GCCTTGGCACCCGAGAATTCCA) was added and the RNA reverse-transcribed using SuperScript III (Invitrogen) according to the manufacturer’s instructions. The libraries were amplified for 10 cycles using the Q5 High-Fidelity DNA polymerase (NEB), size selected by polyacrylamide gel electrophoresis and sequenced on the Illumina Miseq platform to obtain 50-nt single-end reads.
ChIP-seq : Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

treatment_protocol: Transfection of siRNAs was performed using Cell Line 96-well Nucleofector Kit SF and 96-well Shuttle Device (Lonza).

value: Ovarian Somatic Cells (OSC)

value: EGFP-KD OSC

tag: treatment

value: RNAi EGFP


title: Day14_timeseries_replicate2


title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat control 1

description: neg biol rep 1


title: CLASH rep5

value: WT OSC


title: CAGE EGFP KD rep1 #2


title: prostate epithelial cells, C_rep1


title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat control 2

description: neg biol rep 2


title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat 2

description: IP biol rep 2


title: CAGE Piwi KD rep3 #1

value: Piwi-KD OSC

value: RNAi Piwi


title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat 3

description: IP biol rep 3


title: prostate epithelial cells, B_rep5

value: wild type (B)


title: Day11_timeseries_replicate2


title: Day11_timeseries_replicate3


title: CLASH rep4


title: prostate epithelial cells, B_rep4


title: TREx-BCBL1 Rta cell with 24hr lytic KSHV, biological repeat 1

description: IP biol rep 1

value: TREx-BCBL1 Rta


title: CLASH rep3


title: CLASH rep2


title: prostate epithelial cells, C_rep2


title: PBMC, cohort 3, SjD 9

city: New York

first: Maxwell

last: McDermott

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

description: 10x genomics

data_processing:
The demulitplexing, barcode processing, gene counting, and aggregration were made using cell ranger software v 7.0.0(https://www.10xgenomics.com/support/software/cell-ranger/getting-started/cr-what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab delimited includes raw counts for each sample

source_name: PBMC

extract_protocol:
Frozen PBMCs were thawed and stained with Annexin-V (Biolegend, Cat. 640912) and LIVE/DEAD (ThermoFisher, Cat. L23105) in Annexin-V binding buffer (Biolegend, Cat. 422201). Live PBMC were sorted as Annexin-V- Live/Dead- on Aria II (BD Biosciences). Cells were collected in RPMI1640 medium (Corning, Cat. 10040CV) with 10% fetal bovine serum. Collected cells were then stained using Type B hashing antibodies (BioLegend), for patient identification post multiplexing (sequences were shown in Supplementary Table 3), according to manufacturer’s protocol.
Collected cells were also quantified using a Bio-Rad TC20 automated cell counter. Stained cells were encapsulated into emulsion droplets using Chromium Controller (10x Genomics) for library prep. scRNA-seq and antibody multiplexing libraries were constructed using Chromium Single Cell 3′ v3.1 Reagent Kit and 3’ Feature Barcode Kit (PN-1000268 & 1000262 respectively) according to the manufacturer’s protocol.
Individual libraries were diluted to 2nM and pooled for sequencing. Pooled batches were sequenced with 100 cycle run kits (28bp Read1, 8bp Index1 and 91bp Read2) on the NovaSeq6000 Sequencing System (Illumina).  Amplified cDNA was evaluated with an Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies). Final libraries were evaluated with an Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).

value: PBMC

tag: disease state

value: SjD


title: prostate epithelial cells, B_rep3


title: Day9_timeseries_replicate3


title: prostate epithelial cells, B_rep2


title: Day11_timeseries_replicate1


title: PBMC, cohort 3, SjD 8

description: 10x genomics


title: CLASH rep1


title: prostate epithelial cells, B_rep1


title: PBMC, cohort 3, SjD 7

description: 10x genomics


title: Day9_timeseries_replicate1


title: PBMC, cohort 3, Healthy Donor 8

description: 10x genomics

value: healthy


title: Day7_timeseries_replicate3


title: Huh7 cells, pTracer-SV40 empty vector transfected

city: Kolkata

first: UPASANA

last: RAY

state: West Bengal

address: CN-06, CN Block, Sector 5, Bidhannagar

department: Infectious Diseases and Immunology

country: India

institute: CSIR-Indian Institute of Chemical Biology

data_processing:
Illumina Platform
Amplified libraries were analyzed on Bioanalyzer 2100 (Agilent Technologies) using High Sensitivity (HS) DNA chip as per manufacturer's instructions.
Qubit concentration for the library and the mean peak size from Bioanalyzer profile was obtained. Library was loaded into Illumina platform for cluster generation and sequencing
Reference guided transcript assembly was performed for the samples, first by mapping HQ reads on reference genome using hisat2 (v 2.2.1) and then performing transcript assembly by StringTie (v 2.1.4)
Transcript abundance was estimated for individual sample using merged transcript consensus. For each transcript,  read counts  and  transcript assembly obtained from StringTie were taken as input for differential expression analysis using edgeR package.

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degree C

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent. The quality of the isolated RNA was checked on 1% Formaldehyde Denaturing Agarose gel and quantified using Qubit® 2.0 Fluorometer
The libraries were prepared from samples with input total RNA ~1μg  using Illumina TruSeq Stranded mRNA Library Preparation Kit as per the manufacturer’s protocol.

treatment_protocol: Huh7 cells were transiently transfected with endotoxin free plasmid DNA using Lipofectamine 2000 (Invitrogen)

value: differentiated hepatocyte-derived carcinoma cell line

value: Plasmid transfection followed by total RNA extraction


title: PBMC, cohort 3, Healthy Donor 7

description: 10x genomics


title: Day7_timeseries_replicate2


title: Huh7 cells, no transfection control

value: No transfection followed by total RNA extraction


title: H2052 KR_K975_rep1

city: Nagoya

first: Tatsuhiro

last: Sato

state: Aichi

address: 1-1 Kanokoden

department: Division of Cancer Biology

institute: Aichi Cancer Center Research Institute

description: Sample 34

data_processing:
The fastq files were analyzed using the RaNA-seq tool
Assembly: Human, Homo sapiens (GRCh38)
Supplementary files format and content: csv file includes raw counts for each experiments

source_name: mesothelioma

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina and the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured in the presence or absence of 1 μM K-975 for 48 hours

value: mesothelioma


title: PBMC, cohort 3, Healthy Donor 6

description: 10x genomics


title: Day7_timeseries_replicate1

value: Ovary


title: 10x_Retina_WT1

first: Rui

last: Chen

state: Texas

department: Department of Molecular and Human Genetics

description:
10x Genomics
retina_isoform.gtf
retina_isoform_quantify_cellclass

data_processing:
Raw sequencing reads are processed by Sicelore pipeline (https://github.com/ucagenomix/sicelore)
Transcript isoform identification and quantification using Flair (https://flair.readthedocs.io/en/latest/modules.html)
Isoform QC and filtering using SQANTI3 (https://github.com/ConesaLab/SQANTI3)
Assembly: mm10 (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz)
Supplementary files format and content: A .gtf file of information for isoforms and a cell class by isoform count matrix

source_name: retina

extract_protocol:
We have generated 4 scRNA-seq samples of the mouse C57BL6/J retina. After dissection, retinas were dissociated into single cells using papain-based enzyme following the published protocol 10. With activated 45U of papain (Worthington, Cat. #LS003126) solution (1mg L-Cystine, Sigma; 8 KU of DNase I, Affymetrix; in 5 ml DPBS), retina was incubated at 37C for ~20min. Which was followed by the replacement of incubation buffer with 2ml ovomucoid solution (15 mg ovomucoid, Worthington Biochemical; 15 mg BSA Thermo Fisher Scientific; in 10 ml DPBS) and 500ul deactivated FBS. The retina tissue was carefully triturated and filtered by 20 um plastic mesh. Repeat the step with additional 1ml ovomucoid solution until no tissue is visible. Spin the cells down at 300g, 4C for 10 min, and cells were used in the next step.  To deplete the photoreceptors, cells were resuspended in 0.5% BSA and stained with CD73-PE antibody for 10min at 4C (for each million cells, add 98ul 0.5% BSA with 2ul CD73-PE antibody), and washed with 35 ml 0.5% BSA at 4C for 10min. After being stained with Anti-PE microbeads (for each million cells, add 80ul 0.5% BSA and 20ul microbeads), for 15 min at 4C, cells were washed and resuspended in 0.5% BSA. CD73 negative neuronal cells were enriched by autoMACS Pro Separator (Miltenyi Biotec) DEPLETES mode and ready for the next step. Similarly, CD90.2 positive neuronal cells were enriched with CD90.2 microbeads (for each 10million cells, 90ul 0.5% BSA and 10ul CD90.2 microbeads were used) and autoMACS POSSEL-S mode. Cells viability was 85%-87% when checked with DAPI staining under microscope.
Nanopore library was generated from scRNA-seq cDNA following the Nanopore Single-cell transcriptomics with cDNA prepared using 10x Genomics protocol (version Jan2022) using the SQK-PCS111 Ligation Sequencing Kit. 35-55 fmol of the library was sequenced on PromethION FLO-PRO002 R9.4.1 flow cells. The following options were used: 72hr of run time, and real-time basecalling with High-accuracy mode.
Nanopore Protocol for Single-cell transcriptomics with cDNA prepared using 10X Genomics

