title: hUC-MSCs, SCI rats in vivo, 3d, rep4

status: Public on Jun 30 2024

type: SRA

city: Guangzhou city

first: Mangmang

last: Li

state: Guangdong province

address: 1838 N Guangzhou Ave

department: Department of Cell Biology School of Basic Medical Sciences

country: China

institute: Southern Medical University

library_source: transcriptomic

data_processing:
Trimmomatic(v0.39) was employed to eliminate adapter sequences, poly-N sequences, and low_x0002_quality reads (quality scores below 30).
The filtered high-quality reads were aligned to the human reference genome (GRCh38) using the STAR aligner(v2.7.10) with default parameters.
Samtools(v1.16.1) was used to retain properly paired reads using the parameter “-f 4”.
gene expression levels were quantified via featureCounts (v2.0.3) using annotated gene models to generate raw read count data
Assembly: hg19
Supplementary files format and content: comma-separated values file includes raw counts for each Sample
Supplementary files format and content: comma-separated values file includes TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: human umbilical cord

growth_protocol: hUC-MSCs were cultured in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin-streptomycin, and 10 ng/ml recombinant human brain-derived neurotrophic factor (rhBDNF)， and maintained at 37C in a humidified incubator with 5% CO2

extract_protocol:
Total RNA extracted with TRIzol Reagent. Poly(A) RNA purified and used for library construction.
RNA libraries prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: Human umbilical cord-derived MSCs were transplanted 2 week following SCI in rats. As controls, MSCs transplanted to the uninjured spinal cord and non-transplanted MSCs were used. At 1 day and 3 days post transplantation, the MSCs were isolated from the SCI and the sham。

tag: tissue

value: human umbilical cord

tag: cell type

value: mesenchymal stem cells

tag: treatment

value: intrathecal injection in subacute-SCI rats

tag: time

value: Day 3


title: hUC-MSCs, Sham rats in vivo, 3d, rep2

value: intrathecal injection in sham-operated rats


title: hUC-MSCs, Sham rats in vivo, 3d, rep3


title: hUC-MSCs, Sham rats in vivo, 3d, rep4


title: hUC-MSCs, Sham rats in vivo, 1d, rep4

value: Day 1


title: hUC-MSCs, Sham rats in vivo, 1d, rep3


title: hUC-MSCs, SCI rats in vivo, 3d, rep5


title: hUC-MSCs, SCI rats in vivo, 3d, rep2


title: hUC-MSCs, SCI rats in vivo, 1d, rep4


title: hUC-MSCs, SCI rats in vivo, 3d, rep3


title: hUC-MSCs, Sham rats in vivo, 1d, rep2


title: hUC-MSCs, SCI rats in vivo, 1d, rep3


title: PNFLX4_mPFC

type: RNA

city: Mumbai

first: UTKARSHA

last: GHAI

state: Maharashtra

address: Tata Institute Of Fundamental Research, Old Navy Nagar,, Colaba, Mumbai, Maharashtra, India- 400005

department: DEPARTMENT OF BIOLOGICAL SCIENCES

country: India

institute: Tata Institute Of Fundamental Research

description: gene expression in the mPFC of 6 month old PNFlx rats which received fluoxetine from P2-P21

hyb_protocol: 600 ng cy3 labeled samples for 8x15 arrays were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software 10.5.1.1

data_processing: The normalization was done using GeneSpring GX 11 Software. 75th percentile shift normalization was done.

organism: Rattus norvegicus

source_name: mPFC tissue, PNFLX 5

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Pups received either fluoxetine (10mg/kg) or vehicle (5% sucrose solution) from postnatal day 2 (P2) to P21, to give rise to the groups PNFLX and Control respectively.

value: whole mPFC


title: CONTROL_JVeh1_mPFC

description: gene expression in the mPFC of 6 month old JVeh rats which received vehicle from P28-P48

source_name: mPFC tissue, CONTROL 1

treatment_protocol: Pups received either fluoxetine (10mg/kg) or vehicle (5% sucrose solution) from postnatal day 28 (P28) to P48, to give rise to the groups JFLX and Control respectively.


title: PNFLX3_mPFC

source_name: mPFC tissue, PNFLX 3


title: CONTROL_JVeh4_mPFC

description: gene expression in the mPFC of 6 month old JVeh rats which received fluoxetine from P28-P48

source_name: mPFC tissue, CONTROL 4


title: JFLX3_mPFC

description: gene expression in the mPFC of 6 month old JFlx rats which received fluoxetine from P28-P48

source_name: mPFC tissue, JFLX 3


title: PNFLX1_mPFC

source_name: mPFC tissue, PNFLX 1


title: JFLX2_mPFC

source_name: mPFC tissue, JFLX 2


title: JFLX1_mPFC

source_name: mPFC tissue, JFLX 1


title: CONTROL3_mPFC

description: gene expression in the mPFC of 6 month old PNVeh rats which received fluoxetine from P2-P21


title: CONTROL4_mPFC

source_name: mPFC tissue, CONTROL 5


title: CONTROL1_mPFC

description: gene expression in the mPFC of 6 month old PNVeh rats which received vehicle from P2-P21


title: JFLX4_mPFC

source_name: mPFC tissue, JFLX 4


title: CONTROL_JVeh2_mPFC

source_name: mPFC tissue, CONTROL 2


title: CONTROL_JVeh3_mPFC

source_name: mPFC tissue, CONTROL 3


title: CONTROL2_mPFC


title: PNFLX2_mPFC

source_name: mPFC tissue, PNFLX 2


title: hUC-MSCs, SCI rats in vivo, 3d, rep1


title: hUC-MSCs, SCI rats in vivo, 1d, rep1


title: hUC-MSCs, Sham rats in vivo, 1d, rep1


title: hUC-MSCs, Sham rats in vivo, 3d, rep1


title: EN76_42C_rep2

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

data_processing:
mRNA-Seq reads were mapped to reference N. viennensis genome using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER
DEGs was assessed with DESeq2 using getDiffExpression.pl in HOMER.
Assembly: N. viennensis
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Nitrososphaera viennensis EN76

source_name: archaea

growth_protocol: N. viennensis EN76 were cultured in artificial freshwater medium in the dark. The medium contained the following components per liter of culture medium: 0.4 g MgCl2 · 6H2O, 0.5 g KCl, 0.2 g KH2PO4, 1.0 g NaCl, and 0.1 g CaCl2 · 2H2O. After autoclaving, NH4Cl (2 mM), NaHCO3 (2 mM), HEPES (pH 7.4; 3 mM), sodium pyruvate (0.1 mM), 0.1 mL (0.1×) vitamin solution, and 0.1 mL (0.1×) trace metals solution per liter were added aseptically per liter of medium.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To investigate the effect of thermal stress on archaea, N. viennensis was cultured in 5 L of artificial freshwater medium at two different temperatures (33 °C and 42 °C)

tag: strain

value: archaea


title: hUC-MSCs, in vitro, 0d, rep1

value: in vitro

value: Day 0


title: hUC-MSCs, SCI rats in vivo, 1d, rep2


title: EN76_33C_rep2


title: EN76_33C_rep1


title: hUC-MSCs, in vitro, 0d, rep2


title: EN76_42C

library_source: genomic

data_processing:
MNase-Seq reads were mapped to the N. viennensis genome using HISAT2.
We used the makeTagDirectory followed by findPeaks command from HOMER version 4.9.1 to identify peaks of MNase-seq enrichment over background
A false discovery rate (FDR) threshold of 0.001 was used for all data sets. MNase-seq data were visualized by IGV browser.
Assembly: N. viennensis
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: genomic DNA

extract_protocol:
Cells were fixed using formaldehyde and then subjected to washing with MNase buffer. The cell pellet was subsequently mixed with 50 mU of MNase and incubated at 37°C for 15 minutes. DNA was extracted using phenol:chloroform:isoamyl for high-throughput sequencing.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: EN76_42C_rep1


title: scRNA_mSKIN_r2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

country: USA

institute: NIH

library_source: transcriptomic single cell

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: mm9, mm10 (only for scRNAseq), hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

organism: Mus musculus

source_name: skin

growth_protocol: HCT-116 degron cell lines: RAD21- mAID-mClover1 and HCT116-OsTIR1-MED26-AID2 were cultured in McCoy's 5A medium supplemented with L-Glutamine (Gibco), 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), at 37 °C; 5% CO2.  ES (E14) RAD213 and CTCF degron4 cell lines were cultured in knock-out DMEM (Gibco), ES cell qualified FBS (ATCC), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 1:10,000LIF (10,000x) on 0.1% gelatin coated dishes at 37 °C; 5% CO2.  Primary WT and Myc knockout B cells were derived from Myc flox/flox mice (WT) or RosaCreERTam/Myc flox/flox mice (KO) were treated with tamoxifen (Sigma) (three times of i.p. 1mg/mouse at 4, 3 and 1 day before sacrifice).  The deletion of floxed allele was checked as previously5 with PCR or intracellular staining of Myc protein. B cells were isolated from spleen of WT and KO mice, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies) and activated for 4 hours with 50 mg/ml LPS and 2.5 ng/ml IL4 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco), at 37 °C; 5% CO2 B220 positive primary bone marrow B cells were derived from C57BL/6J wild-type mice, enriched with CD45R (B220) MicroBeads Kit (Miltenyi Biotec) and Dead Cell Removal Kit (Miltenyi Biotec). Splenic B cells were derived from C57BL/6J wild-type mice immunized with a keyhole limpet haemocyanin (KLH; 25 µg/footpad, Sigma-Aldrich) in the presence of 10% CFA adjuvant (Sigma-Aldrich). After 5 days B cells were isolated from spleen, enriched with EasySep Mouse B Cell Isolation KIT (STEMCELL Technologies), and activated for 72 hours with 50 mg/ml LPS, 2.5 ng/ml IL4 and anti-CD180 in RPMI-1640 medium (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 1:100 sodium pyruvate (Gibco), 1:100 NEAA (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and HEPES (Gibco),  at 37 °C; 5% CO2.  CH12 B lymphoma cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 1:1000 2-Mercaptoethanol (Gibco), at 37 °C; 5% CO2. LNK (NK cell line) cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% FBS (Gemini), 1:100 Glutamax (Gibco), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco), 10 mM HEPES, 1:100 NEAA (Gibco), 1:100 sodium pyruvate (Gibco), 1:1000 2-Mercaptoethanol (Gibco) and 200 IU/ml IL-2 (Sigma-Aldrich). Skin cells for scRNA-Seq: whole epidermis from mouse neonates. Keratinocytes were isolated from Fvb neonate (P0-P2) skin (n = 2) as described in Lichti et al., 20086. Cells were subjected to MACS Dead Cell removal kit (Miltenyi Biotech) using the manufacturer’s protocol. Skin cells for mRNA half-lives estimation: primary keratinocyte. Skins from a pool of Fvb neonatal mice were collected at P0-P2 and incubated overnight in 2.0 U/mL Dispase II (Sigma) in KBM-Gold (Lonza) on an end-over-end rotator. The following day, skins were washed twice in 1x PBS (Sigma), and epidermises were separated from dermises. Epidermises were placed basal side down and floated in pre-warmed 0.25% Trypsin-EDTA (Thermo Scientific) for 20min on an orbital shaker at room temperature. An equal volume of pre-warmed 2.5mg/mL Soybean Trypsin Inhibitor (Thermo Scientific) was added to finish trypsinization, and epidermises were rubbed vigorously against bottom of plate using curved forceps to dislodge keratinocytes. Dislodged cells were pooled into a tube on ice in KBM-Gold. Pooled cells were pipetted ~40 times with a 10ml serological pipette and strained with a 100um filter before pelleting cells at 300xg for 10min at 4°C. Cells were resuspended in 4.5mL KBM-Gold per epidermis and cell count was obtained using Cellometer ViaStain AOPI Solution (Sigma). The cells were subjected to Percoll (GE LifeSciences; ratio of 10X PBS:Percoll:KBM-Gold media was 1:4:5, where the cells were at a concentration of 1 million per mL of final volume) gradient ultracentrifugation using a swinging bucket rotor (11,000 rpm for 42 minutes at 4°C) to separate the basal and suprabasal fractions. The cells at the top band were suprabasal cells and separated from the pellet at the bottom of the tube which were basal cells. The basal cell sample was carefully pipetted out, washed twice with 4°C 1x PBS, seeded onto collagen-coated (Collage Type I; Corning) 6-well plates at 1x106 cells per well, and incubated at 37°C overnight to allow cells to attach to the plate before proceeding with experiments.  Mast cells: Mouse bone marrow-derived mast cells (BMMC) were differentiated from the marrow of tibias and femurs of C57/BL6 mice and cultured for 8 weeks in RPMI 1640 containing 10% FBS, 1M HEPES, 100 U/mL penicillin, 100 μg/mL streptomycin, 4 mM l-glutamine, 1 mM sodium pyruvate, non-essential amino acids, 50 μM 2-mercaptoethanol, IL-3 (20 ng/mL) and stem cell factor (SCF) (20 ng/mL). The purity of mast cells was monitored by assessing the expression of the receptors for SCF (CD117;Kit) and for IgE (FcεRI) by flow cytometry. By the end of 6-8 weeks in culture more than 98% of the cultured population was FcεRI+/CD117+ double-positive mast cells.

