title: LNCaP_WT_shCtrl_noDOX

description: negative control without endogenous AR knockdown and without BLRP AR-WT overexpression

value: AR-WT:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: WT_shCtrl_noDOX_Veh

status: Public on Oct 31 2023

type: SRA

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

country: USA

institute: Universality of Texas Health Science Center at San Antonio

library_source: genomic

data_processing:
Basecalls performed using Illuminal CASAVA software.
The adaptor was removed by using cutadapt v1.11 with parameters "-m 20 -e 0.1". The clean reads were aligned to the hg19 genome assembly using bowtie2 v2.2.9 with parameters "-mm --very-sensitive --no-discordant -X 2000", and only primary alignments were retained. The alignments were shifted with +4 for plus strand and -5 for minus strand.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Assembly: hg19
Supplementary files format and content: bigWig file

molecule: genomic DNA

organism: Homo sapiens

source_name: prostate cancer cells

growth_protocol: LNCaP obtained from ATCC were cultured in RPMI1640 media supplemented with 10% FBS. The established doxycycline-inducible stable cell lines with pInducer20 vectors that contain different AR cDNAs were maintained at RPMI1640 medium with G418 (600 μg/ml) for stable selection. All cell lines were cultured in a 5% CO2 humidified incubator at 37°C.

extract_protocol: 50,000 cells were harvested for each condition. After purification of nuclei, transposition was performed with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030). ATAC-seq library prep was performed as in Buenrostro et al, 2015. Libraries were sequenced with either High SR 75 on Illumina NextSeq 500 or SR 50 on Illumina HiSeq3000.

treatment_protocol: To test the role of AR condensation on enhancer accessibility, we used 1,6 hexanediol (1,6 HD) to chemically disrupt phase separation in cells. Before experiment, the LNCaP cells were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by three different treatments for 2 hours: 1. ethanol as vehicle control; 2. 100 nM DHT as hormone stimulation sample; 3. 100 nM DHT plus 2.5% 1,6 HD as condensation disruption condition. To test the enhancer regulation function of different AR cDNAs (WT vs mutants), we have set up the doxycycline-inducible stable cell lines with pInducer20 vectors that contain different AR cDNAs. For the rescue experiments, doxycycline-inducible AR-overexpressing LNCaP cell lines were infected by either control or AR shRNA lentivirus and selected with 1 μg/ml puromycin and collected for experiments within 5 days (first two days in regular medium and last three days in stripping media before hormone treatment). 20 ng/ml doxycycline was added to the overexpressing samples for 2 days before the 2 hours of vehicle or DHT treatment and collection for ATAC-seq experiments.

tag: cell line

value: LNCaP

tag: transfection

value: LNCap stable line with pInducer20-AR-WT (G418) (AR cDNA is shAR3718-Resistant)

tag: treatment

value: pInd-AR-WT:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: LNCaP_dIDR_shCtrl_noDOX

description: negative control without endogenous AR knockdown and without BLRP AR-dIDR overexpression

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Assembly: hg19
Supplementary files format and content: bigWig file

growth_protocol: The established BLRP-tagged Tet-On inducible stable lines were established from LNCaP cell line (ATCC) and their growing were maintained at RPMI1640 medium with G418 (300 μg/ml), hygromycin (100ug/ml) and puromycin (0.3 μg/ml) for stable selection. All cell lines were cultured in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with streptavidin magnet beads pull-down.
The extracted ChIP DNA was ligated to specific adaptors using KAPA LTP Library Preparation Kit (KK8230) or KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.

treatment_protocol: To perform Biotin ChIP experiments through Biotin-streptavidin pull-down, we used the BLRP-tagged Tet-On inducible LNCaP stable lines that can in vivo biotinylate BLRP-tagged proteins. For each line, we have prepared two different cell samples for biotin ChIP: the control one was transduced with control shRNA and not treated with doxycycline; the experimental sample was transduced with AR shRNA TRCN0000003718 and treated by 2 μg/ml doxycycline for 24 hours. Both cell samples were hormone-stripped in phenol red-free RPMI1640 medium plus 5% charcoal-treated FBS for 3 days, followed by treatment with 100 nM DHT for 2 hours before collection for biotin ChIP experiments.

value: LNCaP stable cell line with pBirA (G418), pRetro-TetR (Hygromycin), and pRetro-BLRP-AR-dIDR (puromycin) (AR cDNA is shAR3718-Resistant)

value: AR-dIDR:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr

tag: chip antibody

value: Biotin-ChIP using Streptavidin Magnetic beads (Solulink)


title: AngII+Si-NAT10_RNA_2

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

country: China

institute: School of Medicine, Southeast University

library_source: transcriptomic

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For acRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For acRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
For Ribo-seq: The reads were aligned to rRNA and tRNA sequences so as to remove rRNA and tRNA reads using bowtie2 software, remaining reads were used to align to reference genome and transcriptome (Ensembl Version 91) using hisat23 and bowtie2 software separately.
For Ribo-seq:ORF identification was performed using Price5 software.  Read counts were calculated using featureCounts6 software.  Raw counts were further normalized as RPKM values using fpkm function in DESeq27 package.
Assembly: mm10 and hg38
Supplementary files format and content: mRNA-seq_9 mouse_All.count.txt
Supplementary files format and content: Ribo-seq_9 mouse_All.count.txt
Supplementary files format and content: 12hsa_acRIP-seq_input.count.txt
Supplementary files format and content: 12mmu_acRIP-seq_input.count.txt

molecule: total RNA

organism: Mus musculus

source_name: heart ventricular tissue

extract_protocol:
For acRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852).   Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2.   Subsequently, the purified RNA was incubated with anti-ac4c polyclonal antibody  for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments.   The ac4c-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106).   The RNA-seq library was prepared by NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, E7775).  For Ribo-seq:tissue were pulverized manually under liquid nitrogen and treated by ice-cold PBS containing 100 μg/mL cycloheximide.     Ribosome profiling was performed using Epi™ Ribosome Profiling Kit (Epibiotek, R1814).     Subsquently, RPFs (ribosome-protected RNA fragments) was extracted using RNA clean&ConcentratorTM-5 kit (ZYMO, R1016).     EpiTM RiboRNA Depletion Kit  (Epibiotek, R1805) was used for rRNA depletion.     Sequencing libraries were constructed using QIAseq miRNA Library kit (QIAGEN, 1103679).
RNA libraries were prepared for sequencing using standard Illumina protocols
acRIP-seq; Ribo-seq; RNA-seq

treatment_protocol: Silencing and inhibiting NAT10

tag: tissue

value: heart ventricular tissue

tag: genotype


title: Liver_obese_T2D T2D28

type: RNA

city: Lübeck

first: Henriette

last: Kirchner

address: Ratzeburger Allee 160

department: Institute for Human Genetics

country: Germany

institute: University of Lübeck

description:
Liver_obese_T2D
noncoding RNA expression from diabetic and non-diabetic liver of human obese subjects

hyb_protocol: After preparation of the hybridization cocktail using additionaly 3 nM control oligo B2  and hybridiztion controls (GeneChip Hybridization Control Kit, Applied Biosystems), 21.5 µl biotin-labeld sample were injected into one GeneChip miRNA 4.0 Array, multi-species (Applied Biosystems) per sample. Hybridization was performed for 18 h at 48 °C and 60 rpm. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChip miRNA 4.0 Array, multi-species were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data analysis was performed with the Transcriptome Analysis Console software (version 4.0.2.15) with the analysis type 'Expression (Gene)'. As summarization method 'RMA+DABG (Human Only)' was used for signal normalization. ANOVA method 'ebayes' was used for comparison. A probe set was considered expressed if at least 50% of the detection above background (DABG) values were below the DABG threshold.

label: biotin

source_name: liver biopsy of an obese human subject with type-2-dabetes

label_protocol: Biotinylated RNA was prepared according to the FlashTag Biotin HSR RNA Labeling Kit (Applied Biosystems, USA) from 500 ng total RNA.

extract_protocol: RNA was isolated from snap-frozen liver using the miRNeasy mini kit (Qiagen, Germany) according to the manufacturer’s instructions blinded.

value: liver

tag: condition

tag: age

tag: bmi

tag: gender

value: w


title: CRC27

city: shanghai

first: Kong

last: Cheng

address: 270 Dong 'an Road

institute: fudan university shanghai cancer center

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh37_genome_ensembl_v73
Supplementary files format and content: RPKM values for each Sample

source_name: Tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Tumor tissue

value: snap-frozen tissues


title: CRC26


title: H3i, YPGal, RNA-seq biol rep1

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

data_processing:
FastQC
Reads were align to Saccer3 genome using the Hisat2
Sorting and indexing using Samtools
Duplication was removed by Picard tools
Raw read counts were normalized by DEseq2
Assembly: Saccer3
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were cultured in YPGal medium at 30°C and 230 rpm before H3-shutoff experiment. The H3 inducible shut-off strain (i.e., “DGS200.1” or  “H3i”) from the YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter.

extract_protocol:
RNA was extracted by MagMax96 total RNA isolation kit (AM1830, Invitrogen) for the first and second replicates. Trizol reagent (15596026, Invitrogen) was used in extraction with glass beads for the third replicate.
Librarires of the first and second replicates were prepared using the Illumina TruSeq Stranded mRNA Library Prep. For the third replicate, the TruSeq Stranded mRNA LT sample prep kit was used for library construction.

treatment_protocol: Switching media from YPGal to YPD

value: Cell pellet

tag: cell type

value: Yeast cell

value: YPGal


title: CRC25


title: Liver_obese_T2D T2D39

value: m


title: WT, YPGal, RNA-seq biol rep1

value: WT


title: WT, YPD, RNA-seq biol rep1

value: YPD


title: ChIP H3K27Ac MPdiff

city: Berlin

first: Frederic

last: Koch

address: Ihnestraße 63-73

department: Developmental Genetics

institute: Max Planck Institute for Molecular Genetics

data_processing:
Prior to mapping, the forward and reverse reads were trimmed to 50bp using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using bowtie version 1.3.1, providing the options ‘ -y -m 1 -S  -I 100 -X 500’. The mapping information of the paired-end reads was used to elongate each fragment to its original size using a custom pearl script, with the result stored as a BED file. Reads were then sorted and deduplicated such that only one fragment with the same starting and end position was retained. For visualization, wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: FACS sorted T+/Noto- cells from in vitro differentiated cultures

growth_protocol: To initiate NotoP differentiation, ESCs were removed from feeders by dissociation using 0.05% trypsin and then plated onto tissue culture plates for four short successive periods (25’, 20’, 15’, 10’) to remove feeders. To induce differentiation, a protocol slightly modified from Gouti et al. was used. In short, cells were plated on CellBINDSurface dishes precoated with 0.1% gelatin at a density of 1 x 104 cells per cm2 in a medium consisting of ‘N2B27’ medium, supplemented with 10 ng/ml bFGF for 3 days (d1-d3). From d2-d4 µM CHIR99021 was added to the medium. For induction of Foxa2 expression, 1ng/ml doxycycline was applied from d2-d4.

