title: whole heart, B6.Cg-Lepob/J wild type male, TAC, replicate 2, snRNAseq

city: LOS ANGELES

first: Jijun

last: Huang

address: 650 Charles E Young Dr S, CHS 36-100

department: Medicine

institute: UCLA

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggreattion were using Cell Ranger v5.0.0. (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole heart

extract_protocol:
Isolated hearts were processed to obtain nuclei using established protocol 1. In detail, after euthanasia fresh mouse heart were perfused by 15ml PBS with a winged infusion set with a 25g needle to ensure the complete elimination of blood cells. Next, hearts were washed three times in ice cold PBS and minced into small clusters (1-2mm width) on ice. The minced tissues were immediately transferred to an M-Tube (Miltenyi, 130-093-236) in Trition free lysis buffer and spined on a Miltenyi Biotec gentleMACS™ Dissociator (Miltenyi, 130-093-235) at the M-Tube program (1x Run) in 4 °C. After filtering of remaining tissue mass with a 40 um cell strainer (Corning, 352340), nuclei were precipitated by 1M Sucrose solution in lysis buffer with 0.05% Triton. Quality control for nuclei integrity were performed with DAPI staining and observed under Zeiss fluorescent microscope. The nuclei number was measured using Countess™ Cell Counter. A final suspension with concentration of 1200 nuclei/ul was processed for the following steps for single nuclei gene expression library preparation with 10x genomics NEXT GEM 3’ gene expression kit v3.1. Using 10X Genomics Chromium Controller system, we generated 8 snRNA libraries from four conditions (WT_Sham, WT TAC, OB Sham and OB TAC) and were sequenced on the same lane using Illumina NovaSeq6000 S4 at UCLA Technology Center for Genomics & Bioinformatics (TCGB).
Library was performed according to the manufacter's instructions (single cell 3' v3.1 protocl, 10x Genomics). Briefly, single nuclei were resuspended in the master mix and loaded together with partition oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the nuclear lysate contained in each single GEM was retrotranscripited to cDNA, which contains an lluminar R1 primer sequence, UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaened with Silane DynaBeads, amplified by PCR and the apropriated sied fragments with SPRIselet reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: whole heart

tag: treatment

value: TAC


title: whole heart, B6.Cg-Lepob/J wild type male, TAC, replicate 1, snRNAseq

status: Public on Jul 12 2024

type: SRA

state: CA

country: USA

description: 10x Genomics

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: 4C_mz_EKO_4

city: Paris

first: Nicola

last: Festuccia

address: 25-28 Rue du Docteur Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

description:
Trimmed
Gene_expression_resubmission.tsv

data_processing:
Single-end sequences (50-85bp, using 50bp sequencing kits) were generated using an Illumina Next-seq 500 or 2000 instruments. After trimming Illumina adapter sequences with cutadapt (3) using options -b CTGTCTCTTATA --minimum-length=1, reads were split in UMI containing or not with Julia (J. Bezanson, A. Edelman, S. Karpinski, V. Shah, Julia: “A fresh approach to numerical computing.” https://arxiv.org/abs/1411.1607; 2015), trimming 11bp after the sequence “AAGCAGTGGTATCAACGCAGAGTACGATC”. For UMI, reads were further processed in Julia to remove the invariant adapter sequence, extract the identifier, and the UMI/ transcript sequence pairs used to remove duplicates. Conventional or UMI reads were then aligned to the mm10 genome using STAR (A. Dobin et al., “STAR: ultrafast universal RNA-seq aligner. Bioinformatics” 29, 15-21; 2013) and quantified by RSEM (B. Li, C. N. Dewey, “RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.” BMC Bioinformatics 12, 323; 2011) through the RSEM-STAR pipeline,  using gencode.v25 annotations and additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.5” for conventional reads and “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 1” for UMI reads. RSEM estimated read counts per sample were rounded for use with DESeq2 (M. I. Love, W. Huber, S. Anders, “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biol 15, 550; 2014). Genes were considered as differentially expressed if their mean expression exceeded 10 TPM in at least one genotype for a given stage, and using a <> 1.5 fold change and <0.1 FDR cutoff.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Embryo

growth_protocol: Ex-vivo

extract_protocol:
Extraction and library preparation were performed in one reaction (see below)
The protocol employed is derived from FLASH-seq (V. Hahaut et al., “Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.” Nat Biotechnol 40, 1447-1451; 2022), with two main modifications: 1/ Genotyping primers are added during the cDNA amplification step; 2/ A phosphate group is added to the 3’ of the template switching primer to exclude the possibility it might prime DNA synthesis during the cDNA amplification step, which would result in tagging single transcripts with multiple UMI barcodes. Embryos were isolated and directly transferred by mouth pipetting to PCR tubes in 5ul of the following lysis solution: 0.1   μL Triton X-100 (10% v/v, Sigma-Aldrich, T8787); 1.2   μL dNTP mix (25 mM each, ThermoFisher Scientific, R1121); 0.46 μL 5’Bio-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, 100 μM (supplied by IDT). 0.46 μL 5’ Biotin-AGTGGTATCAACGCAGAGTAC G ATC NNNNNNNN rGrGrG-3′Phospate, 100 μM (supplied by IDT); 0.15 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.06 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 1       μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.45 μL dCTP (100 mM, Sigma-Aldrich, DNTP100); Water to 5 μL final. Notes (AGTGGTATCAACGCAGAGTAC is an suppression PCR sequence. Random Ns form the UMI tag, and ATC is a 3bp barcode that can be varied if multiple samples are to be mixed before tagmentation, and only UMI reads are considered. rGrGrG are required for template switching. The 3’ Phosphate inhibits priming in following steps). Tubes were incubated 3 min at 72C in a thermocycler, and immediately transferred on ice. RT-pcr was performed by adding 20ul of the following mix to each sample:1.19 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 4 μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.23 μL magnesium chloride (1 M, ThermoFisher Scientific, AM9530G); 0.48 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.25 uL Superscript IV Reverse Transcriptase (200 U/μL, ThermoFisher Scientific, 18091050); 12.5 μL KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502); Water to a final volume of 20 μL. Samples were incubated in a thermocycler set to execute the following programme: Hold at 50°C, and after placing tubes skip to 60 min at 50°C; 3 min at 90°C; Hold at 4°C. Tubes were transferred on ice and 0.5ul of a 100 uM solution of amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCAGTGGTATCAACGCAGAGTAC G) were added to each sample. 1ul of a solution of genotyping primers (see embryo genotyping section) at 10uM each was also added in each tube. Tubes were then transferred to a thermocycler, set to the following programme: Hold at 4°C and after placing tubes skip to 20 sec 98°C; 20 sec 64°C; 6 min 72°C; Followed by 20 cycles of: (20 sec 98°C; 20 sec 67°C ;6 min 72°C, adding 12 seconds per cycle); then hold at 4°C. Amplification products were purified using 1x volume of SPRI magnetic beads, eluting in 15 ul water. 1ul was set aside to perform a nested PCR for genotyping. Fragment size distribution was checked on a Genomic DNA Screentpape (Agilent Technologies, 5067-5365/6), with a typical lengths ranging from less than 1Kb to more than 10kb. For tagmentation, each sample was diluted to 150 pg/ul. 2 ul of diluted cDNA were mixed with 2ul of Amplicon Tagment Mix (ATM) and 4 μL of Tagment DNA Buffer (TD) from an Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024), and incubated for 8 min at 55°C, in a thermocycler. Tn5 was released from DNA by adding 2μL of Neutralization Buffer (NT), followed by a 5 min RT. Enrichment of UMI containing fragments in the tagmented DNA was performed by adding 5 μL of Nextera PCR Master Mix (NPM) and 1ul of 5 uM amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG AAGCAGTGGTATCAACGCAGAGTAC G, as before). KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502) can substitute the Nextera PCR Master Mix, adapting volumes as required. Tubes were incubated as follows: 72°C for 3 min; 95°C for 30 sec; followed by 10 cycles of linear enrichment PCR: (95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); then hold at 4°C. 4 ul of a 2.5uM solution of each of the following amplification primers were added on ice: Universal primer AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG; Indexed primer CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG. The 8 Ns are to be replaced with the Illumina index sequence of choice. Tubes were returned to the thermocycler held at 4°C and then subjected to 14 iterations of the cycle:( 95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); Followed by 72°C for 5 mi and then hold at 4°C. Amplification products were purified using 1-1.4x volume of SPRI magnetic beads, eluting in 30 ul water. Fragment size distribution was checked on a DNA Hi Sensitivity D1000 HS Screentape (Agilent Technologies, 5067-5584/5).

value: Embryo

tag: date

tag: developmental stage


title: whole heart, B6.Cg-Lepob/J wild type male, Sham, replicate 1, snRNAseq

description: 10x Genomics

value: Sham


title: whole heart, C57BL/6J wild type male, TAC, replicate 2, snRNAseq

description: 10x Genomics

value: C57BL/6J wild type


title: Late_MoO4_rep_D

city: Bozeman

first: Eric

last: Boyd

address: 1 Montana State University

institute: Montana State University

data_processing:
RNA paired-end reads were processed to remove adapter sequences and filter reads before reads were aligned to the reference MmS2 genome using Bowtie2 to generate transcriptional profiles using the HT-Seq software program.
Assembly: ASM1158v1
Supplementary files format and content: tab-delimited text files for each sample contain raw count numbers for genes

molecule: total RNA

organism: Methanococcus maripaludis

source_name: Methanogens

growth_protocol: MmS2 was grown under N2-fixing conditions in defined basal medium as described in Payne et al. 2023 (Communications Biology)

extract_protocol:
Cultures of MmS2 were harvested during late log phase (24 hrs. for molybdate and molybdenite conditions, 30 hrs. for the no Mo condition) of growth for RNA extraction. Cultures were brought into an anaerobic chamber and were vacuum-filtered over 0.2 µm Supor membrane filters that were then transferred into 2 mL microcentrifuge tubes. The tubes and their contents were immediately flash frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted from the filters using the Trizol method. DNA contamination was checked by performing PCR amplification using archaeal-specific 16S rRNA primers.
rRNA depletion was conducted using custom Methanococcus-specific oligonucleotides, and sequenced on the Illumina NovaSeq platform with 2x150 bp paired-end reads at the University of Wisconsin sequencing center.

treatment_protocol: MmS2 was provided with 0.4% w/v sodium formate, 10 mM acetate, and Wolfe’s vitamins. However, the composition of our trace metals solution was modified to exclude molybdate and ferrous iron; sodium molybdate was added separately to a final concentration of 5 µM. Ferrous iron was added in the form of synthetic mackinawite to a final concentration of 10 µM. In the case of MoS2 experiments, Fe was provided as FeCl2 to a final concentration of 25 µM . Where specified, HS- was added to a final concentration of 1 mM or a mixture of sodium thiosulfate and L-cysteine was added as S source to final concentrations of 1 mM each. All cultures were incubated at 37 °C and over-pressurized with 2.04 atm of 80:20 N2:CO2. MmS2 was passaged five times (2% v/v inoculum; ~3x10^8 total cells in 75 mL) in medium without Mo to induce Mo limitation prior to use as an inoculum.

