title: Gland Tissue, DKO, Rep 4

first: Maxwell

last: McDermott

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
RNA-seq reads were trimmed using trimmomatic v0.36
Trimmed RNA-Seq reads were mapped to MM10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
read count extraction from BAM files performed using deeptools
Assembly: mm10
Supplementary files format and content: Tab delimited includes raw counts for each sample

source_name: Submandibular Gland

extract_protocol:
SMGs from 5-week-old WT and Stim1/2Foxp3 male mice were harvested and kept in chilled tubes with prefilled beads in 1 mL TRIzolTM reagent. Organs were processed via tissue homogenizer for 30s to completely disassociate the tissue.  RNA was extracted with the RNeasy Mini Kit followed by cDNA synthesis using the iScript cDNA synthesis kit.
RNA was then depleted of ribosomal RNA
RNA libraries were prepared using automated stranded RNA-seq library prep polyA selection system. The libraries were purified with AMPure bead.

value: male

value: Submandibular Gland

value: Stim1fl/fl Stim2fl/fl Foxp3-Cre


title: B cells, WT non-stim, rep1

status: Public on Nov 04 2024

type: SRA

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

library_source: transcriptomic

data_processing:
The fastq file was demultiplexed using BRBseq Tools software (version 1.6, Gardeux 2021).
Subsequently, the RNA-seq pipeline was executed on each demultiplexed Fastq file, following these steps: Firstly, reads were subjected to adapter and quality trimming using Cutadapt (version 2.5, Martin 2011). Next, reads corresponding to ribosomal RNA sequences were eliminated using fastq_screen (version 0.11.1, Wingett & Andrews, 2018). The remaining reads underwent further filtering for low complexity with reaper (version 15-065, Davis et al. 2013).
These processed reads were then aligned to the Mus musculus genome (build GRCm38) using STAR (version 2.5.3a, Dobin et al. 2013).
UMI deduplication was performed after the mapping step using UMI-tools dedup functionality (version 0.5.3, Smith et al. 2017).
The count of unique UMIs per gene locus was summarized using htseq-count (version 0.9.1, Anders et al. 2015) with Ensembl 102 gene annotation. The quality of the RNA-seq data alignment was evaluated using RSeQC (version 2.3.7, Wang et al. 2012).
Assembly: build GRCm38
Supplementary files format and content: Tab-delimited text file includes umi counts for each Sample
Library strategy: BRB-seq

molecule: total RNA

organism: Mus musculus

source_name: primary cells

growth_protocol: Bone marrow derived plasmacytoid dendritic cells (BM-pDC) were differentiated in IMDM medium supplemented with 10% FBS + antibiotics (penicillin and streptomycin) and was conditioned with 10% of Flt3L containing  media from cell line producing this cytokine. B cells were isolated from spleens by untouched  magnetic separation

extract_protocol:
RNA from BM-pDC was harvested using Qiagen Rneasy Plus Micro kit. RNA from primary splenic B cells was isolated using Zymoresearch Quick-RNA Miniprep kit.
RNA libraries were prepared using BRB-Seq kit from Alithea Genomics, according to the manufacturer's recommendations. A total of 85 ng purified RNA was transferred into the BRB-Seq multiwell plate containing the barcoded oligo-dT primers for the reverse transcription step. All cDNA were pooled into an Eppendorf tube and purified using SPRIselect beads (Beckman) at a 1X ratio. The remaining free primers were digested with an exonuclease step. Second strand synthesis was performed from the purified cDNA pool and cleaned-up with a 0.6X SPRIselect beads step. Double stranded cDNA was then tagmented and purified with a 0.6X SPRIselect beads step. Finally the 3’ terminal fragments were amplified using Unique Dual Indexing (UDI) Illumina adapter primers. After a final 0.7X SPRIselect beads purification step, the library generated was quantified with a fluorimetric method (QubIT, Thermo Scientifics) and its size pattern analyzed with a fragment analyzer (Agilent).

treatment_protocol: Cells were stimulated either with TLR7 agonist (R848 100 ng/ml) or CpG-B (ODN1668 1 uM) for 4 or 6h, respectively

tag: cell line

value: primary cells

tag: cell type

value: B cells

tag: genotype

value: WT

tag: treatment

value: non-stimulated


title: patch-seq sample_S093

city: Houston

first: Junzhan

last: Jing

state: Texas

address: 1250 Moursund St., Suite 0925

department: Neuroscience

country: USA

institute: Baylor College of Medicine

description: patchseq.mtx.csv

data_processing:
snRNA-seq,  Cell Ranger (version 5.0.1) with the Mus musculus genome (GRCm38) and annotation GTF (version M23) was used to generate the output count matrix.
patchseq, raw reads were aligned to the  Mus musculus genome (GRCm38) with annotation GTF (version M23) using STAR 2.7.7a  and an expression matrix was generated with FeatureCounts
Assembly: Mus musculus genome (GRCm38) with annotation GTF (version M23)
Supplementary files format and content: HDF5 Format raw count files generated by Cell Ranger (version 5.0.1)
Supplementary files format and content: patchseq raw count csv file, coma-delimited text file, column names are cell_ids , row names are gene symbols

source_name: cochlear nucleus

extract_protocol:
Single nucleus extraction and patchseq RNA
10x Genomics Chromium Next GEM Single Cell 3'v3 and Smart-seq2

tag: tissue

value: cochlear nucleus


title: B cells, TASL non-stim, rep1

value: TASL Knock-out


title: B cells, TASL TLR9, 6h, rep1

value: ODN1668 1uM


title: patch-seq sample_S092

description: patchseq.mtx.csv


title: Patient225217_CD_Surgery_PBT

city: Los Angeles

first: Rivkah

last: Gonsky

state: California

address: 8700 Beverly Blvd. Davis Building, Room D4062

department: Gastroenterology/IBIRI

institute: Cedars-Sinai

data_processing:
Expression analysis of CD3+ T cells was performed using Nugen human FFPE RNA-seq library system.
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program
Reads were mapped to the UCSC transcript set using Bowtie2 version 2.1.0.
DESeq2 (v.1.18.1) was applied to produce normalized counts and the data were log2-transformed
RNA-Seq data analysis and data mining were performed using the BRB array tools
Assembly: hg19

organism: Homo sapiens

source_name: peripheral blood T cell

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit
total RNA

treatment_protocol: CD3+ T cells were isolated using CD3-immunomagnetic beads (Miltenyi Biotech, Auburn, CA) and were at least 95% pure.

