title: parn1_w03h9_rep2

city: Columbus

first: Wen

last: Tang

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore. Sequences were then collapsed and transformed into fasta files using cutsom shell scripts.
Reads were aligned to contaminating RNAs (rRNAs, tRNAs, snRNAs…) using Bowtie. Reads that failed to align were aligned to the genome using Bowtie.
Aligned reads were normalized and assigned to genomic features using custom shell scripts. Alignments were converted to BigWig files using UCSC Tools.
Downstream analysis was preformed using R/Python/IGV.
Assembly: WormBase WS279
Supplementary files format and content: Unique fasta file of collapsed reads

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 C on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached day 1 adulthood.

extract_protocol:
60,000 L1 larvae were plated to 150 mm NGM plates supplemented with 2 mL of concentrated OP50 food. Approximately 64 hours after plating L1 larvae, day 1 adults with eggs were collected from plates using M9 solution. Harvested animals were washed twice with M9 and once with water. Animals were then suspended in TRI Reagent solution (Sigma) and frozen at -80°C until RNA extraction was performed. To extract RNAs animals suspended in TRI Reagent solution were thawed and lysed using a Bead Mill (Thermo Fisher Scientific). Bromo-chloropropane (Sigma) was added to the lysed worms and centrifuged at 12,000 x g for 15 minutes. Following centrifugation, the aqueous phase was pipetted to an equal volume of cold isopropanol and placed at -20°C for 1 hour to precipitate RNAs. RNAs were pelleted by centrifugation at 20,000 x g for 15 minutes at 4°C. Total RNAs were washed with 75% EtOH twice and suspended in RNAse free water. Small RNAs were enriched from total RNAs using the MirVana miRNA isolation kit according (Thermo Fisher Scientific).
Small RNAs were treated with RNA phosphatase PIR-1 to remove gamma and beta phosphates from the 5' triphosphorylated RNAs (50). Monophosphorylated RNAs were ligated to 3' adapters ( rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/, IDT) using T4 RNA ligase 2 in 25% PEG 8000 (NEB) at 15 C overnight. A 5' adapter (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to RNAs to the product using T4 RNA ligase 1 (NEB) for 4 hours at 15 C. Ligated products were reverse transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) to convert RNA to cDNA libraries. cDNA libraries were amplified by PCR and subsequently sequenced on an Illumina Novaseq platform (SP2 x 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: whole animal


title: t32lps4 (RNA-seq)

status: Public on Oct 01 2023

type: SRA

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

library_source: transcriptomic

data_processing:
Used bcl2fastq for demultiplexing
cutadapt (v1.12) for trimming adapters
FASTX-Toolkit for filtering low-quality reads
FastQC (v0.11.5) for quality control
Clean reads were mapped to zebrafish transcriptome (GRCz11.92) and genome (GRCz11) by STAR (version 020201)
Read counts were extracted from mapping result of STAR, and merged into one matrix
DESeq2 (v1.11.1) was used for differential gene expression analysis
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited matrix containing read counts of each library

molecule: total RNA

organism: Danio rerio

source_name: spleen

growth_protocol: Zebrafish adults were maintained in a recirculating aquatic system at 28 ± 0.5 °C. Eggs were incubated in aquatic system water containing 0.1 mg/L methylene blue (Sigma-Aldrich, USA) until first feeding. One-third of water was refreshed every day. The temperature for embryo incubation and larva growth were maintained at either of 24 ± 0.5 °C, 28 ± 0.5 °C or 32 ± 0.5 °C. The fish were sequentially fed SDS (Special Diets Services, SDS, UK) 100, 200, 300, and 400 according to their ontogeny stages. The photoperiod was 12 h light: 12 h dark.

extract_protocol:
Total RNA was isolated from spleen using the PicoPure RNA Isolation kit (ThermoFisher Scientific, USA) with some modifications. In brief, spleen was mashed in 100 μl Extraction Buffer using a 1 ml pipette tip, and pipetted up and down several times to release cells thoroughly. The homogenate was incubated at 42 °C for 30 min, centrifuged at 3,000 × g for 2 min. The supernatant was transferred to a new microcentrifuge tube, mixed thoroughly with 100 μl 70% Ethanol, and bound to the preconditioned purification column by centrifugation. The RNA was washed by Wash Buffer 1 and 2 sequentially, and dissolved in 30 μl Elution Buffer. RNA quality and concentration were determined using High Sensitivity RNA ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).
Libraries were built following the mannual of the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA). Fifty ng total RNAs from each replicate were purified with Oligo(dT) beads, fragmented to ~200 nucleotides by incubating at 94 °C for 15 min. The first and second strand of complement DNAs (cDNAs) were synthesized sequentially. The double-stranded cDNAs were repaired ends, ligated with universal adaptors on the 5' end and indexed adaptors on the 3' end. The ligated cDNAs were amplified on a PCR thermal cycler with the program of: 98 °C for 30 s, 1 cycle; 98 °C for 10 s, 65 °C for 75 s, 14 cycles; 65 °C for 5 min, 1 cycle. The amplified mRNA libraries were purified with SPRIselect beads, and assessed quality and quantity using High Sensitivity D1000 ScreenTapes on a TapeStation 2200 (Agilent Technologies, USA).

treatment_protocol: Zebrafish adults were anesthetized using 200 mg/L tricaine methanesulfonate (MS-222; Sigma-Aldrich, USA) and gently i.p. injected with 2 μl of 50 mg/ml LPS from Pseudomonas aeruginosa 10 (Sigma-Aldrich, USA), and kept for 12 h. Then, fish were euthanized by immersing in 300 mg/L MS-222. The spleen was dissected immediately, snap-frozen in liquid nitrogen, and stored at -80 °C.

tag: strain

value: AB

tag: developmental stage

value: adult

tag: age

value: 100 d post-fertilization

tag: treatment

value: LPS

tag: temperature

tag: tissue

value: spleen


title: Opossum2_neun_neg_1

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

country: USA

institute: University of Washington

library_source: transcriptomic single cell

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: ASM229v1
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

molecule: nuclear RNA

organism: Didelphis marsupialis

source_name: Retina

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single cell RNA sequecning (10X Genomics)

value: Retina

tag: cell type

value: Retinal neurons


title: parn1_w03h9_rep1

state: Ohio

tag: genotype


title: Opossum2_neun_pos


title: t32lps3 (RNA-seq)


title: Opossum_neun_neg_B5


title: parn1_prg1D654A_rep2


title: Opossum_neun_neg_B4


title: t32lps2 (RNA-seq)


title: parn1_prg1SGmut_rep2


title: Control_B19

city: shijiazhuang

first: zhiming

last: zhao

state: hebei

address: 215 heping west road

country: China

institute: The second hospital of hebei medical university

data_processing:
Illumina Casava1.7 software used for basecalling
The raw reads generated by RNA-seq were processed by removing the Illumina adapters with Trimmomatic and then low-quality regions at the 5' and 3' ends were deleted.
Counculat Counts and TPM with alignment-free software, kallisto, Genome index were build form HUMAN reference genome GRCh38.p13, downloaded from GENCODE (https://www.gencodegenes.org/human/release_36.html).The GTF annotation were also from GENCODE Release 36
Assembly: GENCODE GRCh38.p13
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample

organism: Homo sapiens

source_name: Cumulus granule cells

extract_protocol:
testis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
These libraries were constructed based on the recommendations of the NEBNext®Ultra™ Directed RNA Library Preparation Kit. RNA fragments and short-stranded RNA were carried using NEBNext First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using a random hexamer primer and M-MuLV reverse transcriptase. Subsequently, second strand cDNA was synthesized using DNA polymerase I and RNase h, the purified second strand cDNA ends were repaired, and then poly(A) and A adapters were added. A fragment of approximately 300 base pairs (bp) was selected using the UNG enzyme.

value: Cumulus granule cells

value: manual sorting

tag: disease state

value: control

tag: Sex

value: female


title: t32ct10 (RNA-seq)


title: t32lps1 (RNA-seq)


title: parn1_prg1SGmut_rep1


title: Opossum1_neun_neg_1


title: Ctrl TGFb_R3

type: RNA

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2  Microarrays (Agilent-026655) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HMECT cells

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Immortalized human Mammary Epithelial Cells (HMECT) were grown in Mammary Epithelial Cell Growth Medium (MECGM, C-39115 Promocell) with 1% penicillin/streptomycin (Life Technologies). Cells were maintained at 37°C under a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from HMECT cells in culture using NucleoSpin® RNA (Macherey Nalgen) following the manufacturer's recommendations

treatment_protocol: HMECT were transduced with a retrovirus pWZL control vector or pWZL RSK3 encoding vector. After one week of selection with neomycin, cells were treated or not with TGFβ (PeproTech) at the concentration of 0.5 ng/mL for 48h before RNA extraction.

tag: source

value: Cell culture

tag: transduction

value: control vector pWZL

value: TGFb


title: RSK3 TGFb_R3

value: RSK3 pWZL expression vector


title: parn1_drh3TS_rep2


title: t32ct8 (RNA-seq)


title: Ctrl TGFb_R1


title: NT_R3


title: Opossum_neun_pos_B2


title: parn1_drh3TS_rep1


title: RSK3 TGFb_R2


title: RSK3 TGFb_R1


title: parn1_prg1D654A_rep1


title: Opossum1_neun_pos


title: t32ct3 (RNA-seq)


title: t32ct2 (RNA-seq)


title: THP-1_FOXOi_rep3

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: Gene expression six hours after AS1842856 treatment.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to  Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies)  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: THP-1, FOXO inhibitor (AS1842856) treated cell, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 10% FBS, RPMI1640 + 1%penicillin/streptomycin

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Macherey-Nagel) according to the manufacturer's instructions.