extract_protocol:
Cells were processed using the iDeal ChIP-Seq kit (Diagenode) according to manufacturer’s instructions. Approximately 200,000 cells were used per ChIP with the following antibodies: anti-H3K4me1 (pAb-194-050, Diagenode), anti-H3K4me3 (ab8580, Abcam), anti-H3K27ac (ab4729, Abcam) and anti-H3K9me2 (A90-0042, Diagenode).
ChIP-Seq sequencing libraries were generated using the TrueSeq ChIP-Seq kit (Ilumina) following the manufacturer’s instructions with minor modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter A63880) were used for a single purification and the DNA was eluted using 15 µl of resuspension buffer (RSB, Illumina). After the addition of 1 µl primer mix (25 mM each, Primer 1: 5’-AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 s at 98°C, 5 cycles of [15 seconds at 98°C, 30 s at 63°C and 30 s at 72°C] and a final 1 min incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 µl of RSB. Libraries were directly amplified for additional 13 cycles and purified using AMPure XP beads. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips (Agilent 5067-4626).

value: genetically modified F1G4 (C57BL/6N x SV129) mES cells

value: in vitro generated mesoderm progenitor cells

value: TRE::Foxa2-IRES-EGFP (Rosa26 locus); T::H2B-mCherry-T2A-irTA (BAC); Noto::H2B-mTurquoise (BAC)

value: Cells were washed 2x PBS and dissociated by trypsinization at 37°C for 10min. Trypsin/EDTA was quenched using a double volume of 5%BSA/PBS, resuspended and kept on ice until further procedure. All samples were immediately filtered (35µm mesh) and sorted on a FACS Aria II (Becton Dickinson) flow cytometer. Cells were sorted into PBS 5% BSA in BSA coated glass tubes. After sorting, cells were pelleted by centrifugation, transferred to 1.5 ml low binding tubes and washed in PBS containing  0.05% Triton X-100 to break the surface tension.  Crosslinking was performed by adding 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) to cells resuspended in 500µl PBS for 10 minutes at room temperature with agitation. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Pellets were washed twice using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~0.6x106 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.


title: ChIP H3K4me1 NotoPdiff

source_name: FACS sorted Noto+/T+ cells from in vitro differentiated cultures

value: in vitro generated notochord progenitor-like cells


title: ChIP H3K27Ac NotoPdiff

value: FACS sorted Noto+/T+ cells from in vitro differentiated cultures


title: CRC24


title: ChIP Foxa2 NotoPdiff

data_processing:
Prior to mapping, the forward and reverse reads were trimmed to 50bp using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads were mapped to chromosomes 1-19, X, Y and M of the mouse mm10 genome using bowtie version 1.3.1, providing the options ‘ -y -m 1 -S  -I 100 -X 500’. The mapping information of the paired-end reads was used to elongate each fragment to its original size using a custom pearl script, with the result stored as a BED file. Reads were then sorted and deduplicated such that only one fragment with the same starting and end position was retained. For visualization, wiggle files were generated with BEDTools version 2.23.0, converted to bigwig format and visualized in the Integrated Genome Browser. Peak detection was performed using MACS version 3.0.0b1 (https://github.com/macs3-project/MACS) using the elongated and deduplicated bed files as inputs and setting a q-value cutoff of 0.1.
Assembly: mm10
Supplementary files format and content: *.bw: tag denisty files of ChIP data in bigWig format
Supplementary files format and content: *.narrowPeak: peak files for ChIP-Seq tracks used in analysis obtained by MACS
Supplementary files format and content: RNA_FPKM.txt: normalized per gene abundance measurements (FPKM) for RNA-Seq samples obtained by Cuffdiff

source_name: in vitro differentiated cell cultures

extract_protocol:
For sonication, complete protease inhibitors without EDTA (Roche) at 1x final concentration was added to all lysis buffers (LB) prior to use. Each pellet was resuspended in LB1 (50mM Hepes pH7.5, 140mM NaCl, 1mM EDTA pH8, 10% glycerol, 0.75% NP-40, 0.25% triton X-100) and rotated at 4°C for 20 minutes. The cell suspension was homogenized using a douncer with a tight pestle with 3x 15 strokes, with short resting times on ice in between. The chromatin was pelleted by centrifugation at 1400g and 4°C for 5 minutes and resuspended in 2.5ml LB2 (200mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 10mM Tris pH 8) per cell pellet. After 10 minutes rotation at 4°C, the centrifugation step was repeated and each pellet was resuspended in 1.5ml LB3 (1mM EDTA pH8, 0.5mM EGTA, 10mM Tris pH8, 100mM NaCl, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine), transferred to 15ml Falcon tubes and sonicated using a W-450D Digital Sonifier (Branson) sonicator for 14 cycles of 10s on/50s off in a 4°C coldroom with tubes chilled in ice water. After sonication, 150ul of triton X-100 was added per tube, transferred to two 1.5ml Eppendorf tubes and debris was pelleted by centrifugation at 20,000g and 4°C for 10 minutes. The solubilized chromatin was then pooled and mixed thoroughly. After taking 50ul as an input control, the chromatin was distributed into 1.5ml aliquots, snap frozen and stored at -80C until use. For ChIP, 25ul of protein-coated Dynal beads (Life Technologies) were washed 3x using 1ml of blocking solution (PBS containing 0.5% BSA), resuspended in 500ml of blocking solution together with approximately 2.5ug antibody and rotated overnight at 4C. The antibodies used were a goat polyclonal anti-T (R&D, AF2085) and a rabbit polyclonal anti-Foxa2 (Diagenode, 2683-6041). The next day, three further washes using 1ml blocking buffer were performed and the beads were resuspended in 100ml blocking buffer. Chromatin equivalent to approximately 2x10^6 cells was added and rotated overnight at 4C. The following day, washing steps (8 and 9 washes for Foxa2 and T respectively) were performed using 1ml RIPA buffer (50mM Hepes pH7.6, 500mM LiCl, 1mM EDTA pH8, 1% NP-40, 0.7% Na-Deoxycholate) containing 1x complete protease inhibitors without EDTA and finally once with 1ml of TEN (10mM Tris pH8, 1mM EDTA pH8, 50mM NaCl). The immunoprecipates were eluted in two subsequent steps using 100ml of 1x elution buffer (50mM Tris pH8, 10mM EDTA pH8, 1% SDS) and incubation at 65C while shaking for 10 minutes each. The eluates were combined and incubated overnight (13h-15h) at 65C under agitation. The next day, 200ml of TE were added to dilute the SDS of the elution and the ChIPs were purified with two subsequent phenol:chloroform:isoamylalcohol (25:24:1, pH8) isolations and a MinElute (Qiagen) purification.
ChIP-Seq sequencing libraries were generated using the TrueSeq ChIP-Seq kit (Ilumina) following the manufacturer’s instructions with minor modifications. After adapter ligation, 0.95x of AMPure XP beads (Beckman Coulter A63880) were used for a single purification and the DNA was eluted using 15 µl of resuspension buffer (RSB, Illumina). After the addition of 1 µl primer mix (25 mM each, Primer 1: 5’-AATGATACGGCGACCACCGA*G-3’; Primer2: 5’- CAAGCAGAAGACGGCATACGA*G-3’) and 15µl 2x Kapa HiFi HotStart Ready Mix (Kapa Biosystems), amplification was performed for 45 s at 98°C, 5 cycles of [15 seconds at 98°C, 30 s at 63°C and 30 s at 72°C] and a final 1 min incubation at 72°C. The PCR products were purified using 0.95x of beads and eluted using 21 µl of RSB. Libraries were directly amplified for additional 13 cycles and purified using AMPure XP beads. The libraries were quantified using the Qubit DNA HS assay and the library size was validated using DNA HS bioanalyzer chips (Agilent 5067-4626).

value: in vitro differentiated cell cultures

value: Crosslinking was performed directly on differentiating cells in growth medium with the addition of 1/10th volume of crosslinking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 50mM Hepes pH7.8) for 10 minutes at room temperature, with the dishes placed on a shaker. The crosslinking reaction was quenched with the addition of 1/10th volume of 2.5M glycine and 5 minutes incubation. Dishes were placed on ice or in a 4°C cold room and washed twice with cold PBS. Cells were scraped and washed off using cold PBS, containing 0.05% Triton X-100 to break the surface tension. Cells were pooled in aliquots of ~30-50x10^6 in Eppendorf tubes, snap frozen and stored at -80°C until sonication.


title: ChIP H3K4me3 MPdiff

value: FACS sorted T+/Noto- cells from in vitro differentiated cultures


title: ChIP H3K4me1 MPdiff


title: WT_shCtrl_DOX_DHT

value: LNCaP

value: LNCap stable line with pInducer20-AR-WT (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-WT:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: WT_shCtrl_DOX_Veh

value: pInd-AR-WT:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: WT_shCtrl_noDOX_DHT

value: pInd-AR-WT:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: WT_shAR_noDOX_Veh

value: pInd-AR-WT:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: AngII_RNA_2

value: heart ventricular tissue

value: AngII


title: AngII+Si-NAT10_RNA_1


title: AngII_RNA_3


title: CRC23

value: Tumor tissue

value: snap-frozen tissues


title: AngII_RNA_1


title: WT_shAR_noDOX_DHT

value: pInd-AR-WT:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: Sham_RNA_3

value: Sham


title: CRC22


title: WT_shAR_DOX_Veh

value: pInd-AR-WT:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: Liver_obese_T2D T2D52

value: liver

value: m


title: HCO, BMP2, 35 day, Rep 3

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
For H1 RNA-seq, FASTQ data was evaluated using FASTQC. Tuxedo Suite was used for alignment and differential expression analysis. Reads were aligned to hg19 using TopHat v2.0.13 and Bowtie v2.2.5 using default parameters except "-2-very-sensitive", "-no-coverage-search", and "-no-novel-juncs". Cufflinks with"-mulit-read-correct", "-compatible-hits-norm", and "-upper-quartile -norm" to generate TPM matrix.
For iPSC72 RNA-seq, data was processed through BGI pipeline. Briefly, sequenced samples were filtered, trimmed of adapters and low-quality read, quality controlled, and aligned to hg38.
Assembly: hg19 H1 RNA-seq
Assembly: hg38 iPSC72 RNA-seq
Supplementary files format and content: tab-delimited text files including TPM per sample

source_name: hPSC-derived colonic organoid

extract_protocol:
RNA was extracted using RNA NucleoSpin kit (Macherey-Nagel) according to manufacturer's instructions. >300 ng/sample of RNA used to make RNA library.
For H1, library construction was performed by CCHMC DNA sequencing core using standard Illumina mRNA Stranded Library Preperation protocol. For iPSC72, library construction was performed by BGI.