tag: cell type

value: Methanogens


title: Homosapiens,adultnasalmucosa, male, S00224695, D2

city: Oxford

first: Andre

last: Goncalves

address: Old Road Campus, Roosevelt Dr, Headington

department: Department of Paediatrics

country: United Kingdom

institute: University of Oxford

data_processing:
Quality control of raw sequencing data was done using FastQC tool. Mapping to a human reference genome assembly (GRCh38) was done using STAR 2.5.0a(71). Read counts from the resulting binary alignment map (BAM) files were obtained with featureCounts(72) using a general transfer format (GTF) gene annotation from the Ensembl database(73)The R/Bioconductor package DESeq2 (version 1.34.0) was used to identify differentially expressed genes among the samples after removing absent features (zero counts in more than 75% of samples). Genes with a p-value of < 0.05 and an absolute fold-change of > 2.0 were identified as differentially expressed.
Assembly: GRCh38
Supplementary files format and content: log2cpm_expression; raw_expression

organism: Homo sapiens

source_name: nasal cells

extract_protocol:
Nasal cells were collected in RLT (QIAGEN) and stored at -80°C until extraction. RNA extraction (RNeasy; QIAGEN), sample integrity assessment (Bioanalyzer; Agilent 2100)
Library preparation and RNA sequencing (BGISEQ-500RS) were performed at the Beijing Genome Institute.

value: nasal cells

tag: age

tag: Sex

value: male

tag: timepoint

tag: carriage status

value: NEG

tag: smorkers

value: N

tag: htn

value: Y

tag: renal disease

tag: previous malignancy

tag: statin

tag: charlson index


title: Homosapiens,adultnasalmucosa, male, S00224135, baseline

value: baseline


title: Late_MoO4_rep_C


title: 4C_mz_EKO_2


title: Late_MoO4_rep_B


title: whole heart, C57BL/6J wild type male, sham, replicate 2, snRNAseq

description: 10x Genomics


title: 4C_mz_EKO_1


title: whole heart, C57BL/6J wild type male, TAC, replicate 1, snRNAseq

description: 10x Genomics


title: whole heart, B6.Cg-Lepob/J wild type male, Sham, replicate 2, snRNAseq

description: 10x Genomics


title: whole heart, C57BL/6J wild type male, Sham, replicate 1, snRNAseq

description: 10x Genomics


title: 4C_mz_DHet_6


title: Homosapiens,adultnasalmucosa, female, S00233462, D9

value: female

value: POS


title: Late_MoO4_rep_A


title: Homosapiens,adultnasalmucosa, female, S00232652, D2


title: Late_MoS4_rep_A


title: KP-1 Cells, HRS-4642 Treatment for 2 weeks

city: Shanghai

first: Chongyang

last: Li

address: 131 Dong 'an Road, Xuhui District

country: China

institute: Fudan University

library_source: genomic

data_processing:
Adaptor trimming - CutAdapt version 1.18 (parameters,cutadapt -a)
Alignment - MAGeCK version 0.5.9 (parameters, mageck count -l SGRNA_LIBRARY -n DATA_PATH --sample-label SAMPLE_LABEL --fastq FASTQ_FILE)
Statistical test - MAGeCK version 0.5.9 (parameters, megeck test -k MAGECK_COUNT_OUTPUT -c CONTROL -t TEST -n DATA_PATH)
Assembly: mm10
Supplementary files format and content: FC-Kras.count.txt, FC-Kras.count_normalized.txt, KP-Kras.count.txt, KP-Kras.count_normalized.txt

molecule: genomic DNA

source_name: KP-1 (Lung cancer)

extract_protocol:
Genomic DNA was then extracted using the genomic DNA extraction kit (TIANGEN, DP304).
PCR amplification of sgRNA was performed, and NGS sequencing on an Illumina HiSeq was conducted to determine sgRNA abundance.
CRISPR Screen

value: KP-1 (Lung cancer)

tag: cell line

value: Mouse lung adenocarcinoma

value: HRS4642 Treatment for  2 weeks


title: 4C_mz_DHet_5


title: Homosapiens,adultnasalmucosa, female, S00231884, baseline


title: KP-1 Cells,  Input, no treament

tag: treatment

value: no Treatment


title: Homosapiens,adultnasalmucosa, female, S00224660, D2


title: 4C_mz_DHet_4

tag: tissue


title: Biliary epithelial cells 12hrs hypoxia rep3

type: RNA

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

description:
12hrs hypoxia
HL26 12hrs

data_processing:
The normalization and data analysis were performed according to the manufacturers instructions using R
Normalization uses the average expression of the housekeeping genes B2M, GAPDH and RPLP0. Housekeeping genes were chosen by the RT2 Profiler PCR Array software (GeneGlobe; Qiagen)
Target gene signals were normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: Human biliary epithelial cells

extract_protocol: Cryopreserved sections (or fresh samples of tissue) were defrosted at room temperature and digested for 30 min at 37°C in a solution of Collagenase (2 ug/ml, Gibco)-Dispase (1 ug/ml, Gibco)-Bovine Fetal Calf Serum (2% FCS, Gibco) in Advanced DMEMF12 (LifeTech) supplemented with 1% Penicillin/Streptomycin (P/S, Gibco) and 1% L-Glutamine (Glut, Gibco). When the intrahepatic bile ducts could be observed by microscope inspection the sample was centrifuged at 100g for 5 mins, resuspended in Versene (Thermo Fisher) and incubated at 37°C for 1 hour. Dissociated cells were filtered through a 40 um cell strainer and washed in Advanced DMEMF12. Cells were resuspended in Advanced DMEMF12 underlayered with an equal volume of 20% and 50% (v/v) Percoll (Sigma). Following centrifugation at 1800g for 30 mins at 4°C, the HPC rich fraction lying between the 20 and the 50% Percoll layers was collected, washed and re-suspended in PBS with 2% FCS and 100 mmol EDTA (Sigma) for FACS staining procedure. Cells were incubated for 1 hour with EpCAM-BV650 conjugated antibody, CD24-BV421, CD133-APC, CD45-488 and CD31-488. Samples were stained with SYTOX-AADvanced dead cell stain kit (ThermoFisher) prior analysis in a FACSAria Fusion (BD Biosciences). Cells were grown as two-dimensional cultures and maintained as a cell line.

value: Biliary epithelial cells


title: KP-1 Cells, DMSO Treatment for 2 weeks

tag: genotype

value: DMSO Treatment for 2 weeks


title: 4C_mz_DHet_3

value: Embryo

tag: date


title: Homosapiens,adultnasalmucosa, female, S00227837, D9


title: 4C_mz_EKO_3

tag: developmental stage


title: Biliary epithelial cells 12hrs hypoxia rep2

description:
12hrs hypoxia
HL24 12hrs

tag: cell type


title: Biliary epithelial cells 12hrs hypoxia rep1

description:
12hrs hypoxia
HL23 12hrs


title: Biliary epithelial cells 0hrs hypoxia rep3

description:
Control
HL26 0hrs


title: 4C_mz_DHet_2


title: Homosapiens,adultnasalmucosa, female, S00223966, baseline

tag: age


title: Homosapiens,adultnasalmucosa, female, S00218486, baseline

tag: Sex


title: 4C_mz_DHet_1


title: FC1242 Cells,  Input, no treament

source_name: FC1242 (Pancreatic cancer)

value: FC1242 (Pancreatic cancer)

value: Mouse Pancreatic cancer


title: FC1242 Cells, DMSO Treatment for 2 weeks


title: L2C_z_NrKO_6


title: Homosapiens,adultnasalmucosa, female, S00224138, D9

value: nasal cells

tag: timepoint


title: Biliary epithelial cells 0hrs hypoxia rep2

description:
Control
HL24 0hrs


title: Biliary epithelial cells 0hrs hypoxia rep1

description:
Control
HL23 0hrs


title: L2C_z_NrKO_5


title: Homosapiens,adultnasalmucosa, female, S00223716, D2

tag: carriage status


title: FC1242 Cells, HRS-4642 Treatment for 2 weeks


title: lymph node, Acu, Day15 (Z_28)

city: Tianjin

first: Yue

last: Zhang

address: Poyang Lake Road

institute: Tianjin University of Traditional Chinese Medicine

description: Acupuncture at ST36

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: popliteal lymph node

growth_protocol: BALB/c male mice (6-8 weeks-old, 20-22g) were obtained from the Beijing Vital River Laboratory Animal Technology Co., Ltd. (Beijing, China). All mice were housed under controlled conditions (12 h day/night rhythm, 25 ± 1℃, 55 ± 5% relative humidity), and were fed with free access to food and water.

extract_protocol:
Total RNA samples were extracted from the control, AA, and acupuncture-treaed mice using Trizol (Invitrogen, USA)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: In short, after brief iodine disinfection, mice in AA, acupuncture and sham acupuncture groups were subcutaneous injected with 0.1 ml complete Freund’s adjuvant (Sigma, USA) in right hind paw, while mice in control group were subcutaneous injected with the equal volume of saline.

value: popliteal lymph node

value: Acu


title: PIg blood VDJ

city: Urbana

first: Angad

middle: P.

last: Mehta

state: Illinois

address: 600 S Mathews Ave

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic single cell

data_processing:
The  libraries were pooled; quantitated by qPCR and sequenced on one 10B lane with 28x150nt reads  on a NovaSeq X Plus with V1.0 sequencing kits. Read1 is 28nt in length, Read2 is 150nt in length, I1 and I2 are 10nt in length. cDNA reads are in R2.
Fastq.gz files were generated and demultiplexed with bcl2fastq v 2.20 (Illumina).
Custom references corresponding to Sus scrofa genome (Sscrofa11.1) were made following 10X’s recommendations for the Gene Expression (GEX) data using Cell Ranger v7.2.0 (mkref) on the Ensembl 110 Annotation. The custom V(D)J reference was made using Cell 15 Ranger (mkV(D)Jref) on Sscrofa11.1 and IMGT’s (the international ImMunoGeneTics database) IG and TR nucleotide database (v7.2.0).
To jointly align the GEX and V(D)J data for cell calling and UMI quantification, Cell Ranger multi was run with the references and the 6 inner enrichment oligonucleotides.
Assembly: Sscrofa11.1, Ensembl 110 Annotation
Supplementary files format and content: gene expression counts and barcodes in hdf5 format and vdj annotations in .csv format

organism: Sus scrofa

source_name: blood

extract_protocol:
PBMC isolation followed by sorting CD21 positive B cells
The libraries were constructed with Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index), and with the 10X Single-cell VDJ from 10X Genomics (Pleasanton, CA) following the manufacturer’s protocols with the substitution of custom oligonucleotides for pig V(D)J amplification

value: blood

value: B cells

value: CD21 positive cells

value: sorted from PBMCs using anti-CD21 antibodies

tag: library type

value: VDJ


title: lymph node, Acu, Day15 (Z_4)

description: Acupuncture at ST36


title: lymph node, Acu, Day15 (Z_6)

description: Acupuncture at ST36


title: Homosapiens,adultnasalmucosa, male, S00224137, D9

value: male

value: NEG

tag: smorkers

value: Y

tag: htn

value: N


title: L2C_z_NrKO_4


title: Tb1Lu SINVGFP infected 24hpi

first: Yang

address: 2005 Songhu Rd, Yangpu district

institute: Fudan university

description: 3’-adapters were trimmed  and sRNAs containing any N base or overwhelming 10% of total reads were removed. Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable  reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto.  Reads unmapped to host genome were aligned to viral genome. Alignment was done by Bowtie 1.2.3. Reads mapped to positive and negative strands were used to define positive and negative vsRNAs separately. Characterization of vsRNAs were performed as previously described

data_processing:
3’-adapters were trimmed  and sRNAs containing any N base or overwhelming 10% of total reads were removed.
Trimmed reads were first mapped to genome of Pteropus Alecto with 0 mis match, mappable  reads were futher aligned to miRNAs (pal22-), tRNAs, rRNAs, snRNAs, snoRNAs of Pteropus alecto.
Reads unmapped to host genome were aligned to viral genome.
Characterization of vsRNAs were performed as previously described.
Assembly: Pteropus alecto (GCA_000325575.1), hg38
Supplementary files format and content: *.viralreads.xls for all perfect mapped virus-derived small RNA reads in each library (unnormalized)
Supplementary files format and content: *.miRNAreads.xls for all perfect mapped miRNA reads in each library (unnormalized)

organism: Tadarida brasiliensis

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

extract_protocol:
Cells were washed with PBS twice, TRIzol was then added to the cells, and total RNAs were extracted following the manufacturer's instructions.
Extracted total RNAs were used for the construction of small RNA libraries by the method that depends on the 5’ monophosphate of small RNAs as described previously with the TruSeq Small RNA Sample Preparation Kit of Illumina (San Diego, CA).