value: retina

tag: gender

value: Male

value: wild-type

value: No enrichment


title: H2052 KR_control_rep3

description: Sample 33

value: control


title: PBMC, cohort 2, SjD 6

description: 10x genomics


title: Day5_timeseries_replicate3

value: Chinese hamster ovary (CHO) cells


title: PBMC, cohort 2, SjD 5

description: 10x genomics


title: 10x_RGC_live_AC

tag: age

value: Postnatal month 4

value: CD90.2 enrichment


title: 10x_Retina0426Cd73N

value: Postnatal week 8

value: CD73 enrichment


title: H2052 KR_control_rep1

description: Sample 31


title: PBMC, cohort 2, SjD 4

description: 10x genomics

value: PBMC

value: SjD


title: Day9_timeseries_replicate2


title: Day5_timeseries_replicate2


title: H2052 KR_K975_rep3

description: Sample 36


title: Huh7 cells, pDENV4_NS1 transfected

value: differentiated hepatocyte-derived carcinoma cell line


title: 10x3_Ms_WT_P40

value: Postnatal day 40


title: PBMC, cohort 2, Healthy Donor 5

description: 10x genomics

value: healthy


title: H2052 KR_K975_rep2

description: Sample 35

value: mesothelioma


title: Day3_timeseries_replicate3

value: Ovary


title: Day5_timeseries_replicate1


title: MSTO KR_K975_rep2

description: Sample 29


title: Day3_timeseries_replicate2


title: MSTO KR_K975_rep3

description: Sample 30


title: PBMC, cohort 2, Healthy Donor 3

description: 10x genomics


title: H2052 KR_control_rep2

description: Sample 32


title: MSTO KR_control_rep3

description: Sample 27


title: NEM316 RNA-seq Replicate 3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.10. Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 2.5.1, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 2.0.0 from Subreads package (parameters: -t locus_tag -g ID -s 1).
Count data were analyzed using R version 4.0.5 and the Bioconductor package DESeq2 version 1.30.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with(out) applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological condition. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially  expressed.
Assembly: Streptococcus agalactiae NEM316 (NCBI RefSeq NC_004368)
Assembly: Streptococcus agalactiae 2603 (NCBI RefSeq NC_004116)
Assembly: Streptococcus agalactiae A909 (NCBI RefSeq NC_007432)
Supplementary files format and content: DESeq 2 output matrix

organism: Streptococcus agalactiae

growth_protocol: Bacterial cultures in rich media (THY) incubated at 37°C in static condition are harvested in exponential growth phase (OD600 = 0.5).

extract_protocol:
Total RNA are extracted after cell wall mechanical lysis with 0.1 µm beads (Precellys Evolution, Bertin Technologies) in RNApro reagent (MP Biomedicals), and purified by chloroform extraction and ethanol precipitation.
Depletion of rRNA (FastSelect Bacterial, Qiagen) and libraries construction ((TruSeq Stranded mRNA, Illumina) are done following manufacturer instructions.

treatment_protocol: Bacterial pellets are washed with cold PBS containing RNA stabilization reagents (RNAprotect, Qiagen) before flash freezing and storage at -80°C.

tag: strain

value: WT


title: PBMC, cohort 1, SjD 3

description: 10x genomics


title: Day0_timeseries_replicate3


title: IFNG, TNFA, TGFB, replicate2

first: Rahul

last: Satija

address: 101 6th Ave

institute: New York Genome Center

description: Fixed samples were thawed and single-cell RNA-seq with CRISPR guide capture was performed using the Parse Biosciences EvercodeTM Whole Transcriptome Mega v1 kit. Each sample is divided into 16 libraries.

data_processing:
We processed Perturb-seq gene expression sequence data using the Parse Split-pipe pipeline (version 0.9.6). The pipeline performs barcode correction, read alignment, transcriptomic quantification, and cell filtering. Sequencing reads from the mRNA library were aligned to the human reference genome GRCh38.p12 (Ensembl release 93).
Read count matrices from the Split-pipe were loaded into R (v4.2.2) and converted into a Seurat object by Seurat R-package (v5.0.1). We performed standard log-normalization (NormalizeData), variable gene identification (FindVariableFeatures) and principal component analysis (RunPCA) on the quantified gene expression data (RNA assay). A customized sgRNA calling pipeline was used to call the sgRNA identity of each cell.
Assembly: GRCh38.p12
Supplementary files format and content: RDS files of Seurat object, which contains the raw count of expression and the essential meta data of each cell

source_name: cell line

growth_protocol: All cell lines were monoclonal dCas9-KRAB-MeCP2 cell lines. A549 cells were grown in DMEM with high glucose with L-glutamine and sodium pyruvate (Cytiva SH30243.01), BXPC3 cells were grown in RPMI 1640 (Caisson Labs RPL03), HAP1 and K562 cells were grown in IMDM with GlutaMAXTM Supplement (Thermo Scientific 31980030), HT29 cells were grown in McCoy’s 5A (Caisson Labs MCL02), and MCF7 cells were grown in EMEM (Sigma-Aldrich M4655). All media was supplemented with 10% fetal bovine serum (Corning 35-010-CV) and all cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Samples were then fixed using the Parse Biosciences Cell Fixation kit (ECF100) and stored at -80°C. After fixation, we split cells into two, creating a total of 60 samples that encompass two scRNA-seq replicates. Fixed samples were thawed and single-cell RNA-seq with CRISPR guide capture was performed using the Parse Biosciences EvercodeTM Whole Transcriptome v1 (ECW01030) or Whole Transcriptome Mega v1 (ECW01050) kit with minor modifications to the Parse protocol.
Polyadenylated sgRNAs were reverse transcribed and barcoded using the existing primers in the commercial kit, enriched during cDNA amplification using a guide additive primer, and amplified for sequencing using a two-step guide-specific library preparation protocol (described in Jiang and Dalgarno et al., bioRxiv 2024). We optimized the guide capture conditions through guide additive cDNA amplification primer design, modifying the PCR annealing temperature to perform all cycles at 65°C, optimizing the guide additive primer concentration, and increasing the SPRI cleanup ratio from 0.8X to 1X to preserve shorter random hexamer reverse transcription derived guides.

treatment_protocol: All six CRISPRi cell lines were transduced at a low MOI (0.05 – 0.1) with lentivirus for a pathway-specific guide pool. After three to five days of selection for guide positive cells with 1 μg/mL puromycin (Thermo Scientific A1113803) and seven to ten days of expansion, cells were stimulated for 24 hours with the corresponding cytokine to induce signaling: IFNβ (PBL Assay Science 11415-1,   ), IFNγ (R&D Systems285-IF-100,),TGFβ(ThermoScientificPHG9204,,TNFα(R&D Systems 210-TA-005,   ), or insulin (INS) (Sigma-Aldrich 91077C-250MG,   ).

