title: primary cortical neurons, control, Exp1, rep1, Fos

description: Library name: Fos_Control_Exp1_1

value: primary cortical neurons

tag: bait


title: Female_1_PBS_Injected_P_3

status: Public on May 01 2026

type: SRA

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

country: USA

institute: Van Andel Research Institute

library_source: transcriptomic

data_processing:
RNA-seq: Trimmed fastq files were aligned to MM10/GRCm38 using STAR v2.7 (Dobin and Gingeras, 2015).
RNA-seq: The resulting gene_id map counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
Assembly: GRCm38/MM10
Supplementary files format and content: .xlsx, counts in log2cpm for each gene, statistical significance for muliple comparison tests using LIMMA

molecule: polyA RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Neuronal nuclei were isolated from mouse cortex using flow cytometry and filtering for an anti-NeuN antibody.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase. RNA was sheared to an average of 300 bp . Individually indexed libraries were pooled, and 75-bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer. Base calling was done by Illumina NextSeq Control Software (NCS; v2.0), and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0)
bulk RNA-seq on neuronal nuclei.

tag: tissue

value: cortex

tag: cell line

tag: Sex

value: Female

tag: timepoint (month_post_injection)

tag: injection

value: PBS

tag: hemisphere

value: Injected

tag: cage

value: P

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Female_1_PBS_Non-injected_P_1

tag: tissue

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

value: Non-injected


title: MK2 KO untreated 1

city: Quebec City

first: Jean-Philippe

last: Lambert

state: QC

address: 2705, boulevard Laurier

department: Molecular Medicine

country: Canada

institute: Université Laval

data_processing:
Data cleaning: Trim Galore/Cutadapt
Quality control: FastQC and MultiQC
Pseudo-alignment: Kallisto
Normalization and Differential analyses: tximport/DESeq2
Assembly: GRCh38.p10
Supplementary files format and content: raw_counts.csv: comma separated values containing raw counts as called by tximport
Supplementary files format and content: normalized_counts.csv: comma separated values containing DESeq2 normalized counts

molecule: total RNA

organism: Homo sapiens

source_name: MK2 KO untreated 1

growth_protocol: A375 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (Pen/Strep) in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNAs were extracted using the RNeasy plus mini kit from QIAGEN according to the manufacturer’s instructions. 1 ug of RNA depleted of rRNA was used for the construction of sequencing libraries
The NEBNext Ultra II directional RNA library prep kit for Illumina (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare RNA sequencing libraries, according to manufacturer’s instruction.

treatment_protocol: 500 nM JQ1 or DMSO control were used for 48 hours treatments

value: Skin

tag: cell type

value: Malignant melanoma

tag: genotype

value: MAPKAPK2 knockout

tag: treatment

value: DMSO

tag: time


title: SK-Mel-103, replicate 3 (Input)

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

description: Library name: M9-H-Input-3

library_source: genomic

data_processing:
Bowtie2 aligner (v2.4.2), MACS2 peak caller (v.2.1.1.20160309)
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: Skin

growth_protocol: Melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, High glucose, Biosharp) supplemented with 10% fetal bovine serum (VivaCell), Penicillin-Streptomycin 100 X solution (Hyclone) in a standard incubator with 5% CO2 at 37°C. Cells were passaged every two to three days by Trypsin-EDTA solution (Sigma-Aldrich) after washing with 1 x PBS.

extract_protocol:
Nuclei were sonicated in a Bioruptor to yield chromatin fragments of ~200-500 bp, as confirmed by agarose gel electrophoresis.
ChIP-seq libraries were prepared and sequenced using single-end 50 bp sequencing (SE50) on the BGISEQ-500 platform (BGI, Wuhan, China).

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, washed in cold PBS and lysed in a high-salt lysis buffer.

value: Melanoma

value: WT


title: Female_1_PBS_Injected_P_1

tag: hemisphere

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: SK-Mel-103, replicate 2 (Input)

description: Library name: M9-H-Input-2

tag: tissue

tag: cell line


title: primary cortical neurons, NMDA 10min stim 20min recovery, after a 24hr rec. period, rep3, Npas4

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: UT Southwestern Medical Center

description: Library name: Npas4_ETPNMDA_3

data_processing:
4Cker mapping was performed using Bowtie2 to a reduced genome consisting of all unique x-nt (nucleotide count differs depending on sequencing run and viewpoint specific primers) regions surrounding DpnII sites from the hg38 or mm10 reference genome allowing for zero mismatches.
To define regions with significant interaction with the viewpoint we used either cisAnalysis (cis) or nearBaitAnalysis (nb) of 4Cker inputting three replicates per sample
Mapping with pipe4C was done with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
Assembly: mm10 and hg38
Supplementary files format and content: Bigwig files
Library strategy: 4C-Seq

source_name: primary cortical neurons

growth_protocol: Dissociated primary cortical neurons from E16 Swiss-Webster mice were plated at a density of 0.25 million cells/cm2 in 10 cm culture dishes, 6 well plates, or 24 well plates coated beforehand with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained for 13 days in neurobasal media (GIBCO) and supplemented with L-glutamine, penicillin/streptomycin (final of 1%), and B27. Human embryonic kidney cells, HEK293, were maintained in Dulbecco’s modified Eagle’s medium (DMEM, high glucocse) supplemented with 10% fetal bovine serum and 5% penicillin/streptomycin.

extract_protocol:
Approximately 10 million primary cortical neurons (DIV13) or Hek 293T cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with glycine (0.13M final concentration). Cells were incubated for 20 min on ice in lysis buffer (50mM Tris-HCl pH 75, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100, and protease inhibitors).
Nuclei were resuspended in 450uL 1.2x CutSmart buffer and permeabilized with 15uL 10% SDS for 1hr and 75uL 20% Triton X-100. A sample of undigested chromatin was collected to assess chromatin integrity. DNA was digested with 100U NlaIII at 37°C for 3hrs while shaking at 750rpm and then an additional 100U of NlaIII was added and incubated overnight. The extent of chromatin digestion was assessed via gel electrophoresis. NlaIII was deactivated for 20 min at 65°C. Chromatin was diluted to 7mL, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase for overnight ligation at 16°C while shaking. Ligation efficiency was checked by gel electrophoresis. Crosslinks were reversed and proteins digested with proteinase K (30uL of 10mg/ml) overnight at 65°C. DNA was extracted via phenol:chloroform and precipitated with ethanol. DNA was then digested overnight at 37°C with 50U DpnII supplemented with 10X DpnII Buffer while shaking. Second digestion efficiency was determined via gel electrophoresis. DpnII was deactivated at 65°C for 20 min. DNA circularized in a 7mL reaction, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase overnight at 16°C with shaking. Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using Expand Long Template Polymerase starting with 200ng of 4C library template. Viewpoint-specific primers were used to amplify circular templates with the bait of interest. The first round of amplification with the following thermocycler conditions 94°C  for 2 min; 94°C for 10sec, 58° C for 1 min, 68°C for 3 min, for 16 cycles; and 68°C for 5 min. Five different PCR reactions per sample were pooled and 50uL of the pool was used to perform 0.8 x AMPure XP bead purification. 5uL of purified round 1 PCR product was then used for the second round of amplification conducted with the following cycling conditions 94°C for 2 min; 94°C for 10 sec, 60°C for 1 min, 68°C for 3 min for 20 cycles; and 68°C for 5 min. PCR clean up was doing using Qiagen PCR Purification.  DNA fragment size of final, clean PCR products was assessed via Tapestation (Agilent). Library concentrations for each sample was assessed using fluormetry (dsDNA high sensitivity Qubit assay, Thermo) and RT-qPCR (KAPA Biosystems) library quantification.

treatment_protocol: All ETP treatments were conducted with 10mM final concentration, for at most 1hr. NMDA treatments were with 50mM and lasted for 10 min followed by a recovery in conditional neuron media. Serum starvation of the Hek293 cells was done in 0.5% fetal bovine serum for ~16.5hrs and then serum stimulated in 18% fetal bovine serum.

tag: bait

value: Npas4 promoter

value: WT Swiss Webster Mice


title: wild type rice panicle

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

description: Library name: Osa_panicle_WT

data_processing:
sRNA-seq raw reads were processed to remove 3’-adaptor sequences using Cutadapt (v4.8) with the parameters “-m 18 --trim-n --trimmed-only -a AGATCGGAAGAGCAC”. Reads mapping to rRNA and tRNA were filtered out. The remaining reads were aligned to the rice genome using ShortStack (https://github.com/MikeAxtell/ShortStack) allowing no mismatch, and the assignment of multi-mapping reads was guided by unique mapping reads (--mmap u).
Assembly: TIGR7
Supplementary files format and content: Tab-delimited text file containing sequence and count.

organism: Oryza sativa

source_name: panicle

growth_protocol: Rice cultivars Zhonghua 11 (ZH11, Oryza sativa L. ssp. japonica) were grown in the paddy field.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
Small RNA-seq libraries were constructed using the VAHTS Small RNA Library Prep Kit for Illumina v2 (Vazyme, China), followed by purification with VAHTS DNA Clean Beads (Vazyme). cDNA libraries were quantified using NanoDrop spectrophotometer, and sequenced on an Illumina Hiseq X Ten platform (Illumina Inc., USA).

value: panicle

value: wild type


title: ddm1 rice panicle

description: Library name: Osa_panicle_ddm1

value: ddm1 mutant


title: SK-Mel-103, replicate 1 (Input)

description: Library name: M9-H-Input-1


title: A375 _KOMK2_NT_IgG

data_processing:
Data cleaning: Trim Galore/Cutadapt
Quality control: FastQC and MultiQC
Alignment : BowTie2 + Samblaster to flag duplicates
Peak calling : macs2 callpeak against corresponding IgG sample
Assembly: GRCh38.p10
Supplementary files format and content: *_raw.bw : BigWig alignement with no normalization
Supplementary files format and content: *_BPM.bw : BigWig alignement with bin per millions normalization
Supplementary files format and content: *.narrowPeak : Macs2 peakcalling in narrowPeak mode
Library strategy: CUT&RUN

source_name: MK2 KO untreated + IgG antibody

extract_protocol:
Cells were cross-linked with 0.1% formaldehyde for 1 min at room temperature prior to isolating nucleus and performing CUT&RUN.
The NEBNext Ultra II DNA kit for low-input ChIP kit (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare libraries according to the manufacturer's instruction.

value: Malignant Melanoma

tag: chip antibody

value: IgG


title: Female_1_PBS_Injected_P_0

value: cortex

tag: Sex

value: Female

tag: timepoint (month_post_injection)

tag: injection

value: PBS

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: hiPSC-derived neuron pool (RH and BFP treated, patients 553 and 2607), HTO

city: New York

first: Elizabeth

last: LaMarca

state: NY

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: 1092_HTO_Sample1_8_HTO
see associated metadata for sample-level information

library_source: other

data_processing:
Sequencing data were processed using the 10x Genomics Cell Ranger pipeline, and filtered gene expression and feature barcode count matrices were generated for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Barcodes, features, and matrix files. Sample-level metadata.