value: peripheral blood T cell

tag: phenotype

value: Crohn's disease

tag: time

value: Surgery


title: patch-seq sample_S088

description: patchseq.mtx.csv


title: patch-seq sample_S086

description: patchseq.mtx.csv


title: Patient286243_CD_Surgery_PBT


title: Gland Tissue, WT, Rep 4

city: New York

molecule: polyA RNA

tag: Sex


title: Patient225217_CD_Surgery_LPT

source_name: lamina propria mucosa-derived T cell

value: lamina propria mucosa-derived T cell


title: Gland Tissue, DKO, Rep 3


title: patch-seq sample_S085

description: patchseq.mtx.csv


title: Gland Tissue, DKO, Rep 2


title: piRNA-seq rep3

city: Tokyo

first: Masaru

last: Ariura

address: Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio university

library_source: other

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.

molecule: other

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: WT OSC


title: piRNA-seq rep2


title: Patient283965_CD_Surgery_PBT


title: Patient286243_CD_Surgery_LPT


title: Gland Tissue, WT, Rep 2


title: piRNA-seq rep1


title: Gland Tissue, WT, Rep 3


title: Patient283965_CD_Surgery_LPT


title: Day 5 am luminal layer surrounding the attached embryo

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

data_processing:
raw paired-end RNA-seq reads were aligned to indexed mouse genome (GRCm38/mm10) by HiSAT2
The reads per kilobase of exon per million mapped sequence reads were counted using the FeatureCounts function in Subread (v.2.0.0)
Assembly: mm10
Supplementary files format and content: tab-determined files include raw counts for each sample

source_name: mouse uterus

extract_protocol:
NucleoSpin RNA kit (Takara, Osaka, Japan)
SMART-seq v.4 Ultra Low Input RNA Kit (Takara)

value: mouse uterus

value: wildtype

tag: strain

tag: time point


title: patch-seq sample_S082

description: patchseq.mtx.csv


title: Gland Tissue, WT, Rep 1

value: male

value: Submandibular Gland


title: Patient286188_CD_Surgery_PBT


title: Day 5 am luminal layer away from the attached embryo


title: A_3

city: Beijing

first: Shimeng

last: Zheng

address: Yongan Road

department: Beijing Clinical Research Institute

country: China

institute: Beijing Friendship Hospital

description: with acarbose stimulation

data_processing:
HISAT2 2.1.0 --dta –t –p 4
RNA samples were purified, fragmented, reverse transcribed, end-repaired. After sequenced adapters were added, the target fragments were recovered by magnetic bead screening, and PCR amplification was performed to complete the entire library preparation work.
After the library construction was completed, use Agilent2100 to detect the insert size of the library. If insert size met the expectation, Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN were used to perform q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library was > 10nM) to ensure the quality of the library.
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: tibia and femurs

extract_protocol:
The matured bone-marrow derived macrophages were induced to M1 macrophages by LPS and IFN-γ, then stimulated with acarbose (250uM) for 48h.After that,cells RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tibia and femurs

value: BMDM

value: LPS and IFN-y, acarbose


title: patch-seq sample_S081

description: patchseq.mtx.csv


title: A_2

description: with acarbose stimulation

value: WT


title: Day 4 evening uterine luminal layer

value: Day 4 evening uterine luminal layer


title: patch-seq sample_S080

description: patchseq.mtx.csv

value: cochlear nucleus


title: Gland Tissue, DKO, Rep 1

value: Stim1fl/fl Stim2fl/fl Foxp3-Cre


title: patch-seq sample_S084

description: patchseq.mtx.csv


title: Day 4 morning uterine luminal layer

value: Day 4 morning uterine luminal layer


title: patch-seq sample_S079

description: patchseq.mtx.csv


title: C_3

description: without acarbose stimulation

value: LPS and IFN-y


title: Patient284623_CD_Surgery_PBT

value: peripheral blood T cell

value: Crohn's disease

value: Surgery


title: Day 3 morning uterine luminal layer

value: Day 3 morning uterine luminal layer


title: patch-seq sample_S083

description: patchseq.mtx.csv


title: Patient225276_CD_Surgery_PBT


title: A_1

description: with acarbose stimulation


title: Patient286188_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: patch-seq sample_S077

description: patchseq.mtx.csv


title: Patient225276_CD_Surgery_LPT


title: Embryos collected from Day4 8pm Lif eKO uterus

source_name: embryos

treatment_protocol: Lif eKO mice were treated with rLif

value: embryos

value: Lif-floxed/+

value: PBS


title: C_2

description: without acarbose stimulation

value: tibia and femurs


title: patch-seq sample_S078

description: patchseq.mtx.csv


title: C57BL6_Bifidus_1

city: Gwangju

first: YouMin

last: KIM

address: 123, Cheomdangwagi-ro, Buk-gu

department: DEPARTMENT OF BIOMEDICAL SCIENCE AND ENGINEERING

country: South Korea

institute: Gwangju Institute of Science and Technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10X genomics, v6.1.1) was applied to perform mapping to mm10 mouse reference genome. Gene expression matrices were generated by Cell Ranger and loaded to Seurat (v4.1.1) for quality control16. To exclude empty droplets, we used the emptyDrops() function in DropletUtils 1.16.0. Cells with FDR < 0.01 were used for further analysis17. Quality check was based on mitochondrial ratio using flexmix_model in miQC, and then cells with nFeature > 500 and genes with sum of counts in all cells ≥ 10 are used for integration18. 24,403 cells after quality check were integrated using canonical correlation analysis (CCA) through 2,000 integration anchors genes and then regressed out unique molecular identifiers (UMIs) per cell, mitochondrial ratio (calculated by Seurat PercentageFeatureSet function), and cell cycle score (calculated by Seurat CellCyclescoring function)19.
Assembly: mm10
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Lung

growth_protocol: The C57BL/6J male mice were purchased from Orient Bio (Sungnam, Korea). The mice aged 8-10 weeks weighing 20-26 g were used in all experiments. All purchased animals were acclimated to the new environment for 1 week prior to the experiments. All animal experiments were approved by the Institutional Animal Care and Use Committee of the Yonsei University College of Medicine (Seoul, Korea) and were conducted in accordance with the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals. The probiotics containing Bifidobacterium lactis (IDCC 4301, Bifidus) were supplied by a company specializing in probiotic products (Ildong Pharmaceutical Co., Ltd., Seoul, Korea).

extract_protocol:
Following euthanasia, the chest was exposed, and the abdominal aorta and vena cava were cut above the liver. The left atrium was punctured, and the lungs were perfused with Heparin Sodium through the right ventricle until the lung color became completely white. Lungs were extracted, split into individual lobes, and briefly washed with Dulbecco's PBS. Dissected lungs were then digested in an enzyme mixture in the lung dissociation kit (Miltenyi Biotech, Bergisch Gladbach, Germany) at 37 °C by gentleMACS™ Octo Dissociator (Miltenyi Biotech, Bergisch Gladbach, Germany) as manufacturer’s protocol15.
After dissociation, up to 12,000 cells were targeted for cDNA preparation and put through the 10X Genomics Chromium Next GEM Single Cell 30v3.1 (Pleasanton, CA, USA) pipeline for library preparation. After cDNA preparation and GEM generation and clean-up, cDNA was quality checked and quantified using Agilent High Sensitivity D1000 system. Then, libraries were sequenced using Illumina sequencer.