value: leukemia cell line


title: MN28_skin_post_S67

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
Initial quality control analysis of RNA sequencing FASTQ data was performed using FastQC software (v0.11.5). FASTQ data were trimmed with Trimmomatic (v0.33.0). Kallisto (v0.43.0) was used for pseudoalignment and quantifying transcript abundance.
addition of 3 reads to all values
quantile normalization
Assembly: CanFam3.1
Supplementary files format and content: tab delimited txt file of normalized counts

molecule: polyA RNA

organism: Canis lupus

source_name: skin

growth_protocol: fresh frozen tissues and cell lines

extract_protocol:
RNA was extracted from tumor tissue at baseline, and from tumor tissue samples obtained at amputation, post-treatment. RNA was also extracted from cell lines that were established pre-treatment from each case, and from normal skin tissue from each case as a non-malignant control. When available, RNA was also extracted from lung metastases. Tissue samples were disrupted with a tissue homogenizer, and RNA was extracted using a commercially available kit (QIAGEN RNeasy mini kit). RNA was stored at -80°C.
Dual-indexed sequencing libraries were prepared using the Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit.
(2x50-bp paired-end, on a NovaSeq S2

treatment_protocol: Pre-treatment biopsies were obtained from the lesion using 4mm Michele trephine bone biopsy instruments. One pre-treatment tumor biopsy section was placed in 10% neutral buffered formalin for histopathology. A second pre-treatment section was further divided, with one piece used to establish a cancer cell line and a second piece frozen at -80°C for later RNA extraction.Ten days post-treatment with VSV-cIFNβ-NIS, dogs underwent surgical amputation of the affected limb and removal of the associated lymph node(s). A skin punch biopsy was performed, and the tissue frozen at -80°C for later RNA extraction). The amputated limbs were sectioned longitudinally and tumor sections of approximately 5mm thickness were obtained and placed in 10% neutral buffered formalin. Tumor sections were placed in 10% ethanol for slow decalcification, or in acid for rapid decalcification. Separate sections of the tumor were frozen at -80°C for later RNA extraction.

value: skin

tag: ID


title: parn1_drh3RNAi_rep1

value: whole animal

value: drh-3 RNAi


title: Ctrl TGFb_R2


title: Opossum1_neun_neg_2


title: parn1_drh3RNAi_rep2


title: MN28_bone_pre_1_S65

source_name: osteosarcomaTissue

value: osteosarcomaTissue

value: pretreatment


title: THP-1_FOXOi_rep2

source_name: THP-1, FOXO inhibitor (AS1842856) treated cell, replicate 2


title: THP-1_FOXOi_rep1

source_name: THP-1, FOXO inhibitor (AS1842856) treated cell, replicate 1


title: NT_R2


title: parn1_oma1RNAi_rep2

value: oma-1 RNAi


title: parn1_oma1RNAi_rep1


title: t28lps4 (RNA-seq)

value: AB

value: adult

value: 100 d post-fertilization

value: LPS

value: spleen


title: parn1_ekl1RNAi_rep2

value: ekl-1 RNAi


title: MN28_bone_cell_S68

source_name: cellLine

value: cellLine


title: Peromyscus3_CD73_dpS2

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: HU_Pman_2.1
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Peromyscus maniculatus

extract_protocol:
Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation. They were dissociated in papain, followed by FACS sorting. Cells were stained for either THY1/CD90 to enrich for RGCs or for CD73 to deplete photoreceptors.
Single cell libraries were generated using the Chromium 3’ V3 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single cells were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single cell RNA sequecning (10X Genomics)

value: Retina

value: Retinal neurons

value: Contorl

value: Depleted of CD73+ cells


title: MN27_skin_post_S63

value: skin


title: Peromyscus2_CD73_dpS2


title: t32ct6 (RNA-seq)

value: control


title: t28lps3 (RNA-seq)


title: THP-1_CTL_rep3

source_name: THP-1, negative control cell, replicate 3

value: leukemia cell line


title: t28lps2 (RNA-seq)


title: parn1_ekl1RNAi_rep1

value: whole animal


title: THP-1_CTL_rep2

source_name: THP-1, negative control cell, replicate 2


title: MN27_bone_post_S62

value: osteosarcomaTissue

value: VSV


title: parn1_rde3_rep2


title: NT_R1

value: Cell culture

value: control vector pWZL


title: THP-1_CTL_rep1

source_name: THP-1, negative control cell, replicate 1


title: t28ct7 (RNA-seq)

value: AB

value: adult

value: 100 d post-fertilization


title: Peromyscus2_CD73_dpS1


title: t28lps1 (RNA-seq)

value: LPS

value: spleen


title: MN28_bone_post_1_S66


title: parn1_rrf1_rep2


title: MN27_bone_cell_S64

value: cellLine


title: parn1_rde3_rep1


title: t28ct3 (RNA-seq)


title: t28ct5 (RNA-seq)


title: Peromyscus1_CS73_dpS1

value: Retina

value: Retinal neurons


title: parn1_ego1RNAi_rep2

value: ego-1 RNAi


title: MN26_bone_post_S59

value: Placebo


title: Peromyscus1_CD90_S2

value: Contorl

value: Enriched for CD90+ cells


title: Peromyscus1_CS73_dpS2

value: Depleted of CD73+ cells


title: t28ct2 (RNA-seq)

value: control


title: parn1_rrf1_rep1

value: whole animal


title: MN25_lung_cell_S57


title: parn1_ego1RNAi_rep1


title: t28ct1 (RNA-seq)


title: t24lps8 (RNA-seq)


title: RIP-Seq MSTR-1 RIP rep 2

city: Toronto

first: Matthew

last: Eroglu

state: ON

address: 686 Bay St

department: DSCB

country: Canada

institute: Hospital for Sick Children

description: MSTR-1 RIP rep 2

data_processing:
Concatenate fastq files
alignment with RNA STAR (https://github.com/alexdobin/STAR) on Galaxy
peak calling with PEAKachu (https://github.com/tbischler/PEAKachu) on Galaxy
coverage calculated with bamcoverage deepTools2 (https://github.com/deeptools/deepTools) on Galaxy
Genome_build: WS253
Supplementary_files_format_and_content: peak files, bed; coverage plots, bigwig

source_name: Whole worm lysate

growth_protocol: Standard NGM

extract_protocol:
RNA crosslinked to affinity purified MSTR-1::FLAG
by Donnelly Sequencing Centre, Toronto, Canada, based on a modified small RNA protocol

treatment_protocol: 30 min crosslink with 2% formaldehyde

tag: Stage

value: Young adult


title: Lizard_NEUNneg

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: AnoSag2.1
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Anolis sagrei

extract_protocol:
Frozen retinal tissues were homogenized in a Dounce homogenizer in 1ml Tris-based lysis buffer with 0.1% NP-40. Nuclei were stained with NEUN/RBFOX3 and/or CHX10/VSX2, washed once, pelleted at 500g for 5min, resuspended in PBS/BSA and stained with DAPI. NEUN+ and/or CHX10+ DAPI+ single nuclei were collected using a flow cytometer. The sorted nuclei were pelleted again, resuspended in PBS/BSA solution, and adjusted to a concentration of 1000 nuclei/µL. ~12µL of the nuclei suspension was loaded into a 10X Chromium Single Cell Chip (10X Genomics, Pleasanton, CA) with a targeted recovery of 8000 nuclei.
Single nuclei libraries were generated using the Chromium 3’ V3.1 platform (10X Genomics, Pleasanton, CA) according to the manufacturer’s protocol. Briefly, single nuclei were partitioned into Gel-beads-in-EMulsion (GEMs) where nuclear lysis and barcoded reverse transcription of RNA would take place to yield full-length cDNA; this was followed by amplification, enzymatic fragmentation, and 5’ adaptor and sample index attachment to yield the final libraries.
Single nucleus RNA sequecning (10X Genomics)

value: Control


title: MN26_skin_post_S60

value: skin


title: MN25_lung_2_S55

source_name: metastasis

value: metastasis


title: t24lps4 (RNA-seq)

value: AB

value: adult

value: 100 d post-fertilization


title: Lizard_NEUNpos


title: Peromyscus1_CD90_S1


title: RIP-Seq MSTR-1 input rep 2

description: MSTR-1 input rep 2


title: t24lps3 (RNA-seq)

value: LPS

value: spleen


title: MN26_bone_cell_S61

value: cellLine


title: MN25_bone_pre_1_S52

value: osteosarcomaTissue

value: pretreatment


title: Lizard_Chx_10

value: Retina

value: Retinal neurons


title: Lizard_Nueun_2


title: Peromyscus1_CS73_dpS3

value: Contorl

value: Depleted of CD73+ cells


title: MN25_bone_post_1_S53

value: VSV


title: MN26_bone_pre_S58


title: RIP-Seq MSTR-1 RIP rep 1

description: MSTR-1 RIP rep 1

value: Young adult


title: t24lps2 (RNA-seq)


title: t24lps1 (RNA-seq)


title: RIP-Seq N2 RIP rep 2

description: N2 RIP rep 2


title: MN24_bone_post_S50

value: Placebo


title: Lizard_Anole_S14

value: Control


title: RIP-Seq N2 RIP rep 1

description: N2 RIP rep 1


title: MN24_bone_cell_F12_S56


title: RIP-Seq MSTR-1 input rep 1

description: MSTR-1 input rep 1


title: Lizard_Nueun_1


title: RIP-Seq N2 input rep 2

description: N2 input rep 2


title: fem2-3, BS seq

city: Nanjing

first: Dachao

last: Xu

address: Weigang No.1

institute: Nanjing Agricultural University

library_source: genomic

data_processing:
Low-quality sequences(q<20) and adapters were trimmed using trimmomatic.
Reads were mapped to MSU7.0 using bismark with default parameters
Assembly: MSU version 7.0

molecule: genomic DNA

organism: Oryza sativa

source_name: seedling

extract_protocol:
Genomic DNA was extrated using CTAB method.
Genomic DNA was sonicated and then end-repaired with End repair Enzyme Mix. The blunt-ended DNA were treated with Klenow fragment and dATP to yield a proruding3-"A" and cytosine-methylated adaptors from Illumina were ligated according to manufacture's instructions.

value: seedling

value: 18-day-old seedling cells

value: fem2-3 mutant


title: t24ct4 (RNA-seq)

value: AB

value: adult

value: 100 d post-fertilization

value: control


title: MN25_lung_1_S54

value: metastasis


title: t24ct8 (RNA-seq)

value: spleen


title: RIP-Seq N2 input rep 1

description: N2 input rep 1


title: MN24_bone_cell_F07_S51

value: cellLine


title: t24ct5 (RNA-seq)


title: MN23_skin_post_S48

value: skin


title: fem2-1, BS seq

value: fem2-1 mutant


title: MN23_bone_post_S47

value: osteosarcomaTissue


title: fem1-1, BS seq

value: fem1-1 mutant


title: fem2-3,rep3

data_processing:
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Assembly: MSU version 7.0