extract_protocol:
RNA-Seq Cells (0.5M) were harvested and lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen). RNA was isolated and DNase treated according to manufacturer’s protocol. High RNA quality was confirmed using the Agilent TapeStation system before library preparation. mRNA polyA- purification, reverse transcription and library preparation were performed using NEBNext Poly(A) mRNA Magnetic Isolation Module. For spike-in control ERCC RNA Spike-In Mix (Invitrogen) was added before RNA isolation.   ChIP-Seq Cells were fixed with 1% formaldehyde (Sigma) for 10 min at 37°C, treated with 1/20 volume of 2.5 M Glycine, washed with PBS, snap-frozen on dry ice and stored at -80°C until further processing. After thawing cells were resuspended in RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) supplemented with Complete Mini EDTA free proteinase inhibitor (Roche) and sonicated using ultrasonicator (Covaris) in 1 ml AFA tubes (Covaris): duration (s): 1200, peak power: 75, duty % factor: 15, cycles/burst:1000. Sonicated chromatin was pre-cleared with Dynabeads and incubated overnight at 4˚C with rotation with following antibodies: RAD21: ab992 (Abcam); MED26: 13641S (Cell Signaling Technology); TATA binding protein TBP: ab28175 (Abcam); BRD4: ab128874 (Abcam); RNA Pol II: ab26721 (Abcam). Next day samples were washed (10 min at 4˚C with rotation): 2x with RIPA buffer, 2x with RIPA buffer + 0.3 M NaCl, 2x with 1 ml of LiCl buffer (0.25M LiCl, 0.5% Igepal CA-630, 0.5% NaDOC, store at 4˚C), 1x with 1 ml of TE + 0.2 % Triton X-100, 1x with 1 ml of TE. After washes beads were resuspended with 100 ul of TE, followed by addition of 3 µl of 10% SDS and 5 µl of 20 mg/ml Proteinase K and incubated at 65˚C for 4h. After decrosslinking DNA was purified on columns using ChIP DNA Clean & Concentrator kit (Zymo Research). In the next step DNA was quantified using Qubit system (Invitrogen).  mRNA half-lives estimation  Cells were treated with 5 µg/mL actinomycin D (Sigma) and harvested (0.5M cells) at timepoint 0 hours and up to 24 hours: at 1, 2, 4, 8, 12 and 24 hours timepoints7. After each timepoint the viability of cells was checked with FACS, or Nexcelom cell counter after staining with Acridine Orange/Propidium Iodide (AO/PI) (Nexcelom Bioscience). Some cell types did not survive longer actinomycin D treatment than 8 hours, so the last collected timepoint was determined based on cell type viability (details in Extended Data Fig.1a). Pellets were lysed in 100 µl of the lysis solution (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), ERCC RNA Spike-In Mix (Invitrogen) was added, RNA isolated (RNAqueous™-Micro Total RNA Isolation Kit from Invitrogen), and RNA-Seq was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module.   scRNA-Seq Cells were washed twice with 1x PBS containing 0.04% weight/volume BSA, resuspended in the same buffer and encapsulated into droplets using 10X Genomics system.
RNA-Seq NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).  ChIP-Seq Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).  scRNA-Seq Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).

treatment_protocol: HCT-116 degron cell lines: Starvation: cells were FBS depleted for 14 hours, followed by an additional incubation with FBS free medium for another 6 hours in the presence of DMSO (control), 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) for degradation of the AID-tagged RAD21 and MED26 or 500nM JQ-1 (Sigma-Aldrich) for BRD4 displacement. Cells were analyzed after addition of FBS in the presence of DMSO or drugs at timepoints: 0h (RAD21 degron), 0.5h (RAD21 degron) and 2h (RAD21 and MED26 degron, JQ-1 treatment). ES (E14) For the AID-tagged proteins 500 µM auxin (indole-3-acetic acid, IAA) (Sigma-Aldrich) was added for 6 hours (RAD21) or 24 hours (CTCF). Splenic B cells To measure mRNA half-lives in activated B cells Actinomycin D was added after 2 days of stimulation with LPS, IL4 and anti-CD180 (more details: mRNA half-lives estimation). Skin cells To estimate mRNA half-lives in skin cells we used basal cells.

value: skin

value: keratinocytes

tag: genotype

value: WT


title: scRNA_ESCRad21D_DMSO

source_name: ESC E14

tag: cell line

value: ESC E14

value: ESC

value: DMSO 6h


title: scRNA_mSKIN_r1


title: scRNA_ESCRad21D_AUXIN

value: IAA 6h


title: scRNA_ESCCTCFD_AUXIN

value: CTCF-degron

value: IAA 24h


title: scRNA_ESCCTCFD_DMSO

value: DMSO 24h


title: HNC_input_3

city: Beijing

first: Shuohua

last: Chen

address: Haidian District

institute: Tsinghua University

data_processing:
The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6) to remove the following data: reads containing adapters (adapter contamination); reads with an unknown base N content greater than 5%; and low-quality reads (reads with a base quality value less than 15 and with a proportion of bases with such quality values greater than 20% of the total bases in the read). The resulting clean data was then used for gene expression quantification using RSEM (v1.3.1) software. Subsequently, data analysis was performed using the anota2seq package.
Assembly: The clean data were mapped to the reference genome (GCF_000001405.39_GRCh38.p13)
Supplementary files format and content: TPM

source_name: Lung

growth_protocol: H1299 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 1% antibiotics. The cells were cultured in a constant temperature of 37℃ and a 5% carbon dioxide incubator.

extract_protocol:
Cell lysates and polyriboTRIzol reagent (Invitrogen, Carlsbad, CA, USA) was used to extract the mRNA from the cell lysate and the mRNA bound to the polysomes. RNA dissolved in DEPC-treated ddH2O.some bound mrnas were extracted by TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
The Agilent 2200 TapeStation Nucleic Acid System was employed to detect the RNA integrity number (RIN) and concentration of RNA samples. To construct the cDNA library, RNA samples with a RIN greater than 8.5 were used. A certain amount of RNA was taken, denatured at an appropriate temperature to open its secondary structure, and the mRNA was enriched using oligo(dT) magnetic beads. Fragmentation reagents were added to the mRNA obtained in the previous step. A single-stranded synthesis reaction system was prepared, and the reaction programme was set to synthesize single-stranded cDNA; a double-stranded synthesis reaction system was prepared, and the reaction programme was set to synthesize double-stranded cDNA. The reaction system was prepared, and the reaction programme was set to repair the ends of the double-stranded cDNA, and an A base was added at the 3' end. The adapter ligation reaction system was prepared, and the reaction programme was set to connect the adapter with the cDNA. The PCR reaction system was prepared, and the reaction programme was set to amplify the product. The PCR products were denatured into a single strand, the circularization reaction system was prepared, and the reaction programme was set to obtain a single-stranded circular product and the linear DNA molecules that were not circularized were digested. The single-stranded circular DNA molecule is replicated by rolling circle replication to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are placed into a mesh pore on a high-density DNA nanochip and sequenced using the combined probe anchor polymerization technology (cPAS).

treatment_protocol: When the cell density reached approximately 60%, siEIF3Gs (a mixture of two siRNAs at an equal molar ratio, siEIF3G-4, 5’-GAACAAACTCAAGGGCCAGAA-3’; siEIF3G-5, 5’-GAGGTCATCAACGGAAACATA-3’) and siCtrl (5’-TTCTCCGAACGTGTCACGT-3’) were separately transfected into the cells using jetPRIME Transfection Reagent (Polyplus, NY, USA). After 72 hours, the cells were collected and lysed. The supernatants were collected after centrifugation, and 1/10 of the total lysate volume was taken as input control. The cell lysates were then subjected to sucrose density gradient (10-50%) centrifugation, and the resulting products were separated using Gradient108 and Fractionator (BIOCOMP, Canada). The centrifuged products of the polysome fraction were collected for RNA extraction. Subsequently, the mRNA from both the input control and the mRNA bound to the polysomes were extracted and sequenced.

value: Lung

value: Non-small cell lung cancer

value: siCtrl

tag: fraction

value: input


title: HNC_input_2


title: HCTMED26D_Proseq_DMSO_r2

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
Proseq_density: trim: cutadapt 1.14 for adapter and UMI removal with -O 1 --match-read-wildcards -m {20,26}), seqtk trimfq for R1l
Proseq_density: mapping: bowtie2 on combined genome (dm6 (spikein)+ hg19(primary))
Proseq_density: dedup: umitools (http://github.com/CGATOxford/UMI-tools)
Proseq_density: reads seperation with samtools 1.3.1 and convert to bedGraph through bowtie2stdBedgraph.pl (https://github.com/AdelmanLab/NIH_scripts)
mRNA-seq half-life estimation: alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file
Library strategy: PRO-seq

extract_protocol:
RNA-Seq
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).
ChIP-Seq
Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).
scRNA-Seq
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).
RNA-Seq
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) was used for library construction. Single 50 cycles of sequencing data were acquired on NextSeq2000, NextSeq550, HiSeq3000 or NovaSeq6000 (Illumina).
ChIP-Seq
Library was prepared using Ovation Ultralow System V2 (Tecan) according to manufacturer’s protocol. Before sequencing high quality was confirmed using the Agilent TapeStation system. Single 50 cycles of sequencing data were acquired on NextSeq550, NovaSeq6000 (Illumina).
scRNA-Seq
Libraries were prepared using Chromium Single Cell 3′ Reagent Kits (10X Genomics) according to the manufacturer’s protocol. With double 10bp index cycles, 28 forward and 90 reverse cycles were run on NovaSeq6000 machine (Illumina).