molecule: protein

source_name: hiPSC-derived neuron

growth_protocol: hiPSC-NPCs at passages between 9-11 were seeded at low density (e.g., 500k on a 6-well plate) on Matrigel-coated plates and were cultured for 6-8 weeks in neural differentiation medium, containing DMEM/F-12-Glutamax, 1X N-2, 1X B-27, 1X Antibiotic/Antimycotic, 20 ng/mL BDNF (Peprotech), 20 ng/mL GDNF (Peprotech), 1 mM dibutyryl-cyclic AMP (Sigma), 200 nM ascorbic acid (Sigma), and 1 μg/mL laminin. Half-media changes were performed every other day until cells were harvested.

extract_protocol:
iPSC-derived neurons were dissociated into single-cell suspensions prior to loading onto the 10x Genomics platform. RNA capture and reverse transcription were performed according to the manufacturer’s protocol.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium platform according to the manufacturer’s standard protocol. Briefly, single-cell suspensions were loaded for microfluidic partitioning, barcoding, and reverse transcription, followed by cDNA amplification and library construction for sequencing. Hashtag oligonucleotide (HTO) feature barcode libraries were prepared in parallel using standard 10x Genomics-compatible feature barcoding procedures.

treatment_protocol: hiPSC-NPCs were transduced with either the TRE-RNASEH1ΔMLS-BFP or TRE-BFP viruses at a multiplicity of infection (MOI) of approximately 1.0. All constructs were co-transduced with the rtTA transactivator. Virus was added to cells and allowed to incubate for 1 hour at 37°C, followed by spinfection at 1,000 G for 1 hour at room temperature with slow acceleration and deceleration. Cells were returned to 37°C and after 4 hours the media was changed (Day 0). Starting at Day 3, cells were fed every other day with NPC media containing 0.3 μg/μL puromycin. On Day 7, cells were split and replated at low density (e.g., 500,000 cells per well of a 6-well plate). The following day, cells were switched to neuron differentiation medium containing 0.05 μg/μL puromycin and 0.3 μg/μL doxycycline and were fed every 2-3 days for the course of their 6 week differentiation period.

tag: cell type

value: hiPSC-derived neuron

tag: treatment

value: hiPSC directed neural differentiation

tag: time

value: 6 weeks


title: hiPSC-derived neuron pool (RH and BFP treated, patients 553 and 2607), GEX

description:
Library name: 1091_GEX_Sample1_8_3GEX
see associated metadata for sample-level information

library_source: transcriptomic single cell


title: Female_1_PBS_Non-injected_P_0

tag: tissue

tag: hemisphere

value: Non-injected

tag: cage

value: P

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: UACC-62, H3K27ac, replicate 3 (ChIP)

description: Library name: M7-H3K27ac-3

value: Skin

tag: cell line

value: Melanoma

tag: genotype


title: A375_WT_NT_IgG

source_name: WT untreated + IgG antibody

value: WT

value: DMSO

tag: chip antibody


title: Human prenatal germinal matrix, Patient 9_11073, DRIP-seq input control

description: Library name: prenatalInput.GM2.drip

data_processing:
DRIP-seq FASTQ files were trimmed with Trimmomatic/0.36 and were aligned to GRCh38 with Bowtie2/2.4.1. Duplicates and reads with MAPQ score < 30 were removed with SAMtools/1.1, as well as the ENCODE blacklist with BEDTools/2.29.2. Following tag directory generation, peaks were called and annotated with HOMER/4.10 using an FDR threshold of 0.01 and style = histone against input samples. Standard quality control metrics were assessed with ChIPseeker, ChIPQC, and deepTools/3.4.3 (with Python/3.7.3). BigWig files were generated with Deeptools bamCoverage/3.4.3.
Assembly: GRCh38
Supplementary files format and content: BigWig and peak files for DRIP-seq data.

source_name: germinal matrix of second trimester prenatal brain

extract_protocol:
Genomic DNA was extracted from the specified tissue (~500 mg) via incubation with 20% SDS and 20 mg/mL Proteinase K overnight at 37°C. After standard phenol/chloroform extraction, 3M NaOAc pH 5.2 and 2.4 volumes of 100% ice-cold EtOH was added and DNA was precipitated via gentle spooling with a pipette tip to avoid RNA contamination that can result from centrifugation. After three gentle washes with 70% EtOH and 1-2 hours of air drying, DNA was resuspended in TE and digested with a cocktail of restriction enzymes that avoid GC-rich regions (HindIII, EcoRI, XbaI, and SSPI) overnight at 37°C. DNA was again purified via phenol/chloroform extraction and ethanol precipitation, and complete digestion was confirmed on an agarose gel.  For immunoprecipitation of R-loops, a total of 13.2 μg of digested DNA (split into 3 tubes each containing 4.4 μg DNA) was combined with binding buffer (100 mM NaPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 10 μL of 1 mg/mL S9.6 antibody was added to each tube. Samples were incubated with rotation overnight at 4°C. The next day, magnetic protein A/G beads (Thermo Fisher Scientific, cat. no. #88803) were washed with binding buffer 3 X 10 mins and 50 μL was added to each sample tube followed by a 2 hour incubation on a rotisserie shaker at 4°C. Bead:antibody complexes were washed 3 X 10 mins with binding buffer, then 250 μL of elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and 7 μL of Proteinase K (20 mg/mL) was added to each tube and incubated at 55°C for 45 minutes with agitation to elute DNA from the S9.6 antibody. A standard phenol/chloroform extraction was performed, and DNA concentration and purity was assessed with a NanoDrop spectrophotometer. RNase A was added to samples (0.5 μL of 1 μg/μL stock) and incubated at 37°C for 1 hour. DNA was sheared with a Covaris S220 sonicator to a peak fragment size of 300 bp (duty cycle: 2%, incident power: 105 Watts, cycles per burst: 200, bath temperature: 4°C, processing time: 3 mins).
NGS libraries from DRIP DNA and inputs were constructed according to the manufacturer’s instructions (KAPA Hyper Prep Kit: Roche, cat. no. #KK8502 kit and single-indexed adapters from Illumina, cat. no. #IP-202-1012 + IP-202-1024. Dual-indexed libraries were constructed with Roche, cat. no. #KK8722). Library fragment sizes were restricted to between 100-500 bp with a PippinHT instrument (Sage Science). All library sizes and concentrations used for molarity calculations were confirmed on an Agilent 2100 Bioanalyzer and a Qubit 4 fluorometer (ThermoFisher Scientific) with a Qubit dsDNA HS Assay kit (ThermoFisher Scientific, cat. no. #Q32854), respectively. DRIP--sequencing was performed on an Illumina HiSeq 2500 (single-indexed libraries). All DRIP-sequencing (2x150 bp) was seqeunced to a minimum read depth of 50,000,000 reads.

treatment_protocol: Fresh and frozen de-identified prenatal autopsy samples with 4-72 hour postmortem intervals and lack of pathological abnormalities were collected in accordance with the institutional policies and regulations, along with next-of-kin consent for the de-identified tissue to be used for research purposes. Exclusion criteria included maternal history of drug or alcohol abuse, autolysis interval > 72 hours, and RNA integrity values (RIN) of < 8. Approximately 500 mg of tissue per sample was collected from second trimester prenatal human postmortem brain. Samples were dissected into two segments: 1) The germinal matrix (GM), situated next to the lateral ventricles, from which neurons and glia radially migrate toward the cortical plate (n = 3), and 2) the cortical plate (CP), which gives rise to the adult cerebral cortex (n = 3).

tag: Sex

value: female

tag: donor age

value: 17 gestational week

tag: condition

value: Frozen

tag: postmortem interval_(hr)


title: A375_WT+JQ1_IgG

source_name: WT + JQ1 + IgG antibody

tag: tissue

tag: cell type

value: Malignant Melanoma

tag: treatment

value: JQ1 500nM

tag: time


title: Male_3_PFF_Non-injected_K_3

value: cortex

value: Male

tag: timepoint (month_post_injection)

tag: injection

value: PFF

tag: hemisphere

tag: cage

value: K

tag: animal

tag: gaby's id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Male_3_PFF_Injected_K_3

tag: tissue

tag: cell line

tag: Sex

value: Injected

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: A375 _KOMK2+JQ1_BRD4

source_name: MK2 KO + JQ1 + BRD4 antibody

tag: cell type

tag: genotype

value: MAPKAPK2 knockout

tag: treatment

tag: time

tag: chip antibody


title: UACC-62, H3K27ac, replicate 1 (ChIP)

description: Library name: M7-H3K27ac-1


title: Human prenatal cortical plate, Patient 39_16812, sample 1, DRIP-seq

description: Library name: CP2.drip

source_name: cortical plate of second trimester prenatal brain

value: male

tag: donor age

value: 21 gestational week

tag: condition

value: Fresh

tag: postmortem interval_(hr)

tag: drip antibody


title: UACC-62, H3K27ac, replicate 2 (ChIP)

description: Library name: M7-H3K27ac-2

tag: tissue

value: Skin

value: Melanoma


title: Human prenatal cortical plate, Patient 39_16812, sample 2, DRIP-seq

description: Library name: CP3.drip

value: cortical plate of second trimester prenatal brain


title: A375 _KOMK2_NT_BRD4

source_name: MK2 KO untreated + BRD4 antibody

tag: cell line

value: DMSO


title: UACC-62, H3K9me3, replicate 3 (ChIP)

description: Library name: M7-H3K9me3-3

value: WT


title: Male_3_PFF_Injected_K_1

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: cage

tag: animal

tag: gaby's id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Human prenatal cortical plate, Patient 40_16811, DRIP-seq

description: Library name: CP1.drip

tag: donor age

tag: condition

tag: postmortem interval_(hr)

tag: drip antibody


title: UACC-62, H3K9me3, replicate 2 (ChIP)

description: Library name: M7-H3K9me3-2

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: Human prenatal germinal matrix, Patient 16_12437, DRIP-seq

description: Library name: GM3.drip

value: germinal matrix of second trimester prenatal brain

tag: Sex

value: female

value: 18 gestational week

value: Frozen


title: A375_WT+JQ1_BRD4

source_name: WT + JQ1 + BRD4 antibody

value: Malignant Melanoma

tag: treatment

value: JQ1 500nM

tag: time

tag: chip antibody


title: Male_3_PFF_Non-injected_J_3

value: cortex

value: Male

tag: timepoint (month_post_injection)

tag: injection

value: PFF

tag: hemisphere

value: Non-injected

tag: cage

value: J

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: A375_WT_NT_BRD4

source_name: WT untreated + BRD4 antibody

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Male_3_PFF_Non-injected_K_1

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: K

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Human prenatal germinal matrix, Patient 9_11073, DRIP-seq