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit (NEB) following manufacturer's protocols.


title: t24ct2 (RNA-seq)


title: Cobb broiler with ST infection, replicate 2, scRNAseq

city: Bejing

first: Qi

last: Zhang

address: No2 Yuanmingyuan West Road, Haidian

institute: Chinese Academy of Agricultural Sciences Institute of Animal Science

description: 10× Genomics

data_processing:
CellRanger-3.1.0 (10× Genomics) was used for data analysis and processing.
Assembly: GRCg6a
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: matrix files

organism: Gallus gallus

extract_protocol:
Fresh spleen tissues were mechanically minced in PBS with 5% FBS (HyClone, Logan, UT, USA), and a syringe plunger was used to grind the spleen fragments through 100-μm and 40-μm cell strainers (Corning, NY, USA). The filtrated liquid containing cells was centrifuged at 500 × g for 10 minutes, the supernatant was discarded, and the cells were washed twice with 5% FBS and then suspended in 1640/DMEM with 5% FBS. The cells were incubated on ice with mouse anti-chicken CD45-PE (0.1 mg/mL; SouthernBiotech, UAB, AL, USA) for 30 minutes and 7-AAD (5 μL/105 cells; BIOESTABLISH, Beijing, China) for 10 minutes. CD45+ cells were collected by flow cytometry.
After obtaining the single-cell suspension, we detected the cell activity of all samples (the samples with cell activity >85%, single good dispersion, and low impurity content were collected). Subsequently, single-cell gel bead emulsions (GEMs) were prepared by microfluidic channels, and the cell concentration was controlled within 700-1200 cells/μL. In the GEM reaction system, cells were broken and lysed. The released mRNA and poly-dT primer sequence were activated by reverse transcriptase to generate full-length cDNA and amplify and construct the library. The StepOnePlus Real-Time PCR System was used for q-PCR to accurately quantify the effective concentration of the library (the index of the effective concentration of the library was not less than 10 nM). The qualified library was sequenced by the Illumina platform to obtain raw reads. According to the 10× transcriptome library structure, the data were intercepted to obtain Read1 and target Read2, containing barcode and UMI sequence information.

treatment_protocol: 25 Cobb broiler chicks were purchased from the Poultry Breeding Co., Ltd. (Beijing, China), and 22 Beijing-You chicks were acquired from the Changping Experimental farm of the Institute of Animal Sciences (Beijing, China). All chickens were maintained in sterilized isolation ventilated cages (IVCs) (IPQ-type 3 negative pressure isolator) at the experimental center of China Agricultural University (Beijing, China). At 28 days old, 15 Cobb chicks and 15 Beijing-you chicks were randomly chosen and challenged orally with 1 mL PBS containing 1.83 × 1011 CFU Salmonella typhimurium (ST), the remaining chicks were given orally with 1mL PBS.  We refer to the four groups hereafter as BYS (Beijing-you with ST infection), BYC (Beijing-you control), CBS (Cobb broilers with ST infection), and CBC (Cobb broilers control). At 3 days post-infection (dpi), we randomly selected 3 chickens from each experimental group (BYS, BYC, CBS and CBC) and collected the splenic tissue.Unfortunately, two samples in the BYS group had too few cells collected by FACS to meet the scRNA-seq criteria. The 10 samples were performed the subsequently analysis.

value: CD45+ cell


title: Cobb broiler with ST infection, replicate 3, scRNAseq

description: 10× Genomics


title: MN23_bone_cell_S49


title: Cobb broiler with ST infection, replicate 1, scRNAseq

description: 10× Genomics


title: MN22_bone_post_S44

value: Placebo


title: Cobb broiler control, replicate 3, scRNAseq

description: 10× Genomics


title: fem2-3,rep1


title: Cobb broiler control, replicate 2, scRNAseq

description: 10× Genomics


title: Nip,rep4

source_name: Nip

value: WT


title: MN22_bone_cell_S45


title: t24ct3 (RNA-seq)

source_name: spleen


title: Vero cells, Group3, 24h, rep3

city: Beijing

first: Yunchao

last: Huang

address: Boxing 2nd Road

institute: Beijing Institute of Biological Products Company Limited

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/252/025/GCF_015252025.1_Vero_WHO_p1.0/GCF_015252025.1_Vero_WHO_p1.0_genomic.fna.gz
Supplementary files format and content: Excel files for Group 1 and Group 2 samples analysis

organism: Chlorocebus aethiops

source_name: kidney

growth_protocol: Vero cells were cultured in MEM medium supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere with 5% CO2, and passaged when the cells were cultured to 90% density.

extract_protocol:
RNA is extracted from cells using standard extraction methods, followed by strict quality control of RNA samples, mainly by Agilent 2100 bioanalyzer: precise detection of RNA integrity
RNA libraries for RNA-seq were prepared using NEBNext RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: kidney

tag: cell line

value: Vero

value: epithelial cells

value: 4℃ TrypLE treatment


title: Beijing-you with ST infection, scRNAseq

description: 10× Genomics


title: Nip,rep3

value: seedling

value: 18-day-old seedling cells


title: MN21_lung_RD_2_S38


title: MN21_skin_post_S36


title: Cobb broiler control, replicate 1, scRNAseq

description: 10× Genomics


title: Vero cells, Group3, 24h, rep2


title: MN22_bone_pre_S43

value: pretreatment


title: MN21_lung_RD_1_S37

value: metastasis


title: Beijing-you control, replicate 3, scRNAseq

description: 10× Genomics

value: spleen


title: Vero cells, Group3, 24h, rep1


title: Liver - Female_CARWT_TCPOBOP - Rep3

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

institute: INRAe

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing (two wash batches performed as described in WashBatch characteristics) on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 39 out of 48 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 38874 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 36208 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Mus musculus

source_name: Liver

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Following euthanasia by cervical dislocation, liver was collected, weighted and snap-frozen in liquid nitrogen and stored at −80°C.  Total RNA was extracted using TRI Reagent® (Molecular Research Center, Cincinnati, Ohio, USA). RNAs were quantified using Nanodrop

treatment_protocol: Mice included in TCPOBOP groups received a daily intraperitoneal injection of 1,4-bis[2-(3,5-dichloro pyridyloxy)]Benzene (TCPOBOP, Sigma Aldrich) diluted in corn oil at 3mg/kg for 4 days while CO mice received corn oil only (Sigma Aldrich). At ZT16 (6 hours after the last TCPOBOP injection), mice were anesthetized with Isoflurane and Xylasine (2%, 2mg/kg) and killed by cervical dislocation.

value: CARWT

value: TCPOBOP

value: Female

tag: washbatch

value: Liver

tag: strain background


title: MN21_lung_RCV_S39

value: cellLine


title: Liver - Female_CARKO_TCPOBOP - Rep4

value: CARKO


title: Beijing-you control, replicate 2, scRNAseq

description: 10× Genomics

value: CD45+ cell


title: fem2-3,rep2

value: fem2-3 mutant


title: Liver - Female_CARKO_Corn.Oil - Rep1


title: Beijing-you control, replicate 1, scRNAseq

description: 10× Genomics


title: Liver - Male_CARWT_Corn.Oil - Rep6

value: Male


title: MN21_lung_cell_RD_S41

source_name: celllLine

value: celllLine


title: Liver - Female_CARWT_Corn.Oil - Rep1


title: Vero cells, Group3, 8h, rep2

value: kidney

value: Vero

value: epithelial cells

value: WT


title: Liver - Male_CARWT_TCPOBOP - Rep4


title: LG3

city: Alaer

first: Rong

last: Xuan

state: Xinjiang Uyghur Autonomous Region

address: No. 1487 Tarim Avenue

institute: Tarim University

data_processing:
The libraries were subjected to sequencing using an Illumina/Solexa system
The data were subjected to quality assessment using FastQC software (v 0.11.9). According to the quality assessment results, the sequencing adapters were processed with Cutadapt software (v 4.2) to eliminate reads with 10% or more unknown bases and a length greater than 30 bp or less than 18 bp and to retain reads with a sequencing quality (Q) > 30.
The filtered clean reads were subjected to sequence comparison with the Silva (https://www.arb-silva.de/), GtRNAdb (http://lowelab.ucsc.edu/GtRNAdb/), Rfam (http://rfam.xfam.org/) and Repbase (https://www.girinst.org/repbase/) databases using Bowtie software (v 1.1.1). Subsequently, the reads were annotated as repeat reads and noncoding RNAs (ncRNAs), including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs) and other RNAs.
The comparison results were summarized, and the short reads were annotated with classifications. Unannotated reads containing miRNAs were obtained after filtering ncRNAs and repeated sequences. The filtered unannotated reads were then aligned with the goat reference genome (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/704/415/GCF_001704415.1_ARS1) to determine the locus information on the reference genome. Known miRNAs were identified, and novel miRNAs were predicted with miRDeep2 software using the mature and hairpin sequences of goat, cow and human in the miRBase database (http://www.mirbase.org/).
Transcripts per million (TPM) values of miRNA expression were calculated by miRDeep2 software (v 2.0.1.0). According to the TPM values, miRNAs were divided into four groups: the high-expression group (TPM ≥ 500), medium-expression group (500 > TPM ≥ 10), low-expression group (10 > TPM ≥ 1), and ultra-low-expression group (1 > TPM). The detected known miRNAs and novel miRNAs were subjected to family analysis based on sequence similarity to determine the conservation of miRNAs throughout evolution.
Assembly: GCF_001704415.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw counts for every miRNA and every sample

organism: Capra hircus

source_name: mammary gland

extract_protocol:
Total RNA was extracted using a TRIzol™Reagent Kit (Invitrogen, Carlsbad, CA). RNA concentration and integrity were examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany), and RNA samples with an RNA integrity number (RIN) > 8 were used for subsequent experiments.
Nine small RNA libraries were established using the total RNA isolated from mammary gland tissue at the LL, DP and LG stages (LL1, LL2, LL3, DP1, DP2, DP3, LG1, LG2 and LG3) with an NEBNext®Ultra™RNA Library Prep Kit (Illumina, San Diego, USA). For each small RNA library, 1 μg of total RNA was subjected to electrophoresis using 12% Tris-borate ethylenediaminetetraacetic acid (TBE)-urea polyacrylamide gel electrophoresis (PAGE) gels (Invitrogen) to obtain small RNA fragments with a length between 18 and 30 nt. The 3’ and 5’ ends of the RNA were ligated with T4 RNA ligase 2 and reverse transcribed to obtain cDNA based on the 3’ and 5’ adapters ligated to the small RNA. The target library was amplified using PCR, and dsDNA fragments between 140 and 160 bp in length were extracted using TBE gel electrophoresis. The libraries were subjected to sequencing using an Illumina/Solexa system after quality tests.