treatment_protocol: Cells were plated in 6 cm dishes the day before infection. Infection was done with following titer: PR8delNS1 MOI=1, NoV/NoV∆B2 10 copies of genomic RNA1 per cell, SINVGFP MOI=0.5. Cells infected with NoV∆B2 were cultured at 30℃ during infection. At defined time post infection cells were harvested and total RNAs were extracted by TRIzol reagent then used for further analysis.

value: lung cell

value: wildtype

value: infected with SINVGFP


title: Homosapiens,adultnasalmucosa, female, S00223500, baseline

value: female

value: baseline

tag: renal disease

tag: previous malignancy


title: Pig blood gene expression

value: mRNA


title: L2C_z_NrKO_3

value: Embryo


title: lymph node, AIA, Day15 (M_5)

description: AIA

value: popliteal lymph node

value: AIA


title: L2C_z_NrKO_2


title: Homosapiens,adultnasalmucosa, male, S00223715, D2

value: nasal cells

tag: statin

tag: charlson index


title: lymph node, AIA, Day15 (M_31)

description: AIA

tag: treatment


title: L2C_z_NrKO_1

tag: tissue


title: lymph node, AIA, Day15 (M_38)

description: AIA


title: 3D APOE3 neurons co-cultured with APOE4 astrocytes at 2 neurons:1 astrocytes ratio

city: San Francisco

first: Emmy

email: emmyli0306@gmail.com, emmy.li@ucsf.edu

address: 675 Nelson Rising Lane

institute: UCSF

data_processing:
Data processing and aligmnent for iAssembloids (EL1-3) were performed with CellRanger v6.0.2  (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Data processing and alignment for APOE3 vs APOE4 snRNAseq were performed using PIPseeker v2.1.4-linux (https://www.fluentbio.com/products/pipseeker-software-for-data-analysis/)
Assembly: GRCh38
Supplementary files format and content: tab separated files and matrix files

molecule: nuclear RNA

source_name: iAssembloid

extract_protocol:
iAssembloids were dissociated with dounce homogenization in a sucrose based homogenization buffer and filtered through a cell filter. The suspension were then mixed with optiprep (final concentration 25%) and layered ontop of a 30% and 40% optiprep layer). The columns were spun down at 10000g for 18 min at 4C. The nuclear layer was extracted (layer between 30% and 40% optiprep and snRNAseq was performed
10X Chromium v3, Fluent Biosciences PIP-seq T2

value: iAssembloid

tag: cell line

value: neuorns, astrocytes


title: 3D APOE3 neurons co-cultured with APOE4 astrocytes at 1 neuron:1 astrocyte ratio


title: L2C_z_NrHet_7

tag: date

tag: genotype


title: 3D APOE3 neurons co-cultured with APOE3 astrocytes at 2 neurons:1 astrocytes ratio

tag: cell type


title: Homosapiens,adultnasalmucosa, female, S00223305, D9

tag: age


title: 3D APOE3 neurons co-cultured with APOE3 astrocytes at 1 neuron:1 astrocyte ratio


title: Homosapiens,adultnasalmucosa, female, S00222704, D2

tag: Sex


title: lymph node, AIA, Day15 (M_10)

description: AIA


title: L2C_z_NrHet_6

tag: developmental stage


title: lymph node, Control, Day15 (C_17)

description: control

value: Control


title: L2C_z_NrHet_5


title: lymph node, Control, Day15 (C_16)

description: control


title: Homosapiens,adultnasalmucosa, female, S00222501, baseline

tag: timepoint

tag: carriage status


title: L2C_z_NrHet_4


title: Homosapiens,adultnasalmucosa, male, S00222018, D9

value: male

tag: smorkers


title: lymph node, Control, Day15 (C_15)

description: control


title: Day 28 after iAssembloid culture

value: neurons, astrocytes, microglia


title: Day 14 after iAssembloid culture


title: Homosapiens,adultnasalmucosa, male, S00221080, baseline

value: NEG

tag: htn


title: L2C_z_NrHet_2


title: Homosapiens,adultnasalmucosa, male, S00223499, baseline

value: Y

tag: renal disease

value: N


title: A29

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

institute: Centre de Recherche des Cordeliers

data_processing:
ShortRead, V3.17
HISAT2, V2.2.1
Htseq-count, V2.0.3
Assembly: mm10
Supplementary files format and content: Htseq-count output in .txt file with raw count

source_name: Livers

extract_protocol:
RNeasy Mini Kit Qiagen MAK195
mRNA-sequencing library preparation (1.5ug total RNA/ sample; plant and animal eukaryotic strand-specific mRNA and sequencing)

treatment_protocol: ALZET osmotic pumps containing ACBP/DBI (2.5 mg/mL) or PBS were transplanted into eight-week-old female C57BL/6 J mice. Anorexia was induced by CRS or CDDP fourty-eight hours or seventy-two hours later respectively.

value: Livers

value: Wild type

value: Rec-ACBP+CRS


title: A30


title: 2D monoculture neuron CROP-seq rep 3

data_processing:
Data processing and aligmnent were performed with CellRanger v6.0.2  (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Barcode assignment was performed using a publically available package (https://github.com/powellgenomicslab/CROP-seq)
Assembly: GRCh38
Supplementary files format and content: tab separated files (.tsv), comma seperated files (.csv), and matrix files (.mtx)

source_name: Monoculture

extract_protocol:
iAssembloids and 2D monoculture neurons were dissociated with papain. Neurons were enriched for using PSA-NCAM selecting beads and magnetic activated cell sorting.
10X Chromium v3

value: Monoculture

value: PSA-NCAM enriched hiPSC-derived neurons


title: A28


title: L2C_z_NrHet_1

value: Embryo


title: 2D monoculture neuron CROP-seq sgRNA enrichment PCR rep 2


title: Homosapiens,adultnasalmucosa, female, S00220551, baseline

value: female

value: baseline

value: POS

tag: previous malignancy


title: L2C_mz_DKO_6


title: A27


title: L2C_mz_DKO_5


title: 2D monoculture neuron CROP-seq rep 2


title: Day 1 after iAssembloid culture

value: iAssembloid


title: Homosapiens,adultnasalmucosa, female, S00220552, D9

value: nasal cells

tag: statin


title: iAssembloids neuron CROP-seq sgRNA enrichment PCR rep 2


title: L2C_z_NrHet_3


title: L2C_mz_DKO_4


title: A26


title: Homosapiens,adultnasalmucosa, female, S00219745, D2

tag: charlson index


title: A25

tag: treatment

value: Rec-ACBP+CDDP


title: Homosapiens,adultnasalmucosa, female, S00222019, D9


title: Homosapiens,adultnasalmucosa, female, S00221444, D2


title: 2D monoculture neuron CROP-seq sgRNA enrichment PCR rep 3

tag: tissue


title: iAssembloids neuron CROP-seq sgRNA enrichment PCR rep 1

tag: cell line


title: L2C_mz_DKO_3

tag: date


title: Homosapiens,adultnasalmucosa, female, S00220550, D9


title: A23

tag: genotype


title: A24


title: iAssembloids neuron CROP-seq rep 2

tag: cell type


title: L2C_mz_DKO_2


title: L2C_mz_DKO_1


title: Homosapiens,adultnasalmucosa, female, S00219746, D2

tag: age


title: Homosapiens,adultnasalmucosa, female, S00218519, baseline

tag: Sex


title: L2C_mz_NrKO_9

tag: developmental stage


title: 2D monoculture neuron CROP-seq rep 1


title: A20

value: Rec-ACBP


title: Homosapiens,adultnasalmucosa, female, S00222017, D9

tag: timepoint


title: L2C_mz_NrKO_8


title: Homosapiens,adultnasalmucosa, female, S00219107, baseline

tag: carriage status


title: A19


title: 2D monoculture neuron CROP-seq sgRNA enrichment PCR rep 1


title: Homosapiens,adultnasalmucosa, female, S00220548, baseline

tag: smorkers


title: Homosapiens,adultnasalmucosa, female, S00221442, D2

tag: htn


title: L2C_mz_NrKO_7


title: A18


title: Homosapiens,adultnasalmucosa, male, S00220549, D9

value: male

tag: renal disease


title: A17


title: A16


title: Homosapiens,adultnasalmucosa, male, S00218518, baseline

value: NEG

tag: previous malignancy


title: Pcdhg si + Klf2 si + Klf4 si_OS3

city: New Haven

first: Divyesh

last: Joshi

state: CT

address: 300 George Street, Floor 7, YCVRC, Yale University

department: Internal Medicine, Cardiology

institute: Yale University

data_processing:
Processing was performed using PartekFlow v12.0.0 using default settings
Sequence reads were trimmed for adaptor sequence/low quality sequence
Trimmed reads were aligned using STAR aligner
Read count extraction and normalization was done using CPM
Differential expression analysis was done using DeSeq2
Assembly: hg19
Supplementary files format and content: Excel files comparing normalized read counts

source_name: Primary cells

growth_protocol: HUVECs were maintained in EGM2 complete medium at 5% CO2 and 37 deg C humidified incubator

extract_protocol:
Qiagen RNeasy Plus mini kit
PolyA selection on oligodT beads by random priming

treatment_protocol: HUVECs were treated with silencing RNAs as described and treated with OSS for 16h before collection of RNA