value: hPSC-derived colonic organoid

value: WA01 hESC

value: Pooled organoids epithelium and mesenchyme

value: 35 days post-hPSC

value: BMP2 Day 7-10


title: CRC21


title: CRC20


title: HCO, BMP2, 35 day, Rep 2


title: HCO, BMP2, 35 day, Rep 1


title: CRC19


title: WT_shAR_DOX_DHT

value: LNCaP

value: LNCap stable line with pInducer20-AR-WT (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-WT:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: FS_shCtrl_noDox_DHT

value: LNCap stable line with pInducer20-AR-7F-7S (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-7F-7S:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: HIO, NOGGIN, 35 day, Rep 3

source_name: hPSC-derived intestinal organoid

value: hPSC-derived intestinal organoid

value: NOGGIN Day 7-10


title: CRC18

value: Tumor tissue

value: snap-frozen tissues


title: Sham_RNA_1

value: heart ventricular tissue

value: Sham


title: AngII+Si-NAT10_Ribo_3


title: Sham_RNA_2


title: HIO, NOGGIN, 35 day, Rep 2


title: CRC17


title: AngII+Si-NAT10_Ribo_2


title: HIO, NOGGIN , 35 day, Rep 1


title: AngII+Si-NAT10_Ribo_1


title: HCO, BMP2, 21 day, Rep 3

value: 21 days post-hPSC


title: CRC16


title: CRC15


title: HCO, BMP2, 21 day, Rep 2

value: hPSC-derived colonic organoid


title: CRC14


title: FS_shCtrl_noDox_Veh

value: pInd-AR-7F-7S:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: HCO, BMP2, 21 day, Rep 1

value: WA01 hESC

value: Pooled organoids epithelium and mesenchyme


title: HIO, NOGGIN, 21 day, Rep 3


title: CRC12


title: CRC11


title: HIO, NOGGIN, 21 day, Rep 2


title: CRC10


title: HIO, NOGGIN, 21 day, Rep 1


title: Input Sham_1


title: pQ69_shCtrl_noDox_DHT

value: LNCap stable line with pInducer20-AR-pQ69 (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-pQ69:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: FS_shCtrl_Dox_DHT

value: LNCaP

value: pInd-AR-7F-7S:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: DS_4

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Human seminal small extracellular vesicles (sEVs), normozoospermia (Nz), replicate 4

data_processing:
The small RNA sequencing data analysis was performed with the XICRA pipeline and XICRA.stats, the R companion package (Sanchez Herrero, Pluvinet, Luna de Haro and Sumoy, 2021). See additional details in https://xicra.readthedocs.io/en/latest/ or https://github.com/HCGB-IGTP/XICRA.
We checked raw data quality before and after trimming the reads to discard sequencing adapters using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and cutadapt (Martín, 2011), respectively.
For the mapping and the biotype feature assignment of all reads we used STAR mapping software (Dobin et al., 2013) and featureCounts (Liao et al., 2014) using as a reference GRCh38, Gencode XXX
For miRNA identification, we used miraligner (within the SeqBuster software, which can resolve canonical and other isomiR variants (Pantano et al., 2010) and a miRBase (Kozomara et al., 2019) (v22) as the reference database. Then, using miRTop (Desvignes, Loher, Eilbeck, Ma, Urgese, Fromm, Sydes, Aparicio-Puerta, Barrera, Espín, Thibord, Bofill-De Ros, Londin, Telonis, Ficarra, Friedländer, Postlethwait, Rigoutsos, Hackenberg, Vlachos, Halushka and Pantano, 2020), we formatted results into standardized files and generated expression count matrices.
For the tRNA/tRF analysis, we used MINTmap software (Loher et al., 2017)
For the piRNA analysis we used the PILFER software (Ray and Pandey, 2018) and genome annotation accordingly
The analysis of differentoial expression of small RNA we employed XICRA.stats, running DESeq2 (Love et al., 2014, Zhu et al., 2019) and other packages under the R software environment. Due to the numbers of expression counts in miRNA and tsRNA analysis, to normalize and determine differential expression between groups of interest, we employed the algorithm named Approximate Posterior Estimation for the Generalized Linear Model [GLM] (apeglm) (Zhu, Ibrahim and Love, 2019), designed as a strategy for reducing the number of false positive differentially expressed genes filtering by LFC (log2fold-change) maintaining the fraction of true positive differentially expressed (DE) genes. For piRNA analysis, due to the presence of many clusters with low counts and/or total presence/absence of counts, we used the default strategy to avoid filtering all regions.
Assembly: hg38 (Ensembl release 78, Homo_sapiens.GRCh38.dna.primary_assembly), and mature miRBase v20
Supplementary files format and content: Supplementary excel file includes DESeq2 read counts for miRNAs at the isomiR level, tRNA fragment, and piRNA cluster

source_name: semen

growth_protocol: Semen specimens were obtained from 42 infertile men diagnosed with SA (no sperm in semen sample due to spermatogenic failure) or cryptozoospermia (<0.15 x 106 sperm/ml) and 18 individuals with OA and conserved spermatogenesis including both, men successfully vasectomized (OA-V; n=9) and individuals presenting pathological naturally occurring obstruction in the genital tract (OA-N; n=9), including two cases of post-epididymal obstruction [congenital ejaculatory duct obstruction (sample no. 5) and congenital absence of vas deferens -CBAVD- (sample no. 8)] and two cases of intratesticular obstruction (sample nos. 6 and 7). Additionally, 4 normozoospermic sperm donors were included in the small RNA-seq study as controls. Sperm retrieval outcomes with testicular sperm extraction (TESE) provided information of the overall spermatogenic status in order to classify the azoospermia into obstructive (TESE value >0.2 x106 sperm/mL) or secretory (<0.02 x106 sperm/mL), as well as it allowed to define SA subgroups by discriminating the presence [SA(Sp+); n=16] or the absence [SA(Sp-); n=16] of sperm in a testicular biopsy (Table 1). TESE value is defined as the concentration of spermatozoa that was obtained directly after processing 100 mg of biopsy in 1 ml of medium. Semen analysis was performed on all the individuals in accordance with World Health Organization guidelines (Cooper et al., 2010).

extract_protocol:
For total RNA isolatiojn, sEV suspension samples were homogenized through a 20-gauge needle in the organic solution (phenol-Guanidine Isothiocyanate (GITC)-based solution) and used as input material with the miRNeasy Micro Kit (Qiagen) to isolate RNA following the manufacturer’s instructions. RNA concentration was calculated by using the QUBIT fluorometer and the Quant-iT RNA Assay kit (Invitrogen; California, USA). RNA quality was determined by evaluating the OD 260/280 nm ratio with a Nanodrop UV-Vis spectrophotometer (Thermo Fisher Scientific; Massachusetts, USA). Samples with comparable size distribution profiles and a miRNA 18 to 35% of small RNA composition as determined the Small RNA assay on a Bioanalyzer 2100 (Agilent) were selected for small RNA sequencing.
Deep sequencing was performed on libraries generated with the TruSeq™ small RNA library preparation kit (Illumina) adapted to lower input (150 to 200 ng total RNA from sEVs) and with an extended range of size selection. An equimolar pool of all samples determined by Bioanalyzer was automatically size selected. QIAquick (Qiagen) column purification was performed prior and after separation with the Pippin Prep system (SAGE Science) on 3% dye free cassettes with DF marker F, using two different settings in range mode (115-165 nt, and 165 to 250 nt). The two fractions recovered were pooled together and pre-clustered in two independent lanes of a PE flow cell on a cBot, and run on HiSeq2500 system (Illumina) using v4 SBS reagents, to generate paired end reads (2 x 75nt).

treatment_protocol:
Semen samples were obtained by masturbation after 3-5 days of sexual abstinence. Samples were allowed to liquefy for 30 min at 37ºC and subsequently, they were centrifuged twice (1600 x g for 10 min, then 16000 x g for 10 min) at 4ºC in order to eliminate cells, cellular debris, and apoptotic bodies from the biofluid, and to obtain seminal plasma (supernatant) as previously described (Barceló, Mata, Bassas and Larriba, 2018, Eldh et al., 2012, Li et al., 2012). Collected seminal plasma (SP) was immediately stored at -80ºC until use.
For isolation of small EVs from seminal plasma, first, SP aliquots (200 µl) were passed through a 0.22 μm filter in order to enrich for sEVs. The filtered SP fluid plus 9 ml of PBS was ultra-centrifuged at 100,000 x g in a SW40 rotor for 2h at 4ºC as described elsewhere (Barceló, Mata, Bassas and Larriba, 2018, Eldh, Lotvall, Malmhall and Ekstrom, 2012, Li, Huang, Guo, Guan and Xiong, 2012) to sediment the sEVs. The pellet was resuspended in 100 µl PBS and then treated with RNAse A (Qiagen NV; Germany) (100 μg/ml final reaction concentration; 15 min at 37ºC) to degrade the residual RNA outside the vesicles, and subsequently frozen at -80°C (Barceló, Mata, Bassas and Larriba, 2018, Plata-Peña, López-Rodrigo, Bassas and Larriba, 2022).