value: mammary gland

value: mammary cell

value: late gestation


title: Vero cells, Group3, 8h, rep1

value: 4℃ TrypLE treatment


title: MN21_bone_pre_S70

value: osteosarcomaTissue

value: pretreatment


title: LG1


title: MN21_lung_cell_RCV_S42


title: Vero cells, Group3, 0h, rep3


title: DP3

value: dry period


title: LG2


title: Vero cells, Group3, 0h, rep2


title: MN21_bone_post_S35

value: VSV


title: MN21_bone_cell_S40

value: cellLine


title: Vero cells, Group3, 0h, rep1


title: Vero cells, Group2, 24h, rep3

value: 37℃ TrypLE treatment


title: DP1


title: DP2


title: Vero cells, Group3, 8h, rep3


title: Vero cells, Group2, 24h, rep2


title: MN20_bone_post_1_S32

value: Placebo


title: MN20_bone_pre_S31


title: MN20_skin_post_S33

source_name: skin

value: skin


title: Liver - Male_CARKO_TCPOBOP - Rep5

value: CARKO

value: TCPOBOP

value: Male

value: Liver


title: LL3

value: late lactation


title: LL2

value: mammary gland


title: MN20_bone_cell_S34


title: Vero cells, Group2, 24h, rep1

value: kidney

value: Vero

value: epithelial cells

value: WT


title: Vero cells, Group2, 8h, rep3


title: LL1

value: mammary cell


title: t28lps8 (RNA-seq)

tag: strain

value: AB

value: adult

value: 100 d post-fertilization

value: LPS

value: spleen


title: Liver - Male_CARKO_TCPOBOP - Rep4


title: MN19_bone_pre_2_S28

source_name: osteosarcomaTissue

value: osteosarcomaTissue

value: pretreatment


title: Liver - Male_CARWT_Corn.Oil - Rep2

value: CARWT


title: Vero cells, Group2, 8h, rep2

value: 37℃ TrypLE treatment


title: Liver - Male_CARWT_TCPOBOP - Rep6

value: TCPOBOP

value: Male

value: Liver


title: Liver - Female_CARKO_TCPOBOP - Rep1

value: CARKO

value: Female


title: Liver - Male_CARKO_Corn.Oil - Rep5


title: Liver - Female_CARKO_Corn.Oil - Rep2


title: Vero cells, Group2, 8h, rep1

value: kidney

value: Vero

value: epithelial cells


title: Liver - Female_CARWT_Corn.Oil - Rep2


title: MN19_bone_post_S29

value: VSV


title: Liver - Male_CARKO_Corn.Oil - Rep1


title: Liver - Female_CARWT_TCPOBOP - Rep6


title: MN19_bone_cell_S30

value: cellLine


title: Vero cells, Group2, 0h, rep3

value: WT


title: MN18_skin_post_S26

value: skin


title: MN18_bone_post_S25

value: Placebo


title: Vero cells, Group2, 0h, rep2


title: Liver - Male_CARWT_Corn.Oil - Rep4


title: MN18_bone_cell_S27


title: Vero cells, Group2, 0h, rep1


title: OFT-RV, mutant, biological rep3 (miRNA)

city: Bronx

first: Silvia

middle: Elisa

last: Racedo

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: miRNA expression data from E9.5 OFT-RV

hyb_protocol: A total of 3.8 mg of cDNA from the last step was hybridized to the Affymetrix Mouse GeneST 1.0 or miRNA 4.0 chip. Hybridization, washing, staining and scanning were performed in the Genomics Core at Einstein (https://www.einstein.yu.edu/research/shared-facilities/cores/46/genomics/) according to the Affymetrix manual.

scan_protocol: Scanning were performed in the Genomics Core at Albert Einstein College using Genechip G7 scanner.

data_processing: Data analysis was performed in the R statistical package. GeneChip data were pre-processed by the ‘oligo’ package (PMID: 20688976), which implements Robust Multichip Average (RMA) algorithm with background correction, quantile normalization and gene level summarization (PMID: 12925520).

label: biotin

source_name: OFT-RV, mutant

label_protocol: The sense-strand cDNA was amplified and converted from 100 nanograms (ng) starting total RNA using Ambion WT Expression Kit.

growth_protocol: Embryos at E9.5 (19 - 21 somite pairs) were used for quentitative gene expression studies of microdissected anterior second heart field and outflow tract with the right ventricle.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions-miRNeasy Mini Kit QIAGEN 217004.

treatment_protocol: Embryos were isolated on embryonic day E9.5 and immediate processed for microdissection of aSHF and OFT-RV tissues following by fast freezing at -80C. After multiple litter collections and genotyping, the tissues were pooled according to genotype for total RNA extraction.

value: OFT-RV

value: Mef2c-AHF-Cre/+; Dgcr8 f/f

tag: developmental stage

value: embryonic day E9.5


title: MN17_bone_pre_S22

value: osteosarcomaTissue

value: pretreatment


title: MN17_bone_post_S23


title: Vero cells, Group1, 24h, rep2

value: 37℃ trypsin treatment


title: Vero cells, Group1, 24h, rep1


title: Liver - Male_CARKO_TCPOBOP - Rep2

value: TCPOBOP

value: Male

value: Liver


title: OFT-RV, mutant, biological rep2 (miRNA)

description: miRNA expression data from E9.5 OFT-RV


title: MN17_bone_cell_S24


title: Liver - Female_CARWT_TCPOBOP - Rep2

value: CARWT

value: Female


title: OFT-RV, wild-type, biological rep3 (miRNA)

description: miRNA expression data from E9.5 OFT-RV

source_name: OFT-RV, wild-type

value: Dgcr8 f/+


title: Liver - Male_CARWT_TCPOBOP - Rep3


title: Vero cells, Group1, 8h, rep3

value: kidney

value: Vero

value: epithelial cells


title: OFT-RV, mutant, biological rep1 (miRNA)

description: miRNA expression data from E9.5 OFT-RV


title: Vero cells, Group1, 24h, rep3

value: WT


title: MN16_bone_pre_S19


title: Liver - Male_CARKO_Corn.Oil - Rep2

value: CARKO


title: OFT-RV, wild-type, biological rep2 (miRNA)

description: miRNA expression data from E9.5 OFT-RV

value: OFT-RV


title: Vero cells, Group1, 8h, rep2


title: MN16_bone_post_1_S20

value: VSV


title: Liver - Female_CARKO_Corn.Oil - Rep3


title: Liver - Female_CARKO_Corn.Oil - Rep5


title: OFT-RV, wild-type, biological rep1 (miRNA)

description: miRNA expression data from E9.5 OFT-RV

value: embryonic day E9.5


title: aSHF, mutant, biological rep2 (miRNA)

description: miRNA expression data from E9.5 aSHF

source_name: aSHF, mutant

value: aSHF

value: Mef2c-AHF-Cre/+; Dgcr8 f/f


title: Liver - Female_CARKO_TCPOBOP - Rep3


title: aSHF, mutant, biological rep4 (miRNA)

description: miRNA expression data from E9.5 aSHF


title: Vero cells, Group1, 8h, rep1

value: 37℃ trypsin treatment


title: Liver - Female_CARWT_Corn.Oil - Rep4


title: MN16_bone_cell_S21

source_name: cellLine

value: cellLine


title: MN15_skin_post_S17

value: skin


title: MN15_bone_pre_1_S16

value: osteosarcomaTissue

value: pretreatment


title: Vero cells, Group1, 0h, rep2


title: MN15_bone_cell_S18


title: Vero cells, Group1, 0h, rep1


title: Vero cells, Group1, 0h, rep3


title: fem2-3, sRNA seq

data_processing:
Adapter sequences were trimed and clean reads with sizes ranging from 18 to 45-nt .
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Bowtie with parameter -v 0.
Annotated structure RNAs were excluded.
Read counts were normalized to RPTM.
Assembly: MSU version 7.0

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen).
18-45nt small RNA was cut from PAGE gel.

value: seedling

value: 18-day-old seedling cells

value: fem2-3 mutant


title: MN14_skin_post_S14


title: fem2-1, sRNA seq

value: fem2-1 mutant


title: Vero cells, CTR,  rep1

value: kidney

value: Vero

value: epithelial cells

value: 37℃Non-enzymatic cell lysate


title: fem1-1, sRNA seq

value: fem1-1 mutant


title: MN14_bone_post_2_S13

value: VSV


title: Liver - Female_CARWT_Corn.Oil - Rep5

value: CARWT

value: Female

value: Liver


title: Vero cells, CTR,  rep2

value: WT


title: Liver - Female_CARKO_TCPOBOP - Rep5

value: CARKO

value: TCPOBOP


title: aSHF, mutant, biological rep3 (miRNA)

description: miRNA expression data from E9.5 aSHF

value: aSHF

value: Mef2c-AHF-Cre/+; Dgcr8 f/f

value: embryonic day E9.5


title: aSHF, mutant, biological rep1 (miRNA)

description: miRNA expression data from E9.5 aSHF


title: aSHF, wild-type, biological rep4 (miRNA)

description: miRNA expression data from E9.5 aSHF

source_name: aSHF, wild-type

value: Dgcr8 f/+


title: aSHF, wild-type, biological rep3 (miRNA)

description: miRNA expression data from E9.5 aSHF


title: Liver - Male_CARKO_Corn.Oil - Rep6

value: Male


title: aSHF, wild-type, biological rep2 (miRNA)

description: miRNA expression data from E9.5 aSHF


title: aSHF, wild-type, biological rep1 (miRNA)

description: miRNA expression data from E9.5 aSHF


title: Vero cells, CTR,  rep3

value: kidney


title: Liver - Male_CARKO_TCPOBOP - Rep1


title: 5.5_Escherichia coli strain BW25113, Wildtype with treatment: Negamycin 16 ug/ml for 40 minutes