value: cell line

value: A549, MCF7, HT29, HAP1, BxPC3, and K562

value: lung adenocarcinoma epithelial cells, breast adenocarcinoma cells, colorectal adenocarcinoma cells, cell line derived from the chronic myelogenous leukemia, pancreatic adenocarcinoma cells, and chronic myelogenous leukemia cells

value: Non-targeted and knocked down

value: interferon-beta (IFNB), interferon-gamma (IFNG), transforming growth factor beta (TGFB), tumor necrosis factor-alpha (TNFA), or insulin (INS)


title: MSTO KR_control_rep1

description: Sample 25

value: control


title: NEM316 ∆covR RNA-seq Replicate 3

value: {delta}covR


title: PBMC, cohort 1, SjD 1

description: 10x genomics


title: Day0_timeseries_replicate1

value: Chinese hamster ovary (CHO) cells


title: IFNB, Insulin, replicate2


title: Y27_K975_rep3

description: Sample 24


title: Day0_timeseries_replicate2


title: NEM316 RNA-seq Replicate 1


title: NEM316 ∆covR RNA-seq Replicate 2


title: CHO_multiome_S4_ATAC

data_processing:
Alignment of the raw fastq-data with cellranger-arc-2.0.2 to reference genome.
QC and data filtering with cellranger-arc-2.0.2.
Sample combination with cellranger-arc-2.0.2.
QC with Signac v1.12.
Clustering and visualization with Seurat v.4.0.5. & Signac v.1.12
Assembly: Cricetulus_griseus CHOK1GS_HDv1.108
Supplementary files format and content: RData objects containing the Signac object and the GRanges ATAC peak objects

source_name: Ovaries

extract_protocol:
To isolate the nuclei, the cells were transferred to a 1.5 ml Eppendorf tube and centrifuged at 200 g for 5 mins. The supernatant was discarded and 1 ml of 1x PBS was added. The cells were then centrifuged for 5 minutes at 200 g and the supernatant discarded. Cells were treated for 10 minutes on ice in 125 µl buffer (10 mM HEPES (pH 7.9), 10 mM KCl, 1.5 mM MgCl2, 0.34 M sucrose, 10% glycerol, 1mM DTT) supplemented with 0.1 % Triton X-100 and a freshly added cOmplete mini tablet (Roche). Afterwards, the samples were centrifuged at 1300 g for 5 minutes and the supernatant was discarded. To freeze the nuclei, the samples were resuspended in 1 ml buffer containing 700 µl glycerol and slowly cooled down to -80°C. Prior to library preparation, samples were thawed on ice, filled up with buffer to a total volume of 1.5 ml, and centrifuged for 3 min at 1300 g. Next, the supernatant was discarded without fully exposing the pellet. Samples were subsequently resuspended in 1 ml of buffer, centrifuged for 3 minutes at 1300 g and 4°C. The supernatant was discarded, and the nuclei were resuspended in 100 µl buffer and stored on ice. Subsequently, they were processed with the 10X Multiome Gene Expression + ATAC kit.
Approximately 10,000 nuclei per sample were loaded into the Chromium Controller system, and libraries were subsequently prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10X Genomics), following the manufacturer’s instructions. Libraries were sequenced on a NovaSeq 6000 device (Illumina) using paired-end (50 + 100 bp) settings for 150 cycles for the scRNA-seq, and paired-end (50+100 bp) for 150 cycles for the scATAC-seq.

value: Ovaries

value: Nuclei

tag: library

value: ATAC

tag: treatment (glutamine_adaption)

value: yes

tag: passage

value: Passage 40


title: MSTO KR_K975_rep1

description: Sample 28


title: PBMC, cohort 2, Healthy Donor 4

description: 10x genomics

value: PBMC

value: healthy


title: Day3_timeseries_replicate1

value: Ovary


title: NEM316 ∆covR RNA-seq Replicate 1


title: PBMC, cohort 1, Healthy Donor 1

description: 10x genomics


title: CHO_multiome_S4_RNA

value: RNA


title: Y27_K975_rep1

description: Sample 22

value: mesothelioma


title: Y27_K975_rep2

description: Sample 23


title: PL4 96H stim XQ1

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
Donor 3 96H stim
XQ18_S18

data_processing:
Raw FASTQ files were trimmed for low quality sequence and Illumina adapters using trimmomatic
Aligned to reference genome using HISAT2
gene level count data generated by subread featurecounts
gencode v37 gene annotations were used
Assembly: Ensembl GRCh38
Supplementary files format and content: tab delemited text file of raw counts per genes from featurecounts. Each sample is a column and genes (ensembl IDs) are the rows.

source_name: Peripheral blood T cells

growth_protocol: PBMCs from de-identified, normal, healthy human donors were obtained by automated leukapheresis (StemExpress).CD4+ and CD8+ cells were sorted by immunomagnetic separation using CD4 and CD8 microbeads (Miltenyi Biotec) in combination with a CliniMACS Prodigy cell sorter (Miltenyi Biotec).Sorted T cells were cultured in OpTmizer CTS medium supplemented with 2.6% Optimize CTS supplement, 5% human AB serum, 1x L-glutamine, 1x Pen/Strep 10mM N-Acetylcysteine, 300U/mL IL2, 5ng/mL IL7, and 5ng/mL IL15 or RPMI, 10%FBS, and 1x Pen/Strep at 37°C and 5% CO2 until use.

extract_protocol: At 0, 24, 36, 48, and 72 hours post activation cells were then collected and RNA was extracted with a PureLink RNA Mini kit (Invitrogen).

treatment_protocol: T cells were thawed and activated using Dynabeads Human T-Activator CD3/CD28 at a ratio of 2:1 (beads:cell) for 24-96 hours.

value: Peripheral blood T cells

value: 96 hours stim


title: PBMC, cohort 1, Healthy Donor 2

description: 10x genomics


title: A909 RNA-seq Replicate 3

value: WT


title: MSTO KR_control_rep2

description: Sample 26


title: PBMC, cohort 1, SjD 2

description: 10x genomics

value: SjD


title: CHO_multiome_S3_ATAC

value: no

value: Passage 39


title: NEM316 RNA-seq Replicate 2


title: A909 RNA-seq Replicate 2


title: Y27_control_rep2

description: Sample 20

value: control


title: CHO_multiome_S3_RNA

value: Ovaries


title: PL2 96H stim XQ1

description:
Donor 1 96H stim
XQ16_S16


title: CHO_multiome_S2_ATAC

value: Nuclei

value: Passage 36


title: A909 RNA-seq Replicate 1


title: PL4 72H stim XQ1

description:
Donor 3 72H stim
XQ15_S15

value: 72 hours stim


title: Y27_control_rep1

description: Sample 19


title: CHO_multiome_S2_RNA


title: ACC1_K975_rep3

description: Sample 6


title: L4, tm2321;mir-43(M3), rep3

city: Cambridge

first: Michael

middle: W

last: Stubna

state: MA

address: 455 Main St

institute: Whitehead Institute

description: ebaxM3 L4-3

data_processing:
Trimmed 4N from 5' of each read with fastx_trimmer
Trimmed 3' adapter with cutadapt
Filtered reads for base quality with fastq_quality_filter using parameters -q 30 -p 100
Collapsed fastq files to retain only the sequence of each read, with the sed command in Unix
Counted miRNAs by string-matching to unique 19nt prefixes with a custom Python script
Counts were manually merged and counts to spike-in oligonucleotides removed prior to DESeq2 expression analysis or Excel-based normalization of counts to total miRNA read abundance.
Assembly: miRNAs curated from Jan CH, Friedman RC, Ruby JG, Bartel DP (2011), Nature 469:97-101, Supplementary Table 6; 21U-RNAs from ENSEMBL WBcel235
Supplementary files format and content: Excel file includes raw microRNA counts for each Sample

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol:
Worms were cultured on standard NGM agar seeded with E. coli OP50 at 20 degrees C, except for glp-4 mutants, which were raised at 15 degrees and upshifted to 25 degrees for the experiment.
Worms were synchronized by treatment with an alkaline bleach solution. Early embryos were isolated immediately after bleaching; late embryos were allowed to develop a further 6 h in M9 buffer; samples grown to postembryonic stages were allowed to hatch overnight into M9 buffer in the absence of food.
L1 larvae were collected in a starved state following the overnight hatching period. For older stages, starved L1 were plated on NGM agar with food and grown at 20 degrees C for approximately 16, 28, 42, and 68 h for L2, L3, L4, and adult worms, respectively. glp-4 worms raised at 25 degrees were collected after 48 h.

extract_protocol:
Samples were washed with M9 buffer and then snap-frozen. TRI reagent was added to frozen worm pellets, which were then thawed and snap-frozen twice more to disrupt the embryonic cuticle. Phase separation was achieved with 1-bromo-3-chloropropane, and the aqueous phase was precipitated in isopropanol.
Libraries were prepared from 2–10 µg total RNA essentially as described (Kleaveland, 2018), with the addition of spike-in RNA oligonucleotides in proportion to the total RNA content of each sample. A step-by-step protocol for sRNA-seq library preparation can be found at http://bartellab.wi.mit.edu/protocols.html.