value: Primary cells

value: HUVEC

value: Endothelial

value: Pcdhg and Klf2 and Klf4 triple silencing RNA

value: OSS


title: L2C_mz_NrKO_6


title: Pcdhg si_OS2

value: Pcdhg silencing RNA


title: A22

value: Livers

value: Wild type


title: Pcdhg si + Klf2 si + Klf4 si_OS2


title: L2C_mz_NrKO_4

value: Embryo


title: A15

value: CRS


title: L2C_mz_NrKO_5


title: L2C_mz_NrKO_10


title: Pcdhg si_OS3


title: Homosapiens,adultnasalmucosa, male, S00220554, D9

value: N

tag: statin


title: A21


title: Homosapiens,adultnasalmucosa, male, S00219747, D2

tag: charlson index


title: L2C_mz_NrKO_3


title: Pcdhg si_OS1

tag: treatment


title: Pcdhg si + Klf2 si + Klf4 si_OS1

tag: tissue


title: A14


title: Homosapiens,adultnasalmucosa, male, S00218890, baseline

value: baseline


title: A13


title: L2C_mz_NrKO_2


title: Control si_OS2

tag: cell line

value: Control silencing RNA


title: A12


title: Homosapiens,adultnasalmucosa, male, S00281231, D9

value: nasal cells


title: Control si_OS1


title: L2C_mz_NrKO_1

tag: date


title: L2C_mz_EKO_10

tag: genotype


title: A549 cells, Perth09_Mock

city: urbana

first: christopher

last: brooke

state: IL

address: B103 CLSL, MC-110, 601 South Goodwin Avenue

description: 10x Genomics

data_processing:
Fastq.gz files were generated and demultiplexed with CellRanger 3.1.0
Custom references were made using Cell Ranger 4.0.0 to combine the human and each virus
Cell Ranger's (7.1.0) "count" was used to align each sample to the appropriate custom reference, collapse reads to UMIs and call cells.
Assembly: NCBI GRCh38 (Annotation Release 109) plus either H1N1 (A/California/07/2009) or H3N2 (A/Perth/16/2009)
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: cell line

extract_protocol:
A549 cells were infected with H1N1 or H3N2 for 8 and 16 hrs. Following incubtation cells were stained with anti-HA antibody FI6v3 and sorted for infected or bystander. Mock libraires were prepared by incubating A549 cells with PBS + 0.1% BSA instead of virus and harvested at 16hrs. Cells were steains with FI6v3 and negative population was sorted for library preparation.
The libraries were constructed with the Chromium Single-Cell Gene Expression v3 kit (10x Genomics) and sequenced on an S4 flowcell (4 lanes) with 28x150 reads in a NovaSeq 6000

value: cell line

tag: cell type

value: human alveolar epithelial

value: 0 hours

value: Uninfected


title: A11


title: L2C_mz_EKO_8


title: A549 cells, Perth09_8hrs_infected

description: 10x Genomics

value: 8 hours post infection

value: Infected H3N2 (A/Perth/16/2009)


title: A10

value: CDDP


title: Homosapiens,adultnasalmucosa, male, S00281230, D2

tag: age

value: male

value: NEG


title: L2C_mz_EKO_9


title: A9

value: Livers


title: Homosapiens,adultnasalmucosa, female, S00219106, D2

tag: Sex

value: female

value: POS


title: L2C_mz_EKO_7

value: Embryo

tag: developmental stage


title: A549 cells, Perth09_16hrs_infected_Replicate_2

description: 10x Genomics

value: 16 hours post infection


title: A8

value: Wild type


title: Homosapiens,adultnasalmucosa, male, S00281196, baseline

tag: timepoint

value: baseline

value: N


title: L2C_mz_EKO_6


title: Control si_OS3

value: Primary cells

value: HUVEC

value: Endothelial

value: Control silencing RNA

value: OSS


title: A549 cells, Perth09_16hrs_infected_Replicate_1

description: 10x Genomics

value: cell line

value: human alveolar epithelial

value: Infected H3N2 (A/Perth/16/2009)


title: A7

value: CDDP


title: Homosapiens,adultnasalmucosa, male, S00281239, baseline

value: nasal cells

value: male

tag: carriage status

value: NEG


title: Homosapiens,adultnasalmucosa, male, S00218888, D9

tag: smorkers


title: A6

value: Livers


title: L2C_mz_EKO_5

value: Embryo


title: Homosapiens,adultnasalmucosa, female, S00219857, D9

value: female

value: POS

tag: htn


title: A5

value: Wild type

value: PBS


title: A549 cells, Perth09_16hrs_bystander_Replicate_2

description: 10x Genomics

value: 16 hours post infection


title: A549 cells, Perth09_8hrs_bystander_Replicate_1

description: 10x Genomics

value: 8 hours post infection


title: L2C_mz_EKO_3


title: A4


title: Homosapiens,adultnasalmucosa, female, S00281212, D2

value: N

tag: renal disease


title: A549 cells,Perth09_16hrs_bystander_Replicate_1

description: 10x Genomics


title: A2


title: Homosapiens,adultnasalmucosa, female, S00212688, baseline

value: baseline

tag: previous malignancy


title: L2C_mz_DHet_7


title: A1.


title: L2C_mz_EKO_2


title: A549 cells, Cal07_Mock

description: 10x Genomics

value: cell line

value: 0 hours

value: Uninfected


title: Homosapiens,adultnasalmucosa, female, S00281229, baseline

value: Y

tag: statin


title: L2C_mz_DHet_6


title: A549 cells, Cal07_8hrs_infected

description: 10x Genomics

value: human alveolar epithelial

value: Infected H1N1 (A/California/07/2009)


title: Homosapiens,adultnasalmucosa, female, S00281187, D9

value: nasal cells

tag: charlson index


title: L2C_mz_EKO_4


title: KO2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
library strategy: Visium spatial transcriptomics
Sequencing was performed on NovaSeq 6000 platform in a 28+90-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger (version spaceranger-1.3.0, 10X Genomics).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene name and Ensembl ID
Supplementary files format and content: matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue
Supplementary files format and content: filtered_feature_bc_matrix.h5 : HDF5 format files including counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: spatial.zip : zipped "spatial" foler which is one of output folders of Space Ranger software (10X genomics)

source_name: brain

extract_protocol:
Mouse brain slide gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard Illumina protocols.

value: brain

tag: strain

value: 6-8 weeks old


title: Homosapiens,adultnasalmucosa, male, S00218225, D2

value: male

value: NEG


title: Homosapiens,adultnasalmucosa, female, S00281169, D2

value: female

value: POS


title: A549 cells, Cal07_16hrs_infected_Replicate_1

description: 10x Genomics

tag: tissue

value: 16 hours post infection

tag: treatment


title: A3

value: Livers

value: Wild type

value: PBS


title: L2C_mz_DHet_4

value: Embryo

tag: date


title: A549 cells, Cal07_8hrs_bystander_Replicate_2

description: 10x Genomics

value: cell line

tag: cell line

tag: genotype

value: 8 hours post infection


title: Homosapiens,adultnasalmucosa, female, S00281237, D9

tag: cell type

tag: age

value: N


title: WT2

value: WT


title: L2C_mz_DHet_3

tag: developmental stage


title: L2C_mz_EKO_1


title: WT1


title: Homosapiens,adultnasalmucosa, male, S00281166, D9

tag: Sex

tag: timepoint

value: Y


title: Homosapiens,adultnasalmucosa, male, S00281165, baseline

value: nasal cells

value: baseline

tag: carriage status

tag: smorkers


title: A549 cells, Cal07_8hrs_bystander_Replicate_1

description: 10x Genomics

value: human alveolar epithelial

value: Infected H1N1 (A/California/07/2009)


title: L2C_mz_DHet_2


title: A549 cells, Cal07_16hrs_bystander_Replicate_2

description: 10x Genomics


title: L2C_mz_DHet_1


title: A549 cells, Cal07_16hrs_infected_Replicate_2

description: 10x Genomics


title: A549 cells, Cal07_16hrs_bystander_Replicate_1

description: 10x Genomics


title: Homosapiens,adultnasalmucosa, female, S00281191, baseline

value: NEG

tag: htn

tag: renal disease


title: KO_HFD_5

description: Adipocytes from HFD-fed Sema6d-/- mice

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffnorm v2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: adipocytes

extract_protocol:
Total RNAs were extracted using miRNeasy Mini kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared using TruSeq stranded mRNA Library Prep Kit (Illumina).

value: epididymal white adipose tissue

value: high fat diet


title: Homosapiens,adultnasalmucosa, female, S00281218, D9

value: female

tag: previous malignancy

tag: statin


title: biol rep 2

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

description: 10X Genomics Visium FFPE

data_processing:
Raw sequence files were analysed by SpaceRanger software (v1.3.0) with reads mapped to mouse reference mm39.
Assembly: mm39
Supplementary files format and content: H5 files were generated for each sample following mapping by SpaceRanger.
Supplementary files format and content: Matrix files were generated for each sample following mapping by SpaceRanger.
Supplementary files format and content: JPEG files are provided for H/E stained sections for each sample matching the Visium fiduciary window.
Supplementary files format and content: aligned_fiducials.jpg: Fiducial alignment image
Supplementary files format and content: detected_tissue_image.jpg: Detected tissue image
Supplementary files format and content: scalefactors_json.json: Scale factor json file
Supplementary files format and content: tissue_hires_image.png: high resolution H/E image
Supplementary files format and content: tissue_lowres_image.png: low resolution H/E image
Supplementary files format and content: tissue_positions_list.csv: barcode position file
Supplementary files format and content: filtered_feature_bc_matrix.h5: filter feature h5 file
Library strategy: Spatial Transcriptomics

source_name: Distal tibia fracture callus

extract_protocol: 10X Genomics Visium mouse FFPE

treatment_protocol: Distal tibia fractures were introduced into adult mice. Ten days after fracture, calluses were dissected, fixed in formallin, and decalicified in 14% EDTA for 3 days prior to embedding.

value: Distal tibia fracture callus

value: Nf1[+/flox] and Postn-cre;Nf1[flox/-]

value: 10-day post-surgery


title: Homosapiens,adultnasalmucosa, male, S00281234, D2

value: male

tag: charlson index


title: KO_HFD_4

description: Adipocytes from HFD-fed Sema6d-/- mice

tag: strain

tag: tissue


title: Homosapiens,adultnasalmucosa, female, S00281217, D2


title: brain, KO

description: 10x Genomics

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101+101 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger count pipeline (cellranger-6.0.0, 10x Genomics) for alignment to the mm10 genome, UMI collapsing, and UMI counting for each gene-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: comma-delimited text files include raw counts for all cells detected
Supplementary files format and content: filtered_feature_bc_matrix.h5 : HDF5 format files including counts data for each gene and cell (barcode) combination

extract_protocol:
Sinlge nucleus droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-nucleus level.
Single nucleus RNA library construction was processed following the protocol outlined in (Step.5) 5' GEX Library Construction of the Chromium Next GEM Single Cell 5ʹ Reagent Kits v2 User Guide.
single nucleus RNA sequencing (snRNA-seq)

value: brain

tag: region

value: amygdala

value: 6-8 weeks old


title: brain, Wildtype

description: 10x Genomics

value: WT


title: KO_HFD_1

description: Adipocytes from HFD-fed Sema6d-/- mice

tag: treatment


title: KO_CD_4

description: Adipocytes from CD-fed Sema6d-/- mice

tag: genotype

value: control diet


title: biol rep 1

description: 10X Genomics Visium FFPE


title: Homosapiens,adultnasalmucosa, male, S00281232, baseline

tag: cell type

value: nasal cells

value: Y

value: N


title: KO_CD_2

description: Adipocytes from CD-fed Sema6d-/- mice


title: Homosapiens,adultnasalmucosa, male, S00281182, D2

tag: age


title: WT_HFD_3

description: Adipocytes from HFD-fed WT mice

value: wild type


title: 03 anti-CD74(clone CDLA74-1)