value: Lung

value: male

value: Bifidus


title: Embryos collected from Day4 8pm Lif-floxed uterus


title: patch-seq sample_S075

description: patchseq.mtx.csv


title: C_1

description: without acarbose stimulation

value: BMDM

value: WT


title: C57BL6_ARDS_1

description: 10x Genomics

value: ARDS


title: Patient239532_CD_Surgery_LPT


title: Patient239532_CD_Surgery_PBT


title: Day4 8pm Lif eKO uterine luminal layer, after rLif treated

source_name: uterus

value: uterus

value: Lif-floxed/floxed Ltf-Cre/+

value: rLif


title: patch-seq sample_S074

description: patchseq.mtx.csv

value: cochlear nucleus


title: Patient284623_CD_Surgery_LPT

value: Crohn's disease

value: Surgery


title: C57BL6_NVC_1

description: 10x Genomics

value: NVC


title: Patient225673_CD_Surgery_PBT

value: peripheral blood T cell


title: Day4 8pm Lif eKO uterine luminal layer


title: patch-seq sample_S073

description: patchseq.mtx.csv


title: Embryos collected from Day4 8pm Lif eKO uterus, after rLif treated

value: embryos

value: Lif-floxed/+


title: D381T24: DC_gRNA_Ctrl_LPS_2h_cohortC3

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
fastq files were aligned to mouse reference genome mm10 using STAR
BAM files resulting from the alignments were summarized to genes or TEs counts using analyzeRepeats from HOMER (raw counts + FPKM)
Expression data was normalized using DESeq2 algorithm
Differentially expressed genes or TEs (adjusted p-values <= 0.05) were identified using DESeq2 R package
Genome_build: mouse reference genome mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each Sample

source_name: RAW264.7 Macrophages

growth_protocol: 1.5-2x106 BMDCs or RAW264.7 macrophags/well were plated in 6-well untreated dishes and placed in a 5% CO2 37 °C incubator

extract_protocol:
RNA was first precipitated with Trizol according to the manufacturer's instructions, washed with ethanol and the pellet air-dried before in-solution DNAse (Quiagen) treatment for 30 minutes at room tempurature. DNAse-treated RNA was then column-purified using the RNA Mini kit from Quiagen and eluted in 30µl of nuclease-free H2O.
PolyA+ RNA libraries were prepared using the TruSeq Stranded mRNA kit from Illumina

treatment_protocol: BMDCs were either left unstimulated, or stimulated with LPS (100 ng/mL) for the indicated times

tag: background strain

value: BALB/c

value: RAW264.7 Macrophages

tag: stimulation

value: LPS

value: IfnarWT

value: TrifWT


title: patch-seq sample_S072

description: patchseq.mtx.csv


title: Patient225673_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: D381T23: DC_gRNA_Ctrl_LPS_2h_cohortC2


title: Day4 8pm Lif-floxed uterine luminal layer

value: Lif-floxed/floxed

value: PBS


title: Patient283588_CD_Surgery_PBT


title: D381T22: DC_gRNA_Ctrl_LPS_2h_cohortC1


title: patch-seq sample_S076

description: patchseq.mtx.csv


title: Patient226011_CD_PostSurgery_PBT

value: PostSurgery


title: patch-seq sample_S070

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 84

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

data_processing:
PISA (v0.7) was employed to filter and demultiplex DNBelab C4 RNA-seq raw sequencing reads and STAR (v2.6.1a) was used to align these reads. For alignment, a modified GTF file of the Macaca_fascicularis_5.0 genome was used to involve both introns and exons items. Next, sambamba (v0.7) was performed to sort the aligned sequences.
Assembly: Macaca_fascicularis_5.0
Supplementary files format and content: The Market Exchange (MEX) format was used to represent the UMI counts sparse matrix of the cell to the gene.

organism: Macaca fascicularis

source_name: Brain

extract_protocol:
The nuclear suspension was prepared into droplets using DNBelab C series single-cell library preparation kit (MGI, #1000021082, China) and cell lysis as well as mRNA capture were finished by magnetic beads in the droplets.
The DNBelab C series single-cell library preparation kit (MGI, #1000021082, China) was applied to prepare the snRNA-seq library for the DNBelab C4 RNA-seq analysis based on droplet technology.