value: Whole animal

tag: developmental stage

value: L4 larva


title: PL2 72H stim XQ1

description:
Donor 1 72H stim
XQ13_S13


title: PL3 72H stim XQ1

description:
Donor 2 72H stim
XQ14_S14


title: ACC1_K975_rep2

description: Sample 5


title: A909 ∆covR RNA-seq Replicate 2

value: {delta}covR


title: A909 ∆covR RNA-seq Replicate 1


title: PL4 48H stim XQ1

description:
Donor 3 48H stim
XQ12_S12

value: 48 hours stim


title: L4, tm2321;mir-43(M3), rep2

description: ebaxM3 L4-2


title: L4, tm2321;mir-43(M3), rep1

description: ebaxM3 L4-1


title: Y27_control_rep3

description: Sample 21


title: PL3 96H stim XQ1

description:
Donor 2 96H stim
XQ17_S17


title: ACC1_control_rep3

description: Sample 3


title: 2603V/R RNA-seq Replicate 3


title: PL3 48H stim XQ1

description:
Donor 2 48H stim
XQ11_S11


title: L4, tm2321;mir-43(M2), rep3

description: ebaxM2 L4-3


title: 2603V/R RNA-seq Replicate 2


title: ACC1_control_rep2

description: Sample 2


title: PL2 48H stim XQ1

description:
Donor 1 48H stim
XQ10_S10


title: A909 ∆covR RNA-seq Replicate 3


title: ACC1_control_rep1

description: Sample 1


title: L4, tm2321;mir-43(M2), rep2

description: ebaxM2 L4-2


title: PL3 36H stim XQ1

description:
Donor 2 36H stim
XQ8_S8

value: 36 hours stim


title: PL4 36H stim XQ1

description:
Donor 3 36H stim
XQ9_S9


title: H2052_K975_rep3

description: Sample 18

value: mesothelioma


title: 2603V/R ∆covR RNA-seq Replicate 3


title: ACC1_K975_rep1

description: Sample 4


title: L4, tm2321;mir-43(M2), rep1

description: ebaxM2 L4-1


title: 2603V/R ∆covR RNA-seq Replicate 2


title: H2052_K975_rep1

description: Sample 16


title: 2603V/R ∆covR RNA-seq Replicate 1


title: PL2 36H stim XQ1

description:
Donor 1 36H stim
XQ7_S7

value: Peripheral blood T cells


title: PL4 24H stim XQ1

description:
Donor 3 24H stim
XQ6_S6

value: 24 hours stim


title: L4, tm2321;mir-43(M1), rep2

description: ebaxM1 L4-2


title: PL3 24H stim XQ1

description:
Donor 2 24H stim
XQ5_S5


title: Pacbio DNA-seq

value: Ovarian Somatic Cells (OSC)

value: WT OSC


title: L4, tm2321;mir-43(M1), rep3

description: ebaxM1 L4-3


title: H2052_control_rep3

description: Sample 15


title: L4, tm2321;mir-43(M1), rep1

description: ebaxM1 L4-1


title: L4, mir-43(M3), rep3

description: M3 L4-3


title: CHO-DG44

data_processing:
Reads were trimmed using Trimmomatic  and mapped with BSMAP  version 2.9. The assembly of Cricetulus_griseus CHOK1GS_HDv1.108 was used as genome reference. Duplicate reads were removed using the Picard tool (http://broadinstitute.github.io/picard).
Methylation ratios were determined using a Python script (methratio.py) that is distributed with the BSMAP package. For all further analysis, only CpGs covered by at least five reads were considered.
Assembly: Cricetulus_griseus CHOK1GS_HDv1.108
Supplementary files format and content: BED files containing CpGs with information about coverage (_cov) and methylation ratios (_ratio).

extract_protocol:
Genomic DNA was extracted using the PureLink Genomic DNA Isolation Minikit kit (Invitrogen), including RNAase treatment following the manufacturer's instructions.
Libraries for whole-genome bisulfite sequencing (WGBS) were prepared using the VAHTS Universal Pro DNA Library Prep Kit for Illumina (Vazyme, Catalog #ND608).

value: Ovary

value: Chinese hamster ovary (CHO) cells


title: WT Treg, Ku70, rep2

city: Shanghai

first: Qianru

last: Huang

address: 227 South Chongqing Road Shanghai

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The quality of sequence reads was confirmed using fastQC to confirm that the average of Phred score was over 20.
Raw sequences were trimmed using trim_galore with the default setting; trim_galore --paired ${name}_R1.fq.gz ${name}_R2.fq.gz -o ${name}.
Sequencing reads were mapped to the mouse genome mm10 using Bowtie2 with default setting; bowtie2 -p 16 -x mm10 -1 ${name}_R1_val_1.fq.gz -2 ${name}_R2_val_1.fq.gz -S ${name}.sam.
Duplicated sequences were removed by picard from GATK toolkit; gatk SortSam –Input ${name}.sam == OUTPUT ${name}.sort.sam – SORT_ORDER coordinate; and then gatk MarkDuplicates –INPUT ${name}.sort.sam – OUTPUT ${name}.dedup.bam –REMOVE_DEPLICATES TRUE –METRICS_FILE ${name}.DeDUPLICATE.txt;
Common ChIPseq peaks in the given conditions were identified by merging 2 replicates for each condition, and were defined using MACS2 callpeak method with the following command; macs2 callpeak -t ${name}_rep1.dedup.bam ${name}_rep2.dedup.bam -g mm -n ${name} -B -p 0.05, –nomodel -extsize 140. Bdg2bw tool used for the conversion of bedgraph to bigwig for visualization.
Specific peaks between given conditions were identified by MACS2 bdgdiff method as following; macs2 bdgdiff --t1 ${condition1}_treat_pileup.bdg --c1 ${condition1}_control_lambda.bdg --t2 ${condition2}_treat_pileup.bdg --c2 ${condition2}_control_lambda.bdg -g 60 -l 140 --o-prefix diff.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Regulatory T cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature.  Chromatin was sonicated into~500-bp fragments and purified with the CST SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads, #9005).
The DNA library was sequenced using the DNBSEQ-T7 platform with a PE read length of 150 bp.

value: Regulatory T cells

value: wild type

tag: chip antibody

value: anti-Ku70 (proteintech:66607-6-Ig)


title: 2603V/R RNA-seq Replicate 1

value: WT


title: WT Treg, Ku70, rep1

value: anti-Ku70 (proteintech:66607-5-Ig)


title: L4, mir-43(M3), rep2

description: M3 L4-2

value: Whole animal


title: H2052_control_rep2

description: Sample 14

value: control


title: H2052_K975_rep2

description: Sample 17


title: PL4 24H nostim XQ1

description:
Donor 3 24H nostim
XQ3_S3

value: no stim


title: Treg, Input

value: anti-Ku70 (proteintech:66607-4-Ig)


title: MSTO_K975_rep3

description: Sample 12


title: L4, mir-43(M3), rep1

description: M3 L4-1

value: L4 larva


title: WT Tconv, Ku70, rep2

source_name: Conventional T cells

value: Conventional T cells

value: anti-Ku70 (proteintech:66607-3-Ig)


title: PL3 24H nostim XQ1

description:
Donor 2 24H nostim
XQ2_S2

value: Peripheral blood T cells


title: L4, mir-43(M2), rep2

description: M2 L4-2


title: MSTO_K975_rep2

description: Sample 11

value: mesothelioma


title: WT Tconv, Ku70, rep1

value: anti-Ku70 (proteintech:66607-2-Ig)


title: L4, mir-43(M2), rep3

description: M2 L4-3


title: MSTO_K975_rep1

description: Sample 10


title: Iso-seq Piwi KD rep2

value: Ovarian Somatic Cells (OSC)

value: Piwi-KD OSC

value: RNAi Piwi


title: PL2 24H nostim XQ1

description:
Donor 1 24H nostim
XQ1_S1


title: L4, mir-43(M2), rep1

description: M2 L4-1


title: Iso-seq EGFP KD rep2

value: EGFP-KD OSC

value: RNAi EGFP


title: MSTO_control_rep3

description: Sample 9


title: L4, mir-43(M1), rep3

description: M1 L4-3


title: KO Treg, Foxp3, rep1

value: Regulatory T cells

value: Xrcc6 knockout

value: anti-Foxp3 (eBioscience:14-4774-86)