description: Library name: GM2.drip

tag: donor age

value: 17 gestational week

tag: condition

tag: postmortem interval_(hr)

tag: drip antibody


title: UACC-62, replicate 3 (Input)

description: Library name: M7-H-Input-3

tag: tissue

value: Skin

value: Melanoma


title: A375 _KOMK2_NT_BRD2

source_name: MK2 KO untreated + BRD2 antibody

tag: cell line

value: MAPKAPK2 knockout

value: DMSO

tag: time

tag: chip antibody


title: Male_3_PFF_Injected_J_3

value: Injected

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: A375 _KOMK2+JQ1_BRD2

source_name: MK2 KO + JQ1 + BRD2 antibody

tag: cell type

tag: genotype

tag: treatment


title: Male_3_PFF_Non-injected_J_1

source_name: cortex

tag: tissue

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: UACC-62, H3K9me3, replicate 1 (ChIP)

description: Library name: M7-H3K9me3-1

value: WT


title: A375_WT+JQ1_BRD2

source_name: WT + JQ1 + BRD2 antibody

tag: time

tag: chip antibody


title: UACC-62, replicate 2 (Input)

description: Library name: M7-H-Input-2

source_name: Skin


title: UACC-62, replicate 1 (Input)

description: Library name: M7-H-Input-1


title: Human prenatal germinal matrix, Patient 39_16182, DRIP-seq

description: Library name: GM1.drip

value: germinal matrix of second trimester prenatal brain

value: male

tag: donor age

value: 21 gestational week

tag: condition

value: Fresh

tag: postmortem interval_(hr)

tag: drip antibody


title: RNase H1-transduced hiPSC-derived neurons, Patient 553, culture 1, RNA-seq

description:
Library name: RH1-1_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis

data_processing:
After quality control with the FASTQC package and adapter trimming (Trimmomatic/0.36, RNA-seq FASTQ files were aligned to GRCh38 using STAR/2.7.5b and uniquely mapped reads within genes were counted with FeatureCounts under the subread/2.0.1 package. Ribosomal RNA was removed prior to FeatureCounts with the BEDTools/2.29.2 package. Genes with more than 10 counts in at least two samples were kept for downstream analysis. Sample-level quality control consisted of Principal Component Analysis and hierarchical clustering, both performed on regularized log transformed data. Differential gene expression was calculated with DESeq2/1.40.2, α = 0.05.
Assembly: GRCh38
Supplementary files format and content: Count matrix for RNA-seq data.

extract_protocol:
RNA was extracted from cells by adding 1 mL TRIzol (Invitrogen, cat. no. # 15596026) directly to the culture plate and scraping vigorously with a pipette tip. RNA was extracted with chloroform and precipitated with isopropyl alcohol, then treated with 2 U/10 μg RNA RNase-free DNase I (Invitrogen, cat. no. #AM222) at 37°C for 30 mins to remove DNA contamination. RNA was cleaned with acid phenol/chloroform and ethanol precipitated. Aliquots were stored at -80° prior to NGS library construction.
NGS libraries from total, purified RNA were constructed with the SMARTer Stranded RNA-seq Kit (Takara, cat. no. #634839) according to the manufacturer’s instructions for first-strand cDNA synthesis, purification of first-strand cDNA using SPRI beads, RNA-seq library amplification via PCR (with 12 PCR cycles for 10 ng of starting RNA), and SPRI cleanup. All library sizes and concentrations used for molarity calculations were confirmed on an Agilent 2100 Bioanalyzer and a Qubit 4 fluorometer (ThermoFisher Scientific) with a Qubit dsDNA HS Assay kit (ThermoFisher Scientific, cat. no. #Q32854), respectively. RNA-sequencing was performed on an Illumina HiSeq 2500 (single-indexed libraries). All RNA-sequencing (2x75 bp) was seqeunced to a minimum read depth of 50,000,000 reads. RNA-sequencing libraries were split across three lanes and merged for downsream analysis.

treatment_protocol: hiPSC-NPCs were transduced with either the TRE-RNASEH1ΔMLS-BFP, TRE-RNASEH1ΔMLS-D145N-BFP, or TRE-BFP viruses at a multiplicity of infection (MOI) of approximately 1.0. All constructs were co-transduced with the rtTA transactivator. Virus was added to cells and allowed to incubate for 1 hour at 37°C, followed by spinfection at 1,000 G for 1 hour at room temperature with slow acceleration and deceleration. Cells were returned to 37°C and after 4 hours the media was changed (Day 0). Starting at Day 3, cells were fed every other day with NPC media containing 0.3 μg/μL puromycin. On Day 7, cells were split and replated at low density (e.g., 500,000 cells per well of a 6-well plate). The following day, cells were switched to neuron differentiation medium containing 0.05 μg/μL puromycin and 0.3 μg/μL doxycycline and were fed every 2-3 days for the course of their 6 week differentiation period.

tag: cell type

value: hiPSC-derived neuron

tag: genotype

value: RNase H1 (R-loop knockdown)

tag: treatment

value: hiPSC directed neural differentiation

value: 6 weeks


title: Male_1_PFF_Non-injected_J_0

tag: tissue

value: cortex

tag: cell line

tag: Sex

value: Male

value: PFF

value: Non-injected

tag: cage

value: J

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: A375_WT_NT_BRD2

source_name: WT untreated + BRD2 antibody

value: Skin

tag: cell type

value: Malignant Melanoma

tag: time

tag: chip antibody


title: Male_3_PFF_Injected_J_1

tag: tissue

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Injected

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: RNase H1-transduced hiPSC-derived neurons, Patient 2607, culture 1, RNA-seq

description:
Library name: RH1-2_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis

tag: genotype

tag: Sex

tag: donor age

tag: treatment


title: SK-Mel-28, H3K27ac, replicate 3 (ChIP)

description: Library name: M4-H3K27ac-3

tag: cell line

value: Melanoma

value: WT


title: RNase H1 D145N-transduced hiPSC-derived neurons, Patient 2607, culture 1, RNA-seq

description:
Library name: D145N-2_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis

value: RNase H1-D145N mutant control

value: male


title: SK-Mel-28, H3K27ac, replicate 2 (ChIP)

description: Library name: M4-H3K27ac-2


title: Male_1_PFF_Injected_J_0

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: RNase H1 D145N-transduced hiPSC-derived neurons, Patient 553, culture 1, RNA-seq

description:
Library name: D145N-1_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis

tag: cell type

tag: time


title: Female_3_PBS_Non-injected_Q_1

tag: tissue

tag: Sex

value: Female

tag: timepoint (month_post_injection)

tag: injection

value: PBS

tag: hemisphere

value: Q

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: SK-Mel-28, H3K27ac, replicate 1 (ChIP)

description: Library name: M4-H3K27ac-1

tag: cell line

tag: genotype


title: Male_1_PFF_Non-injected_I_10

tag: cage

value: I

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: case id


title: The RNA precipitated by Flag-tagged FAK

city: Guangzhou

first: Man-Li

last: Luo

address: No.107 Yanjiang West Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen Memorial Hospital

data_processing:
Based on Sequencing By Synthesis (SBS) technology, Illumina HiSeq high-throughput sequencing platform sequencing cDNA libraries to produce large amounts of high-quality Data, known as Raw Data
The specified genome GRCh38 was used as a reference for sequence alignment and subsequent analysis.
The reconstruction of transcripts was carried out with software StringTie, which allows to identify splice variants.
RSeQC was used to analyze the relationship between sequencing data and gene locations on the genome.
Processed data files were based on the fold enrichment (the fold enrichment between Flag-FAK fpkm and IgG fpkm in a experiment) of different experiments. The odds ratio of fold enrichment between two experiment > 2 was used to selected different genes.
Assembly: GRCh38NCBI RefSeq
Supplementary files format and content: Tab-delimited text files include FPKM and gene counts values for each RNA precipitation Sample respectively.
Supplementary files format and content: The coding protein potential score of the sequenced transcripts was calculated.

growth_protocol: Breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen) following manufacturer's protocols

treatment_protocol: We produced FLAG tagged-FAK protein in MDA-MB-231 cells by transfection of FLAG tagged plasmids into cells. Cells were lysed by RIP lysis buffer, and incubated at 4 °C with antibody-conjugated Protein A/G Dynabeads overnight. Specific anti-FLAG antibody (Sigma) and normal mouse IgG (Santa Cruz) were used for the retrieval of RNA. RNA was extracted for subsequent sequencing analysis.

tag: cell type

value: Flag-tagged FAK protein was expressed

tag: treatment

value: Flag antibody immunoprecipitation


title: The RNA precipitated by normal mouse IgG

value: IgG antibody immunoprecipitation


title: Male_1_PFF_Injected_I_10

tag: tissue

value: cortex

tag: Sex

value: Male

tag: timepoint (month_post_injection)

tag: injection

value: PFF

tag: hemisphere

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: BFP-transduced hiPSC-derived neurons, Patient 2607, culture 1, RNA-seq

description:
Library name: BFP-2_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis

value: hiPSC-derived neuron

tag: genotype

value: BFP lentiviral backbone control

tag: donor age

value: hiPSC directed neural differentiation

tag: time

value: 6 weeks


title: BFP-transduced hiPSC-derived neurons, Patient 553, culture 1, RNA-seq

description:
Library name: BFP-1_RNA
RNA-seq files were split across three lanes and FASTQs were merged for downstream analysis


title: SK-Mel-28, H3K9me3, replicate 3 (ChIP)

description: Library name: M4-H3K9me3-3

value: Skin

tag: cell line

value: Melanoma

value: WT


title: 10% input RNA in MDA-MB-231 cells

value: RNA extraction


title: Male_1_PFF_Injected_I_3

value: Injected

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: SK-Mel-28, H3K9me3, replicate 1 (ChIP)

description: Library name: M4-H3K9me3-1

tag: tissue

tag: cell type


title: CpG

city: Changchun

first: Zheng

last: Jin

address: Xinmin Street 126#

department: College of  Basic Medical Science

institute: Jilin University

description: 10x Genomics

data_processing:
Genome alignment, quantification, single cell matrix generation, and clustering were performed using Cell Ranger 6.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
Assembly: hg38
Supplementary files format and content: tap-separated value files and matrix files

source_name: PBMC

extract_protocol:
B cells were sorted from Human PBMC,then stimulated with or without CpG fior 24 hours. The single cells were obtained by the method of grinding through a 70 μm cell strainer.
Library construction was performed according to the manufacture's protocol(Single Cell 3′ library and Gel Bead Kit v.3).Briefly, GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling. The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection. The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: PBMC

tag: agent

value: CpG

value: B cells


title: UN

description: 10x Genomics


title: SK-Mel-28, H3K9me3, replicate 2 (ChIP)