city: Kumamoto

first: Yoshihiro

last: Komohara

address: Honjo 1‐1‐1, Chuouku

department: Department of Cell Pathology

institute: Graduate School of Medical Sciences, Kumamoto University

description: 03 anti-CD74(agonist) e3

data_processing:
illumina Local Run Manager v2.4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore! v0.6.6
Trimmed sequence reads were mapped to UCSC hg19 using STAR v2.7.3a
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: blood

tag: cell line

value: primary

value: macrophage

value: Cocultured with anti-CD74 antibody (clone CDLA74-1)


title: Homosapiens,adultnasalmucosa, female, S00281173, baseline

tag: Sex

value: female

value: baseline

value: NEG


title: WT_HFD_2

description: Adipocytes from HFD-fed WT mice

value: epididymal white adipose tissue

value: high fat diet


title: 02 anti-CD74(clone LN2)

description: 02 anti-CD74(blocking) e2

value: male

value: Cocultured with anti-CD74 antibody (clone LN2)


title: KO_CD_3

description: Adipocytes from CD-fed Sema6d-/- mice


title: KP-1 Cells, Carfilzomib Treatment for 48 hours, rep1

data_processing:
Quality control - fastqc version 0.12.1 (parameters, fastqc -t 8)
Adaptor truncating - fastp version 0.23.4 (parameters, fastp -l 50 -q 20 u 50 -g -c --detect_adapter_for_pe -w 9)
Pseudo alignment - Kallisto version 0.50.1 (parameters, kallisto quant -t 10 -i INDEX)
Assembly: mm10
Supplementary files format and content: Kallisto_raw.counts.csv

source_name: KP-1 (Lung)

extract_protocol:
RNA was harvested using TRNzol Universal Total RNA Extraction Reagent Kit (DP424, TIANGEN). 1 μg of total RNA was used for the construction of sequencing libraries.
mRNA sequencing is based on the Illumina platform, which sequences all transcribed mRNA. The sequencing experiment utilizes the Illumina TruseqTM RNA sample prep Kit method for library construction, with the following specific operational steps: 1. Total RNA is extracted from the sample, and its concentration and purity are assessed using Nanodrop2000. RNA integrity is checked via agarose gel electrophoresis, and the RIN value is determined using Agilent2100. For a single library preparation, RNA totaling 1 μg is required, with a concentration ≥50 ng/μL and an OD260/280 ratio between 1.8 and 2.2. 2. Utilizing magnetic beads with Oligo(dT) to pair with polyA, mRNA is separated from total RNA for transcriptome analysis. 3. Fragmentation buffer is added, and under suitable conditions, mRNA is randomly fragmented into approximately 300 bp fragments. Subsequently, using reverse transcriptase and random primers, a single-stranded cDNA is synthesized from the mRNA template, followed by second-strand synthesis, forming a stable double-stranded structure. 4. The double-stranded cDNA structure has sticky ends, which are repaired to blunt ends by adding End Repair Mix. Then, an A base is added to the 3' end to prepare for adapter ligation. 5. The adapter-ligated products are purified and fragmented, followed by PCR amplification using the selected fragments to obtain the final library. 6. Quantification is performed using the QuantiFluor® dsDNA System, and the samples are mixed according to data proportions. Bridge PCR amplification is conducted on the cBot to generate clusters, followed by sequencing using the Illumina platform.

value: KP-1 (Lung)

value: Mouse lung adenocarcinoma

value: Carfilzomib (200nM) Treatment for 48 hours


title: KP-1 Cells, Carfilzomib Treatment for 48 hours, rep2


title: KP-1 Cells, HRS4642 and Carfilzomib Treatment for 48 hours, rep3

value: HRS4642 (200nM) and Carfilzomib (200nM) Treatment for 48 hours


title: KP-1 Cells, Carfilzomib Treatment for 48 hours, rep3


title: KP-1 Cells, HRS4642 and Carfilzomib Treatment for 48 hours, rep2


title: KP-1 Cells, HRS4642 and Carfilzomib Treatment for 48 hours, rep1


title: WT_HFD_1

description: Adipocytes from HFD-fed WT mice


title: 01 Control

description: 01 Control2 e1

value: Cocultured with isotype matched antibody


title: WT_CD_3

description: Adipocytes from CD-fed WT mice

value: wild type

value: control diet


title: KP-1 Cells, HRS4642 Treatment for 48 hours, rep2

value: HRS4642 (200nM) Treatment for 48 hours


title: MYLA, romidepsin, rep 3

city: New York

first: Bobby

last: Shih

state: NY

address: 1130 St Nicholas Ave

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequence reads aligned to GRCh38.p12 reference genome using STAR (ver 2.7.9a).
Read counting performed using featureCounts (ver 2.0.0).
Genes with fewer than 10 counts in any sample is defined as non-expressed and removed before normalization using DESEQ2 (ver 1.38.1).
Assembly: GRCh38.p12
Supplementary files format and content: count file containing raw counts generated after STAR alignment and featureCounts read counting.
Supplementary files format and content: Comma separated value file of DESEQ2 normalized counts after filtering lowly expressed genes (<10 counts).

growth_protocol: MYLA cells are grown in 1x RPMI, 20% FBS, 1% P/S, 20 ng/mL hIL-2. Cell density maintained between 200,000 - 1,000,000 cells/mL

extract_protocol:
Total RNA was extracted from CTCL cell lines treated with single drugs and combination using the RNeasy kit (Qiagen, Hilden, Germany) following manufacturer’s protocol. RNA quality and concentration was determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA).
RNAseq libraries were prepared from total RNA isolated from treated CTCL cell lines and sequenced by Azenta Life Sciences (South Plainsfield, New Jersey, USA).

treatment_protocol: Cells are seeded in fresh media at a density of 500,000 cells/mL and treated with either romidepsin (3.2 nM), afatinib dimaleate (5.7 uM), or the combination. All conditions are DMSO normalized to the highest class volume (combination). Cells not treated with any drugs are labelled "DMSO". Cells are treated for 24 hours before RNA extraction.

value: cell line

value: MYLA

value: Romidepsin


title: KP-1 Cells, HRS4642 Treatment for 48 hours, rep1


title: KP-1 Cells, HRS4642 Treatment for 48 hours, rep3


title: WT_CD_2

description: Adipocytes from CD-fed WT mice


title: WT_CD_1

description: Adipocytes from CD-fed WT mice


title: MYLA, romidepsin, rep 2


title: KP-1 Cells, DMSO Treatment for 48 hours, rep2

value: DMSO Treatment for 48 hours


title: KP-1 Cells, DMSO Treatment for 48 hours, rep3


title: KO_HFD_4_MPP

description: MPP from HFD-fed Sema6d-/- mice

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2.
The fragments per kilobase of exon per million mapped fragments (FPKM.txts) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 100000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM.txt values for each Sample

source_name: multipotent progenitor cells

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent (Qiagen).
Full-length cDNA was generated using a SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

tag: feed

value: multipotent progenitor cells


title: MYLA, romidepsin, rep 1


title: Homosapiens,adultnasalmucosa, male, S00281233, D9

data_processing:
Quality control of raw sequencing data was done using FastQC tool. Mapping to a human reference genome assembly (GRCh38) was done using STAR 2.5.0a(71). Read counts from the resulting binary alignment map (BAM) files were obtained with featureCounts(72) using a general transfer format (GTF) gene annotation from the Ensembl database(73)The R/Bioconductor package DESeq2 (version 1.34.0) was used to identify differentially expressed genes among the samples after removing absent features (zero counts in more than 75% of samples). Genes with a p-value of < 0.05 and an absolute fold-change of > 2.0 were identified as differentially expressed.
Assembly: GRCh38
Supplementary files format and content: log2cpm_expression; raw_expression

extract_protocol:
Nasal cells were collected in RLT (QIAGEN) and stored at -80°C until extraction. RNA extraction (RNeasy; QIAGEN), sample integrity assessment (Bioanalyzer; Agilent 2100)
Library preparation and RNA sequencing (BGISEQ-500RS) were performed at the Beijing Genome Institute.

value: nasal cells

tag: timepoint

tag: carriage status

value: NEG

value: Y

value: N


title: MYLA, romidepsin + afatinib dimaleate, rep 3

value: Romidepsin + Afatinib Dimaleate


title: A549 cells, Perth09_8hrs_bystander_Replicate_2

description: 10x Genomics

value: human alveolar epithelial

value: 8 hours post infection

value: Infected H3N2 (A/Perth/16/2009)


title: KO_HFD_3_MPP

description: MPP from HFD-fed Sema6d-/- mice

value: high fat diet


title: KP-1 Cells, DMSO Treatment for 48 hours, rep1

value: KP-1 (Lung)

value: Mouse lung adenocarcinoma


title: MYLA, romidepsin + afatinib dimaleate, rep 2


title: KO_HFD_2_MPP

description: MPP from HFD-fed Sema6d-/- mice


title: KO_CD_4_MPP

description: MPP from CD-fed Sema6d-/- mice

value: control diet


title: MYLA, romidepsin + afatinib dimaleate, rep 1

value: cell line


title: NICP, mALB (T) His-

city: Seattle

first: Alyssa

last: La Fleur

state: WA

address: Campus Box 352500 185 Stevens Way

institute: University of Washington

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L67 His-

library_source: other

data_processing:
Trimmed fastq files are clustered with starcode
Clustered barcodes are matched to their proteins using the barcode to protein tables (see supplemental file), and PPIs are counted.
Autoactivators are detected and corrected (see methods of paper)
Deseq2 is used to get  fold changes for each PPI using the His+ and His- condition counts as inputs.
Assembly: N/A
Supplementary files format and content: Proccessed PPI counts per each selection stage (His+ and His-)
The first column of the csv file has the DBD associated protein name, while the columns have the AD associated protein  name.  The values in all other cells correspond to the count of the barcodes for the PPI being measured.
Library strategy: MP3-seq

molecule: other

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: 250uL of transformed yeast from gylcerol stock is first grown in 100mL of synthetic drop out media at 30C and 250rpm lacking tryptophan during an extended outgrowth step. Yeast are allowed to grow for at least 36 hours with periodic 1:250 dillutions into fresh media when optical density at 600nM reaches 1.0. 250uL of cells are used to inoculate 100mL of synthetic dropout media - Tryptophan -Histidine +3mM 3AT. Cells are allowed to incubate at same conditions before until OD600 of 1.0 is reached.

extract_protocol:
All plasmids are extracted after growth selection using a Zymoprep Yeast Plasmid Miniprep II Kit according to the manufacturer's protocol.
All proteins of interest are ordered as twist gene fragements. These fragments are ordered to contain the terminator, barcode, and overlap regions for assembly. These fragmetns are combined with the MP3-seq vector and assembled during yeast transformation through homologous recombination.