value: semen

tag: biofluid

value: seminal fluid

tag: non-cellular fraction

value: small extracellular vesicles (sEV), including microvesicles and exosomes

tag: fertility status

value: Control, healthy sperm donor

tag: clinical classification

value: Normozoospermia (Nz)

value: male

tag: individual

tag: fsh


title: FS_shAR_Dox_Veh

tag: cell line

value: LNCap stable line with pInducer20-AR-7F-7S (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-7F-7S:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: FS_shAR_Dox_DHT

tag: transfection

value: pInd-AR-7F-7S:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: CRC13

value: Tumor tissue

tag: treatment

value: snap-frozen tissues


title: FS_shCtrl_Dox_Veh

value: pInd-AR-7F-7S:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: FS_shAR_noDox_DHT

value: pInd-AR-7F-7S:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: pQ69_shCtrl_Dox_Veh

value: LNCap stable line with pInducer20-AR-pQ69 (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-pQ69:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: pQ69_shCtrl_noDox_Veh

value: LNCaP

value: pInd-AR-pQ69:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: FS_shAR_noDox_Veh

value: pInd-AR-7F-7S:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: prostate, TIL hot

city: Houston

first: Nadim

last: Ajami

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: Gene count matrix columns: GeneName, PGDX8570T1_RNA, PGDX8570T2_RNA

data_processing:
Read trimming with Trimmomatic (0.33)
Alignment to GRCh38 reference genome using HISAT2 (2.1.0)
Sorting BAM files with SAMTools (1.7)
Mapping raw read counts to genes using Subread FeatureCounts
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file including gene level raw count data for both samples

source_name: prostate tumor

extract_protocol:
Personal Genome Diagnostics RNAComplete™ method
Next-generation library preparation and sequencing was performed using the HiSeq2500 system with 100 base pair reads

value: prostate tumor


title: prostate, TIL cold


title: CRC9


title: Input Sham_3

value: heart ventricular tissue

value: Sham


title: Sham_Ribo_2


title: Sham_Ribo_3


title: AngII_Ribo_1

value: AngII


title: Sham_Ribo_1


title: AngII_Ribo_3


title: CRC8


title: AngII_Ribo_2


title: Input Si-NAT10_3


title: CRC7


title: Input Si-NAT10_2


title: pQ69_shCtrl_Dox_DHT

value: pInd-AR-pQ69:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: pQ69_shAR_noDox_Veh

value: pInd-AR-pQ69:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: DS_3

description: Human seminal small extracellular vesicles (sEVs), normozoospermia (Nz), replicate 3

value: semen

value: seminal fluid

value: small extracellular vesicles (sEV), including microvesicles and exosomes

value: Control, healthy sperm donor

value: Normozoospermia (Nz)

value: male


title: DS_2

description: Human seminal small extracellular vesicles (sEVs), normozoospermia (Nz), replicate 2


title: CRC5

value: Tumor tissue

value: snap-frozen tissues


title: CRC6


title: pQ69_shAR_noDox_DHT

value: LNCaP

value: LNCap stable line with pInducer20-AR-pQ69 (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-pQ69:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: CRC4


title: pQ69_shAR_Dox_DHT

value: pInd-AR-pQ69:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: CRC2


title: Input AngII+Input Si-NAT10_2

value: heart ventricular tissue


title: Input AngII_3


title: dIDR_shCtrl_noDOX_Veh

value: LNCap stable line with pInducer20-AR-dIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-dIDR:shCTL, No DOX, stripped 3 days, vehicle 2hr


title: pQ69_shAR_Dox_Veh

value: pInd-AR-pQ69:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: CRC1


title: Input AngII+Input Si-NAT10_1


title: Input AngII+Input Si-NAT10_3


title: dIDR_shCtrl_noDOX_DHT

value: pInd-AR-dIDR:shCTL, No DOX, stripped 3 days, DHT 100nM 2hr


title: dIDR_shCtrl_DOX_Veh

value: pInd-AR-dIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: dIDR_shCtrl_DOX_DHT

value: pInd-AR-dIDR:shCTL, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: Input Si-NAT10_1


title: CRC3


title: AS.REQpos_1

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia with residual sperm (SA(Sp+)), replicate 1

value: semen

value: seminal fluid

value: small extracellular vesicles (sEV), including microvesicles and exosomes

value: Sterile, infertility clinic patient

value: Non-obstructive, secretory azoospermia (SA), testicular sperm extraction positive (Sp+)


title: AS.REQpos_5

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia with residual sperm (SA(Sp+)), replicate 5

value: male


title: DS_1

description: Human seminal small extracellular vesicles (sEVs), normozoospermia (Nz), replicate 1

value: Control, healthy sperm donor

value: Normozoospermia (Nz)


title: AS.REQpos_2

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia with residual sperm (SA(Sp+)), replicate 2


title: AS.REQpos_4

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia with residual sperm (SA(Sp+)), replicate 4


title: AS.REQpos_3

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia with residual sperm (SA(Sp+)), replicate 3


title: AS.REQneg_4

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia without sperm (SA(Sp-)), replicate 4

value: Non-obstructive, secretory azoospermia (SA), testicular sperm extraction negative (Sp-)


title: Exp3_DHT

description: DHT treatment

value: LNCaP

value: No transfection, regular LNCaP cells

value: DHT:stripping 3 days, DHT 100nM 2hr


title: Exp3_Veh

description: Veh

value: Veh:stripping 3 days, ethanol


title: AO.N_1

description: Human seminal small extracellular vesicles (sEVs), naturally occurring obstructive azoospermia (OA_N), replicate 1

value: Obstructive azoospermia, with naturallly occurring obstruction (OA_N)


title: AS.REQneg_2

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia without sperm (SA(Sp-)), replicate 2


title: AS.REQneg_3

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia without sperm (SA(Sp-)), replicate 3


title: organoid_fxs_sac_mRNA_rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

description:
input_fxs_sac_r2
RiboMinus RNA

data_processing:
Adapter trimming by Cutadapt.
Reads mapping by STAR to the transcriptome.
Reads calculation with RSEM.
Assembly: For [Dataset 1], mm10. For [Dataset 2], hg38.
Supplementary files format and content: posterior_mean_estimate.xlsx: For [Dataset 1] and [Dataset 2], Excel file with reads mapped to individual genes by RSEM algorithm.

source_name: forebrain organoid

growth_protocol: The human iPSC lines were reprogrammed from skin biopsy samples of three FXS male patients and three age-matched healthy males at Emory University. All iPSC lines were cultured on irradiated MEFs in human iPSC medium consisting of D-MEM/F12 (Invitrogen), 20% Knockout Serum Replacement (KSR, Invitrogen), 1X Glutamax (Invitrogen), 1X MEM Non-essential Amino Acids (Invitrogen), 100 µM β-Mercaptoethanol (Invitrogen), and 10 ng/ml human basic FGF (PeproTech). Forebrain-specific organoids were generated using established protocols as previously described. Briefly, human iPSC colonies were detached from the MEF feeder layer with 1 mg/ml collagenase treatment for 1 hour and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83 in non-treated polystyrene plates for 4 days with a daily medium change. On days 5-6, half of the medium was replaced with induction medium consisting of DMEM/F12, 1X N2 Supplement (Invitrogen), 10 μg/ml Heparin (MilliporeSigma), 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X Glutamax, 4 ng/ml WNT-3A (R&D Systems), 1 μM CHIR99021 (Tocris), and 1 μM SB-431542 (Tocris). On day 7, organoids were embedded in Matrigel (BD Biosciences) and continued to grow in induction medium for 6 more days. On day 14, embedded organoids were mechanically dissociated from Matrigel by pipetting up and down onto the plate with a 5 ml pipette tip. Typically, 10-20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) containing differentiation medium, consisting of DMEM/F12, 1X N2 and B27 Supplements (Invitrogen), 1X Penicillin/Streptomycin, 100 µM β-Mercaptoethanol (Invitrogen), 1X MEM NEAA, 2.5 μg/ml Insulin (MilliporeSigma). All media was changed every other day.

extract_protocol:
For [Dataset 1] and [Dataset 2], CHX (cycloheximide, Milliporesigma C7698-1G) was added to a final concentration of 100 μg/ml to the medium and incubated for 7 minutes. Then spin down the cells, wash once with cold DPBS with 100 μg/ml CHX and spin down again, flash-freeze with LN2 and store at -80C. RPFs were prepared according to the manufacturer's instructions with riboLace kit (IMMAGINA, RL001). Total RNAs were extracted with standard TRIzol protocol.
For [Dataset 1] and [Dataset 2], RNA libraries for input samples were constructed by SMARTer Stranded Total RNA-Seq Kit v2 (TaKaRa, 634417) with total RNA as input. RNA libraries for RPFs were constructed with NEBNext® Small RNA Library Prep Set for Illumina® (NEB, E7330L) with end-repaired RPFs extracted as inputs.

treatment_protocol:
For [Dataset 1], KCl depolarization was performed as follows: Replace half medium with fresh medium+100 mM KCl (to make final 50 mM). After ten minutes, replace half medium for 3 times. After two hours, harvest cells. SAC incubation was performed as follows: (SAC) at 20 μM for 24 hours.
For [Dataset 2], SAC incubation was performed as follows: (SAC) at 20 μM from day 49 to 56.

value: forebrain organoid

value: FXS

value: 20 uM SAC

tag: Sex


title: AS.REQneg_1

description: Human seminal small extracellular vesicles (sEVs), secretory azoospermia without sperm (SA(Sp-)), replicate 1

tag: tissue

value: semen


title: organoid_fxs_dmso_rpf_rep2

data_processing:
Adapter trimming by Cutadapt.
Reads mapping by STAR to the transcriptome.
Reads calculation with RSEM.
Assembly: For [Dataset 1], mm10. For [Dataset 2], hg38.
Supplementary files format and content: posterior_mean_estimate.xlsx: For [Dataset 1] and [Dataset 2], Excel file with reads mapped to individual genes by RSEM algorithm.
Library strategy: Ribo-seq

tag: genotype

value: DMSO


title: organoid_fxs_sac_rpf_rep1


title: organoid_fxs_sac_rpf_rep2


title: organoid_fxs_dmso_mRNA_rep2

description:
input_fxs_dmso_r2
RiboMinus RNA


title: organoid_fxs_sac_mRNA_rep1

description:
input_fxs_sac_r1
RiboMinus RNA


title: organoid_fxs_dmso_rpf_rep1


title: AO.N_4

description: Human seminal small extracellular vesicles (sEVs), naturally occurring obstructive azoospermia (OA_N), replicate 4

value: seminal fluid

value: small extracellular vesicles (sEV), including microvesicles and exosomes


title: IP AngII+Si-NAT10_3

value: heart ventricular tissue


title: IP Si-NAT10_2


title: organoid_fxs_dmso_mRNA_rep1

description:
input_fxs_dmso_r1
RiboMinus RNA

value: male


title: IP Si-NAT10_1


title: Input AngII_2

value: AngII


title: Input AngII_1


title: IP Sham_1

value: Sham


title: IP Sham_3


title: AO.N_3

description: Human seminal small extracellular vesicles (sEVs), naturally occurring obstructive azoospermia (OA_N), replicate 3

value: Sterile, infertility clinic patient


title: IP Si-NAT10_3


title: IP AngII+Si-NAT10_2


title: AO.N_2

description: Human seminal small extracellular vesicles (sEVs), naturally occurring obstructive azoospermia (OA_N), replicate 2


title: dIDR_shAR_noDOX_Veh

value: LNCaP

value: LNCap stable line with pInducer20-AR-dIDR (G418) (AR cDNA is shAR3718-Resistant)

value: pInd-AR-dIDR:shAR3718, No DOX, stripped 3 days, vehicle 2hr


title: dIDR_shAR_noDOX_DHT

value: pInd-AR-dIDR:shAR3718, No DOX, stripped 3 days, DHT 100nM 2hr


title: dIDR_shAR_DOX_Veh

value: pInd-AR-dIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, vehicle 2hr


title: Exp3_DHT_16HD

description: DHT plus 16HD

value: No transfection, regular LNCaP cells

value: DHT+1,6HD:stripping 3 days, DHT 100nM + 2.5% 1,6 HD  2hr


title: dIDR_shAR_DOX_DHT

value: pInd-AR-dIDR:shAR3718, +DOX (20ng/ml 2d), stripped 3 days, DHT 100nM 2hr


title: organoid_ctrl_sac_rpf_rep1

value: forebrain organoid

value: CTRL

value: 20 uM SAC


title: organoid_ctrl_sac_rpf_rep2


title: IP AngII_3


title: IP AngII_1


title: Mop_4B_rep1 (Multiome Gene Expression)