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

data_processing:
All reads mappings were performed against the reference strain of E. coli K12 substr. MG1655 (RefSeq ID NC_000913.3).
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment).
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.443 based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Supplementary_files_format_and_content: Unnormalized quantified gene expression values as tsv file.

organism: Escherichia coli

source_name: lab grown bacteria

growth_protocol: Strains were grown in lysogeny broth (LB), 0.5% polypeptone (PP) in water (BD BBL polypeptone, catalog no. 211910) or M9 medium (47.74 mM NaHPO4 x 2H2O, 22.04 mM KH2PO4, 8.56 mM NaCl, 18.7 mM NH4Cl, 2 mM MgSO4, 100 µM CaCl2, 0.4% glucose) at 37°C.

extract_protocol:
For RNA extraction from E. coli BW25113, cells were grown in PP at 37°C (190 rpm) until early exponential growth phase. For negamycin treatment, the bacterial liquid culture was split into two. One culture remained untreated and to the other culture a final concentration of 16 µg/ml negamycin was added. Samples were incubated for further 45 min at 37°C (190 rpm). Cells were harvested by centrifugation (10 min, 4,600 g at 4°C) and resuspended in DNA/RNA Shield buffer (Zymo research).
RNA was isolated using the Quick-RNA Miniprep Plus Kit (Zymo Research) and stored at -80°C. The RNA quality was determined with an Agilent 2100 Bioanalyzer and samples with a high RNA integrity number (RIN > 8) were selected for library construction. Per replicate, a total amount of 1.6 µg RNA was subjected to rRNA depletion using the Ribo-Zero™ Plus Kit  (according to the manufacturer’s instructions. The cDNA libraries were constructed using the resulting RNA and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions

value: Wildtype

value: Negamycin 16 ug/ml for 40 minutes


title: Liver - Male_CARWT_TCPOBOP - Rep2


title: MN14_bone_cell_S15

value: cellLine


title: Liver - Male_CARWT_Corn.Oil - Rep5


title: Liver - Male_CARWT_TCPOBOP - Rep5


title: 4.5_Escherichia coli strain BW25113, ΔchiPΔompN with treatment: None


title: MN13_bone_post_S10

value: osteosarcomaTissue


title: MN14_bone_post_1_S12

value: VSV


title: Liver - Female_CARWT_TCPOBOP - Rep1

value: CARWT


title: MN12_skin_post_S8

value: skin


title: MN12_bone_post_S7


title: Liver - Male_CARWT_Corn.Oil - Rep3

value: Liver


title: ovarian tissue, 6-b

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar rat circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

organism: Rattus

source_name: Rats treated with Bushen Ningxin formula

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: group

value: TCM treatment

value: ovarian tissue

tag: fraction

value: circRNA


title: 5.4_Escherichia coli strain BW25113, Wildtype with treatment: Negamycin 16 ug/ml for 40 minutes

tag: treatment


title: 1.5_Escherichia coli strain BW25113, Wildtype with treatment: None


title: 4.4_Escherichia coli strain BW25113, ΔchiPΔompN with treatment: None


title: ovarian tissue, 2-c

source_name: Ovarian tissue of premature ovarian insufficiency (POI) rats

value: model

tag: tissue


title: MN11_bone_pre_S6

value: pretreatment


title: ovarian tissue, 6-c


title: ovarian tissue, 6-a


title: Liver - Female_CARWT_Corn.Oil - Rep6

value: Female


title: Liver - Male_CARKO_Corn.Oil - Rep4

value: CARKO


title: ovarian tissue, 2-b


title: 2.4_Escherichia coli strain BW25113, ΔompN with treatment: None


title: ovarian tissue, 1-c

source_name: Ovarian tissue of control rats

value: control


title: Liver - Female_CARKO_Corn.Oil - Rep6


title: 3.4_Escherichia coli strain BW25113, ΔchiP with treatment: None


title: MN08_bone_pre_2_S5


title: MN06_bone_pre_4_S4


title: Liver - Male_CARKO_TCPOBOP - Rep6

value: TCPOBOP

value: Male


title: ovarian tissue, 2-a


title: Liver - Female_CARWT_TCPOBOP - Rep4


title: 1.4_Escherichia coli strain BW25113, Wildtype with treatment: None

value: Wildtype


title: CRR OE -Pi #3

city: LAUSANNE

first: JOAQUIN

last: CLUA

address: BIOPHORE

department: DBMV

country: Switzerland

institute: UNIL

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Arabidopsis thaliana.TAIR10.39 genome using STAR (v. 2.5.3a, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Arabidopsis thaliana.TAIR10.39 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Reads were also aligned to the Arabidopsis thaliana.TAIR10.39 transcriptome using STAR (v. 2.5.3a, Dobin et al. 2013) and the estimation of the isoforms abundance was computed using RSEM (v. 1.2.31, Li and Dewey 2011).
Statistical analysis was performed for genes in R (R version 3.5.3). Genes with low counts were filtered out according to the rule of 1 count per million (cpm) in at least 1 sample. Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package version 3.24.3; Robinson et al. 2010). Differential expression was computed with limma-trend approach (Ritchie et al. 2015) by fitting all samples into one linear model. Moderated t-test was used for each contrast and F-test was used for interaction. For each group of comparisons, the adjusted p-value is computed by the Benjamini-Hochberg method, controlling for false discovery rate (FDR or adj.P.Val).
Assembly: TAIR10.39
Supplementary files format and content: Normalized expression values all genes. Excel file showing the normalize expression values for each gene in each replicate
Supplementary files format and content: Differential expression testing. Excel file showing the normalized expression value for each gene and the differential expression testing between genotypes and conditions

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis seedlings were grown in 1/6MS agar plates for 7 days with or without phosphate

extract_protocol:
RNA from roots was extracted using Promega ReliaPrep™ RNA Tissue Miniprep System
Illumina Sequencing library preparation

treatment_protocol: The control condition was 1mM phosphate and the treated samples were grown without the addition of phosphate

value: Root

tag: ecotype

value: Col-0 ecotype background over-expressing CRR under the 35S promotor

tag: cell type

value: Minus Pi (-Pi)


title: Liver - Female_CARKO_TCPOBOP - Rep2

tag: genotype


title: MN06_bone_pre_3_S3

value: osteosarcomaTissue


title: ovarian tissue, 1-a


title: 5.1_Escherichia coli strain BW25113, Wildtype with treatment: Negamycin 16 ug/ml for 40 minutes

value: Negamycin 16 ug/ml for 40 minutes


title: Liver - Female_CARKO_Corn.Oil - Rep4

tag: Sex

value: Liver


title: CRR OE -Pi #2

value: over-expressing CRR under the 35S promotor


title: Liver - Female_CARKO_TCPOBOP - Rep6


title: ovarian tissue, 1-b

value: ovarian tissue


title: MN05_bone_post_S69

value: VSV


title: MN03_bone_pre_S2


title: CRR OE -Pi #1


title: CRR OE +Pi #3

value: Control (+Pi)


title: 3.1_Escherichia coli strain BW25113, ΔchiP with treatment: None


title: MN01_bone_pre_S1

value: pretreatment


title: Liver - Male_CARKO_TCPOBOP - Rep3


title: Liver - Female_CARWT_TCPOBOP - Rep5

value: CARWT

value: Female


title: Liver - Male_CARKO_Corn.Oil - Rep3

value: CARKO


title: CRR OE +Pi #2


title: 4.1_Escherichia coli strain BW25113, ΔchiPΔompN with treatment: None


title: 2.1_Escherichia coli strain BW25113, ΔompN with treatment: None


title: CRR OE +Pi #1


title: TreeShrew2_neun_pos

data_processing:
We used cellranger (v7.0, 10X Genomics) to align the sc- and snRNA-seq datasets, following manufacturer’s instructions. For each species, sequencing reads were demultiplexed into distinct samples and the .fastq.gz files corresponding to each sample were aligned to reference transcriptomes to obtain binary alignment map (.bam) files.
Assembly: TS_3.0
Supplementary files format and content: To include both exonic and intronic reads in the quantification of gene expression for each sample, regardless of cellular or nuclear origin, we applied velocyto to the corresponding .bam files. This generated two separate gene expression matrices (GEMs; genes x cells) for each sample, corresponding to “spliced” and “unspliced” reads. The two GEMs were summed element by element to obtain “total” GEM for each sample.
Supplementary files format and content: GEMs from different sample runs were combined (column-wise concatenated) to yield a full species’ GEM.

organism: Tupaia chinensis

source_name: Retina

value: Retina

value: Retinal neurons

value: Enriched for Neun+ nuclei


title: Gastric mucosa with intestinal metaplasia_7

city: Tsukiji, Chuo-ku

first: Chihiro

last: Takeuchi

state: Tokyo

department: Division of Epigenomics

institute: National Cancer Center Research Institute

library_source: genomic single cell

data_processing:
BAM and fragment.tsv files were generated by the Cell Ranger ATAC (v2.0.0).
Fragments.tsv files were used for further analysis by ArchR (v1.0.2) R package.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: fragments.tsv.gz

source_name: Stomach

extract_protocol:
Gastric mucosa from resected specimen was freshly obtained from patients who underwent gastrectomy and stored in STEM-CELLBANKER (ZENOAQ) freezing medium at –80°C until further use. Nuclei isolation was performed according to the protocol descried by 10x Genomics.
Library was prepared using Chromium Next GEM Single Cell ATAC Kit v1.1 (10x Genomics).