title: KO Treg, Foxp3, rep2

value: anti-Foxp3 (eBioscience:14-4774-87)


title: Iso-seq Piwi KD rep1


title: MSTO_control_rep2

description: Sample 8

value: control


title: H2052_control_rep1

description: Sample 13


title: L4, mir-43(M1), rep2

description: M1 L4-2

value: Whole animal


title: MSTO_control_rep1

description: Sample 7


title: Iso-seq EGFP KD rep1


title: KO Treg, Input

value: anti-Foxp3 (eBioscience:14-4774-85)


title: WT Treg, Foxp3, rep2

value: wild type

value: anti-Foxp3 (eBioscience:14-4774-84)


title: PL2 24H stim XQ1

description:
Donor 1 24H stim
XQ4_S4

value: Peripheral blood T cells

value: 24 hours stim


title: L4, mir-43(M1), rep1

description: M1 L4-1

value: L4 larva


title: cADSC_BPA_Smp3

city: Seongnam-si

first: Eun-Jung

state: Gyeonggi-do

address: 1342 Seongnam-daero

department: Food and nutrition

country: South Korea

institute: Gachon University

data_processing:
Quality control test on the sequencing data was done with error rate calculation and a Phred Q20 and Q30 score. All samples passed with error rate (%) < 0.03, Q20 > 98%, and Q30 > 94%.
The preprocessed reads (fastq.gz) were mapped into NCBI reference genome (GCF_014441545.1_ROS_Cfam_1.0_genomic.fna) using Rsubread R package (ver. 2.0.0, Liao et al. 2013).
The transcripts of each sample were assembled based on transcripts per milllion (TPM) mapped reads method. We obtained TPM log2 values and performed quantile normalization for each sample. The sequence read alignment was annotated with gene symbols by NCBI annotation data (GCF_014441545.1_ROS_Cfam_1.0_genomic.gtf).
Assembly: GCF_014441545.1_ROS_Cfam_1.0_genomic.fna
Supplementary files format and content: Tab-delimited text files include TPM log2 values for each Sample.

organism: Canis lupus familiaris

source_name: canine adipose-derived stem cell

growth_protocol: The details of cADSC cell culture and the adipogenic differentiation methods have been described in our previous study (PMID: 34170094 ).

extract_protocol:
We used the standard procedure of Qiagen RNeasy kit (Qiagen, Chatsworth, CA, USA) to extract total RNA from the cADSCs. We calculated total RNA concentration and assessed the integrity.
The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer.
The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582).

value: canine adipose-derived stem cell

tag: treatment/time

value: day14, differentiated adipocyte with 1 μM BPA


title: L4, tm2321, rep1 for miR-43

description: CZ9907 L4-1


title: L4, tm2321, rep2 for miR-43

description: CZ9907 L4-2


title: WT Treg, Foxp3, rep1

value: anti-Foxp3 (eBioscience:14-4774-83)


title: Tconv, Input

value: Conventional T cells

value: anti-Ku70 (proteintech:66607-1-Ig)


title: WT Treg, Input

value: Regulatory T cells

value: anti-Foxp3 (eBioscience:14-4774-82)


title: cADSC_BPA_Smp1


title: cADSC_BPA_Smp2


title: cADSC_Control_Smp3

value: day14, differentiated adipocyte with DMSO


title: L4, WT, rep3 for miR-43

description: WT L4-3

value: wild-type


title: cADSC_Control_Smp2


title: KO1_GAS

status: Public on Nov 03 2024

city: 咸阳市

first: HE

last: Yu

state: 陕西省

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道

institute: 西北农林科技大学

data_processing:
We used the raw data of the samples for gene differential expression analysis.
Assembly: GRCm39
Supplementary files format and content: file includes raw counts for each Sample

source_name: gastrocnemius muscle

growth_protocol: We generated lnc-ORA knockout (KO) mice using the CRISPR genome‐editing system with the C57BL/6 background.

extract_protocol:
RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
After fragmentation of the mRNA, the first-strand cDNA is synthesized using random hexamer primers, followed by the synthesis of the second-strand cDNA. After end repair, A-tailing, adapter ligation, fragment selection, amplification, and purification, the library is ready

treatment_protocol: The specific method is to design two sgRNAs based on the sequence of the lnc-ORA gene (sgRNA1: 5′‐-CATAGAGATCTTTCGTAAACAGG-3′; sgRNA2: 5′-TTGTGCAGGGAAACTTTACGTGG-3′) to delete the 5147 bp genomic region containing the complete lnc-ORA transcript. The sgRNA of mouse lnc-ORA gene and Cas9 mRNA were co-injected into the fertilized eggs to generate targeted knockout offspring. F0 generation animals were identified by PCR and sequence analysis, and mated with wild-type mice for F1 generation animals for transmission experiments.

value: gastrocnemius muscle

value: lnc-ORA KO


title: WT4_GAS

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道

value: WT


title: L4, WT, rep1 for miR-43

description: WT L4-1

value: Whole animal


title: KO3_GAS

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道


title: WT2_GAS

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道


title: L4, WT, rep2 for miR-43

description: WT L4-2


title: KO2_GAS

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道


title: WT3_GAS

address: 陕西省 / 咸阳市 / 杨陵区 / 杨陵街道


title: Rad21het_rep3

city: Dunedin

first: Jisha

last: Antony

state: Otago

address: 58 Hanover Street

country: New Zealand

institute: University of Otago

data_processing:
Sequencing reads were QC using FastQC. Sequencing adapter and low quality (Q<20) were removed using fastq-mcf. Cleaned reads were aligned using HISAT2 (version 2.0.4). Read count were retrieved using FeatureCount summarising data at gene id level.
Transcript per milion were generated using featureCount read count using R.
Assembly: Danio Rerio genome GRCz11
Supplementary files format and content: tab-delimited text file, contains the transcript parts million counts(TPM) for each sample

organism: Danio rerio

source_name: Whole kidney marrow

extract_protocol:
Whole kidney marrow tissue was isolated from adult zebrafish. Total RNA was extracted using the NucleoSpin RNA kit (MACHEREY-NAGEL).
Libraries were prepared using the Illumina TruSeq® RNA Sample Preparation v2

value: Whole kidney marrow


title: Lung, samples 1-6

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

data_processing:
The demultiplexing, matrixd processing, gene counting and aggregation were made using cellranger-7.1.0 with the Chromium Mouse Transcriptome Probe Set v1.0.
Assembly: mm10-2020-A
Supplementary files format and content: matrix, features, and matrix files

source_name: Lung

extract_protocol:
Mice lungs were digested
Mice lungs were harvested, minced with a razor blade, digested in Collagenase IV (1.6mg/ml) + DNAse I (10ug/ml) in DMEM buffer supplemented with Hepes (10mM) for 30 min. Lungs were triturated with a 1mL pipette and cell suspensions were filtered (40um). 2 different mice were pooled for each sample. RBC were lysed (Gibco, #A10492-01) before staining with viability dye (Biolegend 423105) and anti-CD45 (103107). 500000 live immune cells were sorted on a FACS ARIA III (BD) and harvested in collection buffer (PBS+ 0.04% BSA + 50% FBS). Cells were then fixed, before single cell library preparation using Chromium 10x fixed RNA kits and instructions (#PN-1000414 and #PN-1000497).

value: Lung

value: OVA


title: Rad21het_rep2


title: Rad21het_rep1


title: Lung, samples 9, 13-16

value: PBS, OVA+vehicle, OVA+RTX


title: WT_rep3

value: wild type


title: WT_rep2


title: WT_rep1


title: tumor, individual 44

city: Ulm

middle: Karl

last: Melzer

address: Albert-Einstein-Allee 23

institute: Ulm University Hospital

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU44_S158086

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.1 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling was performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and basic Gencode reference transcriptome v46 (May 2024) with STAR 2.7.11b and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.18 package DESeq2 1.40.2, running under R 4.3.3.
Assembly: UCSC hg38 based on GRCh38
Supplementary files format and content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: Bladder cancer

extract_protocol:
Total RNA from organoids was extracted using the Monarch Total RNA Miniprep Kit (NEB, cat.: T2010S) following the manufacturer’s protocol. RNA from parental tumors was extracted from FFPE tissue using the RNEasy FFPE Kit (Qiagen, cat. 73504), also according to the manufacturer’s guidelines. In brief, tumor regions on slides were identified and marked by a board-certified pathologist, then scraped off the slides. Tissue from multiple sections, with a combined thickness of up to 40µm, was pooled before initiating RNA isolation as per the manufacturer's instructions.
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA). RNA-seq libraries were prepared with the Watchmaker RNA Library prep kit with Polaris Depletion (Watchmaker Genomics, Inc., Boulder, CO, USA). All formalin-fixed, paraffin embedded (FFPE) samples, underwent special treatment adhering to the vendor’s protocol. NGS library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent, Santa Clara, CA, USA). For sequencing, samples were diluted and pooled into multiplex NGS libraries in equimolar amounts.