value: yeast cell

value: MATa AGA1::GAL1-AGA1::URA3 ura3-52 trp1 leu2-delta200 his3-delta pep4::BleoMX leu2::pGAL6z-HIS3 prbd1.6R can1 GAL


title: MYLA, DMSO, rep 3

value: MYLA

value: DMSO


title: Bcl & inhibitors His-

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1 mM 3-AT.
L66 His-


title: KO_CD_2_MPP

description: MPP from CD-fed Sema6d-/- mice

value: multipotent progenitor cells


title: MYLA, DMSO, rep 2


title: Bcl & inhibitors His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1 mM 3-AT.
L66 His+


title: KO_CD_1_MPP

description: MPP from CD-fed Sema6d-/- mice


title: NICP, mALB (T) His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L67 His+


title: MYLA, DMSO, rep 1


title: WT_HFD_5_MPP

description: MPP from HFD-fed WT mice

value: wild type


title: MYLA, afatinib dimaleate, rep 3

value: Afatinib Dimaleate


title: NCIP His- (high 3-AT)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  10 mM-AT.
L62 His- 10mM 3-AT


title: PT53_PP_scRNA

city: Tampa

first: Xiaofei

last: Song

state: FL

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Cell Ranger (version 3.0, 10x genomics)
Assembly: GRCh38
Supplementary files format and content: all_contig_annotations.csv: High-level and detailed annotations of all contigs (from cell and background barcodes) in CSV format.
Supplementary files format and content: filtered_contig_annotations.csv: High-level annotations of each high-confidence contigs from cell-associated barcodes. This is a subset of all_contig_annotations.csv.
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: Contains only detected cell-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page. This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier cells, run dimensionality reduction, normalize gene expression).

source_name: PP

extract_protocol:
Cells were encapsulated with NextGEM v1.1 Single Cell 5’ Reagent Kit
cDNA libraries were prepared according to the 10X Genomics protocol
5' scRNA+scVDJ seq

value: PP

tag: disease

value: Cutaneous T-cell lymphoma (CTCL)


title: PT55_Tumor_scRNA

source_name: Tumor

value: Tumor


title: PT52_PP_scRNA


title: PT53_Tumor_scRNA


title: PT11_Tumor_scVDJ

data_processing:
Cell Ranger (version 3.0, 10x genomics)
Assembly: GRCh38
Supplementary files format and content: all_contig_annotations.csv: High-level and detailed annotations of all contigs (from cell and background barcodes) in CSV format.
Supplementary files format and content: filtered_contig_annotations.csv: High-level annotations of each high-confidence contigs from cell-associated barcodes. This is a subset of all_contig_annotations.csv.
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: Contains only detected cell-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the feature-barcode matrix page. This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier cells, run dimensionality reduction, normalize gene expression).
Library strategy: scVDJ-seq


title: PT55_PP_scRNA


title: PT35_Tumor_scRNA


title: PT52_Tumor_scRNA


title: PT35_PP_scVDJ


title: PT35_Tumor_scVDJ


title: PT56_PP_scRNA


title: PT50_PP_scRNA


title: PT11_PP_scVDJ


title: PT47_PP_scRNA


title: PT47_Tumor_scRNA


title: PT50_Tumor_scRNA


title: PT56_Tumor_scRNA


title: PT11_Tumor_scRNA


title: PT35_PP_scRNA


title: PT11_PP_scRNA


title: MYLA, afatinib dimaleate, rep 2


title: NCIP His- Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L62 His- 2mM 3-AT


title: WT_HFD_1_MPP

description: MPP from HFD-fed WT mice


title: WT_HFD_4_MPP

description: MPP from HFD-fed WT mice


title: PT47_PP_scVDJ


title: L2C_mz_DHet_5

city: Paris

first: Nicola

address: 25-28 Rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Single-end sequences (50-85bp, using 50bp sequencing kits) were generated using an Illumina Next-seq 500 or 2000 instruments. After trimming Illumina adapter sequences with cutadapt (3) using options -b CTGTCTCTTATA --minimum-length=1, reads were split in UMI containing or not with Julia (J. Bezanson, A. Edelman, S. Karpinski, V. Shah, Julia: “A fresh approach to numerical computing.” https://arxiv.org/abs/1411.1607; 2015), trimming 11bp after the sequence “AAGCAGTGGTATCAACGCAGAGTACGATC”. For UMI, reads were further processed in Julia to remove the invariant adapter sequence, extract the identifier, and the UMI/ transcript sequence pairs used to remove duplicates. Conventional or UMI reads were then aligned to the mm10 genome using STAR (A. Dobin et al., “STAR: ultrafast universal RNA-seq aligner. Bioinformatics” 29, 15-21; 2013) and quantified by RSEM (B. Li, C. N. Dewey, “RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.” BMC Bioinformatics 12, 323; 2011) through the RSEM-STAR pipeline,  using gencode.v25 annotations and additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.5” for conventional reads and “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 1” for UMI reads. RSEM estimated read counts per sample were rounded for use with DESeq2 (M. I. Love, W. Huber, S. Anders, “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biol 15, 550; 2014). Genes were considered as differentially expressed if their mean expression exceeded 10 TPM in at least one genotype for a given stage, and using a <> 1.5 fold change and <0.1 FDR cutoff.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Embryo

extract_protocol:
Extraction and library preparation were performed in one reaction (see below)
The protocol employed is derived from FLASH-seq (V. Hahaut et al., “Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq.” Nat Biotechnol 40, 1447-1451; 2022), with two main modifications: 1/ Genotyping primers are added during the cDNA amplification step; 2/ A phosphate group is added to the 3’ of the template switching primer to exclude the possibility it might prime DNA synthesis during the cDNA amplification step, which would result in tagging single transcripts with multiple UMI barcodes. Embryos were isolated and directly transferred by mouth pipetting to PCR tubes in 5ul of the following lysis solution: 0.1   μL Triton X-100 (10% v/v, Sigma-Aldrich, T8787); 1.2   μL dNTP mix (25 mM each, ThermoFisher Scientific, R1121); 0.46 μL 5’Bio-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, 100 μM (supplied by IDT). 0.46 μL 5’ Biotin-AGTGGTATCAACGCAGAGTAC G ATC NNNNNNNN rGrGrG-3′Phospate, 100 μM (supplied by IDT); 0.15 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.06 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 1       μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.45 μL dCTP (100 mM, Sigma-Aldrich, DNTP100); Water to 5 μL final. Notes (AGTGGTATCAACGCAGAGTAC is an suppression PCR sequence. Random Ns form the UMI tag, and ATC is a 3bp barcode that can be varied if multiple samples are to be mixed before tagmentation, and only UMI reads are considered. rGrGrG are required for template switching. The 3’ Phosphate inhibits priming in following steps). Tubes were incubated 3 min at 72C in a thermocycler, and immediately transferred on ice. RT-pcr was performed by adding 20ul of the following mix to each sample:1.19 μL Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050); 4 μL betaine (5M, Sigma-Aldrich, 61962-50G); 0.23 μL magnesium chloride (1 M, ThermoFisher Scientific, AM9530G); 0.48 μL recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684); 0.25 uL Superscript IV Reverse Transcriptase (200 U/μL, ThermoFisher Scientific, 18091050); 12.5 μL KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502); Water to a final volume of 20 μL. Samples were incubated in a thermocycler set to execute the following programme: Hold at 50°C, and after placing tubes skip to 60 min at 50°C; 3 min at 90°C; Hold at 4°C. Tubes were transferred on ice and 0.5ul of a 100 uM solution of amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAGCAGTGGTATCAACGCAGAGTAC G) were added to each sample. 1ul of a solution of genotyping primers (see embryo genotyping section) at 10uM each was also added in each tube. Tubes were then transferred to a thermocycler, set to the following programme: Hold at 4°C and after placing tubes skip to 20 sec 98°C; 20 sec 64°C; 6 min 72°C; Followed by 20 cycles of: (20 sec 98°C; 20 sec 67°C ;6 min 72°C, adding 12 seconds per cycle); then hold at 4°C. Amplification products were purified using 1x volume of SPRI magnetic beads, eluting in 15 ul water. 1ul was set aside to perform a nested PCR for genotyping. Fragment size distribution was checked on a Genomic DNA Screentpape (Agilent Technologies, 5067-5365/6), with a typical lengths ranging from less than 1Kb to more than 10kb. For tagmentation, each sample was diluted to 150 pg/ul. 2 ul of diluted cDNA were mixed with 2ul of Amplicon Tagment Mix (ATM) and 4 μL of Tagment DNA Buffer (TD) from an Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024), and incubated for 8 min at 55°C, in a thermocycler. Tn5 was released from DNA by adding 2μL of Neutralization Buffer (NT), followed by a 5 min RT. Enrichment of UMI containing fragments in the tagmented DNA was performed by adding 5 μL of Nextera PCR Master Mix (NPM) and 1ul of 5 uM amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG AAGCAGTGGTATCAACGCAGAGTAC G, as before). KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502) can substitute the Nextera PCR Master Mix, adapting volumes as required. Tubes were incubated as follows: 72°C for 3 min; 95°C for 30 sec; followed by 10 cycles of linear enrichment PCR: (95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); then hold at 4°C. 4 ul of a 2.5uM solution of each of the following amplification primers were added on ice: Universal primer AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG; Indexed primer CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG. The 8 Ns are to be replaced with the Illumina index sequence of choice. Tubes were returned to the thermocycler held at 4°C and then subjected to 14 iterations of the cycle:( 95°C for 10 sec; 55°C for 30 sec; 72°C for 30 sec); Followed by 72°C for 5 mi and then hold at 4°C. Amplification products were purified using 1-1.4x volume of SPRI magnetic beads, eluting in 30 ul water. Fragment size distribution was checked on a DNA Hi Sensitivity D1000 HS Screentape (Agilent Technologies, 5067-5584/5).

value: Embryo

tag: date

tag: developmental stage


title: iAssembloids neuron CROP-seq rep 1

value: iAssembloid

value: PSA-NCAM enriched hiPSC-derived neurons


title: NCIP His+ Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L62 His+


title: MYLA, afatinib dimaleate, rep 1


title: PT47_Tumor_scVDJ


title: KO1

value: brain

value: 6-8 weeks old


title: WT_CD_3_MPP

description: MPP from CD-fed WT mice

value: control diet


title: MOLM-13 pbody 2

city: Houston

first: Srikanth

last: Kodali

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw sequencing files (FASTQ format) were aligned to the reference genome using STAR with default settings.
Duplicates were removed using samtools 1.12.
Differential expression analysis was performed using R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited .txt files including read counts for each sample.

source_name: Blood

growth_protocol: Cells were cultured in RPMI 1640 supplemented with fetal bovine serum (FBS), L-glutamine, beta-mercaptoethanol, and antibiotics.

extract_protocol:
RNAs were extracted using the miRNeasy Micro Kit (QIAGEN).
RNA libraries were constructed according to NEBNext® Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

value: Blood

value: AML


title: KO_HFD_3_HSC

description: HSC from HFD-fed Sema6d-/- mice

source_name: hematopoietic stem cells

value: high fat diet

value: hematopoietic stem cells


title: WT_CD_2_MPP

description: MPP from CD-fed WT mice


title: PT53_PP_scVDJ


title: NCIP His- Biol Rep 1 (from 24 hr start)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L61 His- 2mM 3-AT

value: yeast cell

value: MATa AGA1::GAL1-AGA1::URA3 ura3-52 trp1 leu2-delta200 his3-delta pep4::BleoMX leu2::pGAL6z-HIS3 prbd1.6R can1 GAL


title: MOLM-13 cyto fraction 2


title: PT50_Tumor_scVDJ


title: PT50_PP_scVDJ


title: PT52_PP_scVDJ


title: NCIP His+ Biol Rep 1 60Hr Sample

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L61 His+ 60h


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His- Biol Rep 2 (technical replicate)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L72 His- (technical 2)


title: PT52_Tumor_scVDJ


title: HEL cyto fraction 1

value: HEL


title: MOLM-13 cyto fraction 1


title: NCIP His+ Biol Rep 1 44Hr Sample

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L61 His+ 44h


title: HEL cyto fraction 2


title: MOLM-13 pbody 1


title: KO_HFD_2_HSC

description: HSC from HFD-fed Sema6d-/- mice


title: KO_CD_4_HSC

description: HSC from CD-fed Sema6d-/- mice


title: WT_CD_4_MPP

description: MPP from CD-fed WT mice

value: wild type

value: multipotent progenitor cells


title: KO_HFD_4_HSC

description: HSC from HFD-fed Sema6d-/- mice


title: NCIP His+ Biol Rep 1 24Hr Sample

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  2 mM-AT.
L61 His+ 24h


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His- Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L72 His-


title: HEL pbody 2


title: PT55_PP_scVDJ

value: PP

value: Cutaneous T-cell lymphoma (CTCL)


title: NCIP His- Biol Rep 1 (high 3-AT)  (from 24 hr start)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  10 mM-AT.
L61 His- 10mM 3-AT