value: Stomach

tag: disease state

value: intestinal metaplasia


title: Normal gastric mucosa

value: normal


title: TreeShrew2_chx10_pos

value: Enriched for CHX10+ nuclei


title: RIPseq with DDX20 antibody, mouse testis cells,repeat2

city: beijing

first: dingfeng

last: zou

state: 北京

address: Beijing, Dong Dan San Tiao 5

institute: Institute of Basic Medical Sciences  Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
raw reads were trimmed to remove low-quality bases using Trimmomatic (version 0.36) with defined parameters (-LEADING:3, -MINKEN:36)
Sequencing adapter sequences were removed with Cutadapt-4.1
aligned to the mouse reference genome (GRCm38) with STAR (version 2.7.2b), using the following parameters:  outFilterMismatchNmax 1  outFilterMultimapScoreRange 1
sort by samtools, and raw read counts were calculated using the featureCounts software
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: mouse testis cells

extract_protocol:
Cells were UV cross-linked (200 mJ/cm2 at 254 nm) using a Stratalinker, after which the cells were lysed with IP lysis buffer (thermos fisher) and subjected to DDX20 IP.
Library DNAs were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced by HiseqXten‐PE150 (Berry Genomics).  Library DNAs were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs), and sequenced by HiseqXten‐PE150 (Berry Genomics).

value: mouse testis cells

tag: rip antibody

value: DDX20(Proteintech, #11324-2-AP)


title: Liver - Male_CARWT_Corn.Oil - Rep1

source_name: Liver

value: Male

value: Liver


title: Liver - Female_CARWT_Corn.Oil - Rep3


title: Gastric mucosa with intestinal metaplasia_6_H3K27ac

data_processing:
Fastp (version 0.20.0) was used for sequencing QC and adapter trimming.
All reads were aligned to the human genome GRCh38/hg38 using the short-read aligner Bowtie 2 (version 2.4.1) with default parameters.
The resultant SAM file was converted into a BAM file and duplicates were removed using SAMtools (version 1.16.1).
Peak calling was performed with the input control using MACS2 (version 2.1.0) with default parameters.
Heatmaps of ChIP/input enrichment around the peaks were created from deepTools (v3.5.1) using bamCompare, computeMatrix, and plotHeatmap.
BigWig files were generated using the deeptools (v3.5.1) using bamCompare.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor (Cosmo Bio).
Sequencing library was prepared with GenNext NGS Library Prep Kit (Toyobo, LPK-101) from 10 ng for a final sequencing depth around 30-54 million reads among the samples.

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: RIPseq with DDX20 antibody, mouse testis cells,repeat1

value: DDX20(Proteintech, #11324-1-AP)


title: Col-0 -Pi #2

value: Root

value: Col-0 ecotype

value: wildtype

value: Minus Pi (-Pi)


title: TreeShrew1_neun_chx10_neg

first: Joshua

last: Hahn

institute: University of Washington

value: Retina

value: Depleted of CHX10+


title: Input, mouse testis cells,repeat2


title: Gastric mucosa with intestinal metaplasia_3_H3K27ac


title: Col-0 -Pi #1


title: 1.1_Escherichia coli strain BW25113, Wildtype with treatment: None

value: Wildtype


title: Input, mouse testis cells,repeat1


title: Col-0 +Pi #3

value: Control (+Pi)


title: TreeShrew1_neun_pos

value: Retinal neurons

value: Enriched for Neun+ nuclei


title: Liver - Male_CARWT_TCPOBOP - Rep1

value: CARWT

value: TCPOBOP


title: Gastric mucosa with intestinal metaplasia_3_input


title: TreeShrew2_neun_chx10_neg


title: TreeShrew1_chx10_pos

value: Enriched for CHX10+ nuclei


title: Col-0 -Pi #3


title: TreeShrew_Chx10


title: Ins_RS

city: shanghai

first: Xin

last: Wang

state: shanghai

address: 320 Yue Yang Road, Shanghai 200031

institute: Shanghai Institute of Biochemistry and Cell Biology

description:
MiwiΔIns-RS
Transcriptome_in_RS.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trim_galore (v0.5.0).
Processed reads were mapped to mm10 genome using STAR with the default parameters.
Gene expression (in FPKM) was calculated by RSEM.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Excel file includes FPKM for each Sample.

source_name: MiwiΔIns round spermatids

extract_protocol:
Mouse round spermatids were isolated from 28 days mouse testes by FACS. In brief, total spermatogenic cells were extracted from the seminiferous tubules of 28 days mouse testes, stained by Hoechst 33342 (Acros Organics), and then separated through FACS sorting. The isolated round spermatids were further confirmed by their distinct nuclear morphology (DAPI staining of nuclei). Total RNAs were extracted from mouse round spermatids using RNAiso Plus (Takara).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V3 Library Prep Kit for Illumina protocols.

value: Miwi<delta>Ins

value: Male

value: Round spermatids


title: Normal gastric mucosa_H3K27ac

source_name: Normal gastric mucosa

value: Normal gastric mucosa

value: H3K27ac (ab4729, Abcam)


title: R371W_RS

description:
MiwiR371W-RS
Transcriptome_in_RS.xlsx

source_name: MiwiR371W round spermatids


title: Col-0 +Pi #1

value: Root

value: Col-0 ecotype


title: TreeShrew_Nueun

city: Seattle

address: 3747 W Stevens Wy NE


title: Gastric mucosa with intestinal metaplasia_6_input


title: SH3_input

status: Public on Sep 27 2023

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads were aligned to the mouse (mm10) or human (hg38) genome using default settings of HISAT2.
Alignments were filtered to only include uniquely mapped reads using SAMtools v.1.8.
Peak-calling was normalized to respective inputs for each sample and was performed using MACS v.2.1.1 (44) with default settings and filtered for FDR < 0.05 and fold change > 1.5.
Differential analysis was performed using diffReps (45) with a 1 kb? window size.
Peaks and differential sites were further annotated to nearby genes or intergenic regions using the region analysis tool from the diffReps package.
Assembly: mm10, hg38
Supplementary files format and content: Tab-delimited text files containing peaks

source_name: Brain

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the TruSeq® ChIP Sample Preparation kit. All the DNA was used as starting material for input and ip samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter??? Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Susceptible

tag: condition

value: input

value: Brain


title: SH1_IP

value: H3K4me3Q5ser (MilliporeSigma #ABE2580)


title: SH2_IP


title: SH1_input


title: SF2_IP

value: FLX


title: SF3_input


title: Col-0 +Pi #2

value: wildtype

value: Control (+Pi)


title: SF1_input


title: SF3_IP


title: SH2_input


title: SF1_IP


title: CH3_IP

value: Control


title: CH3_input


title: CH2_IP


title: CH2_input


title: CH1_IP


title: SF2_input


title: CF3_input


title: CF3_IP


title: CH1_input


title: Normal gastric mucosa_input


title: CF2_input


title: CF2_IP


title: SH3_IP


title: CF1_IP


title: CF1_input


title: 3.5_Escherichia coli strain BW25113, ΔchiP with treatment: None


title: 220_S43_L006


title: WT_RS

description:
WT-RS
Transcriptome_in_RS.xlsx

source_name: Wildtype round spermatids

value: Wildtype


title: 219_S49_L006

value: MDD


title: 217_S56_L006


title: 215_S51_L006


title: 213_S45_L006


title: 212_S54_L006


title: 216_S37_L006


title: 218_S38_L006


title: 211_S44_L006


title: 208_S50_L006


title: 203_S39_L006


title: 202_S36_L006


title: 204_S53_L006


title: 207_S41_L006


title: 210_S55_L006


title: 209_S42_L006


title: 201_S48_L006


title: 218input_S48_L007


title: 206_S52_L006


title: 214_S40_L006


title: 205_S47_L006


title: 216input_S47_L007


title: 215input_S30_L005


title: 217input_S35_L005


title: 219input_S28_L005


title: 214input_S50_L007


title: 213input_S55_L007


title: 212input_S33_L005


title: 211input_S54_L007


title: 210input_S34_L005


title: 209input_S52_L007


title: 208input_S29_L005


title: 207input_S51_L007


title: MN12_bone_cell_S9

data_processing:
Initial quality control analysis of RNA sequencing FASTQ data was performed using FastQC software (v0.11.5). FASTQ data were trimmed with Trimmomatic (v0.33.0). Kallisto (v0.43.0) was used for pseudoalignment and quantifying transcript abundance.
addition of 3 reads to all values
quantile normalization
Assembly: CanFam3.1
Supplementary files format and content: tab delimited txt file of normalized counts

extract_protocol:
RNA was extracted from tumor tissue at baseline, and from tumor tissue samples obtained at amputation, post-treatment. RNA was also extracted from cell lines that were established pre-treatment from each case, and from normal skin tissue from each case as a non-malignant control. When available, RNA was also extracted from lung metastases. Tissue samples were disrupted with a tissue homogenizer, and RNA was extracted using a commercially available kit (QIAGEN RNeasy mini kit). RNA was stored at -80°C.
Dual-indexed sequencing libraries were prepared using the Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit.
(2x50-bp paired-end, on a NovaSeq S2

value: cellLine

tag: ID


title: 2.5_Escherichia coli strain BW25113, ΔompN with treatment: None


title: 220input_S53_L007


title: 202input_S46_L007


title: GM12878_indexTag1_scWGS

status: Public on Sep 18 2023

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

data_processing:
Reads were demultiplexed using unidex (github.com/adeylab/unidex), changing the read name to be the error-corrected cell barcode
Alignment was performed using bwa mem
Duplicate reads were removed on a cell-by-cell basis
Fragment files were generated using sinto (ATAC), or reads were tallied for each cell over tiling genomic windows (WGS)
WGS data were processed using RobustCNV and ATAC data using ArchR
Assembly: hg38
Supplementary files format and content: Gzipped fragment files are provided for all ATAC data
Supplementary files format and content: RobustCNV outputs of window biases and copy number calls in gzipped tar files

source_name: Blood, Cell line

extract_protocol:
Nuclei were extracted using NIB-Hepes buffer
Nuclei for scATAC and dTag were carried through tagmentation, dTag nuclei or nuclei for scWGS alone were carried through nucleosome disruption followed by tagmentation. dTag amnd multiplexed scWGS samples used indexed tagmentation using reagents from the ScaleBio scATAC multiplexing kit. Single-plex experiments used the tagmnetaiton enzyme provided in the 10x Genomics scATAC kit. After final tagmentation, nuclei were carried through the 10x scATAC v2 protocol according to the default protocol or using the modifications indicated by ScaleBio for samples that leevraged indexed tagmentation.