value: Bladder cancer

value: Parental Tumor

value: FFPE


title: tumor, individual 45

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU45_S158090


title: tumor, individual 43

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU43_S158088


title: tumor, individual 36

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU36_S158094


title: tumor, individual 41

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU41_S158098


title: tumor, individual 33

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU33_S158096


title: tumor, individual 24

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU24_S158092


title: organoid, individual 45

description:
organoids dervied from corresponding tumor
hBC_OR45_S158091

value: Organoids

value: total RNA


title: organoid, individual 43

description:
organoids dervied from corresponding tumor
hBC_OR43_S158089


title: organoid, individual 38

description:
organoids dervied from corresponding tumor
hBC_OR38_S158101


title: organoid, individual 44

description:
organoids dervied from corresponding tumor
hBC_OR44_S158087


title: organoid, individual 41

description:
organoids dervied from corresponding tumor
hBC_OR41_S158099


title: organoid, individual 33

description:
organoids dervied from corresponding tumor
hBC_OR33_S158097


title: 3DCS_4214

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
FASTQ files were generated using the Cell Ranger v6.0.1 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic mouse reference using Cell Ranger v6.0.1 (10X Genomics) to generate count matrices.
Assembly: GRCh38
Supplementary files format and content: HDF5 gene count matrices

source_name: blood

growth_protocol: Cells were suspended in 10% sucrose solution at 2x106 cells/mL and plated in PuraMatrix Peptide Hydrogel (Corning) diluted 1:1 with a 20% sucrose solution and supplemented with 100 ng/mL stem cell factor (SCF), 100 ng/mL Flt3 ligand (FLT3L), 20 ng/mL thrombopoietin (TPO), 2 ng/mL vascular endothelial growth factor (VEGF), 20 ng/mL IL-3, 20 ng/mL IL-6, 1 µmol/L StemRegenin1 (SR1), and 25 µg/mL Vitamin C.

extract_protocol:
3D hydrogel culture wells were washed with PBS with recovery of the hydrogel and cells by gentle pipetting in PBS buffer, then centrifuged for 5 minutes at 750 x g, then the hydrogel/PBMC pellet was resuspended in TrypLE solution and incubated at 37°C for 10 minutes. RPMI media with 10% FBS was added and centrifuged for 5 minutes at 750 x g. The resultant pellet was washed twice with PBS to remove hydrogel matrix debris. PBMCs were resuspended in PBS and passed through a 40 µM filter, pelleted by centrifugation at 300 x g for 5 minutes, and resuspended in RPMI media with 10% FBS. FACS was then used to isolate cells from any remaining hydrogel debris and recovered cells were concentrated to 1,000 cells/µl in RPMI media with 10% FBS for downstream scRNA-seq.
Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit v3.1 following the manufacturer’s user guide.

value: blood

value: PBMC

value: 3D hydrogel culture system

tag: time

value: day 8


title: organoid, individual 24

description:
organoids dervied from corresponding tumor
hBC_OR24_S158093


title: Endothelial cells, miR-187/NIPBL, rep3

city: shanghai

first: tan

last: zizheng

address: songhu road

institute: Fudan university

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <30 bp) and low quality reads using Fastp (v0.20.0), an ultra-fast all-in-one FASTQ preprocessor. Then FastQC is employed to ensure high reads quality and to process data quality control. The clean reads were mapped to the hg19 human genome using the Bowtie2 (v2.2.6) software and saved with format of bam by SAMtools (v1.10), bigwig and bedgraph by deepTools(v3.3.2) ,which also used for peaks count normalization and visualization. Peaks detection was performed using the MACS2 (v2.2.7.1) peaks finding algorithm with 0.01 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package . Differentially peaks were identified by DiffBind (for sample with replications) or MAnorm2 (for sample with no replication) with a cut-off value of log2|fold-change|>1 and p-value <0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant peaks, the potential peaks in identified modules based on gene ontology (GO) and KEGG pathway categories. HOMER(v4.11) was utilized to Motif prediction of peaks.
Assembly: hg19
Supplementary files format and content: narrowPeak

source_name: Endothelial cells

extract_protocol:
Extract DNA using the ATAC seq library preparation kit (APExBIO) extraction kit
ATAC-seq libraries of cells were prepared as the manufacturer’s protocol (Cat. No. K1157, APExBIO). 50,000 cells of samples were lysed in 50 μL ice ATAC Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.5 μL 10% NP40, 0.5 μL 10% Tween 20, and 0.5 μL 2% Digitonin for 3 min. Lysates were spun at 1000 rpm for 10 min to obtain the pellet nuclei. The nuclei were then incubated with the transposase enzyme and tagmentation buffer at 37 °C for 30 min. The fragmented DNA was then purified using MinElute Reaction Cleanup Kit (Cat No. 28204, QIAGEN) in a final volume of 10 μL. ATAC-Seq Libraries were prepared following the Buenrostro protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/). The DNA libraries were amplified for 10 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 2×150 as the sequencing mode.

value: Endothelial cells


title: organoid, individual 36

description:
organoids dervied from corresponding tumor
hBC_OR36_S158095


title: Endothelial cells, miR-187, rep3


title: Endothelial cells, miR-187, rep1


title: Endothelial cells, miR-NC, rep2


title: Endothelial cells, miR-187, rep2


title: Endothelial cells, miR-187/NIPBL, rep2


title: Endothelial cells, miR-NC, rep1


title: Endothelial cells, miR-NC, rep3


title: EA.hy 926, miR-187, rep1

data_processing:
Raw paired-end fastq reads were filtered by Fastp discard the adapters and low quality bases. The clean reads obtained were then aligned to the hg19 human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie. Differentially expressed genes (DEGs) were identified by Deseq2 (for sample with replications) with a cut-off value of log2 |fold change| >1 and p-adjust < 0.05. The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules based on gene ontology (GO) and KEGG pathway categories. Terms with pvalue<0.05 were considered significant. Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: hg19
Supplementary files format and content: Excel files includes FPKM for each Sample.
Supplementary files format and content: allgenes_sample_FPKM.xls

source_name: EA.hy 926

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12310ES, China) following manufacturer’s recommendations. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

value: EA.hy 926


title: EA.hy 926, miR-NC, rep2


title: Endothelial cells, miR-187/NIPBL, rep1


title: EA.hy 926, miR-187, rep2


title: tumor, individual 38

description:
parental tumor tissue, FFPE-derived RNA
hBC_TU38_S158100


title: Endothelial cells, miR-187, H3K27AC

data_processing:
Raw reads were filtered to obtain clean reads by removing sequencing adapters, short reads (length <30 bp) and low quality reads using fastp (v0.20.0). Then FastQC was used to perform quality control. Clean reads were aligned to the human reference genomehg19 using Bowtie2 (v2.2.6) and filtered to access high-quality bam by SAMtools (v1.10) with (-q 30). Peaks were called utilized MACS2(v2.2.7.1) with the parameters by default. FDR cut-off of 0.05 was used to determine significant peaks. ChIPseeker R package was invoked to annotate nearest genes and genomic features to peaks. Differentially peaks were identified by DiffBind with a cut-off value of log2|fold-change|>1 and p-value <0.05 (according to your research). The clusterProfiler was used to perform functional enrichment analysis for the annotated significant peaks based on Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). HOMER(v4.11)  was employed to search for sequence motif among significant peaks with -len 6,8,10 for length of motifs. E value cutoff of 0.05 was used to select significantly enriched motifs.
Assembly: hg19
Supplementary files format and content: narrow peak (expect for IgG samples)
Library strategy: CUT&Tag

extract_protocol:
The CUT&Tag assay used the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903).
Library construction was performed according to the CUT&Tag library construction protocol with some modifications[1]. Cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine, this step was optional. Concanavalin A coated magnetic activated beads were added per sample and incubated at RT for 15 min. The binding cells to beads were pre-cleared and immunoprecipitated with anti-NIPBL and anti H3K27AC antibodies. For increasing quantity of Protein A binding sites, secondary antibody were employed. After washing, the cells were treated with PA/G-Tn5 adapter complex containing 10mM MnCl2 to get CUT&Tag fragments DNA libraries. The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode.