value: Brain


title: patch-seq sample_S071

description: patchseq.mtx.csv

value: cochlear nucleus


title: D381T21: DC_gRNA_Ctrl_LPS_0h_cohortC3


title: snRNA-seq of Macaque brain sample 85


title: Patient283588_CD_Surgery_LPT

value: Crohn's disease


title: Patient283311_CD_Surgery_PBT

value: Surgery


title: D381T20: DC_gRNA_Ctrl_LPS_0h_cohortC2


title: snRNA-seq of Macaque brain sample 83


title: patch-seq sample_S068

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 82


title: patch-seq sample_S069

description: patchseq.mtx.csv


title: D381T19: DC_gRNA_Ctrl_LPS_0h_cohortC1


title: Patient283311_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 81


title: patch-seq sample_S067

description: patchseq.mtx.csv


title: D381T18: DC_gRNA_2_LPS_2h_cohortC3


title: snRNA-seq of Macaque brain sample 80


title: Patient263335_CD_Surgery_PBT


title: D381T17: DC_gRNA_2_LPS_2h_cohortC2


title: patch-seq sample_S065

description: patchseq.mtx.csv


title: Patient263335_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 79


title: patch-seq sample_S066

description: patchseq.mtx.csv


title: D381T16: DC_gRNA_2_LPS_2h_cohortC1


title: Patient232640_CD_Surgery_PBT


title: patch-seq sample_S063

description: patchseq.mtx.csv


title: D381T14: DC_gRNA_2_LPS_0h_cohortC2


title: snRNA-seq of Macaque brain sample 76


title: Patient263288_CD_Surgery_PBT


title: patch-seq sample_S064

description: patchseq.mtx.csv


title: patch-seq sample_S062

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 77


title: Patient232640_CD_Surgery_LPT


title: Patient263288_CD_Surgery_LPT


title: patch-seq sample_S061

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 75


title: D381T15: DC_gRNA_2_LPS_0h_cohortC3


title: snRNA-seq of Macaque brain sample 74


title: Patient263279_CD_Surgery_PBT


title: patch-seq sample_S060

description: patchseq.mtx.csv


title: D381T12: DC_gRNA_1_LPS_2h_cohortC3


title: D381T13: DC_gRNA_2_LPS_0h_cohortC1


title: D381T11: DC_gRNA_1_LPS_2h_cohortC2


title: snRNA-seq of Macaque brain sample 73


title: Patient263279_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 78


title: patch-seq sample_S059

description: patchseq.mtx.csv


title: D381T10: DC_gRNA_1_LPS_2h_cohortC1


title: Patient226867_CD_Surgery_PBT


title: patch-seq sample_S058

description: patchseq.mtx.csv


title: Patient263273_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 72


title: D381T09: DC_gRNA_1_LPS_0h_cohortC3


title: snRNA-seq of Macaque brain sample 71


title: D381T08: DC_gRNA_1_LPS_0h_cohortC2


title: snRNA-seq of Macaque brain sample 70


title: Patient232763_CD_Surgery_PBT_Duplicate

tag: duplicate

value: Duplicate


title: Patient263273_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 69


title: D381T07: DC_gRNA_1_LPS_0h_cohortC1


title: D273T29: DC_MyD88KO_TrifWT_LPS_4h_cohort3

source_name: bone marrow derived dendritic cells

value: bone marrow derived dendritic cells


title: patch-seq sample_S055

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 68


title: patch-seq sample_S056

description: patchseq.mtx.csv


title: patch-seq sample_S054

description: patchseq.mtx.csv


title: Patient232763_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 67


title: D273T13: DC_MyD88WT_TrifWT_LPS_2h_cohort3


title: Patient232763_CD_Surgery_PBT

value: peripheral blood T cell


title: D273T14: DC_MyD88WT_TrifWT_LPS_4h_cohort3


title: Patient225972_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 66


title: patch-seq sample_S051

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 65


title: Patient225972_CD_Surgery_LPT


title: patch-seq sample_S049

description: patchseq.mtx.csv


title: D273T33: DC_MyD88WT_TrifWT_UT_0h_cohort1

value: UT


title: D273T35: DC_MyD88WT_TrifWT_UT_0h_cohort3


title: patch-seq sample_S057

description: patchseq.mtx.csv


title: Patient262684_CD_Surgery_PBT


title: D273T5: DC_MyD88WT_TrifWT_UT_0h_cohort2


title: patch-seq sample_S047

description: patchseq.mtx.csv


title: patch-seq sample_S053

description: patchseq.mtx.csv


title: D273T46: DC_MyD88WT_TrifKO_LPS_2h_cohort2

value: TrifKO


title: snRNA-seq of Macaque brain sample 63


title: snRNA-seq of Macaque brain sample 62


title: Patient225245_CD_Surgery_PBT


title: D273T37: DC_MyD88WT_TrifWT_LPS_2h_cohort2


title: Patient225245_CD_Surgery_LPT


title: Patient262038_CD_PostSurgery_PBT


title: snRNA-seq of Macaque brain sample 64


title: patch-seq sample_S044

description: patchseq.mtx.csv


title: patch-seq sample_S046

description: patchseq.mtx.csv


title: D273T24: DC_MyD88KO_TrifWT_LPS_4h_cohort2


title: Patient262219_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 61


title: patch-seq sample_S045

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 59


title: patch-seq sample_S043

description: patchseq.mtx.csv


title: D273T47: DC_MyD88WT_TrifKO_LPS_2h_cohort3


title: snRNA-seq of Macaque brain sample 58


title: patch-seq sample_S048

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 57


title: Patient225888_CD_Surgery_PBT


title: D273T1: DC_MyD88WT_TrifWT_UT_0h_cohort1


title: Patient262684_CD_Surgery_LPT


title: Patient262219_CD_Surgery_LPT


title: patch-seq sample_S042

description: patchseq.mtx.csv


title: D273T50: DC_MyD88WT_TrifKO_LPS_4h_cohort3


title: snRNA-seq of Macaque brain sample 60


title: Patient225888_CD_Surgery_LPT


title: D273T34: DC_MyD88WT_TrifWT_UT_0h_cohort2


title: snRNA-seq of Macaque brain sample 56


title: D273T41: DC_MyD88WT_TrifWT_LPS_4h_cohort3


title: patch-seq sample_S039

description: patchseq.mtx.csv


title: patch-seq sample_S040

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 55


title: D273T45: DC_MyD88WT_TrifKO_LPS_2h_cohort1


title: Patient261995_CD_PostSurgery_PBT


title: patch-seq sample_S038

description: patchseq.mtx.csv


title: D273T40: DC_MyD88WT_TrifWT_LPS_4h_cohort2


title: Patient238832_CD_Surgery_PBT_Duplicate


title: patch-seq sample_S037

description: patchseq.mtx.csv


title: D273T49: DC_MyD88WT_TrifKO_LPS_4h_cohort2


title: Patient238832_CD_Surgery_PBT


title: patch-seq sample_S036

description: patchseq.mtx.csv


title: Patient238832_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 51


title: D273T38: DC_MyD88WT_TrifWT_LPS_2h_cohort3


title: D273T23: DC_MyD88KO_TrifWT_LPS_2h_cohort2


title: patch-seq sample_S034

description: patchseq.mtx.csv


title: patch-seq sample_S041

description: patchseq.mtx.csv


title: Patient226011_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 50


title: Patient226800_CD_PostSurgery_PBT


title: D273T42: DC_MyD88WT_TrifKO_UT_0h_cohort1


title: snRNA-seq of Macaque brain sample 53


title: snRNA-seq of Macaque brain sample 54


title: snRNA-seq of Macaque brain sample 49


title: Patient226011_CD_Surgery_LPT


title: patch-seq sample_S032

description: patchseq.mtx.csv


title: patch-seq sample_S033

description: patchseq.mtx.csv


title: D273T44: DC_MyD88WT_TrifKO_UT_0h_cohort3


title: D273T17: DC_MyD88KO_TrifWT_UT_0h_cohort1


title: snRNA-seq of Macaque brain sample 48


title: Patient239153_CD_PostSurgery_PBT


title: patch-seq sample_S031

description: patchseq.mtx.csv


title: Patient262120_CD_Surgery_LPT


title: Patient262120_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 47


title: D273T11: DC_MyD88WT_TrifWT_UT_0h_cohort3


title: snRNA-seq of Macaque brain sample 46