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: UCSD

description:
Mop_4B_rep1_barcodes.tsv.gz
Mop_4B_rep1_features.tsv.gz
Mop_4B_rep1_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Raw sequencing was processed using cellranger-arc (10x Genomics), generating snRNA-seq UMI count matrices for intronic and exonic reads mapping in the sense direction of a gene.
Cells were filtered for low quality nuclei by requiring ≥1000 ATAC fragments and ≥500 genes detected per nuclei.
Genes were annotated with hg38 Gencode v33 for human, mm10 Gencode vM22 for mouse, ensembl release 104 (and Refseq GCF_003339765.1 for 10x multiome) for macaque, and GCA_009663435.2 for marmoset. To maximize the number of orthologous protein-coding quantified in macaque 10x multiome RNA data, we supplemented any missing protein coding genes in GCF_003339765.1 gtf with annotations present in Ensembl release 104.
Assembly: hg38 GRCh38
Assembly: mm10 GRCm38
Assembly: Mmul_10 (rheMac10)
Assembly: cj1700_1.1 (calJac4)
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.   Files provided in tar archives.

source_name: primary motor cortex

extract_protocol:
[nuclei preparation protocol]  Brain tissue was pulverized using a mortar and pestle on dry ice and pre-chilled with liquid nitrogen. Pulverized brain tissue was resuspended in 1mL of chilled NIM-DP-L buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1X Protease Inhibitor (Pierce), 1U/μL Recombinant RNase inhibitor (Promega, PAN2515), and 0.1% Triton X-100). Tissue was Dounce homogenized with a loose pestle (5-10 strokes) followed by a tight pestle (15-25 strokes) or until solution was uniform. Nuclei were filtered using a 30μm CellTrics filter (Sysmex, 04-0042-2316) into a LoBind tube (Eppendorf, 22431021) and pelleted (1000 rcf, 10 min at 4˚C) (Eppendorf, 5920 R). Pellet was resuspended in 1 mL NIM-DP buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl pH 7.5, 1mM DTT, 1x Protease Inhibitor, 1U/μL Recombinant RNase inhibitor) and pelleted (1000 rcf, 10 min at 4˚C). Pelleted nuclei were resuspended in 400uL 2μM 7-AAD (Invitrogen, A1310) in Sort Buffer (1mM EDTA, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor, 1% fatty acid-free BSA in PBS).
120,000 nuclei were sorted (Sony, SH800S) into a LoBind tube containing Collection Buffer (5U/uL Recombinant RNase inhibitor, 1X Protease Inhibitor, 5% fatty acid-free BSA in PBS). 5X Permeabilization Buffer (50mM Tris-HCl pH 7.4, 50mM NaCl, 15mM MgCl2, 0.05% Tween-20, 0.05% IGEPAL, 0.005% Digitonin, 5% fatty acid-free BSA in PBS, 5mM DTT, 1U/μL Recombinant RNase inhibitor, 5X Protease Inhibitor) was added for a final concentration of 1X. Nuclei were incubated on ice for 1 minute, then centrifuged (500 rcf, 5min at 4C). Supernatant was discarded and 650uL of Wash Buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1%.Tween-20, 1% fatty acid-free BSA in PBS, 1mM DTT, 1U/μL Recombinant RNase inhibitor, 1X Protease Inhibitor) was added without disturbing the pellet followed by centrifuging (500 rcf, 5 min at 4˚C). Supernatant was removed, and the pellet was resuspended in 7uL of 1X Nuclei Buffer (Nuclei Buffer (10x Genomics), 1mM DTT, 1 U/μL Recombinant RNase inhibitor). 1 μL of nuclei was diluted in 1X Nuclei Buffer, stained with Trypan Blue (Invitrogen, T10282) and counted. 16-20k nuclei were used for tagmentation reaction and controller loading and libraries were generated following manufacturer’s recommended protocol (https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression).
10x multiome ATAC-seq and RNA-seq libraries were paired-end sequenced on NextSeq 500 and NovaSeq 6000 to a depth of ~50,000 reads per cell for each modality.

value: primary motor cortex

tag: species

value: Mouse

tag: donor id

value: 4 mice are pooled

value: M

tag: mouse strain

tag: library type

value: 10x Genomics Multiome Gene Expression


title: IP AngII_2

value: heart ventricular tissue

value: AngII


title: organoid_ctrl_sac_mRNA_rep2

description:
input_ctrl_sac_r2
RiboMinus RNA

tag: cell type

value: male


title: organoid_ctrl_sac_mRNA_rep1

description:
input_ctrl_sac_r1
RiboMinus RNA


title: organoid_ctrl_dmso_rpf_rep2

value: DMSO


title: organoid_ctrl_dmso_rpf_rep1


title: IP AngII+Si-NAT10_1


title: organoid_ctrl_dmso_mRNA_rep2

description:
input_ctrl_dmso_r2
RiboMinus RNA


title: SupT1/Rec rep3 [Rec_19]

city: Charlottesville

first: Lou

last: Hammarskjold

state: VA

address: 1340 Jefferson Park Avenue

institute: University of Virginia

data_processing:
Raw image files were transformed to sequence reads by CASAVA base calling.
Sequenced reads were trimmed for adapater sequences, then mapped to hg38 using HISAT2.
Differential expression was performed by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: count data and differential expression data

source_name: SupT1_HERV-K Rec

growth_protocol: SupT1 cells were routinely passaged 2-3 times per week. Twenty-four hours prior to transductions, SupT1 cells were split 1:4.

extract_protocol:
Total RNA was extracted using phenol/chlorform prior to ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SupT1 cells (10^6 cells) were transduced with each virus stock using an moi of 2.

value: T-lymphoblast cell line

value: HERV-K Rec


title: SupT1/Rec rep2 [Rec_12]


title: Squamous Cell Carcinoma Sample 3

city: Richmond

first: Michela

last: Saviana

state: Virginia

address: 1101 E Marshall St

department: Department of Internal Medicine, Division of Pulmonary Diseases and Critical Care Medicine

institute: Virginia Commonwealth University

description: miRNA expression of Squamous Cell Carcinoma Sample 3

hyb_protocol: For each sample, 4.0 μL of total exosomal enriched RNA was allowed to anneal with DNA “bridge oligos” that bound both the sample miRNAs and multiplexed RNA tags (miR-tags). Mature miRNAs were then joined to sequence-specific miR-tags using a Ligase enzyme and all tags in excess were removed by a subsequent enzyme clean-up step. Both capture and reporter probes were then allowed to hybridize overnight for 17 h at 65 °C with the ligated and tagged sample miRNAs as per protocol to allow the color-beaded “string” probes to bind with their sequence-specific targets. Probe excess was removed using a two-step magnetic-bead-based purification on an automated fluidic handling system (nCounter Prep Station) and target/probe complexes were immobilized on the cartridge for data collection.

scan_protocol: The nCounter Digital Analyzer collected the data by taking images of immobilized fluorescent reporter probes in the sample cartridge with a CCD camera through a microscope objective lens. For each cartridge, a high-density scan encompassing 550 fields of view was performed. Images were subsequently processed internally into a digital format (RCC files) where raw count results for each miRNA could be analyzed.

data_processing: Normalization was performed using the nSolver Analysis Software (Version 4.0; NanoString Technologies), applying the geometric mean of the negative controls for negative background subtraction; the positive controls for the technical normalization; finally, data were biologically normalized by calculating the geometric mean of the top 100 miRNAs in all samples, as recommended by NanoString company.  P values were calculated using the limma package (v3.54.0) from the Bioconductor R project.   P values were used to rank all genes, retaining those under a significant threshold of 0.05 and with a geometric mean expression of >30 counts (in at least one condition) after negative background subtraction and a |linear fold-change| > 1.25.

source_name: Plasma Extracellular Vesicles

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

extract_protocol: EVs were isolated from plasma using the Total Exosome Isolation Kit (INVITROGEN). EVs were thoroughly resuspended in 200 µl of PBS.  RNA purification was performed with RNA Clean-Up and Concentration Kit (NORGEN).

tag: disease

value: Lung Cancer patient with Squamous Cell Carcinoma

tag: age

tag: race

value: Black

value: Male

tag: Stage

value: IV


title: Small Cell Lung Cancer Sample 1

description: miRNA expression of Small Cell Lung Cancer Sample 1

value: Lung Cancer patient with SCLC

value: IIIA


title: Small Cell Lung Cancer Sample 2

description: miRNA expression of Small Cell Lung Cancer Sample 2

value: IVA


title: L2 GC n1

city: Tübingen

first: Jun-Hoe

last: Lee

address: Otfried-Müller-Str. 37

department: Quantitative Biology Centre (QBiC)

institute: University of Tuebingen

data_processing:
A fork of the Nextflow-based nf-core pipeline nf-core/smrnaseq (version 1.2; https://github.com/qbic-projects/smrnaseq, commit: 306b024) was used for the small RNAseq Bioinformatics analysis
As part of the workflow, FastQC (v0.11.9) (Andrews, 2010) was used to determine the quality of the FASTQ files. Adapter trimming was conducted using TrimGalore based on the recommended parameters by Takara SMARTer® smRNA-Seq Kit. Subsequently, the filtered reads were mapped to the miRBase (Kozomara et al., 2019) database of mature and hairpin human micro-RNas (miRNA) using Bowtie1 (v.1.3.0) (Langmead et al., 2009). The miRNA-seq data quality was assessed using mirTrace (v1.0.1) (Kang et al., 2018), followed by an aggregation of the quality control of the analyses with MultiQC (version 1.7; http://multiqc.info/) (Ewels et al., 2016).
Differential expression analysis was performed using miRNA counts in R (v3.5.1) using DESeq2 (v1.22.1) (Love et al., 2014), through a fork of the Nextflow-based qbic-pipelines/rnadeseq pipeline (v1.32) (https://github.com/qbic-projects/QSCNN, commit: c1aded5) .
The miRNA reads were considered differentially expressed when the Benjamini-Hochberg multiple testing adjusted p-value (Benjamini Y, 1995) was smaller than 0.05 (padj < 0.05). Multiple testing correction was used to minimize the number of false positives.
Assembly: GRCh37
Supplementary files format and content: Raw miRNA counts (hairpin, mature) of all libraries, as standard output from the Bowtie1 mapping step of nf-core/smrnaseq (version 1.20; https://github.com/nf-core/rnaseq) workflow. Each row shows the raw count values for each miRNA across each sample (per column).