title: EA.hy 926, miR-NC, rep1


title: Endothelial cells, miR-NC, IgG


title: Endothelial cells, miR-NC, H3K27AC


title: Normal Rabbit Serum E11.5 TrkC Cut&Run rep4

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

description:
NRS sample
NRS sample

data_processing:
Sequence reads were trimmed for adaptor with cutadapt
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie with ‘--no-mixed --no-discordant’
After alignment, fragments with size ≤ 90 bp were selected for peak calling of Runx3/Brn3a/Islet1 samples. No size selection was applied to the H3K27Ac.
Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Runx3 samples we also used '-p e-5'.
For the ATACseq data, reads were trimmed with cutadapt and aligned to the genome with bowtie. PCR duplicates were removed with Picard (v 1.119). Non-uniquely mapped reads were removed with Samtools using the flags ‘-F 4 -f 0x2’. Nucleosome-free read pairs with an inner distance of up to 120 bp were then selected from the alignment for downstream analyses. MACS2 was applied for peak calling using the setting: -f BAMPE --SPMR -B –Nomodel.
Assembly: mm10
Supplementary files format and content: Excel file for every experiment with the genomic regions of the consensus peaks.
Supplementary files format and content: Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Brn3a samples we also used '-p e-5'.
Library strategy: Cut&Run

source_name: DRG neurons

extract_protocol:
DRG were dissected from E11.5 BacE-GFP expressing embryos (Appel et al 2016) and dissociated with Trypsin B/Collagenase H.  GFP positive cells were FACS isolated and 300,000-600,000 cells were used for Cut&Run analysis with anti-Brn3a (1:200) (kindly provided by E.Turner), anti-Islet1 (1:50) (Abcam 20670), home made anti-Runx3 (1:200), anti-H3K27Ac (1:50) (Abcam 4729) antibodies or Normal Rabbit Serum (NRS, 1:200). GFP positive TrkC neurons were bound to ConA beads, permeabilized, incubated with anti-Brn3a, anti-Islet1, anti-Runx3, anti-H3K27Ac or NRS and targeted by MNase cleavege. Antibody bound DNA was extracted by phenol chloroform. For ATAC analysis 50,000 cells were used. The cells were lysed and the DNA was exposed to the transposition reaction.
Library was prepared using NEBNEXT Ultra II DNA Library Prep Kit for Illumina (#E7645). DNA fragments were PCR amplified with Illumina primers for no more than 15 cycles and library fragments up to ~250 bp (insert plus adaptor and PCR primer sequences) were SPRI (x0.8) purified.

value: DRG neurons

tag: antibody


title: Endothelial cells, miR-NC, NIPBL


title: cADSC_Control_Smp1

last: Park

value: canine adipose-derived stem cell

value: day14, differentiated adipocyte with DMSO


title: Normal Rabbit Serum E11.5 TrkC Cut&Run rep3

description:
NRS sample
NRS sample

tag: tissue


title: Endothelial cell, miR-187/NIPBL, rep2

source_name: Endothelial cell

value: Endothelial cell


title: Endothelial cell, miR-187/NIPBL, rep1


title: Normal Rabbit Serum E11.5 TrkC Cut&Run rep1

description:
NRS sample
NRS sample


title: E11.5 ATAC rep2

description: Processed_file_1_ATAC_consensus_peaks_E11.5.xlsx

data_processing:
Sequence reads were trimmed for adaptor with cutadapt
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie with ‘--no-mixed --no-discordant’
After alignment, fragments with size ≤ 90 bp were selected for peak calling of Runx3/Brn3a/Islet1 samples. No size selection was applied to the H3K27Ac.
Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Runx3 samples we also used '-p e-5'.
For the ATACseq data, reads were trimmed with cutadapt and aligned to the genome with bowtie. PCR duplicates were removed with Picard (v 1.119). Non-uniquely mapped reads were removed with Samtools using the flags ‘-F 4 -f 0x2’. Nucleosome-free read pairs with an inner distance of up to 120 bp were then selected from the alignment for downstream analyses. MACS2 was applied for peak calling using the setting: -f BAMPE --SPMR -B –Nomodel.
Assembly: mm10
Supplementary files format and content: Excel file for every experiment with the genomic regions of the consensus peaks.
Supplementary files format and content: Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Brn3a samples we also used '-p e-5'.


title: E11.5 ATAC rep1


title: Endothelial cell, miR-187, rep2


title: Normal Rabbit Serum E11.5 TrkC Cut&Run rep5

description:
NRS sample
NRS sample


title: Endothelial cell, miR-NC, rep1

value: miR-NC


title: H3K27Ac E11.5 TrkC Cut&Run rep3

description:
as a control TrkC_NRS_E11.5_12_240723 was used
Processed_file_2_H3K27Ac_consensus_peaks_E11.5.xlsx


title: Endothelial cell, miR-187, rep3


title: H3K27Ac E11.5 TrkC Cut&Run rep2


title: H3K27Ac E11.5 TrkC Cut&Run rep5


title: E11.5 ATAC rep3


title: Endothelial cell, miR-NC, rep2


title: Endothelial cell, miR-187, rep1


title: blastocyst_dmso_10

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

institute: Loke Centre for Trophoblast Research

description:
DMSO_SOP5502A65
blastocyst_counts.tsv
blastocyst_tpm.tsv

data_processing:
Technical replicate fastq files were merged and preprocessed using the nf-core/rnaseq pipeline 3.10.1 with Nextflow 22.10.1 (Ewels et al 2020). Briefly, reads were trimmed for adaptors and quality using Trimgalore 0.6.7 and cutadapt 3.4. Trimmed reads were pseudoaligned to GRCh38 with salmon 1.9.0 and used to generate estimated raw abundances and TPM normalized reads.
Resulting gene expression matrices were integrated and normalized to generate log-counts using Bioconductor tools (Amezquita 2019)
Assembly: GRCh38
Supplementary files format and content: blastocyst_counts.tsv raw estimated abundances from Salmon
Supplementary files format and content: blastocyst_tpm.tsv tpm normalized counts

source_name: Blastocyst

growth_protocol: Human blastocysts were thawed using the Blast thaw kit (Origio; Cat# 10542010A) and cultured in GLOBAL culture medium (LifeGLOBAL; Cat# LGGG-20) with HAS protein supplement (LifeGLOBAL; Cat# LGPS-605) for 2h. Inhibitor or DMSO were applied in equilibrated GLOBAL culture medium with HAS protein supplementation for 20 – 24h.

extract_protocol:
Each blastocyst was briefly washed through PBS- (Gibco, 15140-122) and collected in 5 uL 10X Reaction buffer, containing 3.75 uL Lysis Buffer and 0.25 uL RNAse Inhibitor, provided in the the TAKARA SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Cat# v634890), and snap-frozen to -80˚C.
cDNA was generated using the TAKARA SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Cat# v634890). Retrosynthesis was performed using the provided Smart-seq V4 oligonucleotide primer and 3' Smart-seq CDS Primer II A. The samples were amplified over 18 or 21 PCR cycles and purified up with SPRI Beads (Beckman Coulter Cat#B23318). Preparation of the cDNA library was performed using Nextera_XT 15031942 (Illumina, Cat #FC-131-1096) and followed by paired-end 100 bp NovaSeq 600 sequencing.

treatment_protocol: Human blastocysts were treated with 100 uM A8301 or volume-matched DMSO in pre-equilibrated GLOBAL medium with HAS supplement, for 24h.