title: patch-seq sample_S028

description: patchseq.mtx.csv


title: Patient226863_CD_PostSurgery_PBT


title: D273T36: DC_MyD88WT_TrifWT_LPS_2h_cohort1


title: Patient226800_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 45


title: snRNA-seq of Macaque brain sample 44


title: D273T30: DC_MyD88KO_TrifWT_LPS_2h_cohort3


title: patch-seq sample_S027

description: patchseq.mtx.csv


title: patch-seq sample_S025

description: patchseq.mtx.csv


title: D273T8: DC_MyD88WT_TrifWT_LPS_4h_cohort2


title: Patient226800_CD_Surgery_LPT


title: patch-seq sample_S024

description: patchseq.mtx.csv


title: Patient226712_CD_PostSurgery_PBT


title: snRNA-seq of Macaque brain sample 43


title: patch-seq sample_S029

description: patchseq.mtx.csv


title: Patient262042_CD_Surgery_PBT


title: patch-seq sample_S023

description: patchseq.mtx.csv


title: D273T27: DC_MyD88KO_TrifWT_UT_0h_cohort3


title: patch-seq sample_S021

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 42


title: D273T20: DC_MyD88KO_TrifWT_LPS_4h_cohort1


title: D273T3: DC_MyD88WT_TrifWT_LPS_2h_cohort1


title: snRNA-seq of Macaque brain sample 41


title: snRNA-seq of Macaque brain sample 39


title: Patient235932_CD_Surgery_PBT


title: patch-seq sample_S020

description: patchseq.mtx.csv


title: Patient262042_CD_Surgery_LPT


title: patch-seq sample_S019

description: patchseq.mtx.csv


title: D273T39: DC_MyD88WT_TrifWT_LPS_4h_cohort1


title: Patient262038_CD_Surgery_PBT


title: patch-seq sample_S016

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 37


title: D273T19: DC_MyD88KO_TrifWT_LPS_2h_cohort1


title: Patient235932_CD_Surgery_LPT


title: patch-seq sample_S017

description: patchseq.mtx.csv


title: D273T48: DC_MyD88WT_TrifKO_LPS_4h_cohort1


title: Patient262038_CD_Surgery_LPT


title: patch-seq sample_S015

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 36


title: Patient262027_CD_Surgery_PBT


title: D273T21: DC_MyD88KO_TrifWT_UT_0h_cohort2


title: snRNA-seq of Macaque brain sample 34


title: D273T4: DC_MyD88WT_TrifWT_LPS_4h_cohort1


title: snRNA-seq of Macaque brain sample 40


title: Patient225315_CD_Surgery_PBT


title: D273T43: DC_MyD88WT_TrifKO_UT_0h_cohort2


title: patch-seq sample_S013

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 33


title: patch-seq sample_S012

description: patchseq.mtx.csv


title: Patient225315_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 32


title: snRNA-seq of Macaque brain sample 38


title: Patient261953_CD_Surgery_PBT


title: patch-seq sample_S011

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 31


title: D296T33: DC_Suv39h1WT_IfnarWT_UT_0h_cohort2


title: D296T35: DC_Suv39h1KO_IfnarWT_UT_0h_cohort2


title: patch-seq sample_S008

description: patchseq.mtx.csv


title: patch-seq sample_S014

description: patchseq.mtx.csv


title: patch-seq sample_S010

description: patchseq.mtx.csv


title: Patient261953_CD_Surgery_LPT


title: patch-seq sample_S007

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 30


title: Patient262027_CD_Surgery_LPT


title: D296T37: DC_Suv39h1WT_IfnarKO_UT_0h_cohort2

value: IfnarKO


title: Patient261995_CD_Surgery_LPT


title: D296T25: DC_Suv39h1WT_IfnarKO_UT_0h_cohort1


title: snRNA-seq of Macaque brain sample 28


title: D296T29: DC_Suv39h1KO_IfnarKO_UT_0h_cohort1


title: snRNA-seq of Macaque brain sample 29


title: Patient261995_CD_Surgery_PBT


title: D296T23: DC_Suv39h1KO_IfnarWT_UT_0h_cohort1


title: Patient261980_CD_Surgery_PBT


title: Patient261980_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 26


title: D296T21: DC_Suv39h1WT_IfnarWT_UT_0h_cohort1


title: patch-seq sample_S004

description: patchseq.mtx.csv


title: D296T09: DC_Suv39h1KO_IfnarKO_UT_0h_cohort3


title: patch-seq sample_S003

description: patchseq.mtx.csv


title: Patient227015_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 25


title: D296T05: DC_Suv39h1WT_IfnarKO_UT_0h_cohort3


title: Patient227015_CD_Surgery_LPT


title: patch-seq sample_S002

description: patchseq.mtx.csv


title: Patient261956_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 24


title: D296T03: DC_Suv39h1KO_IfnarWT_UT_0h_cohort3


title: snRNA-seq of Macaque brain sample 35


title: snRNA-seq of Macaque brain sample 23


title: single nucleus sample_p3s2


title: patch-seq sample_S006

description: patchseq.mtx.csv


title: Patient261956_CD_Surgery_LPT


title: D296T01: DC_Suv39h1WT_IfnarWT_UT_0h_cohort3


title: D296T41: DC_Suv39h1KO_IfnarKO_UT_0h_cohort2


title: Patient239153_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 22


title: snRNA-seq of Macaque brain sample 27


title: single nucleus sample_p3s1


title: Xrcc6-cKO_2

city: Shanghai

first: Qianru

last: Huang

address: 227 South Chongqing Road Shanghai

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.6).
Bowtie2(v2.3.4.3) was applied to align the clean reads to the reference  gene set.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GRCm38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Regulatory T cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture’s protocols.

value: Regulatory T cells

value: Xrcc6 knockout

value: Lung tumor model


title: patch-seq sample_S005

description: patchseq.mtx.csv


title: snRNA-seq of Macaque brain sample 20


title: snRNA-seq of Macaque brain sample 21


title: snRNA-seq of Macaque brain sample 19


title: single nucleus sample_p2s2


title: WT_3

value: WT


title: Patient226712_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: snRNA-seq of Macaque brain sample 18


title: Patient226712_CD_Surgery_PBT


title: Patient239153_CD_Surgery_LPT


title: Patient226190_CD_Surgery_PBT


title: single nucleus sample_p1s1


title: snRNA-seq of Macaque brain sample 17


title: WT_1


title: WT, Ad

city: Cambridge

first: Michael

middle: W

last: Stubna

state: MA

address: 455 Main St

institute: Whitehead Institute

data_processing:
Reads were aligned to the C. elegans genome (WS245) using STAR v2.7.1a (Dobin et al., 2013) with parameters “ --outFilterMultimapNMax 1 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate”.
Uniquely mapping reads were assigned to genes using featureCounts (Liao et al., 2014) and parameters “-s 2 -F GTF -t CDS”, as well as C. elegans WS245 genome annotations downloaded from Wormbase (www.wormbase.org) and converted from gff3 format to gtf format with the gffread tool.
Raw read counts were merged into a table and inputted to DESeq2 for differential expression analysis. Normalized mRNA abundance was calculated as counts per million mRNA-matching reads (CPM), without pseudocounting.
Assembly: WBcel235/WS245
Supplementary files format and content: Excel file includes raw mRNA counts for each Sample.

organism: Caenorhabditis elegans

growth_protocol: Worms were cultured on standard NGM agar seeded with E. coli OP50 at 20 degrees C.

extract_protocol:
L1 larvae were collected in a starved state following the overnight hatching period. For adult worms, starved L1 were plated on NGM agar with food and grown at 20 degrees C for approximately 68 h
Poly(A)+ RNA-seq libraries were prepared from 3 µg total RNA from either late embryos or L1 larvae (for analysis of miR-35–42 target mRNAs) or from 10 µg total RNA from gravid adults (for analysis of protein-coding genes near dysregulated piRNAs on Chromosome IV) using the stranded NEXTFLEX Rapid Directional RNA-seq kit (Perkin Elmer).