source_name: human dopaminergic neuron

growth_protocol: Two lines of neural progenitor cells (NPCs) carrying the LRRK2 G2019S mutation or the gene corrected LRRK2 wild type were previously generated from patient-derived iPSCs (Reinhardt et al., 2013b, 2013a). NPCs were cultured in base media (50% neurobasal (Thermo Fisher Scientific (Waltham, MA, USA), #21103-049), 50% DMEM/F12 (Thermo Fisher Scientific, #11-330-057), 1% penicillin/streptomycin (Merck (Darmstadt, Germany), #A2213), 1% GlutaMax (Thermo Fisher Scientific, #35050-038), 1% B27 supplement (without vitamin A; Thermo Fisher Scientific, #12587-010) and 0.5% N2 supplement (Thermo Fisher Scientific, #17502-048)) supplemented with 0.5 µM PMA (Merck, #540220), 3 µM CHIR (Axon Medchem (Groningen, Netherlands), #Axon1386) and 200 µM ascorbic acid (Sigma-Aldrich (St. Louis, MO, USA), #A4544).

extract_protocol:
RNA was isolated directly from extracellular vesicles using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN, #217204) and following the vendor’s instructions.
The SMARTer® smRNA-Seq Kit for Illumina® (Takara (Tokyo, Japan), #635030) was used and vendor’s instructions were followed with slight modifications. The libraries were then bead-purified, by  incubating with AMPURE beads (Beckmann Coulter (Brea, California, USA), #A63881).  For size exclusion, a similar protocol was repeated using SPRI beads (Beckmann Coulter, #B23318) and a sample-to-beads ratio of 1:1.  The libraries were sequenced on a Nextseq550 mid output 150 cycles v2.5 flowcell spiking in 30% PhiX control v.3.

treatment_protocol: Once NPCs reached 80% confluency, differentiation into human dopaminergic mid-brain neurons (hDaNs) was initiated. NPCs were incubated in base media supplemented with 20 ng/ml of BDNF (PeproTech (Hamburg, Germany), #450-02), 10 ng/ml of FGF8 (PeproTech, #100-25), 1 µM of PMA and 200 µM of ascorbic acid for 7 days (days 1 to 7). Next, cells were put in base media supplemented with 10 ng/ml of BDNF, 10 ng/ml of GDNF (PeproTech, #450-10), 1 ng/ml of TGF-β3 (PeproTech, #AF-100-36E), 200 µM ascorbic acid, 500 µM dbcAMP (PanReac AppliChem (Darmstadt, Germany), #A0455) and 10 µM DAPT (Selleckchem (Houston, TX, USA), #S2215) for the remainder of the differentiation (days 8 to 23).

value: human dopaminergic neuron

value: Gene corrected LRRK2 G2019S

value: neural differentiation


title: L2 GC n3


title: L2 Mut n3

value: WT LRRK2 mutation


title: L2 GC n2


title: organoid_ctrl_dmso_mRNA_rep1

description:
input_ctrl_dmso_r1
RiboMinus RNA

value: forebrain organoid

value: CTRL


title: Small Cell Lung Cancer Sample 3

description: miRNA expression of Small Cell Lung Cancer Sample 3

value: White


title: Small Cell Lung Cancer Sample 7

description: miRNA expression of Small Cell Lung Cancer Sample 7

value: Female


title: Small Cell Lung Cancer Sample 5

description: miRNA expression of Small Cell Lung Cancer Sample 5

value: IIB


title: Small Cell Lung Cancer Sample 4

description: miRNA expression of Small Cell Lung Cancer Sample 4

value: I


title: Small Cell Lung Cancer Sample 8

description: miRNA expression of Small Cell Lung Cancer Sample 8

value: IVB


title: Small Cell Lung Cancer Sample 6

description: miRNA expression of Small Cell Lung Cancer Sample 6

value: Black


title: SupT1/Rec rep1 [Rec_5]

value: T-lymphoblast cell line

value: HERV-K Rec


title: L2 Mut n2


title: Squamous Cell Carcinoma Sample 4

description: miRNA expression of Squamous Cell Carcinoma Sample 4

value: Lung Cancer patient with Squamous Cell Carcinoma


title: L2 Mut n1


title: L1 Mut n3


title: SupT1/TatRev rep2 [TatRev_14]

source_name: SupT1_HIV TatRev

value: HIV TatRev


title: L1 Mut n2


title: SupT1/TatRev rep1 [TatRev_7]


title: Squamous Cell Carcinoma Sample 2

description: miRNA expression of Squamous Cell Carcinoma Sample 2

value: IB


title: SupT1/Tat rep3 [Tat_18]

source_name: SupT1_HIV Tat

value: HIV Tat


title: L1 Mut n1

value: human dopaminergic neuron


title: SupT1/Tat rep2 [Tat_11]


title: L1 GC n3

value: Gene corrected LRRK2 G2019S

value: neural differentiation


title: Adenocarcinoma Sample 4

description: miRNA expression of Adenocarcinoma Sample 4

value: Lung Cancer patient with Adenocarcinoma

value: II


title: Adenocarcinoma Sample 2

description: miRNA expression of Adenocarcinoma Sample 2

value: White

value: III


title: Squamous Cell Carcinoma Sample 1

description: miRNA expression of Squamous Cell Carcinoma Sample 1

value: Male

value: IIA


title: L1 GC n2


title: SupT1/Tat rep1 [Tat_4]


title: SupT1/Rev rep3 [Rev_17]

source_name: SupT1_HIV Rev

value: HIV Rev


title: SupT1/Rev rep2 [Rev_10]


title: Adenocarcinoma Sample 3

description: miRNA expression of Adenocarcinoma Sample 3

value: I


title: Adenocarcinoma Sample 1

description: miRNA expression of Adenocarcinoma Sample 1

value: Black

value: IV


title: Healty Donor 7

description: miRNA expression of Healty Donor 7

value: Healty Donor

value: Female


title: Healty Donor 8

description: miRNA expression of Healty Donor 8


title: SupT1/Rev rep1 [Rev_3]

value: T-lymphoblast cell line


title: L1 GC n1


title: Healty Donor 6

description: miRNA expression of Healty Donor 6


title: PABNP1-11_S11

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

data_processing:
Partek Flow (build 10.0.21.1116).
Trim bases based on quality score, min Phred score 20.
STAR - 2.7.8a aligned to hg38.
Quantify to annotation model (Partek E/M). Gene level quantification, RPKM normalization.
Assembly: hg38
Supplementary files format and content: Normalized (DESeq2 Median ratio normalization) gene expression data

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in a humidified incubator with 5% CO2 at 37°C in DMEM (01-052-1A, Biological industry) supplemented with 10% heat-inactivated bovine serum (FBS) (04-007-1A, Biological Industries), penicillin/ streptomycin (15240-062, Gibco), and L-Glutamine (G7513, Sigma)

extract_protocol:
RNA was extracted from cell lysate pulldown experiments of RNA binding proteins using Trizol (009010233100 Bio-Lab)
Sequencing libraries were prepared using the INCPM mRNA protocol

treatment_protocol: For nutrient starvation experiments, cells were washed with PBS and treated with HBSS (14025092, Gibco) for 4 h.

value: HeLa cells

tag: rip antibody


title: PABNP1-7_S7


title: Healty Donor 5

description: miRNA expression of Healty Donor 5


title: hnRNPQ-10_S10

value: hnRNPQ


title: SupT1/EV rep2 [EV_9]

source_name: SupT1_empty vector

value: empty vector


title: SupT1/EV rep3 [EV_16]


title: CRD vs LT033NT-C

type: genomic

city: Daejeon

first: Tae Jeong

last: Oh

address: 44-6 10-ro Yuseong-gu

country: South Korea

institute: Genomictree, Inc.

description: methylation profiling in LT033NT sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CRD

label_protocol: The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
Fresh-frozen primary tumors and paired tumor-adjacent normal tissues of lung cancer patients
Genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.

tag: reference

value: pooled DNA of 13 adjacent normal samples

tag: test

value: enriched methylated DNA of adjacent normal tissue

value: male


title: hnRNPQ-6_S6

tag: cell line


title: SupT1/EV rep1 [EV_2]

tag: treatment


title: hnRNPQ-3_S3


title: SupT1 rep3 [SupT1_15]

value: untreated


title: Control-9_S9

value: control


title: SupT1 rep2 [SupT1_8]


title: Healty Donor 4

description: miRNA expression of Healty Donor 4

value: White

tag: Sex

value: Male


title: Control-5_S5


title: Healty Donor 3

description: miRNA expression of Healty Donor 3


title: CRD vs LT037T-C

description: methylation profiling in LT037T sample

value: enriched methylated DNA of primary lung tumor tissue

value: III


title: SupT1 rep1 [SupT1_1]


title: Healty Donor 2

description: miRNA expression of Healty Donor 2


title: Healty Donor 1

description: miRNA expression of Healty Donor 1


title: CRD vs LT031T-C

description: methylation profiling in LT031T sample


title: CRD vs LT031NT-C

description: methylation profiling in LT031NT sample


title: CRD vs LT041T-C

description: methylation profiling in LT041T sample

value: II


title: CRD vs LT027NT-C

description: methylation profiling in LT027NT sample


title: CRD vs LT024T-C

description: methylation profiling in LT024T sample


title: CRD vs LT027T-C

description: methylation profiling in LT027T sample


title: CRD vs LT041NT-C

description: methylation profiling in LT041NT sample


title: BS_high

city: Wuxi

first: Yanfeng

state: Jiangsu

address: No.1800, Lihu Avenue

institute: Jiangnan University

data_processing:
Cutadapt is applied to find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
PANDASEQ is used to assemble paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases.
Genome_build: NCBI number:  AF330636.1
Supplementary_files_format_and_content: csv files include filtered sequences

molecule: other

organism: Bacillus subtilis

source_name: Synthetic construct

extract_protocol:
After FACS-sorting and overnight regrowth in the same media used for growth, sorted fractions were miniprepped. PCR was used to verify that at least 10 plasmids were extracted per sorted cell; minipreps were PCR-amplified, further amplified with the addition of bin-specific barcodes, pooled, and amplified briefly again.
For each sample, >50ng purified PCR fragment was used for library preparation. These PCR products were treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor-ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The final library product for sequencing were then purified by beads and was qualified.