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His+ Biol Rep 2 (technical replicate)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L72 His+ (technical 2)


title: KO_CD_2_HSC

description: HSC from CD-fed Sema6d-/- mice


title: PT53_Tumor_scVDJ

value: Tumor


title: PT56_PP_scVDJ


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His+ Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L72 His+


title: KO_CD_1_HSC

description: HSC from CD-fed Sema6d-/- mice


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His- Biol Rep 1

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L71 His-


title: WT_HFD_5_HSC

description: HSC from HFD-fed WT mice


title: MOLM13 cells, shDDX6, PANDORA-seq, rep2

data_processing:
The raw reads were trimmed by performing SPORTS1.1.2 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Small RNAs were annotated by using SPORTS1.1.2 with the pre-compiled human annotation database.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: DDX6 knockdown


title: HEL pbody 1


title: gt3a-KO, AvrRpt2, 24h, rep1

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds

data_processing:
Sequence data were processed to obtain single cell feature counts by running cellranger (v6.0.1). For snRNA-seq, the –include-introns option was used to align reads to the A. thaliana nuclear transcriptome built with the TAIR10 genome and Araport 11 transcriptome. Count data were analyzed with the R packages Seurat v4 (Hao et al. 2021).
Nuclei were filtered with the following criteria: 200 < RNA UMI count < 7000, RNA gene count > 180, fraction of RNA reads mapped to mitochondrial genome < 5%. Seurat objects of individual samples were merged with the Merge_Seurat_List function of the scCustomize package.
Supplementary files format and content: Processed files except for gt3aKO_snRNA.rds contains snRNA-seq data of each sample after cell filtering

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
Fresh Nuclei purification buffer (NPB; 15mM Tris pH 7.5, 2mM EDTA, 80mM KCl, 20mM NaCl, 0.5mM spermidine, 0.2mM spermine, 1:100 BSA, and 1:100 protease inhibitor cocktail) was prepared before the experiment and chilled on ice. All the following procedures were performed on ice or at 4ºC. Twenty leaves were chopped in 500-1,000 µL of cold NPB with 1:500 Protector RNase IN with a razor blade on ice for 5 min to release nuclei and incubated in 20 mL of NPB. The crude nuclei extract was sequentially filtered through 70 µm and 30 µm cell strainers. Triton-X and NP40 were added to the extract at the final concentration of 0.1% each, and the extract was incubated at 4ºC for 5 min with rotation. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge. When the pellet was green, the pellet was resuspended in 20 mL of NPBd (NPB, 0.1% Triton-X, and 0.1% NP40) with 1:1000 Protector RNase IN by pipetting, followed by centrifugation at 700 x g for 5 min. When the pellet was translucent, this step was skipped. The pellet was then washed by resuspending it in 20 mL of NPB with 1:1000 Protector RNase IN and centrifuging at 500 x g for 5 min with a swing-rotor centrifuge. The pellet was resuspended in 950 µL of 1X Nuclei Buffer (10X Genomics; PN-2000207) with 1:20 Protector RNase IN and 1mM DTT. The nuclei suspension was centrifuged at 50 x g for 3 min in a swing-rotor centrifuge to pellet non-nuclei debris, and the supernatant was taken. This step was repeated one more time. Then, nuclei were counted manually with a hemocytometer. Nuclei were pelleted by centrifugation at 500 x g for 5 min with a swing-rotor centrifuge and removed supernatant leaving approximately 10 µL of buffer. Nuclei were counted again, and up to 16k nuclei were used for the following steps. Single-cell RNA-seq and ATAC-seq libraries were constructed according to the manufacturer’s instruction (10X Genomics, catalog: CG000338). Single-nucleus RNA-seq libraries were sequenced with Illumina NovaSeq 6000 in dual-indexmode with 10 cycles for i7 and i5 index. Single-nucleus ATAC-seq libraries were also sequenced with Illumina NovaSeq 6000 in dual-indexmode with eight and 24 cycles for i7 and i5 index, respectively.
We followed the 10X genomics gene expression assay protocols

value: Leaf


title: gt3a-KO, AvrRpt2, 9h, rep1

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds


title: PT56_Tumor_scVDJ


title: gt3a-KO, AvrRpt2, 9h, rep2

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His- Biol Rep 1  (technical replicate)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L71 His-  (technical 2)


title: WT_HFD_4_HSC

description: HSC from HFD-fed WT mice


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His+ Biol Rep 1 (technical replicate)

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L71 His+ (technical 2)


title: gt3a-KO, AvrRpt2, 24h, rep2

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds


title: WT_HFD_1_HSC

description: HSC from HFD-fed WT mice


title: MOLM13 cells, shDDX6, PANDORA-seq, rep1


title: PT55_Tumor_scVDJ


title: gt3a-KO, Mock, 24h, rep1

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds

value: Mock


title: WT_CD_3_HSC

description: HSC from CD-fed WT mice


title: MOLM13 cells, shDDX6, traditional-seq, rep2


title: mALB (R) His-

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L70 His-


title: MOLM13 cells, shDDX6, traditional-seq, rep1


title: MOLM13 cells, shControl, PANDORA-seq, rep2

value: WT


title: WT_CD_2_HSC

description: HSC from CD-fed WT mice

value: control diet


title: MOLM13 cells, shControl, PANDORA-seq, rep1


title: Hela 4HPP rep 2

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

country: Germany

institute: Max-Planck-Institute for biochemistry

data_processing:
fastqc tool was used to ensure high data quality (v. 0.11.7)
fastq files were mapped to the human genome (Ensembl genome version GRCh38) using the STAR algorithm (v. 2.7.3a)
the reads were counted per gene using the featureCounts tool from the SubRead package (v. 1.4.6-p4)
differential expression analysis was done using DESeq2 (v. 1.26.0)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HeLa cells

growth_protocol: 0.1 x10^6 HeLa cells were plated per well of a 12-well plate in DMEM medium containing 10% FBS and 1% Penicillin-Streptomycin 14 h before treatment.

extract_protocol:
RNA isolation was performed using the RNeasy mini kit from QIAGEN.
mRNA sequencing libraries were prepared from 1ug of total RNA of each sample using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7765, NEB) with NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEB) according to the manufacturer's recommendations.

treatment_protocol: The cells were treated for 24 h in triplicates per treatment with DMEM + 200 µM PP or 4HPP

value: HeLa cells

value: 24h 4HPP


title: NICP, mALB (T), mALb (R),An/Bn, P, N, PA series His+ Biol Rep 1

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L71 His+


title: MOLM13 cells, shControl, traditional-seq, rep2


title: mALB (R) His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L70 His+


title: Ovary Homozygous 6-backup

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Sequencing reads were trimmed of adapters and filtered
STAR alignment was performed against mouse reference
Quantification of reads was determined by Novogene
DEG analysis was performed with DeSeq2
clusterProfiler was used to perform enrichment analyses
Assembly: mm10
Supplementary files format and content: Text files (.txt) containing tab-delimited tables of Raw Counts and Differential Expression of Genes results from Ovary and Uterus samples.

source_name: Ovary

growth_protocol: Mice were housed at animal facilities at the National Institutes of Health, Frederick, MD. Animal handling was conducted in accordance with the ACUC, under protocol number 21-018.

extract_protocol:
RNA isolation was performed with a Zymo tissue RNA isolation kit, then tested via an Agilent BioAnalyzer analysis.
Illumina paired-end total RNA-seq

treatment_protocol: All mice were age matched (20-25 weeks).

value: Ovary

value: ARE-/-


title: Hela 4HPP rep 1


title: MOLM13 cells, shControl, traditional-seq, rep1


title: Hela PP rep 3

value: 24h PP


title: Ovary Homozygous 2


title: WT_CD_4_HSC

description: HSC from CD-fed WT mice

value: hematopoietic stem cells


title: An/Bn, NICP, N, PA series His-

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L68 His-

value: yeast cell

value: MATa AGA1::GAL1-AGA1::URA3 ura3-52 trp1 leu2-delta200 his3-delta pep4::BleoMX leu2::pGAL6z-HIS3 prbd1.6R can1 GAL


title: gt3a-KO, Mock, 9h, rep1

description:
10x Genomics snRNA-seq
gt3aKO_snRNA.rds


title: Hela 4HPP rep 3


title: DHD0, DHD1, DHD2, mALb (T) His- Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L49 His-


title: DHD0, DHD1, DHD2, mALb (T) His+ Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L49 His+


title: An/Bn, NICP, N, PA series His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L68 His+


title: Ovary Heterozygous 4

value: ARE+/-


title: Ovary Homozygous 3


title: Bcl & inhibitors  His-

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L45 His-


title: Ovary Heterozygous 2


title: HEL cells, shDDX6, PANDORA-seq, rep2

source_name: HEL

value: HEL


title: Ovary Heterozygous 1


title: Hela PP rep 1


title: HEL cells, shDDX6, PANDORA-seq, rep1


title: Hela PP rep 2


title: HEL cells, shDDX6, traditional-seq, rep2


title: CeD6_NT_Control2d

city: Stanford

first: Antonio

last: Santos

state: California

address: 265 Campus Dr.