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+IAA 6h, FBS + IAA 2h


title: HNC_input_1


title: HCTMED26D_Proseq_AUXIN_r2

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCTMED26D_Proseq_DMSO_r1


title: HCTMED26D_Proseq_AUXIN_r1


title: UT_Jurkat_TIP60_rep2

city: Boston

first: Melissa

middle: McCalley

last: Inge

state: Massachusetts

address: 24 Cummington Mall

department: Biology

institute: Boston University

hyb_protocol: Microarray DNA double stranding and PBM protocols are as previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937)

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing: Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006). Processed data corresponds to z-scores normalized against the fluorescence distribution obtained at sets of random background probes

label: Alexa fluor conjugated antibody

source_name: Jurkat cells

label_protocol: PBM experiments using cell extracts were performed following the protocols previously described (Berger et al. PMID: 19265799, Mohaghegh et al. PMID: 30657937) and outlined here. The double-stranded microarray was pre-wetted in HBS+TX-100 (20mM HEPES, 150mM NaCl, 0.01% Triton X-100) for 5 min and then de-wetted in an HBS bath. Each of the microarray chambers were then incubated with 180 mL of nuclear extract binding mixture for 1 h in the dark. Nuclear extract binding mixture (per chamber): 400-600 mg of nuclear extract; 20mM HEPES (pH 7.9); 100mM NaCl; 1mM DTT; 0.2mg/mL BSA; 0.02% Triton X-100; 0.4mg/mL salmon testes DNA (Sigma-Aldrich, Catalog #D7656)). The microarray was then rinsed in an HBS bath containing 0.1% Tween-20 and subsequently de-wetted in an HBS bath. After the nuclear extract incubation, the microarray was incubated for 20 min in the dark with 20mg/mL primary antibody for the TF or COF of interest. The primary antibody was diluted in 180 mL of 2% milk in HBS. The array was then rinsed in an HBS bath containing 0.1% Tween-20, de-wetted in an HBS bath, and incubated with 10mg/mL of either Alexa488- or Alexa647-conjugated secondary antibody for 20 min in the dark. The secondary antibody was diluted in 180 mL of 2% milk in HBS. Excess antibody was removed by washing the array twice for 3 min in 0.05% Tween-20 in HBS and once for 2 min in HBS in Coplin jars as described above. After the washes, the microarray was de-wetted in an HBS bath and scanned

growth_protocol: SUDHL4 (CRL-2957), Jurkat E6-1 (TIB-152), and HEK293 (CRL-1573) cells were obtained from ATCC. SUDHL4 and Jurkat cells were grown in suspension RPMI 1640 Glutamax media (Thermofisher Scientific, Catalog #72400120) with 10% heat-inactivated fetal bovine serum (Thermofisher Scientific, Catalog #132903) and Jurkat cells medium was also supplemented with 1mM sodium pyruvate (Thermofisher Scientific, Catalog #16140071). Cells were grown at 37 °C with 5% CO2. T175 (CELLTREAT, Catalog #) non-treated flasks were used when culturing SUDHL4 and Jurkats cells for experiments. HEK293 cells were grown in low glucose DMEM (Cytiva, Catalog # SH30021) supplemented with 10% FBS at 37 °C with 5% CO2. HEK293 cells were grown in cell culture treated T225 flasks (CELLTREAT, catalog #) for experiments.

extract_protocol: Nuclear extracts were obtained as previously described (Bray et al. PMID: 35252945, Mohaghegh et al. PMID: 30657937) with modifications detailed below. To harvest nuclear extracts from Jurkat cells, the cells were collected in a 15 ml falcon tube and placed on ice. To harvest nuclear extracts from SK-MEL-28 cells, the media was aspirated off and the cells were washed once with 1X PBS (Thermofisher Scientific, Catalog #100010049). Once the 1X PBS used to wash the cells was aspirated off, enough 1X PBS was mixed with 0.1mM Protease Inhibitor (Sigma-Aldrich, Catalogue #P8340) to cover the cells was added to each flask. A cell scraper was used to dislodge the cells from the flask, and cells were collected in a 15 ml falcon tube and placed on ice. Jurkat and SK-MEL28 cells were pelleted by centrifugation at 500xg for 5 min at 4˚C. Both pellets were washed with 2mL of 1X PBS with Protease Inhibitor and pelleted again at 500xg for 2 min at 4˚C. To lyse the plasma membrane, the cells were resuspended in Buffer A (1 mL Buffer A for Jurkat cells, 1.5 mL Buffer A for SK-MEL28 cells) (10mM HEPES, pH 7.9, 1.5mM MgCl, 10mM KCl, 0.1mM Protease Inhibitor, Phosphatase Inhibitor (Santa-Cruz Biotechnology, Catalog #sc-45044), 0.5mM DTT (Sigma-Aldrich, Catalog #4315) and incubated for 10 min on ice. After the 10 min incubation, Igepal detergent (final concentration of 0.1%) was added to the cell and Buffer A mixture and vortexed for 10 s. To separate the cytosolic fraction from the nuclei, the sample was centrifuged at 500xg for 5 min at 4˚C to pellet the nuclei. The cytosolic fraction was collected into a separate microcentrifuge tube. The pelleted nuclei were then resuspended in Buffer C (100 µL for Jurkat nuclei and 150 µL for SK-MEL-28 nuclei) (20mM HEPES, pH 7.9, 25% glycerol, 1.5mM MgCl, 0.2mM EDTA, 0.1mM Protease Inhibitor, Phosphatase Inhibitor, 0.5mM DTT, and 420mM NaCl) and then vortexed for 30 s. To extract the nuclear proteins (i.e., the nuclear extract), the nuclei were incubated in Buffer C for 1 h while mixing at 4˚C. To separate the nuclear extract from the nuclear debris, the mixture was centrifuged at 21,000xg for 20 min at 4˚C. The nuclear extract was collected in a separate microcentrifuge tube and flash frozen using liquid nitrogen. Nuclear extracts were stored at -80˚C

treatment_protocol: Jurkat cells intended to be stimulated as well as paired untreated cells were plated at 1 x 106 cell/ml 2 hours prior to stimulation. To stimulate selected cells, soluble anti-CD28, CD3 & CD2 (ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, Catalog #10970) was added to media at manufacturers recommended 25 ul/ml. Cells were agitated slightly and placed back in the incubator for 45 minutes. After 45 minutes, both the untreated and stimulated cells were processed for nuclear.

value: untreated

tag: target protein

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)

tag: secondary antibody concentration


title: EN76_33C

value: archaea


title: UT_SUDHL4_TBL1XR1_rep2

source_name: SUDHL4 cells


title: UT_SUDHL4_P300_rep2


title: UT_SUDHL4_BRD4_rep1

value: Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: UT_SUDHL4_P300_rep1


title: UT_SUDHL4_BRD4_rep2


title: UT_Jurkat_TBL1XR1_rep1


title: UT_SUDHL4_TBL1XR1_rep1


title: UT_Jurkat_PCAF_rep2

value: PCAF


title: UT_Jurkat_PCAF_rep1


title: UT_Jurkat_TBL1XR1_rep2


title: HNC_3

value: polysomal


title: HCTJQ_Proseq_JQ1_r1

value: WT

value: JQ1 2h


title: HCTJQ_Proseq_JQ1_r2


title: HCTJQ_Proseq_DMSO_r2

value: DMSO 2h


title: HNC_2


title: HCT_mRNA_Med26Degron_IAA_r2_8h

data_processing:
scRNAseq: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
base calling: illumina CASAVA 1.8.2
Proseq_density: trim: cutadapt 1.14 for adapter and UMI removal with -O 1 --match-read-wildcards -m {20,26}), seqtk trimfq for R1l
Proseq_density: mapping: bowtie2 on combined genome (dm6 (spikein)+ hg19(primary))
Proseq_density: dedup: umitools (http://github.com/CGATOxford/UMI-tools)
Proseq_density: reads seperation with samtools 1.3.1 and convert to bedGraph through bowtie2stdBedgraph.pl (https://github.com/AdelmanLab/NIH_scripts)
mRNA-seq half-life estimation: alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-seq half-life estimation: htseq count file generation from mRNA-seq aligned both for ERCC spike-in control and genomic sequence
mRNA-seq half-lfe estimation:estimate the decay rate constant (kdecay) by fitting the exponential curve on concentration changes upon timepoints using SSasymp R function. From the decay constant, we calculated the mRNA half-lives using the following equation: ln(2)/kdecay
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: bigwig file

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 8h


title: UT_Jurkat_P300_rep3


title: HNC_1

value: Lung


title: HCT_mRNA_Med26Degron_IAA_r2_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 2h


title: HCT_mRNA_Med26Degron_IAA_r2_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 4h


title: HCT_mRNA_Med26Degron_IAA_r2_0h


title: UT_Jurkat_TIP60_rep1


title: HC5_input_1

value: Non-small cell lung cancer

value: input


title: HCT_mRNA_Med26Degron_DMSO_r2_2h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 2h


title: UT_Jurkat_P300_rep2

value: untreated


title: HC5_input_2


title: HCT_mRNA_Med26Degron_IAA_r2_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 24h


title: HC5_3


title: UT_Jurkat_PCAF_rep3

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: HC5_input_3


title: HCT_mRNA_Med26Degron_IAA_r2_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 12h


title: HCT_mRNA_Med26Degron_DMSO_r2_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 8h


title: HCT_mRNA_Med26Degron_DMSO_r2_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 1h


title: HCT_mRNA_Med26Degron_DMSO_r2_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 4h


title: UT_Jurkat_MOZ_rep2

value: MOZ

value: Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: HCT_mRNA_Med26Degron_DMSO_r2_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 24h


title: UT_Jurkat_MOZ_rep1


title: HC5_2

value: Lung

value: polysomal


title: UT_Jurkat_MOF_rep3

value: MOF


title: HCT_mRNA_Med26Degron_IAA_r2_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 1h


title: HC5_1

value: Non-small cell lung cancer


title: HCT_mRNA_Med26Degron_DMSO_r2_0h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCT_mRNA_Med26Degron_DMSO_r2_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 12h


title: UT_Jurkat_P300_rep1

value: untreated


title: HGG_70, Truseq

city: Temuco

first: Mauricio

middle: A.