value: Blood, Cell line

tag: cell line

value: Lymphoblastoid Cell Line


title: GM12878_dTag1_scWGS

description: RobustCNV.dTag.tgz


title: K562_dTag_multiPlex2_scATAC

value: CML Lymphoblast Cells


title: K562_dTag_multiPlex1_scATAC


title: 204input_S32_L005


title: K562_dTag_multiPlex1_scWGS

description: RobustCNV.dTag.tgz


title: 205input_S26_L005


title: GM12878_dTag_multiPlex1_scWGS

description: RobustCNV.dTag.tgz


title: GM12878_10x_scATACv2


title: GM12878_dTag_multiPlex2_scWGS

description: RobustCNV.dTag.tgz


title: K562_dTag_multiPlex2_scWGS

description: RobustCNV.dTag.tgz


title: 201input_S27_L005


title: GM12878_dTag_multiPlex2_scATAC


title: GM12878_dTag1_scATAC


title: GM12878_scWGS


title: Sftpc-trace_rep_bleo

city: Nashville

first: Jonathan

middle: A

last: Kropski

state: TN

department: Medicine

institute: Vanderbilt University Medical Center

library_source: other

data_processing:
CellRanger_7.0.1
Cellbender remove-background
Assembly: mm10-2020a
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: output_filtered.h5

molecule: other

source_name: lung

value: lung

value: Sftpc-CreER;tDtomato

value: Rep Bleo


title: WT_unchallenged

value: WT

value: Cntrol


title: MN13_bone_cell_S11

city: Minneapolis

first: Aaron

last: Sarver

institute: University of Minnesota

source_name: cellLine


title: Hif1/2_unchallenged

value: SPC-Cre; Hif1/2 f/f


title: WT_sd_bleo

value: SD Bleo


title: Hif1/2_rep_bleo


title: WT_rep_bleo


title: 206input_S31_L005

value: input

value: Brain


title: GM12878_dTag_multiPlex1_scATAC


title: Human_organoid_veh

source_name: Lung

value: Lung

value: Vehicle


title: Scgb1a1_trace_rep_bleo


title: 203input_S49_L007


title: Human_organoid_pt


title: GBM_24_I

status: Public on Sep 14 2023

city: Regensburg

first: Markus

middle: J.

last: Riemenschneider

address: Franz-Josef-Strauß-Allee 11

department: Neuropathology

institute: Regensburg University Hospital

data_processing:
fastq files were aligned to version 102 of Homo_sapiens reference genome GRCh38 using the HiSat2 aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm (v2.0.1).
Batch effects (RNA Seq RUN) were removed with Combat_Seq of the SVA package using a negative binomial regression model
Expression data was normalized using the normalization function of DeSeq2 package or TPM/RPKM values
Differentially expressed genes (logFC±1, padj ≤ 0.05) were identified by negative binomial generalized linear models statistics using the DeSeq2 package
Assembly: version 102 of Homo_sapiens reference genome GRCh38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: CNS brain

extract_protocol:
RNA was isolated using the Maxwell® RSC Simply RNA Tissue kit (AS1340, Promega) and processed as per manufacturer’s instructions.
Illumina Stranded total RNA Prep kit (#20040529, Illumina) and processed as per manufacturer’s instructions.
RNA-seq with 75 cycles single-end read protocol and a NextSeq 500/550 High Output Kit v2.5 (#20024906, Illumina).

value: CNS brain

tag: rna seq_run

tag: tspo expression

value: LOW

tag: tspo cluster

value: LOW I

tag: diagnosis

value: IDH-wt WHO grade 4 solid glioblastoma tumor


title: GBM_26


title: GBM_17


title: GBM_18


title: GBM_14

value: HIGH

value: HIGH II


title: GBM_16


title: GBM_09


title: GBM_15

value: HIGH III


title: GBM_01


title: GBM_11_II


title: GBM_03


title: GBM_08


title: GBM_05


title: Posterior fragment, amputation, 6H [Amp_Illumina_6P6]

status: Public on Sep 11 2023

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
NPv6.final_annotation.csv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.ORF.tsv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.fasta.gz
NPv6.busco_summary.specific.eukaryota_odb10.txt
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.sample_annotation.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.counts.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.TPM.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.TPM.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.counts.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.counts.tsv.gz
Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.TPM.tsv.gz

data_processing:
We filtered Illumina reads using Trimmomatic (v 0.39) with the following parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, and Nanopore and Pacbio reads using NanoFilt (v 2.7.1) with the following parameters œ-q 10 -l 150 --headcrop 75 -- tailcrop 75. We assembled an initial transcriptome draft with RATTLE assembler using the filtered Nanopore reads. We then aligned filtered Illumina and Pacbio reads to the initial draft using Minimap2 (v 2.17-r941) to perform base polishing using Pilon (v 1.23). To remove chimeric transcripts or regions with poor read support, we performed a coverage scan with a rolling window size of 10 bp to trim both ends of the transcript that have less than 33% of the maximum alignment coverage. After trimming, transcripts that have lengths shorter than 300 bp were removed. We then re-mapped the Illumina reads to the initial draft using Salmon quant (v 1.3.0) and clustered similar transcripts with Grouper (https://github.com/COMBINE-lab/grouper) to remove duplicate transcripts. Illumina and Pacbio reads were then re-mapped against the clustered transcriptome using Minimap2 for a second round of base polishing, yielding the final version of the transcriptome. We predicted the open reading frame (ORF) for each transcript using TransDecoder (v 5.5.0) (https://github.com/TransDecoder/TransDecoder) with default parameters, keeping only the predicted ORF with the longest length. We performed functional annotation using Trinotate (v 3.2.1). To identify putative homologs, we performed blastx on the transcriptome against the NCBI â€œrefseq_proteinâ€ database. To evaluate the completeness of our transcriptomes, we performed BUSCO (v 4.0.5) analysis.
Assembly: NPv6
Supplementary files format and content: NPv6.final_annotation.csv.gz : comma-separated values of NPv6 transcriptome annotation.
Supplementary files format and content: transcriptome.NPv6.trimmed.grouped.pilon_corrected.ORF.tsv.gz : Tab-separated values of predicted open reading frames for NPv6 transcriptome reference.
Supplementary files format and content: transcriptome.NPv6.trimmed.grouped.pilon_corrected.fasta.gz : NPv6 transcriptome reference in fasta format.
Supplementary files format and content: NPv6.busco_summary.specific.eukaryota_odb10.txt : BUSCO analysis summary for NPv6 transcriptome.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.sample_annotation.tsv.gz : Tab-separated values of meta information for amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.counts.tsv.gz : Tab-separated non-normalized counts of algal transcripts in amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.TPM.tsv.gz : Tab-separated TPM values of all transcripts in amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.TPM.tsv.gz : Tab-separated TPM values of algal transcripts in amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.counts.tsv.gz : Tab-separated non-normalized counts of acoel transcripts in amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.counts.tsv.gz : Tab-separated non-normalized counts of all transcripts in amputation treated group.
Supplementary files format and content: Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.TPM.tsv.gz : Tab-separated TPM values of acoel transcripts in amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.sample_annotation.tsv.gz : Tab-separated values of meta information for Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.counts.tsv.gz : Tab-separated non-normalized counts of algal transcripts in Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.TPM.tsv.gz : Tab-separated TPM values of all transcripts in Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.TPM.tsv.gz : Tab-separated TPM values of algal transcripts in Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.counts.tsv.gz : Tab-separated non-normalized counts of acoel transcripts in Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.counts.tsv.gz : Tab-separated non-normalized counts of all transcripts in Runt RNAi+amputation treated group.
Supplementary files format and content: Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.TPM.tsv.gz : Tab-separated TPM values of acoel transcripts in Runt RNAi+amputation treated group.

organism: Convolutriloba longifissura

source_name: Posterior fragment

growth_protocol: Acoels were cultured in a 16 gallon Coralife Biocube Aquarium in artificial seawater (ASW, 34 ppt, Instant Ocean) at 26°C with a 14h:10h light:dark cycle. Acoels were fed freshly hatched Artemia shrimp every 1-3 days ad libitum in the tank. Animals used in experiments were kept in individual wells in an incubator at 26°C with a 14:10h light:dark cycle, with filtered ASW. These animals were fed and their water was changed every 1-3 days.

extract_protocol:
Nextera XT library prep
Three replicates each containing five animals were used for RNA extraction for each condition. We rinsed the animals in ASW twice and then removed as much ASW as possible. 300 ulof Trizol was added, followed by a 2-3 min incubation at room temperature and vigorous vortexing to dissociate the tissue. Samples were then flash frozen on dry ice and kept at -80 °C until extraction so that all samples for each RNA-seq experiment could be processed in parallel. On the day of the extraction, samples were thawed on ice and 700 ulof fresh Trizol was added. After brief vortexing, 200 ulof chloroform was added and the sample was shaken vigorously for 15 s followed by a 2 min incubation. Samples were then centrifuged (16,000 g, 15 min at 4 °C) and the aqueous phase was carefully transferred into new tubes and processed with the Direct-zol RNA Purification Kit (Zymo Research, cat. #R2051) following the manufacturerâ€™s instructions, which includes a DNAse treatment step. RNA concentration and quality was quantified on a Bionanalyzer.

treatment_protocol: Animals were kept individually or in groups smaller than 10 individuals in 12-well or 24-well plates in an incubator (Danby Fresh 1.7 cu. ft. Herb Grower, cat. #DFG17A1B). RNA were extracted from anterior or posterior fragments 0 hour or 3 hours after amputation. Double stranded RNA (dsRNA) was synthesized using pJC53.2 plasmids, and resuspended in 50 uL MilliQ water. RNAi was performed through microinjection into the gut using a XenoWorks Digital Microinjector. Needles were pulled with a vertical micropipette puller (Sutter Instruments Model P-30, with settings heat: 750 and pull: 750). The dsRNA was diluted 1:1 with ASW and mixed with food coloring dyes for visual confirmation of successful delivery. runt RNAi injections were done every 2 days over a week (3 injections total). Animals were fed brine shrimp before injections to ensure the formation of the acoel gut, and water was changed every couple of days. As the negative control, acoels were injected with the ccdB and camR insert from the pJC53.2 plasmid. Control RNAi was administered with the same frequency and for the same time span as runt respectively. After control or runt RNAi treatment, animals were amputated and only the tail fragment was kept for RNA extraction.