department: Hematology

institute: Stanford University

description: 10X Genomics

data_processing:
Sequences from scRNA-seq were processed with Cell Ranger (v.3.0.2) software (10X Genomics) with demultiplexing, UMI (unique molecular identifier) collapsing and alignment to the GRCh38 human transcriptome. scRNA-seq data from CLIP versus gliadin treatment were loaded into Seurat objects following their standard pipeline
Assembly: GRCh38
Supplementary files format and content: mtx
Supplementary files format and content: clonotypes, contig_annotations

source_name: organoid

extract_protocol:
Organoids were dissociated in 2030 units ml-1 collagenase IV (Worthington, LS004212) at 37°C for 40 min, washed twice in PBS, and digested in 400 μg ml-1 Liberase-TL (Roche, 5401020001) and 416 units ml-1 DNase I (Worthington, LS006328) at 37°C for 30 min with intermittent shaking. Samples were washed twice in FACS buffer (0.6 mM EDTA (Invitrogen, AM9261), 5% FBS, in PBS)
FACS-isolated organoid cells were subjected to droplet based scRNA-seq with the 10X Genomics Chromium single cell 5’ platform, with or without single-cell TCR/Ig V(D)J library, per the manufacturer’s protocol using Chromium Next GEM Single Cell 5' Kit v2 (PN-1000263), Library Construction Kit (PN-1000190), Chromium Single Cell Human TCR Amplification Kit (PN-1000252) and Chromium Single Cell Human BCR Amplification Kit (PN-1000253). Cell capture, library construction, and sequencing were performed as previously described

tag: patient

tag: batch

tag: stimulation

value: CLIP 2d

value: organoid

tag: culture medium

value: WENR

value: EpCAM+ and CD45+


title: Ovary Wildtype 3

tag: tissue

tag: strain


title: Bcl & inhibitors  His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L45 His+

tag: genotype


title: HEL cells, shDDX6, traditional-seq, rep1

value: DDX6 knockdown


title: DHD0, DHD1, DHD2, mALb (T) His- Biol Rep 1

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L44 His-

tag: cell type


title: DHD0, DHD1, DHD2, mALb (T) His+ Biol Rep 1

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L44 His+


title: Ovary Wildtype 2

value: WT


title: Ovary Wildtype 1


title: CeD5_NT_Control2d

description: 10X Genomics

value: control


title: DHD0 (subset), DHD2, mALb (T) His+-

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM-AT.
L43 His-


title: Uterus Homozygous 2

source_name: Uterus

value: Uterus


title: CeD5_D2_Gliadin2d

description: 10X Genomics

value: Gliadin 2d


title: HEL cells, shControl, PANDORA-seq, rep1


title: DHD0 and DHD1  His- Barcodes Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  No 3-AT.
L39(3) His+


title: Uterus Homozygous 1


title: CeD4_CA2D_CLIP2d

description: 10X Genomics


title: CeD6_D2_Gliadin2d

description: 10X Genomics


title: CeD4_GL2D_Gliadin2d

description: 10X Genomics


title: Uterus Heterozygous 3


title: Uterus Heterozygous 2


title: DHD0 and DHD1  His- Barcodes Biol Rep 1

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  No 3-AT.
L39(2) His+


title: H460-IR-2 (S75)

city: Atlanta

first: Xingming

last: Deng

state: GA

address: 1701 Uppergate Dr NE, Radiation Oncology, Building C, 3rd floor, bench 48-54

department: Radiation Oncology

institute: Winship Cancer Institute, Emory University

description: CRISPR GeCKO v2 library (A and B)

data_processing: Other. This is a DNA sequence and especially for the CRISPR screen. The primers target the barcodes which are designed to bind to every gRNA. The sequence method is described in Feng Zhang's paper.

source_name: cell line

growth_protocol: H460 cells were cultured in RPMI-1640 medium with 10% FBS

extract_protocol:
We extracted whole genome DNA of each sample by Blood & Cell Culture DNA Maxi Kit (QIAGEN-13362)
We purchased the library from Addgene (1000000049). The library preparation and infection were following Feng Zhang's paper (Julia Joung, et al. Nature Protocol, 2017)

treatment_protocol: The three repeats in IR group were treated with 4 Gy ionizing radiation

value: cell line

value: NSCLC

tag: treatment

value: 4 Gy ionizing radiation


title: HEL cells, shControl, PANDORA-seq, rep2

tag: cell line


title: Uterus Heterozygous 1


title: H460-IR-1 (S74)

description: CRISPR GeCKO v2 library (A and B)


title: Uterus Homozygous 3

value: ARE-/-


title: Uterus Wildtype 3


title: CeD2_AS7

description: 10X Genomics


title: Adult hermaphrodite, prg-1(∆PAZ-domain), rep 2

first: Jacob

middle: Manuel

last: Ortega

state: Texas

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description: Small RNA sample

data_processing:
Raw data was evaluated for quality control by Novogene Co, Ltd by an in house data filtration process. In brief, raw reads are evaluated for poor base quality, 5' primer contaminants, lack of 3' primer, lack of insert tag, presence of polyA/T/G/C, and finally reads are trimmed of adapters. On average, 98% of reads for each sample were retained after Novogene filtration. Trimmed data was used for downstream analysis.
Reads were aligned to C. elegans piRNAs (piRNAdb.cel.v1_7_6.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Aligned piRNA reads for each sample were normalized to total number of reads mapping to the C. elegans genome (per million).
Assembly: piRNAdb.cel.v1_7_6
Assembly: ce11genome
Supplementary files format and content: xlsx file includes includes raw counts of genome mapped reads and piRNA mapped reads
Supplementary files format and content: xlsx file includes normalization of piRNA reads to the total number of reads aligning to the C. elegans genome per million

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Plates of C. elegans hermpahrodite stocks for each genotype were synchronized and cultured at 25°C. Once animals had reached adulthood, they were collected and a lysate was prepared from whole worms. This lysate was used to perform RNA IP of V5-tagged Wild Type or ∆PAZ mutant PRG-1 protein.

extract_protocol:
Small RNAs bound to PRG-1 protein were extracted from RNA IP samples by standard chloroform-phenol RNA extraction and sent to Novogene Co, Ltd for library construction and sequencing.
Libraries were constructed by Novogene Co, Ltd using an in house protocol.

value: Whole Animal


title: H460-Control-3 (S73)

description: CRISPR GeCKO v2 library (A and B)

value: No treatment


title: HEL cells, shControl, traditional-seq, rep2


title: CeD1_Sample3_CLIP2d

description: 10X Genomics

value: Live single cells


title: CeD1_Sample5_Gliadin2d

description: 10X Genomics


title: DHD0 and DHD1 His+ Barcodes Biol Rep 2

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  No 3-AT.
L39(3) His-

value: yeast cell

value: MATa AGA1::GAL1-AGA1::URA3 ura3-52 trp1 leu2-delta200 his3-delta pep4::BleoMX leu2::pGAL6z-HIS3 prbd1.6R can1 GAL


title: Uterus Wildtype 2


title: DHD0 (subset), DHD2, mALb (T) His+

description:
An all-by-all PPI assay collected with version one of MP3-Seq.  1mM 3-AT.
L43 His+


title: H460-Control-2 (S72)

description: CRISPR GeCKO v2 library (A and B)


title: Adult hermaphrodite, Wild Type, rep 2

description: Small RNA sample

value: Wild Type


title: HEL cells, shControl, traditional-seq, rep1

value: HEL


title: CeD2_AS8

description: 10X Genomics

value: organoid

value: WENR


title: H460-Control-1 (S71)

description: CRISPR GeCKO v2 library (A and B)


title: H460-IR-3 (S76)

description: CRISPR GeCKO v2 library (A and B)


title: Uterus Wildtype 1-backup

value: WT


title: Adult hermaphrodite, Wild Type, rep 1

description: Small RNA sample


title: S-PRT3

status: Public on Jul 11 2024

city: Philadelphia

first: Ioannis

last: Verginadis

state: PA

address: 3400 Civic Center Blvd, Perelman School of Medicine, TRC 8-155

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq datasets were quality checked and pre-processed using FastQC and Cutadapt. Alignment of the trimmed sequencing reads was conducted against the Mus musculus (version GRCm39) genome using the STAR aligner.
Gene-level quantification was performed using RSEM and expected counts for each gene were extracted for downstream analysis.
Trimmed mean of M-values (TMM) normalization was applied to RSEM read counts and differential expression analysis was conducted using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files that includes raw counts for each sample

source_name: Heart (apex)

extract_protocol:
The tissue was minced, homogenized, embedded in a lysing solution, and total RNA was isolated using a Macherey–Nagel kit. RNA concentrations were measured with Qubit Flourometric Quantification (Theromo Fisher Scientific), RNA integrity number (RIN) was determined with Bioanalyzer on RNA 6000 Nano Kit (Agilent Technologies), all samples were high quality with RIN > 9.
RNA-seq libraries were generated using NEBNext Poly(A) + ultra–Directional RNA library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s instructions.

treatment_protocol: Hearts have been focally irradiated in the apex with 40 Gy (S-PRT or F-PRT). Un-irradiated controls were used (NR)

value: Heart (apex)

value: 40 Gy S-PRT


title: S-PRT4


title: F-PRT2

value: 40 Gy F-PRT


title: F-PRT3


title: F-PRT4


title: S-PRT1


title: NR4


title: NR3


title: S-PRT2


title: NR2


title: NR1


title: adult forebrain, genome-wide, rep3

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

description:
Rep3
Forebrain_CIMERA-seq_sample_1-4_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.mouse.annotation.txt

data_processing:
Sequencing data were processed using SCRAP (SCRAP release 2.0) bioinformatic pipeline to identify the significant sncRNA:targetRNA interactions in each sample (Eadara et al. 2023; Mills et al. 2022), for which code is deposited at https://github.com/Meffert-Lab/SCRAP.
Peak calling was performed by setting SCRAP variables to consider only high confidence sncRNA binding sites across the genome supported by at least 3 chimeric sncRNA:target RNA reads in at least 2 sample libraries.  Peak calling was performed as groups: group1: Forebrain CIEMRA-seq sample 1-4 group 2: Forebrain CIMERA-seq sample 5-7 group 3: Excitatory neuron selective CIMERA-seq sample 1-3 group 4: IgG CIMERA-seq sample 1-2
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include counts for each chimeric RNA (sncRNA:target RNA pairs)
Library strategy: CIMERA-seq

source_name: forebrain

extract_protocol:
Mouse brain tissue in Homogenization buffer (1X HBSS supplemented with 5 mM MgCl2, 10 mM HEPES (pH 7.4) and 1X HALT protease/phosphatase inhibitor) is homogenized by 12 passes through a 21G needle. UV irradiate homogenates 3x with (4000 µJ/cm2 x 100) on a perfluoroalkoxy (PFA) petri dish, mixing samples between rounds. Transfer irradiated tissue homogenate to a microfuge tube and centrifuge 900 x g for 5 minutes at 4 °C.  Immunoprecipitation from the cell pellets were done with anti-Ago2 (2D4, Wako, 018-22021)  for total CIMERA-seq, anti-myc (9B11, Cell Signaling, 2276) for cell-selective CIMERA-seq, and anti-IgG1 (Invitrogen, 14-4714-82) for negative control.
Libraries were prepared by intermolecular ligation of small non-coding RNA and target RNA, RNA isolation from Ago protein, ligation of 3’ and 5’ adaptors, reverse transcription, minimal PCR amplification, gel purification and size selection.
custom sequencing libraries with 150 base-pair paired-end sequencing and a read depth of 61 – 138 million reads per sample (Illumina HiSeq X or NovaSeq)

treatment_protocol: The mouse line with conditional tAgo2 expression in excitatory neurons was generated by crossing B6Tg(Camk2a-Cre/ERT2) (Erdmann et al. 2007), and B6.Cg-Gt(ROSA)26Sortm1(CAG-GFP/Eif2c2)Zjh/J (Jackson Laboratory #017626). Tamoxifen (2 mg) was administered to mice intraperitoneally once per day for 5 days. Gene induction was allowed to occur for 14-21 days after the final injection before tissue harvest at 10-12 weeks of age.

value: forebrain


title: adult forebrain, genome-wide, rep2

description:
Rep2
Forebrain_CIMERA-seq_sample_1-4_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.mouse.annotation.txt


title: adult forebrain, genome-wide, rep4

description:
Rep4
Forebrain_CIMERA-seq_sample_1-4_peakcalling.summary.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.txt
Forebrain_CIMERA-seq_sample_1-4_peaks.bed.mouse.annotation.txt