last: Saez

address: Manuel Montt 56

country: Chile

institute: Universidad Catolica de Temuco

data_processing:
Reads of low quality and adapter contamination were removed using the trim_galore tool. Processed reads were aligned to the GRCh38 reference genome using the Bowtie2 tool. The aligned *.sam results were then converted to *.bam files using the samtools application for subsequent analysis.
Somatic mutations were called according to GATK recommendations, including additional considerations for amplicon panels, as described below. Bam files were analyzed with MarkDuplicatesSpark and BaseRecalibrator, using gnomadV2 database, to finally recalibrate with ApplyBQSR to meet GATK standards. Somatic variants were detected using Mutect2 , only on target regions. To identify and discard artifactual variants, GetPileupSummaries with CalculateContamination, LearnReadsOrientation and a panel of normal were used, Additionally, the Integrative Genomics Viewer (IGV 2.10) was used to identify and correct potential errors. Finally, we used FilterMutectCalls to recover clustered events and to discard variants with an allelic frequency <0.05 or <10 reads supporting the variant.
Variants in vcf files were annotated with Funcotator and reports were generated in vcf and maf files. All genomic coordinates are mapped to the GRCh 38 assembly. Posterior analysis was performed with Variant Effect Predictor (McLaren et al., 2016) to predict pathogenicity. Novel variants and variants not previously reported in gliomas that are predicted to result in singleamino acid substitutionswere subsequently evaluated using Sorting Intolerant From tolerant (SIFT) and polymorphism phenotyping-2 (PolyPhen-2) to predict the effect of the change on protein function while variants that resulted in frameshifts were evaluated using SIFT indel . Maftools R package was used to prepare oncoplots.
Assembly: GRCh38
Supplementary files format and content: vcf files for each sample, containig snp and short indel, after pass filters for quality, and  allelic frequency <0.05 and/or <10 reads supporting the variant.
Supplementary files format and content: maf file used for oncoplots after removing known polymorphisms

source_name: Tumor

extract_protocol:
Formalin-fixed paraffin-embedded tissue samples were obtained from the Pathology Service at the Asenjo Neurosurgery Institute. After neuropathologist confirmation of a tumor percentage greater than 70% in each area to be extracted, 3-6 sections of 10 microns were prepared from each paraffin block using the GeneJET FFPE DNA Purification Kit. No matched blood samples were available. The extracted DNA was quantified using fluorescence-based methods (Quant-iT™ PicoGreen™ dsDNA and/or Qubit™ dsDNA HS), resulting in an average concentration of 40 ng/µL. We
For both AmpliSeq™ and TruSeq™ libraries, library generation efficiency was evaluated with different initial amounts of DNA to adjust the various stages of the process based on the specific sample and panel characteristics. Automated electrophoresis of the first libraries were performed for quality control and size estimation using the DNA 1000 kit on the Agilent 2100 Bioanalyzer system. All libraries were quantified by qPCR using the Illumina KAPA library quantification kit and were pooled at a concentration of 10 nM before sequencing. A Mid Output Kit v2.5 (150 cycles) was used on a NextSeq sequencer with 25% phi-X for all Ampliseq™ libraries, and a Micro Kit v2 (300 cycles) with 25% phi-X on a MiSeq sequencer was used for all TruSeq™ libraries.
Amplicon sequencing

value: Tumor

tag: Sex

value: Male

tag: histological diagnosis

value: Glioblastoma

tag: age at_diagnosis

tag: overall survival_(months)


title: iPSC-derived thyroid follicular cells (day 29) cultured in thyroid maturation medium in absence of BMP4

first: Pushpinder

last: Bawa

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38 supplemented with sequences for tdTomato reporter and lentiviral BFP
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38
Supplementary files format and content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: BU3 NGP8T

growth_protocol: Directed differentiation toward thyroid follicular cells, cultured in medium without BMP4 from day 15 to day 29

extract_protocol:
Cells were resuspended in buffer at a concentration of 1000 cells/ul and captured using a 10X chromium instrument (10X Chromium, Pleasanton, CA), following standard Chromium 10x guidelines.
Libraries were prepared using a Chromium Single Cell 3' v3 kit (10x Genomics) and loaded on a NextSeq 2000 system (Illumina) aiming for sequencing depth of approximately 89,000 reads/cell

value: BU3 NGP8T

value: iPSC-derived thyroid follicular cells

value: thyroid maturation medium with FGF2, FGF10, IGF-1, EGF, TSH, Isulin, Trasferrin, Selenium and Heparin Salt


title: iPSC-derived thyroid follicular cells (day 29) cultured in thyroid maturation medium containing BMP4

growth_protocol: Directed differentiation toward thyroid follicular cells, cultured continuously in presence of BMP4.

value: thyroid maturation medium with FGF2, FGF10, IGF-1, EGF, TSH, Isulin, Trasferrin, Selenium, Heparin Salt and BMP4


title: HGG_68, Truseq

tag: tissue


title: FFPE,  RNA-seq, 06S21001909

city: Tampa

first: Daniel

last: Abate-Daga

state: Florida

address: 12902 Magnolia Dr.

department: Immunology

institute: H. Lee Moffitt Cancer Center and Research Institute

description: TruSeq RNA Exome

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt 1.16
Trimmed sequence reads were mapped to hg19 using STAR-2.5.3a
Gene-level quantification was determined with HTSeq 0.6.1 using gencode ver30 gene model
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: melanoma tumor

extract_protocol:
The Qiagen RNEasy FFPE kit with a DNase treatment step was used to extract RNA from one to ten 20-micron FFPE sections following the manufacturer's protocol.  Samples were eluted in water, quantiated with the Qubit fluorometer, and screened for quality on the Agilent TapeStation 4200 gDNA ScreenTape.
200 ng of RNA was used with the Illumina TruSeq RNA Exome kit with four-plex enrichments following the manufacturer's protocol.  Final post-capture ibraries were quantitated using the Roche KAPA Library Quantification kit accoridng to the protocol.

value: melanoma tumor


title: HGG_69, Truseq


title: FFPE,  RNA-seq, 06S21001908

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001907

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001906

description: TruSeq RNA Exome


title: iPSC-derived thyroid follicular cells (day 12) cultured in thyroid specification medium

growth_protocol: Directed differentiation toward thyroid follicular cell progenitors

tag: cell type

value: iPSC-derived thyroid follicular cell progenitor

value: thyroid specification medium with FGF2, BMP4 and Heparin Salt


title: HGG_67, Truseq

value: Female


title: FFPE,  RNA-seq, 06S21001905

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001904

description: TruSeq RNA Exome


title: hUC-MSCs, in vitro, 0d, rep3

source_name: human umbilical cord

value: human umbilical cord

value: mesenchymal stem cells

tag: treatment

value: in vitro

value: Day 0


title: UT_Jurkat_GCN5_rep2

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: UT_Jurkat_MOF_rep2

value: untreated

value: MOF

value: Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: UT_Jurkat_MOF_rep1


title: HGG_66, Truseq

value: Tumor

value: Male

value: Glioblastoma


title: UT_Jurkat_GCN5_rep1


title: FFPE,  RNA-seq, 06S21001902

description: TruSeq RNA Exome


title: HGG_65, Truseq


title: FFPE,  RNA-seq, 06S21001903

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001896

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001895

description: TruSeq RNA Exome


title: HGG_64, Truseq


title: UT_Jurkat_CBP_rep1

value: CBP


title: FFPE,  RNA-seq, 06S21001892

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001894

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001900

description: TruSeq RNA Exome


title: HGG_62, Truseq


title: FFPE,  RNA-seq, 06S21001891

description: TruSeq RNA Exome


title: UT_Jurkat_CBP_rep2


title: HGG_63, Truseq


title: FFPE,  RNA-seq, 06S21001887

description: TruSeq RNA Exome


title: HGG_61, Truseq


title: FFPE,  RNA-seq, 06S21001885

description: TruSeq RNA Exome


title: HCTJQ_Proseq_DMSO_r1

value: colorectal carcinoma cell

value: WT

value: DMSO 2h


title: FFPE,  RNA-seq, 06S21001890

description: TruSeq RNA Exome

value: melanoma tumor


title: UT_Jurkat_BRD4_rep2


title: HGG_60, Truseq


title: FFPE,  RNA-seq, 06S21001884

description: TruSeq RNA Exome


title: FFPE,  RNA-seq, 06S21001882

description: TruSeq RNA Exome


title: Colon TRPM6 KO mice 3

city: Nijmegen

first: Joost

last: Hoenderop

address: Geert Grooteplein Zuid 28-30

department: Medical Biosciences

country: Netherlands

institute: Radboudumc

data_processing:
RNA-Seq data were analyzed using the seq2science pipeline (https://vanheeringen-lab.github.io/seq2science/content/workflows/rna_seq.html).
Reads were aligned with the preindexed mm10 transcript assembly from UCSC
Samtools (RRID: RRID:SCR_002105) was used to filter reads with a quality score lower than 20, and PCR duplicates were removed
Reads per gene were counted with the htseq-count script from the Hisat2 software suite using the GTF file corresponding to the transcript assembly. Read counts were analyzed with DESeq2 (RRID: SCR_002285) to identify significant dynamics
Assembly: mm10
Supplementary files format and content: Tab delimited file, raw read counts per transcript
Supplementary files format and content: Tab delimited file, TPM values per transcript

source_name: Distal colon

growth_protocol: After acclimatization of two weeks to synthetic chow with regular composition (E15000-04, Ssniff Spezialdiäten, GmbH, Germany), mice were housed individually in meta¬bolic cages for 24 hours to collect urine and feces and monitor food and water intake.

extract_protocol:
Total RNA was extracted from the distal colon using TRIzol reagent according to manufacturer's protocol
Total RNA was used for the preparation of the RNA-Seq libraries using the KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA). In short, oligo hybridization and rRNA depletion, rRNA depletion cleanup, DNase digestion, DNase digestion cleanup, and RNA elution were performed according to the protocol. Fragmentation and priming were performed at 94°C for 6 min. First-strand synthesis, second-strand synthesis, and A-tailing were performed according to the protocol. For the adaptor ligation, a 1.5 mM stock was used (NextFlex DNA barcodes, Bio Scientific, Austin, TX). First and second postligation cleanup was performed according to the protocol. A total of 11 PCR cycles were performed for library amplification. The library amplification cleanup was done using a 0.8× followed by 1.0× bead-based cleanup.  Library size was determined using the High Sensitivity DNA bioanalyzer kit, and the library concentration was measured using the dsDNA High Sensitivity Assay (DeNovix, Wilmington, DE). Paired-end sequencing reads of 50 bp were generated using an Illumina NextSeq 2000.