description: Library name: M4-H3K9me3-2

tag: genotype


title: SK-Mel-28, replicate 3 (Input)

description: Library name: M4-H-Input-3


title: RNase H1-transduced hiPSC-derived neurons, culture 1, DRIP-seq input control

description: Library name: RH1-input_neuron_drip

extract_protocol:
Genomic DNA was extracted from cells (roughly 1X10^6 iPSC-neurons on a 6-well plate, enzymatically detached with Accutase (Millipore) and pelleted with centrifugation for 5 mins at 1,000 G), via incubation with 20% SDS and 20 mg/mL Proteinase K overnight at 37°C. After standard phenol/chloroform extraction, 3M NaOAc pH 5.2 and 2.4 volumes of 100% ice-cold EtOH was added and DNA was precipitated via gentle spooling with a pipette tip to avoid RNA contamination that can result from centrifugation. After three gentle washes with 70% EtOH and 1-2 hours of air drying, DNA was resuspended in TE and digested with a cocktail of restriction enzymes that avoid GC-rich regions (HindIII, EcoRI, XbaI, and SSPI) overnight at 37°C. DNA was again purified via phenol/chloroform extraction and ethanol precipitation, and complete digestion was confirmed on an agarose gel.  For immunoprecipitation of R-loops, a total of 13.2 μg of digested DNA (split into 3 tubes each containing 4.4 μg DNA) was combined with binding buffer (100 mM NaPO4 pH 7.0, 1.4 M NaCl, 0.5% Triton X-100) and 10 μL of 1 mg/mL S9.6 antibody was added to each tube. Samples were incubated with rotation overnight at 4°C. The next day, magnetic protein A/G beads (Thermo Fisher Scientific, cat. no. #88803) were washed with binding buffer 3 X 10 mins and 50 μL was added to each sample tube followed by a 2 hour incubation on a rotisserie shaker at 4°C. Bead:antibody complexes were washed 3 X 10 mins with binding buffer, then 250 μL of elution buffer (50 mM Tris pH 8.0, 10 mM EDTA, 0.5% SDS) and 7 μL of Proteinase K (20 mg/mL) was added to each tube and incubated at 55°C for 45 minutes with agitation to elute DNA from the S9.6 antibody. A standard phenol/chloroform extraction was performed, and DNA concentration and purity was assessed with a NanoDrop spectrophotometer. RNase A was added to samples (0.5 μL of 1 μg/μL stock) and incubated at 37°C for 1 hour. DNA was sheared with a Covaris S220 sonicator to a peak fragment size of 300 bp (duty cycle: 2%, incident power: 105 Watts, cycles per burst: 200, bath temperature: 4°C, processing time: 3 mins).
NGS libraries from DRIP DNA and inputs were constructed according to the manufacturer’s instructions (KAPA Hyper Prep Kit: Roche, cat. no. #KK8502 kit and single-indexed adapters from Illumina, cat. no. #IP-202-1012 + IP-202-1024. Dual-indexed libraries were constructed with Roche, cat. no. #KK8722). Library fragment sizes were restricted to between 100-500 bp with a PippinHT instrument (Sage Science). All library sizes and concentrations used for molarity calculations were confirmed on an Agilent 2100 Bioanalyzer and a Qubit 4 fluorometer (ThermoFisher Scientific) with a Qubit dsDNA HS Assay kit (ThermoFisher Scientific, cat. no. #Q32854), respectively. DRIP--sequencing was performed on an Illumina HiSeq 2500 (single-indexed libraries). All DRIP-sequencing (2x150 bp) was seqeunced to a minimum read depth of 50,000,000 reads.

value: RNase H1 (R-loop knockdown)

tag: Sex

value: male

tag: treatment


title: Male_1_PFF_Non-injected_I_3

value: cortex

tag: cell line

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Non-injected

value: I

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: RNase H1-transduced hiPSC-derived neurons, culture 3, DRIP-seq

description: Library name: RH1-3_neuron_drip

value: hiPSC-derived neuron

tag: time

tag: drip antibody


title: Male_1_PFF_Injected_I_0

tag: tissue

value: Male

value: PFF

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Male_1_PFF_Non-injected_I_0

tag: cell line

tag: Sex

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: rna date_isolated

tag: case id


title: RNase H1-transduced hiPSC-derived neurons, culture 2, DRIP-seq

description: Library name: RH1-2_neuron_drip

tag: cell type

tag: genotype

tag: treatment

value: hiPSC directed neural differentiation

tag: time

value: 6 weeks

tag: drip antibody


title: Male_3_PBS_Non-injected_D_10

tag: tissue

value: PBS

tag: cage

value: D

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: OGD-R_2

city: Beijing

first: He

last: Zhu

address: Dongcheng street

institute: Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: OGD-R group

data_processing:
CLC Genomics orkbench v 11.0.1
Assembly: CRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts values for each Sample
Supplementary files format and content: tab-delimited txt files include FPKM values for each Sample

source_name: HaCaT

extract_protocol:
RNA was harvested using NEBnext® ultratm RNA Library Prep Kit for  Illumina. 1.5ug of total RNA was used for the constructio of sequencing libraries.
RNA libraries for RNA-SEQ were prepared using SMARTER MRNA-SEQ Library Prep Kit following manufactures protocols.

tag: cell line

value: HaCaT

value: Human Keratinocytes Cells

value: OGD/R


title: OGD-R_3

description: OGD-R group


title: RNase H1-transduced hiPSC-derived neurons, culture 1, DRIP-seq

description: Library name: RH1-1_neuron_drip

source_name: hiPSC-derived neuron

tag: Sex


title: OGD-R_4

description: OGD-R group

tag: cell type


title: OGD-R_1

description: OGD-R group


title: SK-Mel-28, replicate 1 (Input)

description: Library name: M4-H-Input-1

value: Skin

value: Melanoma

tag: genotype

value: WT


title: Male_3_PBS_Injected_D_10

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Injected

tag: rna date_isolated

tag: case id

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Achilles tendon_earth_3

city: Tokyo

first: Taro

last: Kasai

address: Bunkyoku Hongo7-3-1

country: Japan

institute: The University of Tokyo

description:
Library name: Sample 6
Column name in read_counts.csv: Achilles tendon_earth_3

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 System using 2 × 150 bp paired-end reads. The sequenced reads were aligned to the mouse reference genome (GRCm39/mm39), and gene expression counts along with transcripts per million values were calculated using DRAGEN version 4.3.
Assembly: GRCm39/mm39
Supplementary files format and content: csv files include read counts for each Smaple

source_name: Achilles tendon

extract_protocol:
Total RNA was extracted from the Achilles tendons, quadriceps femoris muscles, and brown adipose tissue. These tissues were homogenized using zirconia beads in TRI Reagent (Cosmo Bio, Tokyo, Japan). Total RNA was then extracted using the Direct-zol RNA Kit (Zymo Research, CA, USA) according to the manufacturer’s protocol.
Sequence libraries were prepared using the SMART-Seq mRNA (Takara Bio, Japan) and Nextera XT DNA Library Preparation Kit (Illumina, USA) according to the manufacturer’s protocol.

tag: tissue

value: Achilles tendon


title: SK-Mel-28, replicate 2 (Input)

description: Library name: M4-H-Input-2


title: RNase H1 D145N-transduced hiPSC-derived neurons, culture 2, DRIP-seq

description: Library name: D145N-2_neuron_drip

value: RNase H1-D145N mutant control

value: male

tag: treatment

tag: time

tag: drip antibody


title: SK-Mel-19, H3K27ac, replicate 3 (ChIP)

description: Library name: M3-H3K27ac-3

tag: cell line


title: RNase H1 D145N-transduced hiPSC-derived neurons, culture 1, DRIP-seq

description: Library name: D145N-1_neuron_drip

value: hiPSC-derived neuron

tag: Sex


title: Male_3_PBS_Non-injected_D_3

value: cortex

value: Male

value: Non-injected

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: Control_4

description: Control group

tag: cell type


title: Control_3

description: Control group


title: Male_3_PBS_Injected_D_3

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: rna date_isolated

tag: case id

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: SK-Mel-19, H3K27ac, replicate 2 (ChIP)

description: Library name: M3-H3K27ac-2

tag: tissue

tag: cell line

tag: genotype


title: SK-Mel-19, H3K27ac, replicate 1 (ChIP)

description: Library name: M3-H3K27ac-1


title: BFP-transduced, hiPSC-derived neurons, culture 1, DRIP-seq input control

description: Library name: BFP-input_neuron_drip

value: BFP lentiviral backbone control

tag: Sex

tag: treatment

value: hiPSC directed neural differentiation

tag: time

value: 6 weeks


title: Control_2

description: Control group

value: HaCaT


title: Control_1

description: Control group

value: Human Keratinocytes Cells


title: Male_3_PBS_Non-injected_D_1

value: PBS

tag: cage

value: D

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)


title: BFP-transduced hiPSC-derived neurons, culture 2, DRIP-seq

description: Library name: BFP-2_neuron_drip

tag: cell type

tag: drip antibody


title: SK-Mel-19, H3K9me3, replicate 3 (ChIP)

description: Library name: M3-H3K9me3-3

tag: tissue

value: Skin

value: Melanoma


title: Male_3_PBS_Injected_D_1

tag: cell line

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Injected

tag: rna date_isolated

tag: case id

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue

tag: volume to_genomics


title: Male_3_PBS_Non-injected_D_0

tag: Sex

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue


title: BFP-transduced hiPSC-derived neurons, culture 3, DRIP-seq

description: Library name: BFP-3_neuron_drip

tag: cell type

tag: genotype

tag: treatment

tag: time

tag: drip antibody


title: SK-Mel-19, H3K9me3, replicate 2 (ChIP)

description: Library name: M3-H3K9me3-2

tag: tissue

tag: cell line

value: WT


title: SK-Mel-19, H3K9me3, replicate 1 (ChIP)

description: Library name: M3-H3K9me3-1


title: BFP-transduced hiPSC-derived neurons, culture 1, DRIP-seq

description: Library name: BFP-1_neuron_drip


title: Male_3_PBS_Injected_D_0

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)


title: Eu-eMSCs-Exos-2

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

description:
Processed data file column header:
21214899_UMIs

data_processing:
The sequencing data was processed using Cutadapt (version 2.7) to remove sequencing adapters, low-quality reads, short reads with more N, and reads shorter than 16 bp.
Subsequently, perl5 (version 26) was used to process reads with UMIs shorter than 12 bp and reads without UMIs, and to identify UMIs.
The bowtie software (version 1.3.0) was then employed to compare the reads against the miRBase database.
Finally, small RNA quantification was performed by comparing the mapped reads to the miRBase.
The R package edgeR is used to calculate the expression difference based on grouping information from the obtained expression UMI counts matrix, aiming to identify miRNAs that are significantly differentially expressed (either being up-regulated or down-regulated).
Assembly: miRBase v 22
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: adenomyotic eutopic endometrium

growth_protocol: Eutopic endometrial tissue and normal endometrial tissue were obtained from patients with adenomyosis ( AM ) or uterine fibroids who underwent hysterectomy in Jiangsu Provincial Hospital of Integrated Traditional Chinese and Western Medicine. They were purchased from ( Nanjing, China ) for primary culture of endometrial mesenchymal stem cells ( e MSCs ). Eu-e MSCs were obtained from eutopic endometrium of AM patients, and normal e MSCs ( N-e MSCs ) were obtained from eutopic endometrium of control group. Eu-eMSCs and N-eMSCs were cultured in DMEM / F12 ( 1 : 1 ) + 10 % FBS ( Viva Cell, China ) + 1 % Pen-Strep, 37 °C, 5 % CO2 incubator.