tag: strain

value: wild type

tag: plasmid type

value: reporter gene with synthetic NCS

tag: expression level

value: high


title: S00HM-0033

status: Public on Oct 30 2023

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

data_processing:
Paired-end sequencing (150 bp x 2) was done on a NextSeq 500 in medium-output mode.
Shotgun metagenomic sequence reads were processed with the Sunbeam pipeline. Initial quality evaluation was done using FastQC v0.11.5 1. Processing took part in four steps: adapter removal, read trimming, low-complexity-reads removal, and host-sequence removals. Adapter removal was done using cutadapt v2.6 2. Trimming was done with Trimmomatic v0.36 3 using custom parameters (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Low-complexity sequences were detected with Komplexity v0.3.6 4.
High-quality reads were mapped to the human genome (Genome Reference Consortium Human Reference 37) and the Rat Genome (GCF_000001895.5_Rnor_6.0) and those that mapped to it were with at least 50% similarity across 60% of the read length were removed.  The remaining reads were taxonomically classified using Kraken2 with the PlusPF database from 2021-01-275. For functional profiling, high-quality (filtered) reads were aligned against the SEED database via translated homology search and annotated to Subsystems, or functional levels, 1-3 using Super-Focus 6.
Sequence quality was good, and as we expected, quality decreased over the sequences length, specially for the second pairs. Host contamination was generally low, averaging 0.37%.  Reads removed because they matched one of the pre-specified host/contaminant genomes are grouped into the ‘Host/Contaminant’ category. Reads removed due to low complexity or quality are grouped into the ‘Low Quality’ category.
Taxonomic profiles (species-level) were compared using Bray-Curtis dissimilarities and samples were visualized using non-metric multidimensional scaling (NMDS). Samples clustered by sex and strain.
Genome_build: bacteria
Supplementary_files_format_and_content: We use a Permutational multivariate analysis variation to estimate the effects of experimental factors on both taxonomic and functional profiles. For the taxonomic profiles we used only the abundance of bacterial species.  We observed significant differences in the four group combinations for both taxonomic and functional profiles (general model). We created a sequential model to further investigate the influence of each factor and found significant differences between sexes after controlling for strain differences but only for the functional profiles.  When we test for strain differences in male- and female-only models, we found significant differences in both taxonomic and functional profiles but only in females. We used Negative binomial models (DESEq2 R package) for differential abundance testing of taxonomic and subsystem level 3 features. We looked for differences between among groups, and also for difference in disease status after controlling for age differences. P-values were calculated with LRT test. Adjusted p-value = 0.01.  Our general model tested for differences between the four groups. The sequential model looked the Sex:Strain interaction, i.e. groups that showed differences in strains according to their sex. We also build models for male and female subsets. Here we only plot up to 20 taxa. For full results, see the linear_models files. Alpha diversity was calculated from taxonomic profiles using Shannon’s diversity index.

organism: Rattus norvegicus

source_name: fecal matter from cecum

extract_protocol:
DNA was extracted using the Qiagen MagAttract PowerSoil DNA KF kit (Formerly MOBio PowerSoil DNA Kit) using a KingFisher robot. DNA quality was evaluated visually via gel electrophoresis and quantified using a Qubit 3.0 fluorometer (Thermo-Fischer, Waltham, MA, USA).
Libraries were prepared using an Illumina Nextera library preparation kit with an in-house protocol (Illumina, San Diego, CA, USA).
MagAttract PowerSoil DNA KF kit

treatment_protocol: Fecal matter was collected from the rat cecum at endpoint.

value: Wistar Kyoto (WKY) rats

value: female

tag: ratid


title: S00HM-0032


title: BS_low

last: Liu

tag: genotype

value: low


title: S00HM-0027


title: S00HM-0031


title: S00HM-0025


title: S00HM-0026


title: S00HM-0029


title: S00HM-0024


title: S00HM-0028


title: S00HM-0023


title: S00HM-0030


title: S00HM-0022


title: S00HM-0021


title: Control-2_S2

value: HeLa cells


title: S00HM-0020


title: S00HM-0019


title: S00HM-0009

value: Spontaneous hypertensive Rats (SHR)


title: S00HM-0017


title: S00HM-0011


title: S00HM-0008


title: S00HM-0015


title: S00HM-0018


title: S00HM-0010


title: S00HM-0016


title: S00HM-0007


title: S00HM-0013


title: S00HM-0014


title: S00HM-0006


title: S00HM-0012


title: S00HM-0005


title: S00HM-0003


title: S00HM-0001


title: S00HM-0004


title: SINV: zebrafish 3 dpi

city: Shanghai

first: Yang

last: Li

address: 2005 Songhu Road

institute: Fudan University

description: zebrafish infection with SINV by microinjection

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Genome_build: AF174533.1,AF174534.1;J02363.1;NC_001560.1
Supplementary_files_format_and_content: mapping results files generated by bowtie1.1.2

organism: Danio rerio

source_name: zebrafish whole body

extract_protocol:
Total RNA was extracted from zebrafish using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: tissue

value: whole body

tag: infection

value: SINV

tag: injection way

value: microinjection

tag: zebrafish background

value: AB


title: S00HM-0002


title: MCF7 HSF1 HS polyclonal Ab rep 2

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Raw files were adapter-trimmed with trimmomatic and aligned to hg19 genome using hisat2. For HSF1 ChIP-seq, raw fastq files were randomly subset to 40M read pairs prior to alignment. After removing PCR duplicates with MarkDuplicates (Picard),   peaks were called using MACS2 with FDR cutoff 0.01 and then merged between replicates . Read coverage was calculated using bamCoverage and read counts were normalized to sequencing depth. Signal was calculated using multibigwigsummary.
Assembly: hg19
Supplementary files format and content: bw - bigwig files.
Supplementary files format and content: narrowPeak - peaks called for each replicate

growth_protocol: All cells were purchased from the American Type Culture Collection and used within the first 15 passages. Cells were grown in 15 cm dishes as before {Samarakkody et al., 2015, #72840} and growth media was replaced with fresh media 24 hours before treatments {Mahat and Lis, 2017, #290391; Vihervaara et al., 2017, #282616}.

extract_protocol:
Approximately 2x107 cells were crosslinked with 1% ethanol-free formaldehyde (Thermo) in serum-free DMEM/F12 media at 25C for 10min, quenched with 125mM Glycine, and lysed in buffer (1% Sodium-Dodecyl Sulfate (SDS), 50mM Tris (pH=8), 10mM EDTA, 1X PMSF and protease inhibitor cocktail) followed by disruption in the Covaris S2 sonicator for 6 minutes (with peak power = 140, Duty factor = 5, Cycles/burst = 200). Protein A and Protein G Dynabeads (Invitrogen) premixed at 1:1 ratio were used for pre-clearing for 1 hour at 4C. One percent of each precleared sample was taken as input, with at least two inputs taken for each sample and averaged for ChIP percent input calculation. Samples were incubated with 5g of primary antibodies in 2 ml of dilution buffer (1% Triton-X, 2mM EDTA, 20mM Tris pH=8.0, 150mM NaCl, 1X Phenylmethylsulfonyl fluoride (PMSF) and cOmplete protease inhibitor cocktail (Sigma)) with slow rotation overnight at 4C followed by washing
DNA library was prepared from validated ChIP material using NEBNext Ultra II DNA library kit (New England Biolabs) protocol without size selection. Final PCR amplification of cDNA templates was done using TruSeq Illumina Small RNA PCR primers, 250 M dNTP mix, 1x HF buffer, 1M Betaine, 1xEvagreen dye (Biotium) and Phusion DNA polymerase.

treatment_protocol: Heat-Shock treatment was started by placing a dish onto a heated water surface for 1 minute to raise the temperature quickly and continued in a 42°C 5% CO2 incubator for the remaining time. Arsenic treatment was performed by the addition of 500 mM Sodium meta-arsenite (Sigma) at the ambient 37°C with 5% CO2 {Khalil et al., 2006, #243125}.

tag: cell type

value: mammary gland, adenocarcinoma

tag: chip antibody

value: HSF1 SCBT #sc-9144

value: Heat shock


title: MCF7 HSF1 HS polyclonal Ab rep 1


title: MCF7 HSF1 NHS polyclonal Ab rep 1

value: Untreated


title: G4

city: Beijing

first: yongpan

last: an

address: xueyuanlu

institute: Peking University

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: muscle tissue

growth_protocol: The animals were housed in a temperature-controlled animal room (24 ± 2 ℃) with a relative humidity of 60-80%.

extract_protocol:
Muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GW8510 was dissolved in 0.5% Sodium Carboxymethylcellulose  and administered i.p. once a day for 14 days at doses of 2mg/kg.

value: GW8510-treated normal group

tag: age

value: 18 months

value: ICR

value: muscle


title: G3


title: MCF7 HSF1 NHS polyclonal Ab rep 2


title: G1


title: C4

value: vehicle-treated normal group


title: C3


title: MCF7 NHS H3K4me3 rep 2

value: H3K4me3 (Abcam #ab8580)


title: MCF7 HS H3K4me3 rep 2


title: MCF7 NHS H3K4me3 rep 1


title: MCF7 HS H3K4me3 rep 1


title: C1


title: detached 24 hours MCF10A rep1.miRNA

city: Worcester

first: Junhui

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

data_processing:
Oasis(version 2.0) was used to identify and quantify miRNAs
miRNAs with less than 5 reads in all samples were excluded for differential miRNA expression analysis using DEseq2
To control the false discovery rate, Benjamini & Hochberg method was used to adjust the p-value and miRNAs with BH-adjusted p-value < 0.01 and logFC > 1 were considered as significant.
Assembly: hg38
Supplementary files format and content: Gene expression matrix: This is a tabular file that represents the gene expression levels for each sample in the dataset. It typically includes rows representing genes or transcripts and columns representing individual samples. The values in the matrix can be raw read counts, normalized expression values (e.g., TPM or FPKM), or log-transformed expression values.
Supplementary files format and content: Differential expression analysis results: These files contain the results of differential gene expression analysis, identifying genes that show significant expression differences between different conditions or groups. The files may include statistics such as fold change, p-values, adjusted p-values, and gene annotations.