treatment_protocol: Six days after the metabolic cages, mice were subjected to daily administration with vehicle (0.5% (w/v) methylcellulose and 0.2% (w/v) NaHCO3, adjusted with NaOH to pH 9.0) via oral gavage for 4 days. One day before sacrifice, the feed for all groups was switched from normal Mg2+ to a low (0.02%, w/w) Mg2+ diet. Mice were anesthetized with 4% (v/v) isoflurane and sacrificed via exsanguination via orbital sinus bleeding and subsequent cervical dislocation. Organs were collected for further analyses.

value: Distal colon

tag: age

value: 8 weeks


title: UT_Jurkat_BRD4_rep1


title: UT_HEK293_TBL1XR1_rep1

source_name: HEK293 cells


title: HGG_59, Truseq

value: Female


title: Colon TRPM6 KO mice 2

tag: strain


title: UT_HEK293_P300_rep2


title: Colon TRPM6 WT mice 3

tag: genotype


title: Colon TRPM6 KO mice 1

tag: cell line


title: HGG_58, Truseq


title: UT_HEK293_P300_rep1


title: UT_HEK293_BRD4_rep2


title: HGG_57, Truseq


title: Colon TRPM6 WT mice 1


title: UT_Jurkat_CBP_rep3


title: Colon TRPM6 WT mice 2


title: UT_HEK293_BRD4_rep1


title: UT_HEK293_TBL1XR1_rep2


title: HGG_56, Truseq


title: HCTMED26D_ChIPseq_Rad21_DMSO_r1


title: HCTMED26D_ChIPseq_TBP_DMSO_r1

value: DMSO 6h


title: HCTMED26D_ChIPseq_TBP_AUXIN_r1

value: IAA 2h


title: HCTMED26D_ChIPseq_Rad21_AUXIN_r1


title: HGG_55, Truseq


title: HGG_54, Truseq


title: 45mT_Jurkat_TIP60_rep1

source_name: TCR-stimulated Jurkat cells

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (Catalog #10970)

tag: treatment concentration

value: 25 ul/ml

tag: treatment duration

value: 45 min

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: 45mT_Jurkat_TIP60_rep2

tag: target protein

tag: primary antibody


title: HCTMED26D_ChIPseq_PolII_DMSO_r1


title: 45mT_Jurkat_PCAF_rep3

value: PCAF

tag: primary antibody concentration

tag: secondary antibody


title: HCTMED26D_ChIPseq_PolII_AUXIN_r1


title: HGG_53, Truseq

value: Tumor

tag: Sex

value: Male


title: 45mT_Jurkat_PCAF_rep2

tag: secondary antibody concentration


title: HCTMED26D_ChIPseq_Med26_DMSO_r1


title: HGG_52, Truseq

tag: histological diagnosis

value: Glioblastoma

tag: age at_diagnosis


title: HCTMED26D_ChIPseq_Med26_DMSO_r2

value: colorectal carcinoma cell


title: HCTMED26D_ChIPseq_Med26_AUXIN_r2


title: HCTMED26D_ChIPseq_Med26_AUXIN_r1


title: HGG_51, Truseq

tag: tissue

tag: overall survival_(months)


title: HCTMED26D_ChIPseq_Brd4_AUXIN_r1

tag: cell type

tag: treatment


title: Nasopharyngeal tissue, negative, sample 4

city: Bandung

first: Miftahul

last: Faridl

state: Jawa barat

address: Jalan Ganeca No. 12, Dago, Coblong, Bandung, Jawa Barat, Indonesia

department: School of Life Sciences and Technology

country: Indonesia

institute: Bandung Institute of Technology

description:
raw_read_count_negative.csv
NEG4

data_processing:
Four FASTQ files per sample were preprocessed before mapping the reads to the reference sequences. We used the BBDuk+ (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/) plugin provided through Geneious Prime (version 2022.2.2) to quality-process the paired-end reads. We discarded reads shorter than 30 bp and reads with Q score less than 30.
The quality-processed reads were then mapped to the Homo sapiens genome reference (GRCh38.p14) using the Geneious Prime Geneious RNA mapper. The four technical replicates for each sample were formerly merged before mapping. We used the medium-low sensitivity and set the mapper to span annotated CDS introns. Then, we calculated the gene raw read count by subjecting the generated reads assemblies to the Geneious Prime expression level calculator. The ambiguously mapped reads were excluded from the calculation.
Assembly: GRCh38.p14
Supplementary files format and content: comma-separated value file including the raw read count values for each gene in each Sample

source_name: Nasopharyngeal tissue

extract_protocol:
140 µL of a nasopharyngeal swab in a viral transport medium (VTM) is extracted with QIAamp Viral RNA Mini Kit (QIAGEN, Germany) using the factory protocol. An 60 µL elution of total RNA was acquired. The RNA integrity and concentration were then measured using the Agilent RNA 6000 Pico Kit on The Agilent 2100 Bioanalyzer system (Agilent Technologies, Inc., USA) and the Qubit dsDNA HS (High Sensitivity) assay on the Qubit 4 Fluorometer system (ThermoFisher Scientific, USA) respectively.
11 uL of 10-100 ng of RNA was used as the cDNA library preparation and pooling input. The pooled library was prepared using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, USA).

value: Nasopharyngeal tissue

tag: disease state

value: negative control

tag: level of_severity

tag: age

value: 24 years

tag: sex assigned_at_birth


title: HCTMED26D_ChIPseq_Brd4_DMSO_r1

tag: cell line

tag: genotype

value: DMSO 2h


title: Nasopharyngeal tissue, negative, sample 5

description:
raw_read_count_negative.csv
NEG5

value: 50 years


title: HGG_49, Truseq


title: HGG_50, Truseq


title: Nasopharyngeal tissue, negative, sample 1

description:
raw_read_count_negative.csv
NEG1

value: 22 years


title: HGG_48, Truseq

value: Female


title: Nasopharyngeal tissue, negative, sample 3

description:
raw_read_count_negative.csv
NEG3

value: 23 years


title: Nasopharyngeal tissue, severe, patient 8

data_processing:
Four FASTQ files per sample were preprocessed before mapping the reads to the reference sequences. We used the BBDuk+ (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/) plugin provided through Geneious Prime (version 2022.2.2) to quality-process the paired-end reads. We discarded reads shorter than 30 bp and reads with Q score less than 30.    The quality-processed reads were then mapped to the Homo sapiens genome reference (GRCh38.p14) using the Geneious Prime Geneious RNA mapper. The four technical replicates for each sample were formerly merged before mapping. We used the medium-low sensitivity and set the mapper to span annotated CDS introns. Then, we calculated the gene raw read count by subjecting the generated reads assemblies to the Geneious Prime expression level calculator. The ambiguously mapped reads were excluded from the calculation.
Assembly: GRCh38.p14
Supplementary files format and content: comma-separated value file including the raw read count values for each gene in each Sample

tag: level of severity

value: Severe

value: 60 years


title: 45mT_Jurkat_P300_rep2

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (Catalog #10970)

tag: treatment concentration

value: 25 ul/ml

tag: treatment duration

value: 45 min

tag: target protein

tag: primary antibody

tag: primary antibody concentration


title: HGG_47, Truseq

value: Tumor

tag: Sex

tag: histological diagnosis

tag: age at_diagnosis


title: Nasopharyngeal tissue, negative, sample 2

description:
raw_read_count_negative.csv
NEG2

tag: tissue

value: 40 years

value: Male


title: 45mT_Jurkat_P300_rep3

tag: treatment

tag: secondary antibody

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)

tag: secondary antibody concentration


title: 45mT_Jurkat_PCAF_rep1

value: PCAF


title: Nasopharyngeal tissue, severe, patient 7

value: Nasopharyngeal tissue

tag: disease state

tag: age


title: 45mT_Jurkat_P300_rep1


title: 45mT_Jurkat_MOZ_rep2

value: MOZ

value: Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: Nasopharyngeal tissue, severe, patient 6

tag: sex assigned_at_birth


title: HGG_45, Truseq

value: Glioblastoma

tag: overall survival_(months)


title: 45mT_Jurkat_MOZ_rep1


title: HGG_46, Truseq


title: 45mT_Jurkat_MOF_rep3

value: MOF


title: Nasopharyngeal tissue, severe, patient 3

tag: level of severity

value: 61 years

value: Female


title: Nasopharyngeal tissue, severe, patient 5

value: Severe

value: 68 years


title: Nasopharyngeal tissue, severe, patient 2

value: 55 years


title: Nasopharyngeal tissue, mild, patient 5

value: Mildly symptomatic

value: 33 years


title: HGG_43, Truseq

value: Tumor


title: HGG_44, Truseq


title: Nasopharyngeal tissue, mild, patient 3

value: 31 years


title: Nasopharyngeal tissue, mild, patient 2

value: 19 years

value: Male


title: HGG_41, Truseq


title: Nasopharyngeal tissue, asymptomatic, patient 2

value: Asymptomatic

value: 53 years


title: Nasopharyngeal tissue, mild, patient 1

value: Nasopharyngeal tissue

value: 63 years


title: Nasopharyngeal tissue, severe, patient 4

value: 45 years


title: Nasopharyngeal tissue, mild, patient 4

value: 34 years


title: 45mT_Jurkat_MOF_rep2

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (Catalog #10970)

tag: treatment concentration

value: 25 ul/ml

value: 45 min

value: MOF

value: Goat anti-rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: 45mT_Jurkat_MOF_rep1

tag: treatment duration


title: 45mT_Jurkat_GCN5_rep1

tag: target protein

value: Goat anti-mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: 45mT_Jurkat_CBP_rep3

value: CBP

tag: primary antibody


title: 45mT_Jurkat_GCN5_rep2

tag: primary antibody concentration


title: Nasopharyngeal tissue, severe, patient 1

value: Severe

value: 37 years


title: HGG_40, Truseq

value: Tumor

tag: Sex

value: Glioblastoma


title: Nasopharyngeal tissue, asymptomatic, patient 1

value: Asymptomatic

value: 35 years

value: Male


title: HGG_39, Truseq

tag: histological diagnosis


title: rfISCs_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. 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 of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: embryo

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: cell line

tag: cell type

value: Intermediate stem cells between rosette and formative stem cells


title: Black_RNA-seq_rep2

city: Xuzhou

first: Tao

last: Xu

state: Jiangsu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
Clean data for each sample were obtained from the raw data using Trimmomatic (version 0. 39) with default parameters.
The obtained clean data were mapped  to the genome of S. indicum (https://www.ncbi.nlm.nih.gov/genome/?term=Sesamum+indicum) using HISAT2.
New transcripts were assembled using StringTie software, and annotated with databases such as Pfam, SUPERFAMILY.
The featureCounts(v2.0.1) tool was used the to quantitatively analyze the gene expression level, and the FPKM values for each gene were obtained using RSEM (v1.3.1).
DEseq2 package was employed to perform DEG analysis between white and black sesame seeds.
Supplementary files format and content: Gene_expression_fpkm.txt
Supplementary files format and content: Genes.txt

organism: Sesamum indicum

source_name: Seeds

extract_protocol:
Total RNA was extracted from each sample using Trizol Reagent Kit (Invitrogen, China) following the instructions given by manufacturer.
The cDNA library was constructed following the NEB library manufacturer's protocols.