extract_protocol:
When eMSCs reached approximately 70% confluence, the medium was replaced with DMEM/F12 containing 10% exosome depleted FBS (Exo-FBS) (System Biosciences, USA) for 48 h. The cell culture supernatants of eMSCs were collected for microRNA (miRNA) sequencing (miRNA-seq). Exosomes derived from eMSCs (eMSCs-Exos) were isolated using the exoEasy Maxi Kit (Qiagen, USA), and their miRNA content was extracted using the miRNeasy Micro Kit (Qiagen, USA). 4μg total RNA was used for construction of sequencing libraries.
MicroRNA libraries for miRNA-seq were prepared using the QIAseq miRNA Library Kit (Qiagen, Germany) following the manufacturer’s standard protocol.

value: adenomyotic eutopic endometrium

tag: cell type

value: endometrial mesenchymal stem cells

tag: cell component

value: exosome


title: SK-Mel-19, replicate 3 (Input)

description: Library name: M3-H-Input-3

tag: genotype


title: Eu-eMSCs-Exos-3

description:
Processed data file column header:
23209259_Eu_UMIs


title: Eu-eMSCs-Exos-1

description:
Processed data file column header:
21215121_UMIs


title: Male_1_PBS_Non-injected_C_10

value: cortex

tag: Sex

tag: cage

value: C

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: ug/mg tissue

tag: volume to_genomics


title: HaCaT cells, siFn14, C.albicans, rep 1

city: nanjing

first: x

last: wang

address: jiefang road 76,nanjing

institute: jinling hospital

description:
Library name: sample 4
FPKM.Lv_Fn14_1

data_processing:
Read count extraction and normalization were performed using CLC genomic benchwork
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: GRCh38/hg38
Supplementary files format and content: Processed data are provided as tab-delimited text files. Rows correspond to genes (Ensembl gene IDs ), and values are FPKM expression estimates.

source_name: skin

growth_protocol: HaCaT keratinocytes were cultured in RPIM 1640 supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2. Cells were seeded 24 h prior to infection and grown to ~70–80% confluence.

extract_protocol:
Total RNA was extracted from keratinocytes and skin tissue using TRIZOL reagent (Life Technologies), according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the SMARTer Stranded mRNA-Seq Library Prep Kit (Takara Bio) with poly(A) selection, according to the manufacturer’s instructions. Libraries were indexed, pooled equimolarly, and sequenced on an Illumina platform .

treatment_protocol: Fn14 was knocked down using siRNA (sequence provided in supplementary methods) transfected with Lipofectamine RNAiMAX for 48 h. Cells were infected with Candida albicans SC5314 at MOI = 10 for 1 h. After infection, cells were washed with PBS to remove non-adherent fungi and harvested for RNA extraction.

tag: tissue

value: skin

tag: cell line

value: keratinocytes

value: Fn14 konckdown

tag: treatment

value: Infection with Candida albicans


title: SK-Mel-19, replicate 2 (Input)

description: Library name: M3-H-Input-2


title: HaCaT cells, siFn14, C.albicans , rep 2

description:
Library name: sample 5
FPKM.Lv_Fn14_2

value: HaCaT


title: HaCaT cells, siFn14, C.albicans , rep 3

description:
Library name: sample 6
FPKM.Lv_Fn14_3


title: Male_1_PBS_Injected_C_10

value: Male

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

tag: rna date_isolated

tag: case id

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)


title: HaCaT cells, siControl, C.albicans ,rep 3

description:
Library name: sample 3
FPKM.Lv_Con_3

tag: cell type

tag: genotype


title: N-eMSCs-Exos-3

description:
Processed data file column header:
23205838_UMIs

source_name: normal eutopic endometrium

value: normal eutopic endometrium

tag: cell component


title: HaCaT cells, siControl, C.albicans, rep 2

description:
Library name: sample 2
FPKM.Lv_Con_2


title: SK-Mel-19, replicate 1 (Input)

description: Library name: M3-H-Input-1


title: RNA-seq of young_7  (PVM, young)

city: Wuhan

first: Huang

last: Hongqing

address: 1095 Jiefang Avenue, Qiaokou District, Wuhan, Hubei, P.R. China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: young_7

data_processing:
Raw sequencing data were filtered using SOAPnuke (v1.5.2) to remove reads containing adapters, reads with >5% unknown bases (N), and low-quality reads (defined as reads with >20% of bases having a quality value <10). Clean reads were aligned to the mouse reference genome using HISAT2 (v2.0.4). Gene expression levels were quantified using RSEM (v1.2.12) with Bowtie2 (v2.2.5) for alignment to reference gene sequences. Differential expression analysis was performed using DESeq2 (v1.4.5) with a significance threshold of Q value ≤ 0.05.
Assembly: GRCm38(mm10)
Supplementary files format and content: Processed data files are provided as a tab-delimited text matrix (expression_matrix.csv) containing raw counts for each gene across all 12 samples (5 aged, 7 young adult).

source_name: brain

extract_protocol:
Single-cell lysis was performed using the SMART-Seq2 lysis buffer provided by BGI Genomics. The lysis buffer typically contains Rnase inhibitors and dNTPs, and cells were lysed to release total RNA for subsequent reverse transcription.
First-strand cDNA was synthesized using SMART-seq2 amplification technology. Briefly, RNA was denatured with oligo-dT primers on a thermal cycler. Reverse transcription mix was prepared and first-strand cDNA was synthesized. Second-strand cDNA was synthesized using KAPA HiFi HotStart DNA Polymerase. The double-stranded cDNA product was purified using Agencourt AMPure XP beads. The amplified product quality was assessed using an Agilent 2100 Bioanalyzer. For qualified cDNA products, libraries were constructed using the Nextera XT DNA Library Preparation Kit. Library fragment size and concentration were measured using an Agilent 2100 Bioanalyzer. For sequencing, libraries were denatured, circularized to generate single-stranded circular products, and library concentration was measured using a Qubit Fluorometer. DNA nanoballs (DNBs) were generated via rolling circle amplification. DNBs were loaded onto patterned array chips, and sequencing was performed using combinatorial Probe-Anchor Synthesis (cPAS) technology.

value: brain


title: Male_1_PBS_Injected_C_3

extract_protocol:
Neuronal nuclei were isolated from mouse cortex using flow cytometry and filtering for an anti-NeuN antibody.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase. RNA was sheared to an average of 300 bp . Individually indexed libraries were pooled, and 75-bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer. Base calling was done by Illumina NextSeq Control Software (NCS; v2.0), and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0)
bulk RNA-seq on neuronal nuclei.

tag: Sex

value: PBS

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: total (ug)

tag: ug/mg tissue


title: Male_1_PBS_Non-injected_C_3

tag: tissue

tag: cell line

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Non-injected

tag: rna date_isolated

tag: case id

tag: volume to_genomics


title: RNA-seq of young_6  (PVM, young)

description: Library name: young_6


title: N-eMSCs-Exos-1

description:
Processed data file column header:
425785_UMIs

tag: cell type

tag: cell component


title: HaCaT cells, siControl, C.albicans, rep 1

description:
Library name: sample 1
FPKM.Lv_Con_1

tag: genotype

tag: treatment


title: Muscle_Deltoid_SPTAN

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

data_processing:
nf-core rnaseq pipeline
aligned to hg38 using STAR
Salmon for gene counts
Assembly: hg38
Supplementary files format and content: salmon.merged.gene_counts.tsv; gene counts for patient
Supplementary files format and content: salmon.merged.gene_tpm.tsv; transcript per million counts

source_name: deltoid muscle

extract_protocol:
Total RNA wsas extracted using Trizol followed by Qiagen RNAeasy columns.
cDNA

value: deltoid muscle


title: N-eMSCs-Exos-2

description:
Processed data file column header:
431625_UMIs


title: Male_1_PBS_Non-injected_C_1

data_processing:
RNA-seq: Trimmed fastq files were aligned to MM10/GRCm38 using STAR v2.7 (Dobin and Gingeras, 2015).
RNA-seq: The resulting gene_id map counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
Assembly: GRCm38/MM10
Supplementary files format and content: .xlsx, counts in log2cpm for each gene, statistical significance for muliple comparison tests using LIMMA

tag: Sex

tag: cage

tag: animal

tag: gaby's id

tag: tube weight

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)


title: RNA-seq of young_5  (PVM, young)

description: Library name: young_5

tag: tissue


title: RNA-seq of young_4  (PVM, young)

description: Library name: young_4


title: Male_1_PBS_Injected_C_1

tag: cell line

tag: timepoint (month_post_injection)

tag: injection

tag: hemisphere

value: Injected

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: total (ug)

tag: ug/mg tissue


title: Male_1_PBS_Non-injected_C_0

tag: Sex

tag: cage

tag: animal

tag: case id

tag: volume to_genomics


title: RNA-seq of young_3  (PVM, young)

description: Library name: young_3


title: Donor 10B Burn Whole Blood

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

data_processing:
All raw FASTQs reads were aligned to Homo sapiens (GRCh38) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Assembly: Homo_sapiens : GRCh38
Supplementary files format and content: Filtered gene - barcode matrix output from CellRanger