treatment_protocol: Worms were synchronized by treatment with an alkaline bleach solution and allowed to hatch overnight into M9 buffer in the absence of food.

tag: developmental stage

value: Gravid adult

value: wild-type


title: tm2321, Ad


title: WT_2


title: Patient225439_CD_Surgery_PBT


title: snRNA-seq of Macaque brain sample 16

value: Brain


title: snRNA-seq of Macaque brain sample 52


title: Patient226190_CD_Surgery_LPT


title: tm2321, L1, rep2

value: L1 larva


title: put2.mock2.H3

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

data_processing:
For RNA-seq quality analysis, the FastQC v0.11.9 tool was used (Andrews, S. 2010; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The minimum read Phred score for the reads was 33. All reports from FastQC were collected using MultiQC v1.14. Neither adapter bias nor poor quality at the 3' end was evident in the RNA-seq data. There was no need to process the fragments. Then, the Hisat v2.1.0 tool was used to map fastq files to the Arabidopsis genome. R internal scripts were used to carry out the Hisat2 mapping statistics process [https://www.r-project.org/]. The featureCounts tool from the SubRead package was used to quantify the mapped fragments (Liao et al. 2019). Using these quantifications, an internal R script [R Core Team (2022)] produced a counts matrix.
Assembly: Arabidopsis_thaliana.TAIR10.52
Supplementary files format and content: Data frame separated by tabs

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
Total RNA was isolated using the TRI Reagent® method (Sigma-Aldrich) following SAR assays. First, the lower (8, 9, and 10) leaves were inoculated with Pst (OD600=0.005) to induce local priming (SAR) or mock (MgCl2 10 mM, pH 7.0), and 24 hpi the uninoculated upper leaves (13, 14, and 15) were collected for RNA extraction. Then, 48 h after primary infection, upper leaves (13, 14, and 15) were systemically challenged with Pst (OD600=0.0005). These systemically challenged leaves were collected for RNA extraction at 24 hpi.
Three biological replicates, each containing over 20 µg total RNA, were submitted to GENEWIZ® (https://www.genewiz.com/) for standard mRNA sequencing (by poly-A selection) using the Illumina HiSeq platform with a 2x150 bp configuration.

value: Leaf


title: single nucleus sample_p2s1

value: cochlear nucleus


title: put2.mock2.H1


title: snRNA-seq of Macaque brain sample 15


title: Patient227596_CD_Surgery_PBT

value: Crohn's disease

value: Surgery


title: put2.mock2.H2


title: WT, L1, rep1


title: Xrcc6-cKO_1


title: put2.mock.D3

value: mock


title: put2.mock.D2


title: Patient227596_CD_Surgery_LPT


title: tm2321, L1, rep1


title: snRNA-seq of Macaque brain sample 14


title: snRNA-seq of Macaque brain sample 13


title: snRNA-seq of Macaque brain sample 12


title: L1, ju699, rep2

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

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


title: put2.mock.D1


title: snRNA-seq of Macaque brain sample 10


title: snRNA-seq of Macaque brain sample 9


title: WT, L1, rep2


title: L1, ju699, rep1


title: L1, WT, rep2 for ju699


title: Patient225601_CD_Surgery_LPT


title: Patient225439_CD_Surgery_LPT


title: put2.Pst2.G3


title: snRNA-seq of Macaque brain sample 8


title: Patient225302_CD_Surgery_PBT

value: peripheral blood T cell


title: Patient225302_CD_Surgery_LPT


title: L1, WT, rep1 for ju699


title: snRNA-seq of Macaque brain sample 7


title: glp-4 tm2321 adult, rep2

value: Conditionally germlineless adult raised at 25C


title: put2.Pst2.G2


title: snRNA-seq of Macaque brain sample 6


title: Patient226649_CD_Surgery_PBT


title: Xrcc6-cKO_3

value: Regulatory T cells


title: glp-4 tm2321 adult, rep1


title: put2.Pst.C3

value: Pst


title: Patient224667_CD_PostSurgery_PBT

value: PostSurgery


title: snRNA-seq of Macaque brain sample 11


title: snRNA-seq of Macaque brain sample 5


title: glp-4 adult, rep2


title: put2.Pst.C2


title: glp-4 adult, rep1


title: put2.Pst.C1


title: Adult, tm2321, rep2


title: Patient226001_CD_Surgery_LPT


title: snRNA-seq of Macaque brain sample 4


title: Col0.mock2.F3


title: Patient226001_CD_Surgery_PBT


title: Adult, tm2321, rep1


title: Col0.mock2.F2


title: Patient226432_CD_PostSurgery_PBT


title: Adult, WT, rep1


title: Col0.mock2.F1


title: snRNA-seq of Macaque brain sample 1


title: Adult, WT, rep2


title: Patient226946_CD_PostSurgery_PBT


title: snRNA-seq of Macaque brain sample 3


title: Patient225601_CD_Surgery_PBT


title: Patient226649_CD_Surgery_LPT


title: Patient225781_CD_Surgery_PBT


title: L4, tm2321, rep2

value: L4 larva


title: Patient225781_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: Col0.mock.B2


title: L4, tm2321, rep1


title: Col0.mock.B1


title: Col0.mock.B3


title: Patient226536_CD_PostSurgery_PBT


title: L4, WT, rep2


title: Col0.Pst2.E3


title: Patient226262_CD_Surgery_PBT


title: L4, WT, rep1


title: Ceramic_dynamic_StemSpan-AOF_D24_ChipM3

city: Basel

first: Daniel

last: Marbach

address: Grenzacherstrasse 124

department: pRED Pharmaceutical Sciences

institute: F. Hoffmann - La Roche Ltd

data_processing:
Base calling was performed with BCL to FASTQ file converter bcl2fastq2 version 2.20.0 (Illumina).
Paired-end reads were mapped onto the human genome (build hg38) with read aligner STAR version 2.7.10a using default mapping parameters.
Read counts for all RefSeq genes were computed using featureCounts version 2.0.1.
Assembly: hg38
Supplementary files format and content: The file raw_counts.txt provides the gene read counts for all samples in tab-separated value format. The first line is a header. The first two columns provide the Entrez Gene ID and Gene Symbol, followed by one column for each sample.

source_name: primary human stromal cells

growth_protocol: Mesenchymal stromal cells were grown in Mesencult-ACF Plus (StemCell Technologies) during monolayer expansion and the first 8 days of 3D culivation on ceramic scaffolds, with media exchanges every two to three days.