source_name: breast

growth_protocol: MCF10A cells  were maintained in DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor, 10 mg/ml insulin, 1 ng/ml cholera toxin, 100 mg/ml hydrocortisone, 50 U/ml penicillin , and 50 mg/ml streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA (50 µg) was isolated from MCF10A cells cultured under attached or detached (for 24 hours) conditions using TRIzol (Invitrogen), from which small RNAs 18-24 nucleotides in length were size selected and gel purified.
Adapter ligation for pyrosequencing

treatment_protocol: MCF10A were plated either on uncoated

value: breast

value: immortalized mammary epithelial cells

value: detached conditions

tag: time


title: attached MCF10A cells rep2.miRNA

value: adherent conditions

value: 0 h


title: attached MCF10A cells rep3.miRNA


title: Y4

value: 2 months


title: detached 24 hours MCF10A rep2.miRNA


title: attached MCF10A cells rep1.miRNA


title: Y3


title: Y2


title: Beta_Donor4_Control

city: Stanford

first: Mollie

middle: F

last: Qian

address: 279 Campus Drive W

institute: Stanford University

data_processing:
Barcodes were trimmed using Trimgalore_0.5.0.
Reads were aligned to the human genome index (GRCh38, Ensembl release 104) using STAR v2.6.1d (Dobin et al. 2013).
Estimated counts and transcripts per million (TPM) were quantified using RSEM v1.3.1 (Li and Dewey 2011).
Differentially expressed genes with fold change were detected using the DESeq2 R package (Love et al. 2014).
Assembly: hg38 (GRCh38) transcriptome
Supplementary files format and content: csv file containing raw estimated counts
Supplementary files format and content: csv file containing transcripts per million (TPM)

molecule: polyA RNA

source_name: cadaveric pancreatic tissue

growth_protocol: Primary human islets were disersed/ transduced with lentiviruses and cultured for 5 days.

extract_protocol:
SMART-seq v4 Ultra Low input RNA kit (Clontech).
Nextera XT DNA Library Preparation Kit (Illumina)
Paired-end 150bp reads on the Illumina NovaSeq 6000 platform.

treatment_protocol: Lentiviral shRNAs against HNF1A versus non-targeting shRNA control.

value: cadaveric pancreatic tissue

value: primary islet cells

value: beta cells

tag: developmental stage

value: adult

tag: genotype/variation

value: Control


title: Beta_Donor2_Control

tag: cell line


title: Beta_Donor1_Control


title: Beta_Donor2_HNF1AKD

value: HNF1A knockdown


title: Beta_Donor4_HNF1AKD


title: Beta_Donor3_Control


title: Beta_Donor3_HNF1AKD


title: Beta_Donor1_HNF1AKD


title: Alpha_Donor4_HNF1AKD

value: alpha cells


title: SK-N-SH cells, WT-2

city: GuangZhou

first: zhongwei

address: No. 1023 - 1063, Shatai South Road, Baiyun District, Guangzhou, China

institute: Southern Medical University

data_processing:
All sequencing data passed the initial base quality control using FASTQC
Paired reads data was aligned to the hg19 reference genome using HISAT2 with default parameters and convert the sam file to the bam file（binary format）using SAMTOOLS.
Read counts were derived from the GTF file generated by Stringtie with the parameters -A, -e and using the Python scripts provided by Stringtie
Differentially expressed genes (DEGs) were generated by DESeq2 in R
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: brain; derived from metastatic site: bone marrow

growth_protocol: SK-N-SH cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Trizol method. 2 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene.

value: brain; derived from metastatic site:bone marrow

value: SK-N-SH

value: human neuroblastoma cells

value: WT


title: Alpha_Donor2_Control


title: SK-N-SH cells, rs4558409-KO-2

value: rs4558409 knockout


title: Alpha_Donor3_HNF1AKD


title: Alpha_Donor2_HNF1AKD


title: CandR_Donor7_IgG

data_processing:
Trimmomatic (Bolger et al. 2014) was used for trimming.
Bowtie2 (Langmead and Salzberg 2012) was used for alignment.
HOMER (Heinz et al. 2010) was used for peak calling.
The GREAT algorithm was used for gene annotation (McLean et al. 2010).
Assembly: hg19 (GRCh37) transcriptome
Supplementary files format and content: txt file containing peaks data
Library strategy: CUT&RUN

extract_protocol:
CUTANA ChIC/CUT&RUN protocol v3.1 (Epicypher 14-1048)
CUTANA CUT&RUN Library Prep Kit (Epicypher 14-1001)
Paired-end 150bp reads on the Illumina NovaSeq platform.

treatment_protocol: Lentiviruses expressing HNF1A-FLAG.

value: HNF1A-FLAG overexpression

tag: cut&run antibody

value: Rb anti-IgG (EpiCypher 13-0042)


title: SK-N-SH cells, rs4558409-KO-1


title: Alpha_Donor1_Control


title: Alpha_Donor4_Control


title: SK-N-SH cells, WT-1


title: Alpha_Donor3_Control


title: CandR_Donor7_FLAG

value: Rb anti-FLAG (Sigma-Millipore F7425)


title: Alpha_Donor1_HNF1AKD


title: CandR_Donor5_IgG


title: CandR_Donor6_FLAG


title: CandR_Donor6_IgG


title: CandR_Donor5_FLAG

value: primary islet cells, whole pseudoislets


title: CRD vs LT021NT-C

description: methylation profiling in LT021NT sample

tag: reference

value: pooled DNA of 13 adjacent normal samples

tag: test

value: enriched methylated DNA of adjacent normal tissue

tag: Sex

value: female

tag: Stage

value: II


title: CRD vs LT037NT-C

description: methylation profiling in LT037NT sample

value: male

value: III


title: CRD vs LT018NT-C

description: methylation profiling in LT018NT sample

value: I


title: CRD vs LT033T-C

description: methylation profiling in LT033T sample

value: enriched methylated DNA of primary lung tumor tissue


title: CRD vs LT030T-C

description: methylation profiling in LT030T sample


title: CRD vs LT021T-C

description: methylation profiling in LT021T sample


title: Pd-59F,grade 4, SDD 3, scRNAseq

city: Guangzhou

first: Jianru

last: Wang

state: Guangdong

address: No. 58, Zhongshan road II, Guangzhou 510080, People’s Republic of China

institute: Sun Yat-sen University First Affiliated Hospital

description: singlecellRNA-Seq

data_processing:
scRNA-seq: The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38) using Cell Ranger v6.1.1
bulk RNA-seq: Hisat2 2.1.0 mapping to reference genome
bulk RNA-seq: count counting
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files
Supplementary files format and content: bulk RNA-seq: TXT file contain FPKM for each sample

source_name: nucleus pulposus tissue

extract_protocol:
scRNA-seq: cut the outer layer of AF , then the inner layer of AF), and then  start to achieve NP. After that we washed the NP tissues with 0.9% normal saline three times. And transport it in ice-cold preservation solution.
bulk RNA-seq: Total RNA was extracted from NP tissue, and treated with the GeneRead™ rRNA Depletion kit (Qiagen) to remove ribosomal RNA
scRNA-seq: Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, scRNA-seq data analysis was performed by NovelBio Bio-Pharm Technology Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp with default parameter filtering of the adaptor sequence to remove the low-quality reads and obtain the clean data. Then the feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38 Ensemble: version 104) using CellRanger v6.1.1. We performed the down sample analysis of samples sequenced according to the mapped barcoded reads per cell of each sample and finally created the aggregated matrix. Cells containing over 200 expressed genes and a mitochondrial UMI rate below 20% passed the cell quality filtering and mitochondrial genes were removed from the expression table.
bulk RNA-seq: a VAHTS Stranded RNA-seq Library preparation kit for Illumina (Vazyme) was used to construct strand-specific libraries

value: nucleus pulposus tissue

value: nucleus pulposus cells(NPCs)

tag: grade

value: grade 4

tag: status

value: SDD


title: CRD vs LT018T-C

description: methylation profiling in LT018T sample


title: Pd-62F,grade 4, SDD 2, scRNAseq

description: singlecellRNA-Seq

tag: tissue


title: CRD vs LT024NT-C

description: methylation profiling in LT024NT sample


title: Pc-41M,grade 3, SDD 1, scRNAseq

description: singlecellRNA-Seq

value: grade 3


title: Pab-30M,grade 2, MDD 4, scRNAseq

description: singlecellRNA-Seq

value: grade 2

value: MDD


title: Pab-24M,grade 2, MDD 3, scRNAseq

description: singlecellRNA-Seq


title: Pb-55F,grade 1, MDD 2, scRNAseq

description: singlecellRNA-Seq

value: grade 1


title: Pa-17F,grade 1,  MDD 1, scRNAseq

description: singlecellRNA-Seq


title: CRD vs LT017NT-C

description: methylation profiling in LT017NT sample


title: CRD vs LT030NT-C

description: methylation profiling in LT030NT sample


title: .NC-1

city: Suzhou

first: Fang

last: Fang

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description: U937 sample with no treatment

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

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

tag: treatment


title: sh-ZNF217-2

description: MV4-11 sample with ZNF217 knockdown

value: ZNF217 knockdown


title: U937_IgG

data_processing:
Raw data of CUT-TAG was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.4.4)
Peaks were identified using MACS3 (v3.0)
Assembly: hg38
Supplementary files format and content: peak text files
Library strategy: CUT&TAG

extract_protocol: HyperactiveUniversalCUT&TagAssayKitfor Illumina (Vazyme #TD903)

value: IgG

value: untreated


title: .NC-2

description: U937 sample with no treatment


title: .sh-ZNF217-2

description: U937 sample with ZNF217 knockdown


title: NC-1.

description: MV4-11 sample with no treatment


title: MV4-11-ZNF217


title: sh-ZNF217-1

description: MV4-11 sample with ZNF217 knockdown


title: MV4-11-MEF2D


title: MV4-11-RUNX2


title: MV4-11-IgG


title: NC-2.

description: MV4-11 sample with no treatment


title: MV4-11-ELF1


title: U937_ZNF217


title: MV4-11-FOXP1


title: .sh-ZNF217-1

description: U937 sample with ZNF217 knockdown


title: CRD vs LT020NT-C

description: methylation profiling in LT020NT sample

value: pooled DNA of 13 adjacent normal samples

value: enriched methylated DNA of adjacent normal tissue


title: CRD vs LT020T-C

description: methylation profiling in LT020T sample

value: male