source_name: Whole Blood

extract_protocol:
For lymphocyte isolation, whole blood heparinized vacutubes were used. To isolate lymphocytes by immunomagnetic negative selection, 100 μl of Isolation Cocktail and 100 μl of Rapid Spheres (EasySep Direct Human Total Lymphocytes Isolation Kit, 19655, STEMCELL Technologies) were added to 2 ml of whole blood. After mixing and 5-min incubation at room temperature, the sample volumes were topped up to 2.5 ml with 0.04% BSA in PBS. The diluted sample was incubated in the magnet without a lid for 5 min at room temperature, and negatively selected lymphocytes were decanted into a new 5-ml polystyrene tube. Except for the addition of Isolation Cocktail, all steps were repeated once. The final lymphocyte cell suspension was transferred to a 15-ml polypropylene tube, and a volume of 5 ml of 0.04% BSA in PBS was added to the sample. Lymphocytes were precipitated by centrifugation for 5 min at 300g; the supernatant was discarded; and cells were resuspended in 5 ml of 0.04% BSA in PBS. This step was repeated, and cells were resuspended in 100 μl of PBS + 0.04% BSA. Cell density was quantified with a hemacytometer; cell viability was assessed with trypan blue staining (T8154, Sigma-Aldrich); and 7,500 live lymphocytes were transferred to a sterile 1.5-ml microcentrifuge tube.  For leukocyte isolation, 1 ml of whole blood from heparin-containing vacutubes was transferred to 5-ml polystyrene round-bottom tubes, and 12 μl of 0.5 M EDTA was added. Next, 2% FBS in PBS (1 ml) and 50 μl of EasySep RBC Depletion spheres (EasySep RBC Depletion Reagent, 18170, STEMCELL Technologies) were added to immunomagnetically deplete red blood cells. After 5 min of magnet incubation at room temperature, cell suspension containing leukocytes was decanted into a new 5-ml polystyrene tube. To ensure complete removal of red blood cells, red blood cell depletion was repeated, and cell suspension containing leukocytes was decanted into a new 15-ml polypropylene tube. Leukocytes were precipitated by centrifugation at 300g for 5 min at 20 °C and resuspended in 5 ml of 0.04% BSA in PBS. This step was repeated, and leukocytes were resuspended in 2 ml of 0.04% BSA in PBS. Cell viability and cell density were assessed, and 7,500 live leukocytes were transferred to the microcentrifuge tube containing the lymphocyte cell suspension in a total volume of 50 μl of 0.04% BSA in PBS.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

value: Whole Blood

tag: condition

value: burn patient

tag: individual

value: Donor 10B


title: Donor 9B Burn Whole Blood

tag: tissue

value: Donor 9B


title: Donor 2B Burn Whole Blood

value: Donor 2B


title: Donor 4B Burn Whole Blood

value: Donor 4B


title: RNA-seq of young_2  (PVM, young)

description: Library name: young_2


title: Neural Stem Cells - APLP1 Control

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
long (150 bp paired-end) reads to capture 3'UTRs
Sample 3

data_processing:
Library strategy: CITE-seq
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

source_name: Neural Stem Cells

growth_protocol: Neural stem cells were isolated from the sub-ventricular zone of adult mice

extract_protocol:
10X genomics, oligo(dT) capturing (Hash tag oligos conjugated to anti-MHC1 and anti-CD45; HTO_1: 155803 TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody BioLegend, HTO_2: 155805 TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody BioLegend, HTO_3: 155807 TotalSeq™-A0304 anti-mouse Hashtag 4 Antibody BioLegend)
10X Genomics library preparation

treatment_protocol: cultured NSC were treated either with BMP4 for 3 days or EGF

value: Neural Stem Cells

tag: nsc isolation

value: freshly isolated

tag: treatment

value: no treatment

tag: genotype

value: wildtype

tag: sequenced molecule

value: mRNA


title: cKO_WaveNeg_rep3.4

city: Cold Spring Harbor

first: Lucas

last: Cheadle

address: 1 Bungtown Rd

department: Neuroscience

institute: Cold Spring Harbor Laboratory

data_processing:
BCL files were downloaded from Illumina BaseSpace platform after sequencing on an Illumina Next-Seq 500
BCL files were converted into FastQ format.
Files were filtered and demultiplexed using .yaml files specifying the indices used for each sample, .yaml file are provided in this upload.
Raw counts files were generated for each sample then used as input for downstream analyses in R.
Putative doublets were identified and removed using Doublet Finder in R.
QC was performed, data were normalized, and cells were clustered using Seurat version 3 in R.
Differential gene expression analysis was performed using Monocle version 2 in R.
Assembly: Custom transcriptome was built from Ensemble GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1.
Supplementary files format and content: Counts tables (.tsv) files for each sample are provided. These files can be fed directly into Seurat for re-analysis.

extract_protocol:
Single-nuclear RNA-sequencing was performed using the inDrops strategy on nuclei from anterior and posterior V1 micro-dissected from Beta2fl/fl; Pax6α-Cre mice and Beta2fl/fl; Cre-negative controls
Library was constructed by single-cell core facility at Harvard Medical School

tag: strain

tag: age

value: Postnatal day 7


title: GA0518 Control biol rep2

city: houston

first: Xueshuai

last: Han

state: texas

address: 1881 East Rd

institute: MD anderson cancer center

description: Library name: G2CT2

data_processing:
RNA samples were submitted to Novogene (California, USA) for library construction and high-throughput sequencing. Sequencing reads were aligned to the human reference genome (GRCh38), and gene-level read counts were generated using the Novogene standard bioinformatics pipeline. Differential gene expression analysis between CYD-4-61–treated and vehicle-treated cells was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: raw counts, TPM  for each sample

growth_protocol: GA0518 and AGS cells were maintained in DMEM with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: AGS and GA0518 cells were treated with CYD-4-61 (25 nM) or vehicle for 48 h

tag: cell line

tag: cell type

value: gastric cancer cells

value: WT

value: DMSO


title: GA0518 CYD-4-61 treatment biol rep2

description: Library name: G2A2


title: GA0518 Control biol rep3

description: Library name: G2CT3


title: GA0518 Control biol rep1

description: Library name: G2CT1


title: RNA-seq of young_1  (PVM, young)

description: Library name: young_1

value: brain


title: GA0518 CYD-4-61 treatment biol rep1

description: Library name: G2A1


title: GA0518 CYD-4-61 treatment biol rep3

description: Library name: G2A3


title: cKO_WaveNeg_rep3.3


title: RNA-seq of old_5  (PVM, aged)

description: Library name: old_5


title: Male_1_PBS_Injected_C_0

city: Grand Rapids

first: Gerry

last: Coetzee

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

value: cortex

value: Male

tag: timepoint (month_post_injection)

tag: injection

value: PBS

tag: hemisphere

value: Injected

value: C

tag: gaby's id

tag: tube weight

tag: tube +_sample_weight

tag: mg of_tissue

tag: rna date_isolated

tag: rna tube_label

tag: plate id

tag: conc. (ng/ul)

tag: volume (ul)

tag: total (ug)

tag: ug/mg tissue


title: U266 cells,Dihydroartemisinin, 12h, 2

city: Su*zhou City

first: Wang

last: Zhiming

address: No. 199, Ren'ai Road

institute: Soochow University

description:
Dihydroartemisinin,12h
cell20230106-U266D2_L3

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: hg13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

growth_protocol: U266 and LP-1 cells were cultured at 37°C in an atmosphere containing 5% CO2 and in RPMI-1640 medium (Hyclone) supplemented with 10% fetal bovine serum.

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.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The experimental group was treated with Dihydroartemisinin (DHA) at its IC50 concentration, while the solvent control group was treated with an equal amount of DMSO. After 12 hours, cells were collected and subjected to transcriptome sequencing.

tag: tissue

value: bone marrow

value: Multiple Myeloma

tag: genotype

tag: treatment


title: cKO_WaveNeg_rep3.2

tag: strain

tag: age


title: U266 cells,Dihydroartemisinin, 12h, 1

description:
Dihydroartemisinin,12h
cell20230106-U266D1_L3

tag: cell line

tag: cell type


title: RNA-seq of old_3  (PVM, aged)

description: Library name: old_3


title: U266 cells,Dihydroartemisinin, 12h, 3

description:
Dihydroartemisinin,12h
cell20230106-U266D3_L3


title: cKO_WaveNeg_rep3.1


title: RNA-seq of old_4  (PVM, aged)

description: Library name: old_4


title: U266 cells,DMSO, 12h, 3

description:
control
cell20230106-U2663_L3


title: AGS control biol rep3

description: Library name: AGSCT3

source_name: AGS

value: AGS


title: AGS control biol rep2

description: Library name: AGSCT2


title: primary cortical neurons, 24hrs post 1hr ETP treatment, rep3, Fos

city: Dallas

first: Ram

last: Madabhushi

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Library name: Fos_ETP_rec_3

data_processing:
4Cker mapping was performed using Bowtie2 to a reduced genome consisting of all unique x-nt (nucleotide count differs depending on sequencing run and viewpoint specific primers) regions surrounding DpnII sites from the hg38 or mm10 reference genome allowing for zero mismatches.
To define regions with significant interaction with the viewpoint we used either cisAnalysis (cis) or nearBaitAnalysis (nb) of 4Cker inputting three replicates per sample
Mapping with pipe4C was done with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
Assembly: mm10 and hg38
Supplementary files format and content: Bigwig files
Library strategy: 4C-Seq

source_name: primary cortical neurons

extract_protocol:
Approximately 10 million primary cortical neurons (DIV13) or Hek 293T cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with glycine (0.13M final concentration). Cells were incubated for 20 min on ice in lysis buffer (50mM Tris-HCl pH 75, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100, and protease inhibitors).
Nuclei were resuspended in 450uL 1.2x CutSmart buffer and permeabilized with 15uL 10% SDS for 1hr and 75uL 20% Triton X-100. A sample of undigested chromatin was collected to assess chromatin integrity. DNA was digested with 100U NlaIII at 37°C for 3hrs while shaking at 750rpm and then an additional 100U of NlaIII was added and incubated overnight. The extent of chromatin digestion was assessed via gel electrophoresis. NlaIII was deactivated for 20 min at 65°C. Chromatin was diluted to 7mL, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase for overnight ligation at 16°C while shaking. Ligation efficiency was checked by gel electrophoresis. Crosslinks were reversed and proteins digested with proteinase K (30uL of 10mg/ml) overnight at 65°C. DNA was extracted via phenol:chloroform and precipitated with ethanol. DNA was then digested overnight at 37°C with 50U DpnII supplemented with 10X DpnII Buffer while shaking. Second digestion efficiency was determined via gel electrophoresis. DpnII was deactivated at 65°C for 20 min. DNA circularized in a 7mL reaction, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase overnight at 16°C with shaking. Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using Expand Long Template Polymerase starting with 200ng of 4C library template. Viewpoint-specific primers were used to amplify circular templates with the bait of interest. The first round of amplification with the following thermocycler conditions 94°C  for 2 min; 94°C for 10sec, 58° C for 1 min, 68°C for 3 min, for 16 cycles; and 68°C for 5 min. Five different PCR reactions per sample were pooled and 50uL of the pool was used to perform 0.8 x AMPure XP bead purification. 5uL of purified round 1 PCR product was then used for the second round of amplification conducted with the following cycling conditions 94°C for 2 min; 94°C for 10 sec, 60°C for 1 min, 68°C for 3 min for 20 cycles; and 68°C for 5 min. PCR clean up was doing using Qiagen PCR Purification.  DNA fragment size of final, clean PCR products was assessed via Tapestation (Agilent). Library concentrations for each sample was assessed using fluormetry (dsDNA high sensitivity Qubit assay, Thermo) and RT-qPCR (KAPA Biosystems) library quantification.