tag: tissue

value: Seeds

tag: cultivar

value: Black


title: Black_RNA-seq_rep3


title: 45mT_Jurkat_CBP_rep1

tag: treatment

value: ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (Catalog #10970)

value: 25 ul/ml

tag: secondary antibody

tag: secondary antibody concentration


title: 45mT_Jurkat_CBP_rep2

value: 45 min


title: rfISCs_1


title: HGG_42, Truseq

tag: age at_diagnosis


title: HGG_38, Truseq

value: Female

tag: overall survival_(months)


title: White_RNA-seq_rep3

value: White


title: HGG_37, Truseq


title: White_RNA-seq_rep1


title: HCT_mRNA_Rad21Degron_IAA_r2_8h

value: colorectal carcinoma cell

tag: genotype

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 8h


title: ESCs_1

value: 46C embryonic stem cells


title: HCT_mRNA_Rad21Degron_IAA_r2_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 4h


title: HCT_mRNA_Rad21Degron_IAA_r2_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 12h


title: HCT_mRNA_Rad21Degron_IAA_r2_0h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HGG_35, Truseq

value: Tumor

value: Glioblastoma


title: Black_RNA-seq_rep1


title: HCT_mRNA_Rad21Degron_IAA_r2_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 1h


title: HGG_34, Truseq


title: HCT_mRNA_Med26Degron_IAA_r1_8h


title: HGG_33, Truseq


title: HCT_mRNA_Med26Degron_IAA_r1_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 2h


title: HCT_mRNA_Med26Degron_IAA_r1_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500uM IAA 12h, FBS+actinomycin D 24h


title: HCT_mRNA_Med26Degron_IAA_r1_1h


title: HCT_mRNA_Med26Degron_IAA_r1_4h


title: ESCs_2

value: embryo


title: White_RNA-seq_rep2

value: Seeds


title: HGG_32, Truseq


title: HGG_31, Truseq

value: Male


title: HCT_mRNA_Med26Degron_IAA_r1_12h


title: HCT_mRNA_Rad21Degron_IAA_r2_24h


title: HGG_36, Truseq


title: HCT_mRNA_Med26Degron_DMSO_r1_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 8h


title: HCT_mRNA_Med26Degron_DMSO_r1_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 4h


title: HCT_mRNA_Med26Degron_DMSO_r1_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 24h


title: HGG_29, Truseq


title: HCT_mRNA_Med26Degron_DMSO_r1_2h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 2h


title: M0_D1_EV_DGAT1i_1

city: Lund

first: Mattias

last: Belting

state: Skåne

address: Barngatan

department: Clinical Sciences Lund

country: Sweden

institute: Lund University

description: RNA extracted from peripheral blood monocytes obtained from healthy donor differentiated into macrophages in vitro and treated with Evs derived from GBM cells + DGAT1 inhibitor (under hypoxic conditions)

hyb_protocol: 5.2 µg of fragmented and labelled sscDNA target was hybridized to Clariom™ D Human Arrays for 16 hours at 45°C under rotation in Affymetrix Gene Chip Hybridization Oven 645 (ThermoFisher Scientific). Washing and staining was carried out on Affymetrix GeneChip® Fluidics Station 450 (ThermoFisher Scientific), according to the manufacturer’s protocol.

scan_protocol: The fluorescent intensities were determined with Affymetrix GeneChip Scanner 3000 7G (ThermoFisher Scientific).

data_processing: Processing of gene array was performed with R statistical language within Rstudio environment. Using oligo (v1.62.2; RRID:SCR_015729) package, raw CEL files were input into R (oligo::read.celfiles), and Robust Multichip Average (RMA)-based background correction and quantile normalization were performed with rma function, using pd.clariom.d.human (v3.14.1) for Affymetrix Clariom D Human platform design specification. Annotation of probe IDs was performed with affycoretools (v1.70.0) package (annotateEset function), using clariomdhumantranscriptcluster.db (c8.8.0) as reference ChipDb package. Analysis of differentially expressed genes was performed with limma package in R,

label: biotin

source_name: Differentiated Macrophages, treated with Evs derived from GBM cells, and treated with DGAT1 inhibitor

label_protocol: Fragmentation and labeling were performed with the GeneChip® WT Plus Labeling Kit according to the manufacturer’s instructions. The sample volume was 10ul ranging from 100-500ng of total RNA used for generation of amplified sense strand cDNA targets using GeneChip® WT Plus Reagent Kit (ThermoFisher Scientific) followed by fragmentation and labelling of 5.5 ug sscDNA.

growth_protocol: Differentiated, primary Macrophages from healthy donor were exposed to hypoxia with or without GBM-EVs (100 µg/mL) and with or without DGAT1 inhibitor (5mM). After 24 h, cells were extensively washed with 1M NaCl in PBS.

extract_protocol: Samples were dissolved in 350 μl lysis solution provided by the AllPrep DNA/RNA Micro Kit for RNA isolation according to the manufacturer’s instructions. Total RNA quality was assessed by Agilent Technologies 2200 Tapestation and concentrations were measured by NanoDrop ND-1000 Spectrophotometer.

treatment_protocol: Monocytes were isolated by positive selection for CD14+ with antibody-coated microbeads according to the manufacturer's instructions and differentiated in vitro for 7 days by MCSF induction. After washing, cells were directly re-suspended in 350 μL lysis buffer.

value: Bone marrow Derived macrophages (BMDM)


title: HGG_28, Truseq

value: Female


title: M0_D1_EV_DGAT1i_3

value: differentiated into macrophages in vitro and treated with Evs derived from GBM cells + DGAT1 inhibitor (under hypoxic conditions)


title: M0_D1_EV_3

description: RNA extracted from peripheral blood monocytes obtained from healthy donor differentiated into macrophages in vitro and treated with Evs derived from GBM cells (under hypoxic conditions)

source_name: Differentiated Macrophages, treated with Evs derived from GBM cells


title: HCT_mRNA_Med26Degron_DMSO_r1_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 1h


title: M0_D1_EV_2

value: differentiated into macrophages in vitro and treated with Evs derived from GBM cells (under hypoxic conditions)


title: HCT_mRNA_Med26Degron_IAA_r1_0h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCT_mRNA_JQ1_r2_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 8h


title: M0_D1_EV_1


title: FFPE,  RNA-seq, 06S21001886

description: TruSeq RNA Exome

value: melanoma tumor


title: HCT_mRNA_Med26Degron_DMSO_r1_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 12h


title: HCT_mRNA_JQ1_r2_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 4h


title: HCT_mRNA_JQ1_r2_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 24h


title: HGG_26, Truseq

value: Tumor

value: Glioblastoma


title: HCT_mRNA_JQ1_r2_2h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 2h


title: HGG_25, Truseq


title: M0_D1_CTRL_DGAT1i_3

description: RNA extracted from peripheral blood monocytes obtained from healthy donor differentiated into macrophages in vitro and treated with DGAT1 inhibitor (under hypoxic conditions)

source_name: Differentiated Macrophages treated with DGAT1 inhibitor (LDDD)


title: M0_D1_EV_DGAT1i_2


title: HCT_mRNA_JQ1_r2_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 1h


title: HGG_27, Truseq

value: Male


title: HCT_mRNA_Med26Degron_DMSO_r1_0h

value: colorectal carcinoma cell


title: M0_D1_CTRL_DGAT1i_2

value: Bone marrow Derived macrophages (BMDM)

value: differentiated into macrophages in vitro and treated with DGAT1 inhibitor (under hypoxic conditions)


title: HCT_mRNA_JQ1_r2_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, 500nM JQ1 12h, FBS+actinomycin D 12h


title: M0_D1_CTRL_DGAT1i_1


title: M0_D1_CTRL_3

description: RNA extracted from peripheral blood monocytes obtained from healthy donor differentiated into macrophages in vitro (under hypoxic conditions)

source_name: Differentiated Macrophages


title: HCT_mRNA_DMSO_r2_8h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 8h


title: HCT_mRNA_DMSO_r2_4h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 4h


title: E03-9, scRNA-seq

city: Changsha

first: Xueqin

state: Hunan

address: Medical College of Xiangya, No.172 Tongzipo Road, Changsha City, Hunan Prov, China

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Central South of University

description:
E03-9
Each sample represents a cell from the arrested embryo.

data_processing:
Raw sequencing reads were trimmed to remove low-quality bases and adaptor sequences using fastp (v0.20.0).
The filtered clean reads were then mapped to the human reference genome of GRCh38 (without masking repeats) using STAR (v2.7.8a) and expression count values were calculated using StringTie (v2.0.4).
Differential gene expression analysis in our study was performed by comparing the arrested embryos with previously published data (GEO: GSE133856) from healthy controls. Differential gene expression analysis results are not included in this dataset.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: arrested embryo from patient with MEIKIN gene mutations

extract_protocol:
mRNA was captured with oligo-dTs and reverse transcribed using Superscript II (Invitrogen, 18064-071), then amplified with KAPA HiFi HotStart ReadyMix (KAPA, KK2602)
After amplification, the PCR products were purified using Ampure XP beads (Beckman Coulter, Cat#A63881). The fragment size and yield of the product of each sample were inspected on an Agilent 2100 Bioanalyzer (Agilent Technologies). Single-cell libraries were constructed using a Nextera XT DNA Library Preparation Kit (Illumina, Cat#FC-131-1096), and all libraries were sequenced on an BGISEQ-500 instrument, according to the manufacturer’s instructions.
Smart-seq2

treatment_protocol: To remove the zona pellucida, the arrested embryos were exposed to Tyrode’s solution (Sigma-Aldrich, USA) for 3–5 s and then washed thoroughly in PBS containing 1.0% bovine serum albumin (BSA). Zona-free embryos were incubated at 37°C for 5-10 min in Accutase medium, and then disaggregated by careful and gently pipetting. Single blastomeres were placed into individual tubes containing 4.0μL of lysis buffer on ice.

value: embryo blastomere

value: MEIKIN mutations

tag: sample type

value: a single cell


title: HCT_mRNA_DMSO_r2_0h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO 2h


title: HCT_mRNA_DMSO_r2_24h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 24h


title: HCT_mRNA_DMSO_r2_12h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 12h


title: Nipponbare, overexpression, biol rep 3

city: Shanghai

first: xinwei

last: Zhang

state: Shanghai

address: No. 2005, Songhu Road, Yangpu District

department: State Key Laboratory of Genetic Engineering

institute: Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Oryza Sativa L. spp. Japonica
Supplementary files format and content: TPM values for each Sample

organism: Oryza sativa

source_name: panicle

extract_protocol:
RNA was harvested using the FastPure® Plant Total RNA Isolation Kit (Vazyme, Nanjing, China). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: panicle

value: natural


title: E03-5, scRNA-seq

description:
E03-5
Each sample represents a cell from the arrested embryo.