value: Blastocyst

tag: batch

value: DMSO


title: H3K27Ac E11.5 TrkC Cut&Run rep4


title: H3K27Ac E11.5 TrkC Cut&Run rep1


title: R3 E11.5 TrkC Cut&Run rep8

description:
as a control TrkC_NRS_FACS_21_250121 was used
Processed_file_3_Runx3_consensus_peaks_E11.5.xlsx


title: Endothelial cells, miR-187, NIPBL

tag: cell type


title: Endothelial cell, miR-NC, rep3

tag: cell line

tag: genotype


title: R3 E11.5 TrkC Cut&Run rep7

description:
as a control TrkC_NRS_CnR_260220 was used
Processed_file_3_Runx3_consensus_peaks_E11.5.xlsx


title: blastocyst_dmso_9

description:
DMSO_SOP5502A64
blastocyst_counts.tsv
blastocyst_tpm.tsv

tag: treatment


title: blastocyst_dmso_11

description:
DMSO_SOP5502A66
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Normal Rabbit Serum E11.5 TrkC Cut&Run rep2

description:
NRS sample
NRS sample


title: R3 E11.5 TrkC Cut&Run rep6


title: blastocyst_dmso_5

description:
DMSO_SOP5502A60
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: R3 E11.5 TrkC Cut&Run rep4


title: blastocyst_dmso_7

description:
DMSO_SOP5502A62
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: R3 E11.5 TrkC Cut&Run rep3

description:
as a control TrkC_NRS_MACS_021220 was used
Processed_file_3_Runx3_consensus_peaks_E11.5.xlsx


title: Combined Anti-CXCR4 and Anti-PD1 Rep2

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

data_processing:
Raw sequencing data was subjected to quality control using FastQC.
After quality control, Cutadapt was employed to remove low-quality bases and adaptor contaminations. The quality of the resulting clean data was examined again using FastQC software.
Hisat2 was utilized to align the clean data to the mouse reference genome mm10, obtained from the Illumina iGenomes database. Following data mapping, SAM files and BAM files were manipulated using samtools.
The number of reads aligned to gene features was counted using HTSeq-count from the HTSeq package. Differentially expressed genes were identified by edgeR, using a cutoff of |log(fold change)| > 1 and a p-value < 0.01.
GSEA analysis was performed using GSEA software with standard gene sets from the MSigDB database.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Tumor

growth_protocol: Cell line authentication and mycoplasma contamination testing were performed before all experiments. RIL-175 cells were maintained in Dulbecco's modified medium (DMEM) with 20% fetal bovine serum (FBS) with pyruvic acid and 1% penicillin/streptomycin.

extract_protocol:
Tumors were collected from mice treated with control IgG, anti-PD1 antibody alone, anti-CXCR4 antibody alone, and anti-PD1 antibody in combination with anti-CXCR4 antibody. Total RNA was extracted from the freshly isolated tumor tissues using Qiagen RNeasy Mini Kit (Cat. 74104).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from [200ng] of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7.

treatment_protocol: Treatments were administered intraperitoneally every three days for 21 days at 10 mg/kg (anti-PD1 antibody, anti-CXCR4 antibody, and immunoglobulin G [IgG] control) in survival studies. For the time-match study, all the mice with orthotopic grafted models were sacrificed on day 8.

value: Tumor

value: RIL-175 (p53/Hras mutant)

value: hepatocellular carcinoma

value: p53/Hras mutant

value: Combined Anti-CXCR4 and Anti-PD1


title: blastocyst_dmso_4

description:
DMSO_SOP5502A59
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Combined Anti-CXCR4 and Anti-PD1 Rep3


title: R3 E11.5 TrkC Cut&Run rep1


title: Islet1 E11.5 TrkC Cut&Run rep3

description:
as a control TrkC_NRS_FACS_21_250121 was used
Processed_file_5_Isl1_consensus_peaks_E11.5.xlsx


title: Combined Anti-CXCR4 and Anti-PD1 Rep1


title: blastocyst_A8301_9

description:
A8301_SOP5502A179
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: blastocyst_dmso_6

description:
DMSO_SOP5502A61
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Islet1 E11.5 TrkC Cut&Run rep2


title: Islet1 E11.5 TrkC Cut&Run rep1


title: Anti-CXCR4 Rep2


title: blastocyst_A8301_8

description:
A8301_SOP5502A178
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Brn3a E11.5 TrkC Cut&Run rep2

description:
as a control TrkC_NRS_FACS_2804_50521 was used
Processed_file_4_Brn3a_consensus_peaks_E11.5.xlsx


title: blastocyst_A8301_6

description:
A8301_SOP5502A176
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Brn3a E11.5 TrkC Cut&Run rep1


title: blastocyst_A8301_7

description:
A8301_SOP5502A177
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: R3 E11.5 TrkC Cut&Run rep5

description:
as a control TrkC_NRS_FACS_2804_50521 was used
Processed_file_3_Runx3_consensus_peaks_E11.5.xlsx


title: Anti-PD1 Rep2


title: Anti-PD1 Rep1


title: WT_2_dLN RNA

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

data_processing:
Bulk RNA-seq data were preprocessed on Google Cloud via Terra.Bio. The BCL files were converted to FASTQ format using bcl2fastq (v2.20.0.422)
The fastq files were aligned to mouse genome mm10 using STAR version 2.7.5a.
Picard MarkDuplicates was used to identify the duplicate reads.
RNA-SeQC 2 was used for assessing sequencing depth and mapping quality.
Raw counts and TPMs were computed using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each sample

source_name: 2D2 Th17cells

growth_protocol: EX VIVO SAMPLES HARVESTED FROM DRAINING CERVIVAL LYMPH NODES

extract_protocol:
Samples provided in a 96 well plate preserved in 5-10 uL of lysis buffer (1000-5000 cells per well). RNA-SPRI used for RNA isolation and purification.
Modified protocol adapted for low yield non-nuclei samples from Picelli S, et al. (Nat Protocols, 2014)
Samples received, RNA extracted and libraries made following adapted bulk RNA-seq protocol. Libraries barcoded for sequencing using Nextera i5 and i7 primers. Pooled at 4nM and sequenced in house using Illumina Next-seq 75cycle high throughput kit. R1- 38cycles, R2- 38, i1- 8, i2- 8. All QCs done by qubit/bioA.

value: 2D2 Th17cells

value: 2D2 dlck-Cre- Tcf7fl/fl IL17aGFP+


title: WT_4_dLN RNA


title: blastocyst_A8301_5

description:
A8301_SOP5502A175
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: WT_1_dLN RNA


title: Control Rep3

value: Control


title: R3 E11.5 TrkC Cut&Run rep2

description:
as a control TrkC_NRS_FACS_21_250121 was used
Processed_file_3_Runx3_consensus_peaks_E11.5.xlsx


title: KO_4_dLN RNA

value: 2D2 dlck-Cre+Tcf7 fl/fl IL17aGFP+


title: Anti-CXCR4 Rep1


title: blastocyst_A8301_4

description:
A8301_SOP5502A174
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: KO_3_dLN RNA


title: WT_3_dLN RNA


title: KO_1_dLN RNA


title: blastocyst_A8301_2

description:
A8301_SOP5502A172
blastocyst_counts.tsv
blastocyst_tpm.tsv


title: Control Rep2


title: KO_7_dLN

data_processing:
The BCL files were demultiplexed using bcl2fastq (v2.20.0.422)
ENCODE ATAC-seq pipeline (v1.5.4) was used for read alignment, filtering, peak calling, and quality control. Briefly, reads trimmed by cutadapt were aligned to the mm10 genome with Bowtie2, then filtered for duplicates using Picard MarkDuplicates.
After removing the mitochondrial reads, peaks were called using MACS2 with p-value threshold 0.01, smoothing window size 73, and IDR threshold 0.05.
The top 100,000 most significant peaks from each replicate were merged into a set of union peaks using bedtools merge (v2.26.0).
Read counts per peak were computed using featureCounts function in the R package Rsubread (v2.6.4). Peaks wider than 250 bp were selected for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigwig files of processed ATAC-seq read

extract_protocol:
Provide samples in well labeled individual eppendorf tubes of, ideally, ~5000-6000 cells each (frozen in BamBanker solution). Wash/lyse/purify during transposition using Buenrostro ATAC protocol.
Modified protocol adapted for low yield bulk ATAC from Buenrostro J, et al. (current protocols in molecular biology, 2015)
Samples received, lysed and transposed using adapted bulk ATAC protocol. Cleaned using Qiagen MinElute spin columns. QC for amplification using KAPA quant. Libraries barcoded for sequencing using Nextera i5 and i7 primers. Pooled at 4nM and sequenced in house using Illumina Next-seq 75cycle high throughput kit. R1- 38cycles, R2- 38, i1- 8, i2- 0. All QCs done by qubit/KAPA/qPCR


title: blastocyst_A8301_1

description:
A8301_SOP5502A171
blastocyst_counts.tsv
blastocyst_tpm.tsv