tag: individual

value: acoel Convolutriloba longifissura

value: Posterior fragment

value: Amputation


title: Posterior fragment, amputation, 3H [Amp_Illumina_3P3]

tag: treatment


title: GBM_02

tag: tissue


title: Posterior fragment, amputation, 3H [Amp_Illumina_3P2]


title: GM12878_indexTag7_scWGS

value: Blood, Cell line

value: Lymphoblastoid Cell Line


title: Posterior fragment, amputation, 0H [Amp_Illumina_0P4]


title: Posterior fragment, amputation, 3H [Amp_Illumina_3P1]


title: Posterior fragment, amputation, 0H [Amp_Illumina_0P3]


title: GBM_22


title: Anterior+Posterior fragment, amputation [Amp_Pacbio]

description:
Pacbio SMRT
NPv6.final_annotation.csv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.ORF.tsv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.fasta.gz
NPv6.busco_summary.specific.eukaryota_odb10.txt

source_name: Anterior+Posterior fragment

extract_protocol:
Sequel II binding kit 2.0
Three replicates each containing five animals were used for RNA extraction for each condition. We rinsed the animals in ASW twice and then removed as much ASW as possible. 300 ulof Trizol was added, followed by a 2-3 min incubation at room temperature and vigorous vortexing to dissociate the tissue. Samples were then flash frozen on dry ice and kept at -80 °C until extraction so that all samples for each RNA-seq experiment could be processed in parallel. On the day of the extraction, samples were thawed on ice and 700 ulof fresh Trizol was added. After brief vortexing, 200 ulof chloroform was added and the sample was shaken vigorously for 15 s followed by a 2 min incubation. Samples were then centrifuged (16,000 g, 15 min at 4 °C) and the aqueous phase was carefully transferred into new tubes and processed with the Direct-zol RNA Purification Kit (Zymo Research, cat. #R2051) following the manufacturerâ€™s instructions, which includes a DNAse treatment step. RNA concentration and quality was quantified on a Bionanalyzer.

value: Anterior+Posterior fragment


title: Anterior+Posterior fragment, amputation [Amp_Nanopore]

description:
NPv6.final_annotation.csv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.ORF.tsv.gz
transcriptome.NPv6.trimmed.grouped.pilon_corrected.fasta.gz
NPv6.busco_summary.specific.eukaryota_odb10.txt

extract_protocol:
ONT library prep
Three replicates each containing five animals were used for RNA extraction for each condition. We rinsed the animals in ASW twice and then removed as much ASW as possible. 300 ulof Trizol was added, followed by a 2-3 min incubation at room temperature and vigorous vortexing to dissociate the tissue. Samples were then flash frozen on dry ice and kept at -80 °C until extraction so that all samples for each RNA-seq experiment could be processed in parallel. On the day of the extraction, samples were thawed on ice and 700 ulof fresh Trizol was added. After brief vortexing, 200 ulof chloroform was added and the sample was shaken vigorously for 15 s followed by a 2 min incubation. Samples were then centrifuged (16,000 g, 15 min at 4 °C) and the aqueous phase was carefully transferred into new tubes and processed with the Direct-zol RNA Purification Kit (Zymo Research, cat. #R2051) following the manufacturerâ€™s instructions, which includes a DNAse treatment step. RNA concentration and quality was quantified on a Bionanalyzer.


title: Posterior fragment, amputation, 0H [Amp_Illumina_0P2]


title: GBM_07


title: Anterior fragment, amputation, 0H [Amp_Illumina_0A2]

source_name: Anterior fragment

value: Anterior fragment


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_R6-1]

description:
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.sample_annotation.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.counts.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.TPM.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.algae.TPM.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.counts.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.counts.tsv.gz
Runt_Amp_bulk_Illumina_RNAseq_NPv6_Illumina.acoel.TPM.tsv.gz

value: Runt RNAi + Amputation


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_R6-3]


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_R3-3]


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_R0-1]


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_R0-2]


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_R3-1]


title: GBM_25


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_R0-3]


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_R3-2]


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_C6-2]

value: control RNAi + Amputation


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_C6-3]


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_C3-2]


title: Posterior fragment, amputation, 6H [Amp_Illumina_6P3]


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_C0-2]


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_C0-3]


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_C3-1]


title: Brown adipose tissue, 4 days after primary cold challenge (1cyc), snRNAseq

city: Philadelphia

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Cellranger v3
Supplementary files format and content: mm10
Supplementary files format and content: matrix, barcodes, and gene files

source_name: Brown adipose tissue (BAT)

extract_protocol:
Nuclei were isolated as described in manuscript, sorted based on DAPI positivity, and loaded into 10X Genomics platform
10X Genomics according to manufacturers protocol
snRNAseq

value: Brown adipose tissue (BAT)

value: mice that had undergone transient acute cold exposure 4 days previously (1cyc)


title: BCBL1_ADNP_1

status: Public on Sep 08 2023

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Base calling and quality scoring were performed using bcl2fastq v2.17 for Novaseq 6000 output.
CUT&RUN reads were processed with fastp and aligned to the GRCh38 (hg38) human reference genome assembly with Bowtie2.
Hypergeometric Optimization of Motif EnRichment (HOMER) v4.11 was used for peak detection were annotated utilizing the defalt parameters described in the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
CPM-normalized  data files in bigWig format were generated. Mapped reads in BAM format were converted and scaled, using CPM (Counts Per Million mapped reads) normalization, to bedGraph using bedtools. BedGraph files were then converted to bigwig files for visualization.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data are in bigWig format.
Library strategy: CUT&RUN

growth_protocol: Primary effusion lymphoma cell lines (BCBL-1, BC1, BC3) were cultured in RPMI 1640 medium supplemented with 15% FBS, 2 mM L-glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humidified atmosphere with 5% CO2 at 37C. iSLK cells were cultured with DMEM medium with 10% FBS 2 mM L-glutamine, and antibiotics (100 U/ml penicillin and 100 μg/ml streptomycin) in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were washed with PBS and wash buffer (20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine (Sigma, S2626) and proteinase inhibitor (Roche). After removing wash buffer, cells were captured on magnetic ConA beads (Polysciences), in presence of CaCl2. Beads/cells complexes were washed with digitonin wash buffer (0.02% digitonin, 20mM HEPES-KOH pH7.5, 150mM NaCl, 0.5mM spermidine and 1x proteinase inhibitor) three times, and incubated with specific antibodies in 250 mL volume. After incubation, unbound antibody was washed by digitonin wash buffer 3 times. Beads were then incubated with the recombinant pAG-MNase, in 250μl digitonin wash buffer (1.0 mg/mL final concentration) for an hour at 4°C with rotation. Unbound pAG-MNase was removed by washing with digitonin wash buffer 3 times. Pre-chilled 2 mM CaCl2 containing digitonin wash buffer (200 mL) was added to beads and incubate on ice for 30 min. The pAG-MNase digestion was halted by the addition of 200μl 2× STOP solution (340mM NaCl, 20mM EDTA, 4mM EGTA, 50μg/ml RNase A, 50 mg/ml Glycogens). The beads were incubated/shaked at 37°C for 10min in tube shaker at 500 rpm to release digested DNA fragments from the insoluble nuclear chromatin. The supernatant was collected after centrifuge (16,000 x g for 5 min at 4°C) and place on magnetic stand. DNA was extracted using the NucleoSpin & PCR kit (Takara Bio, Kusatsu, Shiga, Japan).
Sequencing libraries were prepared from 3 ng of CUT&RUN DNA with the Kapa HyperPrep Kit (Roche) according to the manufacturer’s standard protocol. Libraries were multiplex sequenced (2 x 150bp, paired-end) on an Illumina NovaSeq 6000 sequencing system.

value: B-cell

value: No treatment

tag: cut&run antibody

value: Invitrogen Cat# 16H17L68


title: BCBL1_ADNP_2

tag: cell type


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_R6-2]


title: Posterior fragment, amputation, 0H [Runt_RNAi_Illumina_C0-1]


title: BCBL1_BRD4_Control_2

value: BRD4 (CST, E2A7X)


title: BCBL1_SMARCA5_2

value: Invitrogen Cat# PA5-52601


title: BC1_BRD4_Control_2


title: BC1_SMARCA5_1


title: BC1_SMARCA5_2


title: BCBL1_SMC1_2

value: SMC1 (CST Cat #4802)


title: Posterior fragment, amputation, 6H [Runt_RNAi_Illumina_C6-1]

value: acoel Convolutriloba longifissura


title: BCBL1_RNA_pol_II_2

value: Millipore CTD4H8


title: BCBL1_RNA_pol_II_1


title: BC1_BRD4_Control_1


title: Posterior fragment, amputation, 3H [Runt_RNAi_Illumina_C3-3]

value: Posterior fragment


title: BCBL1_SMC1_1


title: BCBL1_BRD4_Control_1


title: BC1_RNA_pol_II_1


title: BC1_RNA_pol_II_2


title: BC1_MLL1_2

value: Epicypher 13-2004


title: BCBL1_MLL1_2


title: BCBL1_CTCF_2

value: CTCF (CST D31H2)


title: BCBL1_H3K27me3_2


title: BCBL1_CTCF_1


title: BC1_CTCF_2


title: BCBL1_H3K27me3_1


title: BC1_CTCF_1


title: iSLK_57Wt_H3KK27me3_2

source_name: SLK cells

value: SLK cells

value: renal carcinoma cells


title: iSLK_57Wt_H3KK27me3_1


title: BC3_H3K27me3_2


title: BC3_H3K27me3_1


title: BC1_H3K27me3_2


title: BCBL-1_H327Ac_1

value: Active motif  #91193


title: BCBL1_MLL1_1


title: BCBL-1_H327Ac_2


title: BC1_MLL1_1


title: BCBL1_K4me2_1

value: H3K4me2 (CST C64G9)


title: BCBL1_H3K4me3_1

value: H3K4me3 (CST C42D8)


title: BCBL1_H3K4me3_2


title: BC1_K4me2_1

value: H3K4me1 (CST D1A9)


title: BC1_K4me2_2

value: B-cell


title: BC1_H3K27me3_1

value: No treatment


title: BC1_H3K4me1_2


title: BCBL-1_K4me1_2