title: E03-8, scRNA-seq

description:
E03-8
Each sample represents a cell from the arrested embryo.


title: HGG_23, Truseq

value: Tumor

value: Female

value: Glioblastoma


title: HCT_mRNA_DMSO_r2_2h

value: colorectal carcinoma cell

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 2h


title: HCT_mRNA_DMSO_r2_1h

value: 10% FBS 14h, noFBS+DMSO 6h, FBS + DMSO2h, FBS+actinomycin D 1h


title: HGG_22, Truseq

value: Male


title: E03-4, scRNA-seq

description:
E03-4
Each sample represents a cell from the arrested embryo.


title: HGG_18, Truseq


title: HCT_mRNA_JQ1_r2_0h


title: HGG_30, Truseq


title: HGG_21, Truseq


title: E03-6, scRNA-seq

description:
E03-6
Each sample represents a cell from the arrested embryo.


title: Nipponbare, overexpression, biol rep 2


title: HGG_24, Truseq


title: HGG_20, Truseq


title: Nipponbare, WT, biol rep 3


title: E03-7, scRNA-seq

description:
E03-7
Each sample represents a cell from the arrested embryo.


title: Nipponbare, overexpression, biol rep 1


title: HGG_19, Truseq

value: Anaplastic Astrocytoma


title: M0_D1_CTRL_1

value: Bone marrow Derived macrophages (BMDM)

value: differentiated into macrophages in vitro (under hypoxic conditions)


title: Nipponbare, WT, biol rep 1


title: E03-2, scRNA-seq

description:
E03-2
Each sample represents a cell from the arrested embryo.

value: embryo blastomere

value: MEIKIN mutations


title: mouse hippocampus tissue, GFP+, tdTomato+(learning-associated) astrocytes rep3

city: Houston

first: Yeunjung

last: Ko

address: 1 Baylor Plz

institute: Baylor College of Medicine

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.11).
Reads were mapped to the mouse genome mm10 assembly using STAR (v2.5.0a). Mapped reads were used to build count matrices using Bioconductor packages GenomicAlignments (v1.26.0) and GenomicFeatures (v1.42.2).
UCSC transcripts were downloaded from Illumina iGenomes in GTF file format.
DESeq2 (v1.30.1) was used for normalization and differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPM values

source_name: hippocampus

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen #74004)
cDNA synthesis and library construction with 8-bp single indices were done from 10 ng total RNA using Trio RNASeq System (NuGEN #0507-96).
A final library dilution of 1.3 pM was subjected to paired-end sequencing.

treatment_protocol: After tamoxifen treatment and fear conditioning, we used FACS to purify the respective populations and performed transcriptomic RNA-sequencing.

value: hippocampus


title: E03-3, scRNA-seq

description:
E03-3
Each sample represents a cell from the arrested embryo.

value: a single cell


title: E03-1, scRNA-seq

description:
E03-1
Each sample represents a cell from the arrested embryo.


title: HGG_16, Truseq

source_name: Tumor


title: mouse hippocampus tissue, GFP+, tdTomato+(learning-associated) astrocytes rep2

value: After tamoxifen treatment and fear conditioning


title: Selinexor

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description: 10X Genomics

data_processing:
The demultiplexing, bardoded processing,  gene count and aggregation were make with CellRanger v6.1.2
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files.

source_name: Cultured cell

growth_protocol: DMSO and Sleninexor (50 nM) treated MDSCs were generated in vitro in presence of rmIL-6 and rmGM-CFS (40 ng/mL each).

extract_protocol:
On day 4 post differentiation, single cell libraries were generated using the 10X Genomics platform.  First, Feature Barcode conjugated molecules were bound to cell surface proteins.  Then live-CD11b+ cells were isolated using the SONY MA900 cell sorter (Sony Biotechnology).  Single-cell suspensions were pooled together and assessed with AOPI stain using a Cellometer K2 automated cell counter (Nexcelom), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells were loaded into the Chromium Controller (10X Genomics) where they were partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription was performed, and the resulting cDNA is amplified.
Amplified cDNA is separated into full-length and Feature Barcode fractions using SPRISelect beads (Beckman Coulter).  The full-length amplified cDNA was used to generate libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  Feature barcode derived cDNA was PCR amplified to incorporate Illumina adapter sequences and unique sample indexes.  The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies) and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina.  They were then pooled, denatured, and diluted to 300 pM with 1% PhiX control library added.  The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Cells were treated with DMSO or Sleninexor (50 nM)

value: Cultured cell

value: MDSC

value: Selinexor


title: CD45-/CD45+, PDG-p53 Recurrent, c

city: Amsterdam

first: Daan

middle: Juri

last: Kloosterman

address: Plesmanlaan 121

department: Tumor Biology & Immunology

institute: The Netherlands Cancer

data_processing:
NextSeq paired-end sequencing was performed using 28 cycles for Read 1, 8 cycles for Read i7 and 56 cycles for Read 2. Novaseq paired-end sequencing was performed using 26 cycles for Read 1, 10 cycles for each Read i7 and i5 and 90 cycles for Read 2.
Assembly: mm10
Supplementary files format and content: rds file containing all integrated and pre-processed samples with annotations

source_name: Brain tumor

extract_protocol:
The Chromium Controller platform of 10X Genomics was used for single cell partitioning and barcoding. Each cell’s transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5’ Gene expression libraries were prepared according to the manufacturer’s protocol (CG000207 Rev E and CG000331 Rev A, 10X Genomics).
The Single Cell 5’ Gene Expression libraries were pooled to create three sequencing pools. The sequencing pools were quantified by qPCR, according to the KAPA Library Quantification Kit Illumina® Platforms protocol (KR0405, KAPA Biosystems). The Single Cell 5’ Gene Expression libraries were sequenced on a NextSeq550 or NovaSeq 6000 system (Illumina) using a NextSeq 500/550 High Output Kit v2.5 (cat. no. 20024906, Illumina) and NovaSeq SP Reagent Kit v1.5 (cat.no. 20028401, Illumina), at a sequencing depth of 20.000 reads pairs/cell.

value: Brain tumor

value: 5 x 2Gy Irradiation


title: DMSO

description: 10X Genomics

value: DMSO


title: CD45-/CD45+, PDG-p53 Recurrent, b


title: E01-11, scRNA-seq

description:
E01-11
Each sample represents a cell from the arrested embryo.


title: E02-7, scRNA-seq

description:
E02-7
Each sample represents a cell from the arrested embryo.


title: HGG_13, Truseq

value: Tumor

value: Glioblastoma


title: mouse hippocampus tissue, GFP+, tdTomato+(learning-associated) astrocytes rep1


title: mouse hippocampus tissue, GFP+, tdTomato-(non-learning-associated) astrocytes rep3


title: CD45-/CD45+, PDG-Ink4a Recurrent, d


title: Nipponbare, WT, biol rep 2

value: panicle

value: natural


title: HGG_14, Truseq

value: Female


title: mouse hippocampus tissue, GFP+, tdTomato-(non-learning-associated) astrocytes rep1


title: HGG_11, Truseq


title: E01-10, scRNA-seq

description:
E01-10
Each sample represents a cell from the arrested embryo.


title: M0_D1_CTRL_2

value: Bone marrow Derived macrophages (BMDM)

value: differentiated into macrophages in vitro (under hypoxic conditions)


title: HGG_12, Truseq

value: Male


title: E01-9, scRNA-seq

description:
E01-9
Each sample represents a cell from the arrested embryo.

value: embryo blastomere

value: MEIKIN mutations


title: mouse hippocampus tissue, GFP+, tdTomato-(non-learning-associated) astrocytes rep2

value: hippocampus

value: After tamoxifen treatment and fear conditioning


title: HGG_17, Truseq


title: E01-7, scRNA-seq

description:
E01-7
Each sample represents a cell from the arrested embryo.

value: a single cell


title: ATAC, E9.5 pro-HSC/HPC, rep 3

city: Oxford

first: Marella

last: de Bruijn

address: MRC MHU, WIMM, John Radcliffe Hospital

department: Radcliffe Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Alignment, PCR duplicate filtering, and blacklist region filtering were performed using the NGseqBasic pipeline (Telenius et al. 2018).
Briefly, paired end reads were mapped using Bowtie (v1.0.0) to the mouse genome assembly (mm9).
Unmapped reads were trimmed using trim_galore (v0.3.1) and remapped. Short unmapped reads were combined using flash (v1.2.8) and remapped.
PCR duplicates were removed using samtools rmdup (v0.1.19). Reads mapping to Duke blacklisted regions (UCSC) were removed using BEDtools (v2.17.0).
BigWigs were created using DeepTools bamCompare (v3.0.1), and peaks were identified using MACS2 (v2.0.1) with parameters -BAMPE and -q 0.05.
Consensus peaks were generated using DiffBind (v1.14.6) and counts underlying each consensus peak were calculated using DiffBind dba.count with parameters bUseSummarizeOverlaps = T and score = DBA_SCORE_READS
Assembly: mm9
Supplementary files format and content: Output from DiffBind dba.count: TSV file including read counts over consensus peaks.

source_name: E8.5 PAS+VU

extract_protocol:
1500 cells were sorted directly into 100% FCS, then nuclei were isolated by resuspending in  lysis buffer (10 mM Tris-HCl pH7.5; 10 mM NaC; 3 mM MgCl2; 10% IGEPAL CA-630; 0.1% TritoxX-100), and incubating 10 min on ice.
Protocol adapted from Buenrostro et al. 2015. Nuclei were resuspended in 10 uL tagmentation mix (0.35 uL Tn5 transposase; 5 uL 2X tagmentation buffer; 4.65 uL nuclease free water) (Illumina Nextera FC-121-1030), then incubated 37C for 30 min.
Tagmentation reaction was quenched using 1.1 uL 500 mM EDTA, and 10 uL 50 mM MgCl2 was added to the sample.
The library was amplified using 13 PCR cycles  on the thermocycler, then purified using a MinElute kit (Qiagen).

value: E8.5 PAS+VU

value: pro-HSC/HPC

value: 23GFP transgenic


title: HGG_10, Truseq


title: CD45-/CD45+, PDG-p53 Primary, c

value: Brain tumor

value: No Treatment


title: HGG_15, Truseq

value: Tumor

value: Glioblastoma


title: ATAC, E9.5 pro-HSC/HPC, rep 2


title: HGG_9, Truseq


title: HGG_8, Truseq


title: E01-6, scRNA-seq

description:
E01-6
Each sample represents a cell from the arrested embryo.