value: primary cortical neurons

tag: bait

value: Fos promoter

value: WT Swiss Webster Mice


title: cKO_WaveNeg_rep2.4


title: RNA-seq of old_2  (PVM, aged)

description: Library name: old_2


title: AGS CYD-4-61 treatment biol rep3

description: Library name: AGSA3


title: cKO_WaveNeg_rep2.3


title: RNA-seq of old_1 (PVM, aged)

description: Library name: old_1


title: AGS control biol rep1

description: Library name: AGSCT1


title: cKO_WaveNeg_rep2.2


title: U266 cells,DMSO, 12h, 2

description:
control
cell20230106-U2662_L3


title: AGS CYD-4-61 treatment biol rep2

description: Library name: AGSA2


title: U266 cells,DMSO, 12h, 1

description:
control
cell20230106-U2661_L3


title: Mel270 HM3#1 IP

first: bei

address: Jinsui street

institute: Zhongshan Ophthalmic Center

description: Library name: HM3#1_IP_H3K27ac

data_processing:
RNA-seq：HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. ChIP-seq：Reads were mapped to the reference genome using BWA v0.7.12 and BWA mem v0.7.12. Wiggle files for gene tracks were generated using MACS2, and peaks were visualized in Integrative Genomics Viewer. ChIP-seq reads were first processed to remove adapter sequences using Cutadapt (v2.5) and then aligned to the human genome (hg38) using bowtie2 (v2.3.5.1) with default parameters. Significant H3K27ac enrichment peaks were identified using MACS2 (v2.1.2), generating narrowPeak files. Peaks overlapping blacklist regions were removed based on the ENCODE blacklist database. The remaining peaks were analyzed using the ROSE algorithm to identify active enhancers and super-enhancers. Enhancers were stitched, and super-enhancers were ranked based on input-subtracted H3K27ac signal. Typical enhancers were defined as peaks within 2.5 kb of transcription start sites (TSS), while super-enhancers were distinguished by an inflection point in the rank versus signal curve. ATAC-seq：Library DNA was sequenced in paired-end mode with 150 bp reads on an Illumina HiSeq X Ten platform.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include gene expression matrices in XLS format containing FPKM values for each gene across samples.Processed data include TDF files representing genome-wide ChIP-seq and ATAC signal tracks for visualization in IGV.

extract_protocol:
RNA-seq：1) For THZ1 treatment, Mel270 cells were incubated in medium containing THZ1 at the indicated.concentrations or DMSO for 6 h, RNA was isolated with Rneasy Micro Kit (Qiagen). 2) For exosomal RNA-Seq, RNA extraceted from HUVEC exosomes was treated with terminator 5’-Phosphate-Dependent Exonuclease (Epicenter, Madsion, WI) to degrade 5’-monophosphate RNA in exosomal RNA, and subsequently treated with 5’ polyphosphatase (Epicenter, Madsion, WI) to convert 5’ppp to 5’p, yielding specifically ligated RNA adaptor P5_RNA to RNAs that originally have 5’ppp. ChIP-seq：EZ-ChIP Kit (EMD Millipore, Burlington, MA) was used for ChIP according to our previous reports⁹. In brief, Mel270 cells (1×10⁷) were crosslinked in 1% formaldehyde for 10 min at room temperature and quenched unreacted formaldehyde with glycine. The cell lysates were sonicated to shear DNA to length of 200–500 bp and centrifuged at 12,000 g at 4 °C for 10 min. Protein G agarose (60 μL) was added to each tube to preclear the chromatin before immunoprecipitated with anti-H3K27ac antibodies (5 μg), anti-ELK-1 antibodies (5 μg), anti-STAT1 antibodies (5 μg) or rabbit IgG (negative Parental) overnight at 4 °C with rotation. The protein-DNA complexes underwent reverse crosslinks overnight. RNase A and Proteinase K were used to digest RNA and protein, respectively. DNA was then purified with spin columns. ATAC-seq: CFPAC-1 (pTSB-Vector or pTSB-KLF4; Scramble, shKLF4#1 or shKLF4#2) cells were digested with 0.25% Trypsin. After washing with PBS, 5 × 10^4 cells were lysed in ice-cold lysis buffer (10 mmol/L Tris-HCl pH 7.5, 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.5% IGEPAL CA-630, and 0.1% Tween-20) for 10 min. After nuclei were collected by centrifuging at 500 g for 5 min, Tn5 transposase reactions (#TD501, Vazyme Biotech, Nanjing, China) were immediately performed at 37°C for 30 min. The transposed DNA fragments were purified with VAHTS DNA Clean Beads (#N411, Vazyme Biotech, Nanjing, China).
RNA-seq：Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit.for Illumina® (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. ChIP-seq： Illumina sequencing libraries were generated using TruSeq PE Cluster Kit v3-cBot-HS and sequenced on an Illumina HiSeq platform. ATAC-seq：The purified DNA fragments were amplified using TruePrep Index Kit V2 for Illumina (#TD202, Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions.

value: Uveal melanoma


title: LP-1 cells, Dihydroartemisinin, 12h, 3

description:
Dihydroartemisinin,12h
Lp-1-Med3_L1


title: LP-1 cells, Dihydroartemisinin, 12h, 2

description:
Dihydroartemisinin,12h
Lp-1-Med2_L1


title: cKO_WaveNeg_rep2.1

value: Postnatal day 7


title: cKO_WaveNeg_rep1.4


title: LP-1 cells, Dihydroartemisinin, 12h, 1

description:
Dihydroartemisinin,12h
Lp-1-Med1_L1


title: AGS CYD-4-61 treatment biol rep1

description: Library name: AGSA1

value: gastric cancer cells


title: Mel270 HM3#15 IP

description: Library name: HM3#15_IP_H3K27ac

value: WT


title: LP-1 cells, DMSO, 12h, 3

description:
control
LP-1-N3_L1


title: CYD-4-61 treated GA0518 SOX9 KO cells biol rep3

description: Library name: a35g2s9k3

value: SOX9 KO


title: Mel270 HM3#1 Input

description: Library name: HM3#1_input


title: CYD-4-61 treated GA0518 SOX9 KO cells biol rep2

description: Library name: a35g2s9k2


title: cKO_WaveNeg_rep1.3


title: Mel270 HM3#11 IP

description: Library name: HM3#11_IP_H3K27ac


title: cKO_WaveNeg_rep1.2


title: LP-1 cells, DMSO, 12h, 2

description:
control
LP-1-N2_L1


title: LP-1 cells, DMSO, 12h, 1

description:
control
LP-1-N1_L1


title: Mel270 HM3#15 Input

description: Library name: HM3#15_input


title: CYD-4-61 treated GA0518 cells biol rep3

description: Library name: a35g2c3


title: Mel270 Parental IP

description: Library name: Parental_IP_H3K27ac

value: Parental


title: cKO_WavePos_rep3.4


title: Mel270 HM3#11 Input

description: Library name: HM3#11_input


title: cKO_WaveNeg_rep1.1


title: CYD-4-61 treated GA0518 cells biol rep2

description: Library name: a35g2c2


title: CYD-4-61 treated GA0518 cells biol rep1

description: Library name: a35g2c1


title: Non-tumor liver tissue, DEN-exposed, Brca1-KO, bio rep2

city: To

first: Martha

last: Ghebreselassie

address: 10-601D, Princess Margaret Cancer Research Tower 101 College Park

institute: University of Toronto

description:
Library name: DEN_KO_2
10x Genomics

library_source: genomic single cell

data_processing:
Resulting raw sequencing data was converted into FASTQ files using Cell Ranger software.
Assembly: GRCh38 human transcriptome
Supplementary files format and content: Tab-separated value files and matrix files

source_name: liver

extract_protocol:
Nuclei were isolated as described in this article: Andrews, T. S., Atif, J., Liu, J. C., Perciani, C. T., Ma, X. Z., Thoeni, C., Slyper, M., Eraslan, G., Segerstolpe, A., Manuel, J., Chung, S., Winter, E., Cirlan, I., Khuu, N., Fischer, S., Rozenblatt-Rosen, O., Regev, A., McGilvray, I. D., Bader, G. D., & MacParland, S. A. (2022). Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity. Hepatology communications, 6(4), 821–840. https://doi.org/10.1002/hep4.1854
Library was constructed in accordance to the manufacturer's instructions in Single Cell 3’ v1 Reagent Kit from 10X Genomics.

treatment_protocol: 25mg/kg of DEN at 14 days of age

value: liver

value: 12 months old

tag: Sex

value: male

value: 25 mg/kg DEN at 14 days old


title: Ovary tissue, EMS 5

city: Seoul

first: YunSoo

last: Chung

address: Yonseiro 50-1, Yonsei University College of Medicine

department: OBGY

country: South Korea

institute: Severance Hospital

description: Library name: Sample 19

data_processing:
FastQCvv011.7 and Trimmomatic 0.38 Preprocessed data were mapped to reference genomes by hierarchical indexing for spliced alignment of transcript 2 (HISAT2) version 2.1.0 (Johns Hopkins University, Baltimore, MD, USA), to produce aligned reads.
Assembly: Transcript assembly was carried out using StringTie version 2.1.3b (National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA). The pre-filtered data were then analyzed using DESeq2 (R package, v. 1.36.0).
Supplementary files format and content: Processed data saved as excel file

source_name: Ovary tissue

extract_protocol:
RNA was purified after removal of DNA contamination using DNase and a Ribo-Zero rRNA Removal Kit (Illumina, San Diego, CA, USA).
SureSelectXT RNA Direct For Preparation of Strand-Specific Sequencing for the Illumina Platform Version A0, July 2017

value: Ovary tissue


title: CYD-4-61 treated GA0518 SOX9 KO cells biol rep1

description: Library name: a35g2s9k1


title: cKO_WavePos_rep3.2


title: Mel270 shKLF4 IP

city: Guangzhou

description: Library name: shKLF4_IP


title: cKO_WavePos_rep3.1


title: cKO_WavePos_rep3.3


title: Mel270 Parental Input

description: Library name: Parental_input


title: Non-tumor liver tissue, DEN-exposed, Brca1-KO, bio rep1

description:
Library name: DEN_KO_1
10x Genomics


title: HCASMC, siKDM4A, Rep_4

city: New Haven

first: Kathleen

last: Martin

state: CT

address: 300 George Street

institute: Yale School of Medicine

description: Library name: Sample 29

data_processing:
Primary analysis - sample de-multiplexing and alignment to the human genome - is performed using Illumina's CASAVA 1.8.2 software suite. Partek flow was used for RNA-seq analysis and pathway analysis employed Ingenuity pathway analysis tools.
Assembly: hg19
Supplementary files format and content: txt (expression matrix)

source_name: Smooth muscle

extract_protocol:
The RNA was extracted from human coronary artery smooth muscle cells (hCASMCs) using the RNA extraction kit from Qiagen.
Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel, which measures the ratio of the ribosomal peaks. mRNA is purified from approximately 500 ng of total RNA with oligo-dT beads and sheared by incubation at 94°C. Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries. The cDNA library is then end-repaired, and A-tailed, adapters are ligated, and second-strand digestion is performed by Uracil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the Lab Chip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing. Samples are sequenced using 75 bp single end sequencing on an Illumina Hi-Seq 2500 according to Illumina protocols. Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.