extract_protocol:
The scaffolds were washed with PBS and total RNA was extracted using the NucleoSpin 8 RNA Core Kit (Macherey-Nagel, Düren, Germany). RNA was quantified by spectrophotometric analysis using the NanoDrop 2000 UV-vis instrument (Thermo Fisher Scientific) and quality controlled by capillary electrophoresis on the 2100 Bioanalyzer Instrument (Agilent Technologies, Santa Clara, CA, USA) using the RNA 6000 Nano Kit (Agilent Technologies).
Paired-end (PE) sequencing libraries were prepared from 100 ng of RNA using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Sequencing libraries were quantified using the Qubit dsDNA High Sensitivity Kit (Thermo Fisher Scientific) on Qubit 4.0 Fluorometer (Thermo Fisher Scientific)

treatment_protocol: The seeded ceramic scaffolds were then either continuously cultured in Mesencult-ACF Plus (StemCell Technologies)  in 24 well plates or switched to StemSpan AOF (StemCell Technologies) cell culture medium supplemented with 10 ng/mL TPO, 25 ng/mL FLT-3L, 20 ng/mL SCF, 20 ng/mL GM-CSF (all Peprotech), 10 ng/mL IL-3 (Miltenyi Biotec), 100 µg/mL holo-transferrin (Sigma Aldrich, St. Louis, MO, USA), 100 IU/mL penicillin + 100 µg/mL streptomycin and 5 µg/mL gentamicin (both Corning) and either cultured under static culture conditions in 24-well plates or placed in the microfluidic system under flow for 24 days with media exchanges every two to three days.

value: primary human stromal cells

value: 3D scaffold cultivation + hematopoietic cell culture medium + flow

tag: condition

value: dynamic chip

tag: timepoint

value: day 24

tag: culture medium_at_sampling

value: StemSpan-AOF


title: Ceramic_dynamic_StemSpan-AOF_D24_ChipM6


title: put2.Pst2.G1

value: Leaf


title: Patient226262_CD_Surgery_LPT

value: Crohn's disease


title: Col0.Pst2.E2


title: Ceramic_static_MesenCult-ACF Plus_D24_3

value: 3D scaffold cultivation

value: static well plate

value: MesenCult-ACF Plus


title: Col0.Pst2.E1


title: L3, tm2321, rep2

value: Whole animal

value: L3 larva


title: Ceramic_static_MesenCult-ACF Plus_D24_2


title: Patient226218_CD_Surgery_PBT

value: peripheral blood T cell

value: Surgery


title: Col0.Pst.A3

value: Pst


title: Ceramic_static_MesenCult-ACF Plus_D24_1


title: L3, WT, rep2

value: wild-type


title: Patient226218_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: Patient226260_CD_Surgery_PBT


title: Col0.Pst.A2


title: L3, WT, rep1


title: Col0.Pst.A1


title: Patient226260_CD_Surgery_LPT


title: Ceramic_static_StemSpan-AOF_D24_2

value: primary human stromal cells

value: 3D scaffold cultivation + hematopoietic cell culture medium


title: L2, tm2321, rep2

value: L2 larva


title: L3, tm2321, rep1


title: L2, tm2321, rep1


title: Ceramic_static_MesenCult-ACF Plus_D0_2

value: day 0


title: IFNB, Insulin, replicate1

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

tag: 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: L2, WT, rep2


title: Ceramic_static_MesenCult-ACF Plus_D0_1

tag: cell type

value: 3D scaffold cultivation

value: static well plate

value: MesenCult-ACF Plus


title: snRNA-seq of Macaque brain sample 2

value: Brain


title: Ceramic_static_MesenCult-ACF Plus_D0_3


title: Patient227440_CD_Surgery_LPT

value: Crohn's disease

value: Surgery


title: Patient226536_CD_Surgery_LPT


title: Monolayer_static_MesenCult-ACF Plus_D-8

value: 2D cultivation

value: day -8


title: Patient226536_CD_Surgery_PBT

value: peripheral blood T cell


title: L1, tm2321, rep1

value: Whole animal

value: L1 larva

tag: genotype


title: Patient225295_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: L1, WT, rep2

value: wild-type


title: L2, WT, rep1

value: L2 larva


title: IFNG, TNFA, TGFB, replicate1

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

tag: treatment


title: sgMYB_rep2 [RNA-seq]

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Assembly: hg19
Supplementary files format and content: tab delimited text file containing TPM values for each sample

extract_protocol:
RNA was extracted using the RNEasy micro kit following manufacturer's guidelines
RNA libraries for RNA-seq were prepared using Truseq library prep protocol with ribodepletion (Ribo-zero) step

value: T-ALL

value: sgMYB


title: sgMYB_rep1 [RNA-seq]


title: Patient226425_CD_Surgery_LPT

tag: tissue


title: L1, tm2321, rep2


title: Ceramic_static_StemSpan-AOF_D24_1

value: primary human stromal cells

value: 3D scaffold cultivation + hematopoietic cell culture medium

value: static well plate

value: day 24

value: StemSpan-AOF


title: Late embryo, tm2321 rep 2

value: Late embryo


title: sgCTRL_rep1 [RNA-seq]

value: sgCTRL


title: Patient239853_CD_Surgery_PBT

value: peripheral blood T cell

tag: phenotype

value: Crohn's disease

value: Surgery


title: Patient225295_CD_Surgery_PBT

tag: time


title: L1, WT, rep1

value: Whole animal

value: L1 larva

value: wild-type


title: Late embryo, tm2321, rep1


title: Patient239853_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: IA_15, H3K27ac (HiChIP)

library_source: genomic

data_processing:
Read alignment: The Hi-C reads were aligned by the BWA aligner (v0.7.17). Params: "-A1 -B4 -E50 -L0"
Filtering: Mapped reads were filtered by the GenomicTools tools-hic filter command integrated in HiC-bench for known artifacts of the Hi-C protocol.
Valid pairs: We used the accepted intra-chromosomal read-pairs (‘ds.accepted intra’) and filtered out multi-mapped reads (‘multihit’), read-pairs with only one mappable read (‘single sided’), duplicated read-pairs (‘ds.duplicate’), low mapping quality reads (MAPQ < 20), read-pairs resulting from self-ligated fragments.
Normalization: Contact matrices were generated using the HiC-Bench pipeline and ICE correction was performed using the algorithm detailed in Imakaev et. al (2012) publication. For this, we used the matrix-ic functionality built into HiC-bench which uses the ‘mirnylib.numutils’ python library.
Loop calling: We used the HiC valid pairs with the FitHiC tool (v2.0.7) to identify significant interactions. Parameters:  resolution=10kb ; q-value <= 0.01; Min. distance=30kb; Max. distance=1Mb.
Virtual4C: HiC-Bench ‘virtual4C’ pipeline was used to compute the interactions of each selected viewpoint in a roll-window fashion. We summed the valid read pairs in a 5 kb area centered at 200 bp bins that covered the area of +-2.5 Mb from the viewpoint (25k bins per viewpoint). The interactions were normalized by the total number of valid pairs of the sample.
Assembly: hg19
Supplementary files format and content: The ‘*_filtered.reg.txt.gz’ files contains all the HiChIP valid intra and inter-chromosomal read pairs.
Library strategy: HiChIP