title: MPA-SiNC-3

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

institute: Qilu Hospital of Shandong University

data_processing:
Raw image data files obtained from high-throughput sequencing were processed by CASAVA for base calling, and transformed into raw sequencing data (Raw Data). The results are stored in the FASTQ format (commonly abbreviated as fq), which encompasses both the sequence information of the sequencing data and its corresponding quality information. Reads that pass filtering are termed "Clean Reads" and are saved in the FASTQ format.
Clean reads were aligned to the reference genome using HISAT2 (Kim D, et al. 2015).
Gene expression quantification was conducted using the StringTie software combined with the ballgown package in R. The results from StringTie were integrated using ballgown, and gene expression levels were represented by FPKM values.
Differential gene expression detection was carried out using algorithms DESeq2 (Michael I 2014), EBseq (Leng N 2013), NOIseq (Tarazona S 2011), and PossionDis (S 1997).
Assembly: RefSeq GRCh38
Supplementary files format and content: AllSamples.GeneExpression.Count.xls contains raw counts for each sample
Supplementary files format and content: A-VS-B.DEseq2.GeneDiffExpFilter.xls contains the differential gene expression profiles between the experimental and control groups.

source_name: Ishikawa

extract_protocol:
RNA extraction：Cell toal RNA isolation kit(FOREGENE, Chengdu, China)RNA quality examination： The purity of the sample was determined by NanoPhotometer ®（IMPLEN, CA, USA）； RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,  CA, USA)
After the total RNA samples were tested to be qualified, the MGIEasy RNA library preparation kit was used for library construction. Magnetic beads  with oligo (DT) were used for enrichment and purification; Fragment  buffer was added to the purified mRNA to make its fragment into a short  fragment; the fragment mRNA was used as a template for reverse  transcription into double stranded cDNA with six base random primers,  and then the product was purified. The purified double stranded cDNA was  subjected to end repair, addition of dA tail, linker connection and PCR  amplification. After the amplified product was qualified, it was denatured  and single stranded cyclized, and the cyclized product was inspected.

value: Ishikawa

value: Control


title: CD45-/CD45+, PDG-Ink4a Primary, d


title: Lipid-laden microglia, mn:545

data_processing:
The recorded ATAC-seq data were mapped to the mm10 reference genome with BWA-MEM (version 0.7.17-r1188).104 SAMtools (version 1.10)105 was used to discard the mapped reads with a mapping quality score <15, and PICARD tools (version 2.12.0) was applied to remove optical PCR duplicates. The coverage files were generated with the ‘normalize to 1× genome coverage’ methods in deepTools (version 3.5.1).106
Assembly: mm10
Supplementary files format and content: tab delimited tekst file with feature counts

extract_protocol:
Nuclei of the FACS sorted cells were isolated, permeabilized and tagmented by using in-house-generated Tn5 transposase. The resulting DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter).
ATAC-seq libraries were prepared using an optimized protocol.103  The resulting DNA fragments underwent a first 9-cycle PCR amplifications using KAPA HiFi HotStart ReadyMix (7958935001, Roche), and we selected the fragments between 150 and 700 bp in size using with SPRI beads (A63881, Backman Coulter). The size-selected fragments were amplified for a second 9-cycle PCR reactions, and the resulted libraries were purified using SPRI beads.

value: Lipid-Laden Microglia

value: Ink4a/ArfKO, PDGFB


title: Non-lipid-laden microglia, mn:545

value: Microglia


title: HGG_7, Truseq

data_processing:
Reads of low quality and adapter contamination were removed using the trim_galore tool. Processed reads were aligned to the GRCh38 reference genome using the Bowtie2 tool. The aligned *.sam results were then converted to *.bam files using the samtools application for subsequent analysis.
Somatic mutations were called according to GATK recommendations, including additional considerations for amplicon panels, as described below. Bam files were analyzed with MarkDuplicatesSpark and BaseRecalibrator, using gnomadV2 database, to finally recalibrate with ApplyBQSR to meet GATK standards. Somatic variants were detected using Mutect2 , only on target regions. To identify and discard artifactual variants, GetPileupSummaries with CalculateContamination, LearnReadsOrientation and a panel of normal were used, Additionally, the Integrative Genomics Viewer (IGV 2.10) was used to identify and correct potential errors. Finally, we used FilterMutectCalls to recover clustered events and to discard variants with an allelic frequency <0.05 or <10 reads supporting the variant.
Variants in vcf files were annotated with Funcotator and reports were generated in vcf and maf files. All genomic coordinates are mapped to the GRCh 38 assembly. Posterior analysis was performed with Variant Effect Predictor (McLaren et al., 2016) to predict pathogenicity. Novel variants and variants not previously reported in gliomas that are predicted to result in singleamino acid substitutionswere subsequently evaluated using Sorting Intolerant From tolerant (SIFT) and polymorphism phenotyping-2 (PolyPhen-2) to predict the effect of the change on protein function while variants that resulted in frameshifts were evaluated using SIFT indel . Maftools R package was used to prepare oncoplots.
Assembly: GRCh38
Supplementary files format and content: vcf files for each sample, containig snp and short indel, after pass filters for quality, and  allelic frequency <0.05 and/or <10 reads supporting the variant.
Supplementary files format and content: maf file used for oncoplots after removing known polymorphisms

value: Male


title: HGG_6, Truseq

value: Female


title: CD45-/CD45+, PDG-p53 Primary, d


title: MPA-SiNC-2


title: MPA-SiNC-1


title: ATAC, E9.5 HE, rep 2

value: Hemogenic endothelium


title: ATAC, E9.5 HE, rep 3


title: E01-8, scRNA-seq

description:
E01-8
Each sample represents a cell from the arrested embryo.

value: embryo blastomere

value: MEIKIN mutations


title: Non-lipid-laden monocyte-derived macrophages, mn:545

value: Monocyte-derived macrophage


title: Lipid-laden monocyte-derived macrophages, mn:545

value: Lidid-Laden Monocyte-derived macrophage


title: ATAC, E9.5 HE, rep 1

value: E8.5 PAS+VU

value: 23GFP transgenic


title: MPA-SiNCF2-3


title: HGG_4, Truseq


title: Lipid-laden microglia, mn:546

value: Brain tumor


title: ATAC, E9.5 EC, rep 4

value: Endothelial cells


title: CD45-/CD45+, PDG-p53 Primary, b

value: No Treatment


title: HGG_3, Truseq

value: Tumor

value: Anaplastic Astrocytoma


title: MPA-SiNCF2-1

value: Ishikawa


title: Non-lipid-laden microglia, mn:546

value: Ink4a/ArfKO, PDGFB


title: ATAC, E9.5 pro-HSC/HPC, rep 1

value: pro-HSC/HPC


title: ATAC, E9.5 EC, rep 3


title: ATAC, E9.5 HE, rep 4


title: SCC7IR-3

city: Wuhan

first: An

last: Song

address: Luoyu Road 237

institute: Wuhan University

data_processing:
BGISEQ-500 sequencer
Clean reads were mapped to the reference genome using HISAT/Bowtie2tools.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

growth_protocol: The SCC7  cells were grown in high glucose (Gibco) with 10% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
DNase I was used to digest double-stranded and single-stranded DNAin total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA

treatment_protocol: The SCC7  cells were received with radiotherapy in 9 Gy.

value: cancer cell

value: radiotherapy

tag: time

value: Day 0


title: Lipid-laden monocyte-derived macrophages, mn:546


title: ATAC, E9.5 EC, rep 2


title: HGG_2, Truseq

extract_protocol:
Formalin-fixed paraffin-embedded tissue samples were obtained from the Pathology Service at the Asenjo Neurosurgery Institute. After neuropathologist confirmation of a tumor percentage greater than 70% in each area to be extracted, 3-6 sections of 10 microns were prepared from each paraffin block using the GeneJET FFPE DNA Purification Kit. No matched blood samples were available. The extracted DNA was quantified using fluorescence-based methods (Quant-iT™ PicoGreen™ dsDNA and/or Qubit™ dsDNA HS), resulting in an average concentration of 40 ng/µL. We
For both AmpliSeq™ and TruSeq™ libraries, library generation efficiency was evaluated with different initial amounts of DNA to adjust the various stages of the process based on the specific sample and panel characteristics. Automated electrophoresis of the first libraries were performed for quality control and size estimation using the DNA 1000 kit on the Agilent 2100 Bioanalyzer system. All libraries were quantified by qPCR using the Illumina KAPA library quantification kit and were pooled at a concentration of 10 nM before sequencing. A Mid Output Kit v2.5 (150 cycles) was used on a NextSeq sequencer with 25% phi-X for all Ampliseq™ libraries, and a Micro Kit v2 (300 cycles) with 25% phi-X on a MiSeq sequencer was used for all TruSeq™ libraries.
Amplicon sequencing

value: Female

value: Glioblastoma


title: Non-lipid-laden monocyte-derived macrophages, mn:546

value: Monocyte-derived macrophage


title: HGG_1, Truseq

value: Male


title: HGG_5, Truseq


title: ATAC, E9.5 EC, rep 1

value: E8.5 PAS+VU


title: STARR_10bp_plDNA

city: Lausanne

first: Bart

last: Deplancke

address: SV Station 19

country: Switzerland

institute: EPFL

library_source: other

data_processing:
Insert seqeunes were mapped to the 12bp barcodes located at the 3 prime end with respect to the TSS using a custom script. STARR activity for each insert sequence was computed by taking the log2 ratio of mRNA over input DNA counts.
Library strategy: STARR-seq

molecule: other

growth_protocol: MEC1 cells were cultured in IMDM media (Gibco) supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin.

extract_protocol: Cells were harvested 24h post transfection and lysed in Trizol. RNA was extracted by Chloroform extraction, followed by Isopropanol precipitation with a 1:1 ratio. RNA pellets were resuspended in RNAse-free water and digested with DNAseI for 20 min at room-temperature. DNAseI-treated RNA was purified with a RNA-clean&concentrator-25 kit (Zymo). A total of 10-12 μg RNA was reverse transcribed using the STARR-seq specific RT prime. For each μl of Maxima H minus RT 3 μg input was used. RT reactions were diluted 1:4 with RNAse & DNAse-free water before further amplification. The splice-junction PCR was run using the STARR-seq thio-splice-junction primer and a custom reverse primer spanning the SalI restriction site used for linearizing the STARR-seq vector and the read1 Nextera adapter sequence inserted with the library. About one third of the RT reaction was amplified for 19-22 cycles. Illumina barcodes were added by a final PCR with 8 cycles using the Illumina Nextera guidelines. After each amplification step, PCR products were cleaned up using AMPure XP magenetic beads (Beckman Coulter). Plasmid libraries were directly amplified with a 8-cycle PCR using NEXTERA-specific index primers.

treatment_protocol: Transfections of 5-bp and 10-bp libraries were done in duplicates using ~ 6 Mio cells and 30 μg plasmid per replicate. Transfections were carried out with the Neon Transfection System (Thermo Fisher) as follows: 3 pulses of 20 ms at 1200 V in R buffer using 100 ul tips.

value: CLL cell line

value: WT

value: not applicable


title: SCC7IR-2


title: SCC7IR-1


title: Lipid-laden microglia, mn:547

value: Brain tumor

value: Lipid-Laden Microglia


title: Non-lipid-laden microglia, mn:547

value: Microglia


title: STARR_5bp_mRNA_rep2


title: STARR_5bp_mRNA_rep1