value: Smooth muscle

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: Smooth muscle cells

value: KDM4A knockdown


title: HCASMC, siKDM4A, Rep_5

description: Library name: Sample 30


title: A375 _KOMK2+JQ1_IgG

city: Quebec City

first: Jean-Philippe

last: Lambert

address: 2705, boulevard Laurier

institute: Université Laval

data_processing:
Data cleaning: Trim Galore/Cutadapt
Quality control: FastQC and MultiQC
Alignment : BowTie2 + Samblaster to flag duplicates
Peak calling : macs2 callpeak against corresponding IgG sample
Assembly: GRCh38.p10
Supplementary files format and content: *_raw.bw : BigWig alignement with no normalization
Supplementary files format and content: *_BPM.bw : BigWig alignement with bin per millions normalization
Supplementary files format and content: *.narrowPeak : Macs2 peakcalling in narrowPeak mode
Library strategy: CUT&RUN

source_name: MK2 KO + JQ1 + IgG antibody

extract_protocol:
Cells were cross-linked with 0.1% formaldehyde for 1 min at room temperature prior to isolating nucleus and performing CUT&RUN.
The NEBNext Ultra II DNA kit for low-input ChIP kit (New Englands Biolabs Inc., Ipswich, MA, USA) was used to prepare libraries according to the manufacturer's instruction.

value: Skin

value: Malignant Melanoma

value: MAPKAPK2 knockout

value: JQ1 500nM

tag: time

tag: chip antibody

value: IgG


title: Mel270 SCR IP

last: Jin

description: Library name: SCR_IP

value: Uveal melanoma

value: WT

value: Scramble


title: cKO_WavePos_rep2.4

value: Postnatal day 7


title: Non-tumor liver tissue, DEN-exposed, Brca1-WT, bio rep1

description:
Library name: DEN_WT_1
10x Genomics

value: liver

value: 12 months old


title: HCASMC, siKDM4A, Rep_3

description: Library name: Sample 28


title: HCASMC, siKDM4A, Rep_2

description: Library name: Sample 27


title: cKO_WavePos_rep2.3


title: Mel270 SCR Input

description: Library name: SCR_Input


title: Non-tumor liver tissue, DEN-exposed, Brca1-WT, bio rep2

description:
Library name: DEN_WT_2
10x Genomics

value: male

value: 25 mg/kg DEN at 14 days old


title: HCASMC, siKDM4A, Rep_1

description: Library name: Sample 26

value: Smooth muscle


title: cKO_WavePos_rep2.2


title: Mel270 Monoculture IP

description: Library name: Monoculture_IP

value: Mono-culture


title: Liver, CR6, STAT1KO, biol rep 4

city: Vancouver

first: Lisa

middle: C

last: Osborne

state: BC

address: 3507-2350 Health Sciences Mall

department: Microbiology & Immunology

institute: University of British Columbia

description:
Library name: Sample 9
liver_9

data_processing:
FASTQ files were mapped and aligned using the Salmon Aligner v1.10.1. Reads were mapped to an index created using the GRCm38 mouse transcriptome assembly with decoy sequences generated using SalmonTools.
Differential gene expression analysis was performed with R on Salmon output files. The tximeta package was used to convert transcript quantifications to Ensembl mouse transcriptome (mm10) gene counts. DESeq2 was used for variance stabilization. Gene count expression values were extracted following log2 transformation with variance stabilizing transformations.
Assembly: mm10/GRCm38
Supplementary files format and content: csv file contains batch normalized expression values for each sample (log2 transformed with variance stabilizing transformations).

source_name: Liver

extract_protocol:
RNA from liver biopsies was extracted with TRIzol (Invitrogen) as per manufacturers instructions.
Library was constructed following standard protocol for Illumina Stranded mRNA prep (Illumina) by the UBC SBME Sequencing (UBC SBME-Seq) core facility.

treatment_protocol: STAT1Het or KO (C57BL/6 background, n = 5 per group) mice were infected with murine norovirus strain CR6 (2E05 pfu) intravenously by tail vein injection.

value: Liver

tag: batch


title: Liver, CR6, STAT1KO, biol rep 5

description:
Library name: Sample 10
liver_10


title: Mel270 Monoculture Input

description: Library name: Monoculture_Input


title: Liver, CR6, STAT1Het, biol rep 5

description:
Library name: Sample 11
liver_11


title: HCASMC, siCtrl, Rep_5

description: Library name: Sample 25

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: Smooth muscle cells


title: cKO_WavePos_rep2.1


title: Mel270 shKLF4 Input

description: Library name: shKLF4_Input


title: Liver, CR6, STAT1Het, biol rep 4

description:
Library name: Sample 7
liver_7


title: cKO_WavePos_rep1.4


title: Liver, CR6, STAT1Het, biol rep 3

description:
Library name: Sample 6
liver_6


title: HCASMC, siCtrl, Rep_4

description: Library name: Sample 24


title: Liver, CR6, STAT1KO, biol rep 3

description:
Library name: Sample 5
liver_5


title: Mel270 Coculture IP

description: Library name: Coculture_IP

value: Co-culture


title: cKO_WavePos_rep1.3


title: cKO_WavePos_rep1.2


title: Mel270 Coculture Input

description: Library name: Coculture_Input


title: HCASMC, siCtrl, Rep_3

description: Library name: Sample 23


title: HCASMC, siCtrl, Rep_2

description: Library name: Sample 22


title: HUVEC exosomes 5PPP

description: Library name: HUVEC exosomes_RNA_S1_5PPP-F

source_name: HUVEC

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: 5′-ppp enzyme treatment


title: Liver, CR6, STAT1KO, biol rep 1

description:
Library name: Sample 3
liver_3


title: HUVEC exosomes Control

description: Library name: HUVEC exosomes_RNA_S1_Control

value: NON


title: Liver, CR6, STAT1KO, biol rep 2

description:
Library name: Sample 4
liver_4


title: cKO_WavePos_rep1.1


title: HCASMC, siTET2, Replicate 5

description: Library name: Sample 20

value: TET2 knockdown


title: HCASMC, siCtrl, Rep_1

description: Library name: Sample 21

value: WT


title: Mel270 THZ1(250 nM)

description: Library name: Mel270_RNA_S1_250 nM

value: Uveal melanoma


title: WT_WaveNeg_rep3.3

value: Beta2fl/fl; Cre-negative

value: Postnatal day 7


title: WT_WaveNeg_rep3.4


title: Liver, CR6, STAT1Het, biol rep 2

description:
Library name: Sample 2
liver_2


title: Mel270 THZ1(62.5 nM)

description: Library name: Mel270_RNA_S1_62.5 nM


title: HCASMC, siTET2, Replicate 3

description: Library name: Sample 18


title: Mel270 Control

description: Library name: Mel270_RNA_S1_Control


title: HCASMC, siTET2, Replicate 4

description: Library name: Sample 19


title: WT_WaveNeg_rep3.1


title: WT_WaveNeg_rep3.2


title: Neuro Sphere RIP - KO CPEB4 IP Repl. 1

description:
immunoprecipitation (IP) fraction with CPEB4 antibody
cpeb4_rip_counts.csv
Sample 13

data_processing:
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

source_name: Neuro Sphere

value: Neuro Sphere

tag: nsc isolation

value: cultured

value: no treatment

tag: sequenced molecule

value: mRNA


title: HCASMC, siTET2, Replicate 2

description: Library name: Sample 17

value: Smooth muscle


title: Neuro Sphere RIP - KO CPEB4 IP Repl. 2

description:
immunoprecipitation (IP) fraction with CPEB4 antibody
cpeb4_rip_counts.csv
Sample 14


title: Liver, CR6, STAT1Het, biol rep 1

description:
Library name: Sample 1
liver_1

value: Liver


title: Neuro Sphere RIP - WT CPEB4 IP Repl. 2

description:
immunoprecipitation (IP) fraction with CPEB4 antibody
cpeb4_rip_counts.csv
Sample 12

value: wildtype


title: WT_WaveNeg_rep2.4


title: The hepatocytes within the liver of 7 dpf transgenic Tg(fabp10:GFP) zebrafish

city: chengdu

first: Zhilin

last: Deng

state: sichuan

address: sichuan chengdu chengdu medical college

department: School of Basic Medical Sciences

institute: Chengdu medical college

description: Library name: D7_GFP

data_processing:
Raw reads were quality filtered and adapters were trimmed using fastp v0.23.2.
Clean reads were aligned to the zebrafish reference genome GRCz11 using STAR v2.7.9a.
Gene-level read counts were generated using featureCounts (subread v2.0.3).
Differential expression analysis was performed using DESeq2 (v1.38.3) in R.
Assembly: GRCz11 (Ensembl release 104)
Supplementary files format and content: Processed data includes gene expression matrix (TPM) listing gene IDs and other information

organism: Danio rerio

extract_protocol:
For the four samples sorted by flow cytometry (D3_Cont, D3_GFP, D7_GFP, Adult_GFP), the total RNA in the cells was extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's protocol.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) following the manufacturer’s instructions.

value: liver

value: hepatocyte


title: The hepatocytes within the liver of adult transgenic Tg(fabp10:GFP) zebrafish

description: Library name: Adult_GFP


title: HCASMC, siTET2, Replicate 1

description: Library name: Sample 16

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: Smooth muscle cells


title: HCASMC, siCtrl, Replicate 5

description: Library name: Sample 15


title: The hepatocytes within the liver of 3dpf transgenic Tg(fabp10:GFP) zebrafish

description: Library name: D3_GFP


title: The non-hepatocytes within the liver of 3dp transgenic Tg(fabp10:GFP) zebrafish

description: Library name: D3_Cont

value: non-hepatocyte


title: WT_WaveNeg_rep2.3


title: Neuro Sphere RIP - WT CPEB4 IP Repl. 1

description:
immunoprecipitation (IP) fraction with CPEB4 antibody
cpeb4_rip_counts.csv
Sample 11


title: WT_WaveNeg_rep2.2


title: Neuro Sphere RIP - WT IgG Repl. 2

description:
immunoprecipitation (IP) IgG fraction
cpeb4_rip_counts.csv
Sample 10


title: HCASMC, siCtrl, Replicate 3

description: Library name: Sample 13


title: HCASMC, siCtrl, Replicate 4

description: Library name: Sample 14