molecule: genomic DNA

source_name: Peripheral blood

extract_protocol:
Chromatin was extracted and processed by Arima HiC+ kit following manufacturer's instructions
HiChIP libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit

value: Peripheral blood

tag: chip antibody


title: Late embryo, WT, rep1

tag: strain


title: IA_06, H3K27ac (HiChIP)

source_name: Bone marrow aspirate

value: Bone marrow aspirate

value: ETP-ALL


title: ALL_p17, H3K27ac (HiChIP)

value: T-ALL


title: Patient226434_CD_Surgery_PBT

source_name: peripheral blood T cell


title: Patient226434_CD_Surgery_LPT

source_name: lamina propria mucosa-derived T cell


title: Late embryo, WT, rep 2


title: Early embryo, tm2321, rep 2

value: Early embryo


title: Patient226425_CD_Surgery_PBT


title: Patient224667_CD_Surgery_PBT


title: T-ALL_PATENL [scATAC-Seq]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and peak calling were made using the Cell Ranger ATAC software v1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow Aspirate

extract_protocol:
Nuclei were extracted using 10X genomics Chromium Single Cell ATAC Reagent Kits (v1.1 Chemistry) (lysis step for 2 minutes on ice)
Library construction was performed according to 10X genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 User Guide, Rev G

value: Bone Marrow Aspirate

value: primary sample


title: sgCTRL_rep2 [RNA-seq]


title: Early embryo, tm2321, rep1


title: Patient224667_CD_Surgery_LPT


title: T-ALL_p20 [scATAC-Seq]

description: 10x Genomics

value: Patient-derived xenograft


title: Early embryo, WT, rep1


title: Patient226946_CD_Surgery_PBT


title: Patient227440_CD_PostSurgery_PBT

value: PostSurgery


title: ETP-ALL_p16 [scATAC-Seq]

description: 10x Genomics


title: T-ALL_p09 [scATAC-Seq]

description: 10x Genomics


title: Patient226946_CD_Surgery_LPT


title: Early embryo, WT, rep2


title: Mnase-ChIP H3K4me3 antisense

value: Ovarian Somatic Cells (OSC)

value: antisense TF OSC

value: antisense TF


title: Patient226432_CD_Surgery_PBT

value: peripheral blood T cell

value: Crohn's disease

value: Surgery


title: ETP-ALL_IA-06 [scATAC-Seq]

description: 10x Genomics


title: Mnase-ChIP H3K4me3 sense

value: sense TF OSC

value: sense TF


title: Mnase-ChIP H3K9me3 antisense


title: Patient226432_CD_Surgery_LPT

value: lamina propria mucosa-derived T cell


title: Mnase-ChIP H3K9me3 sense


title: T-ALL_PAWLSN [scATAC-Seq]

description: 10x Genomics


title: prostate epithelial cells, F_rep7

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

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

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


title: T cell electroporated with buffer only replicate 2

first: Keqiang

last: Xie

address: 625 Mount Auburn Street, Suite 105

institute: Full Circles Therapeutics, Inc.

data_processing:
CLC Genomics workbench
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file

source_name: Primary T cells

extract_protocol:
RNA were extracted from treated T cells RNAeasy kit (Qiange)
The mRNA was then purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490), processed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, E7770), followed by deep sequencing analysis using Illumina sequencing (2 × 150-base pair paired end; ~30G for each sample).

value: Primary T cells

value: Healthy volunteer

value: Electroporation only


title: T cell electroporated with buffer only replicate 3


title: Mnase-ChIP ni antisense

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.

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.


title: Mnase-ChIP ni sense


title: prostate epithelial cells, F_rep6


title: Mnase-ChIP input antisense


title: prostate epithelial cells, F_rep5


title: prostate epithelial cells, F_rep4


title: T cell electroporated with dsDNA donor template replicate 2

value: ds DNA only


title: T cell electroporated with buffer only replicate 1


title: prostate epithelial cells, F_rep3


title: T cell electroporated with cssDNA donor template replicate 3

value: cssDNA only


title: prostate epithelial cells, F_rep1


title: CAGE Piwi KD rep3 #2

value: Piwi-KD OSC

value: RNAi Piwi


title: T cell electroporated with cssDNA donor template replicate 2


title: prostate epithelial cells, F_rep2


title: prostate epithelial cells, F_rep8


title: CAGE Piwi KD rep2 #2

value: Ovarian Somatic Cells (OSC)


title: CHO-K1

city: Heidelberg

first: Elias

last: Böhl

address: Im Neuenheimer Feld 580

department: Divison of Epigenetics

country: Germany

institute: German Cancer Research Center (DKFZ)

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).

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

value: Chinese hamster ovary (CHO) cells


title: CAGE Piwi KD rep2 #1


title: T-ALL_p03 [scATAC-Seq]

institute: NYU Langone Health

description: 10x Genomics

value: Bone Marrow Aspirate

value: Patient-derived xenograft


title: CAGE Piwi KD rep1 #2


title: T cell electroporated with GFP mRNA replicate 3

value: mRNA only


title: Humira431


title: T cell electroporated with GFP mRNA replicate 2


title: prostate epithelial cells, E_rep5

value: Ptenpe{delta}/{delta} (E)


title: CHO_DXB11

value: CHO DXB11


title: prostate epithelial cells, E_rep2


title: T cell electroporated with cssDNA donor template replicate 1


title: Agarabi_CHO

value: Agarabi CHO


title: T cell electroporated with dsDNA donor template replicate 3


title: prostate epithelial cells, E_rep4

value: prostate


title: CHO_1-15


title: Mnase-ChIP input sense

value: sense TF OSC

value: sense TF


title: prostate epithelial cells, E_rep3


title: T cell electroporated with dsDNA donor template replicate 1

value: Primary T cells

value: Healthy volunteer


title: CAGE Piwi KD rep1 #1


title: CAGE EGFP KD rep3 #2

value: EGFP-KD OSC

value: RNAi EGFP


title: T cell electroporated with GFP mRNA replicate 1


title: FreeStyle_CHO-S

value: FreeStyle CHO-S


title: prostate epithelial cells, C_rep4

value: L-gp130peKI/KI (C)


title: CAGE EGFP KD rep2 #2

value: Ovarian Somatic Cells (OSC)


title: Human periosteal cell replicate 4, scRNA-seq

first: Dongsu

last: Park

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: 10x genomics

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

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).

value: Periosteum

value: Periosteal cells


title: CAGE EGFP KD rep3 #1


title: ExpiCHO-S

value: Ovary

value: ExpiCHO-S

value: Chinese hamster ovary (CHO) cells


title: prostate epithelial cells, C_rep5


title: prostate epithelial cells, E_rep1

value: Ptenpe{delta}/{delta} (E)


title: CAGE EGFP KD rep2 #1