title: THP1, CYR61 0.5, rep3

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample13


title: C57_MA_BCR_ASC1350A5

status: Public on Oct 18 2023

type: SRA

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

country: USA

institute: University of Pittsburgh

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Gene Expression (GEX) FASTQ files were aligned and a cell barcode x gene count matrix was generated with CellRanger 6, in reference to 10X Genomics' mouse refdata-gex-mm10-2020-A transcriptome.  BCR and TCR FASTQ files were aligned using CellRanger 6 to 10X Genomics' mouse V(D)J reference, vdj_GRCm38_alts_ensembl-5.0.0
Secondary analysis was performed with raw_feature_bc_matrix.h5 files for gene expression data and respective all_contig_annotations.csv and clonotypes.csv for TCR and BCR data. R 4.2.1 was utilized with the Seurat package (v4.3.0) and nichenetr (v1.1.0)
The raw_feature_bc_matrix.h5 files were initially loaded into Seurat and filtered such that only cells expressing at least 200 genes were retained.  Only cells containing less than 1% hemoglobin content were retained.
Wilcoxon rank sum test with Bonferroni FDR correction was used for DEG testing.
Assembly: refdata-gex-mm10-2020-A for transcriptome and vdj_GRCm38_alts_ensembl-5.0.0 for V(D)J reference
Supplementary files format and content: 10x Genomics output scRNA files: raw_feature_bc_matrix.h5
Supplementary files format and content: VDJ output files:  all_contig_annotations.csv and clonotypes.csv

molecule: polyA RNA

organism: Mus musculus

source_name: Hindlimb muscle

extract_protocol: Llibraries were constructed according to the manufacturer's directions as described in 10X Genomics' Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index), Protocol CG000331

treatment_protocol: As outlined in the experimental protocol, scRNAseq was performed on muscle-resident/infiltrating cells isolated from mice immunized with vehicle (PBS) versus recombinant HRS protein.  No additional treatment was administered to experimental mice.

tag: tissue

value: Hindlimb muscle

tag: strain

tag: treatment

value: MA

tag: chemistry


title: Camellia-seq-lineage_LL653-E1-P2-RC_rep2

city: Hangzhou

first: SHOU-WEN

last: WANG

state: Zhejiang Province

address: Shilongshan ST #18, Xihu District

country: China

institute: Westlake University

library_source: transcriptomic

data_processing: DATA are processed with CARLIN pipeline, except CARLIN libraries from Camellia-seq, which were analyzied with a customized script.

molecule: total RNA

source_name: FetalLiver-HSC

extract_protocol:
Each sample has its corresponding CARLIN protocol as shown above. The CARLIN DNA or RNA materials are extracted from either 1) bulk cell populations sorted with FACS or 2) single-cell samples prepared with 10X encapsulation or individually sorted single cells from Camellia-seq
We used bulk RNA or DNA as starting material. RNA were converted to DNA with SuperScrit III. Then we used a nested PCR approach with locus specific primers to perform targeted amplification with Q5 High-Fidelity DNA Polymerase (New England Biosciences, M0491L). We used 1.5X Ampure XP beads (Beckman Coulter, A63881) to purify the PCR product from each step once except the final indexing PCR product (0.8X, twice purification). The final indexing libraries were pooled and quantified (Kappa Biosystems, KK4835) and sequenced on Illumina MiSeq using paired-end 500 cycles v2 kits (Illumina, MS-102-2003) with 5% PhiX sequencing control v3 (Illumina, FC-110-3001).

tag: cell type

value: FetalLiver-HSC

tag: carlin protocol

tag: carlin locus

value: RC


title: K8_WT_D0_071421

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
reads were trimmed using Cutadapt v2.3
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a
assigned count estimates to genes with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited text of raw counts

source_name: Alveolar epithelial cells

extract_protocol: RNA was isolated from cells using the RNeasy Micro kit (Qiagen 74004) according to the manufacturer’s instructions.

value: Alveolar epithelial cells

tag: batch

tag: time

tag: genotype

value: WT

tag: biological replicate

value: Biol Rep 2


title: Camellia-seq-lineage_LL653-E1-P2-TC

value: TC


title: Camellia-seq-lineage_LL744-P2-TC

source_name: AGM-HSC

value: AGM-HSC


title: M1-Right-03-Glia-H3K27me3-R1

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: MOWChIP-seq data. Name format: Mouse number-Left/right hemisphere-Slice number-Neuron/glia-Marker-Replicate number

library_source: genomic

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools and bedtools to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Assembly: mm10
Supplementary files format and content: Normalized ChIP-seq and RNA-seq signal in BigWig format

molecule: genomic DNA

source_name: C57BL/6J brain

extract_protocol:
Nuclei extraction from dissected brain tissue was performed using previously described protocol with minor modifications. All steps were conducted on ice and centrifugation was conducted at 4 ℃. A neocortex slice was thawed on ice and transferred to a glass tissue homogenizer (Sigma, d9036-1SET). 3 ml of ice-cold nuclei extraction buffer was added [0.32 M sucrose, 5mM CaCl2, 2 mM Mg(Ac)2 , 0.1 mM EDTA, 10 mM tris-HCl, 0.1% (v/v) Triton X-100, freshly added 1% protease inhibitor cocktail (PIC, Sigma-Aldrich), 0.1 mM PMSF, 1 mM DTT, and 0.06 U/µl ribonuclease (RNase) inhibitor (2313A,Takara Bio, needed when mRNA extraction was performed)]. The tissue was homogenized with 10 times of slow douncing using a loose pestle and 15 times of douncing using a tight pestle (D9063, Sigma-Aldrich). The homogenate was filtered through a 40-µm cell strainer (22363547, Thermo Fisher Scientific) into a 15-ml centrifuge tube and centrifuged at 1000 rcf for 10 min at 4 ℃. Supernatant was discarded and the pellet was resuspended in 0.5 ml of ice-cold nuclei extraction buffer. 0.75 ml of 50% (w/v) iodixanol (made by mixing 4 ml of OptiPrepTM gradient (Sigma-Aldrich) and 0.8 ml of diluent [150 mM KCl, 30 mM MgCl2, and 120 mM tris-HCl]) was added. The suspension was gently mixed by inverting the tube up and down 5 times and then centrifuged at 10,000 rcf for 20 min. Supernatant was carefully removed and the pellet incubated with 100 µl of 2% (w/v) normal goat serum (50062Z, Life Technologies) in Dulbecco’s PBS (DPBS, Life technologies) on ice. The pellet was then resuspended and transferred into a new Eppendorf tube with an addition of 200 µl of 2% normal goat serum. To differentiate neurons from glia, 10 µl of 2 ng/µl Anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was mixed with the suspension. The mixture was incubated at 4 ℃ for 1 h on a rotator. The nuclei solution was sorted using FACS (BS FACSAria, BD Bioscience) to separate neuronal (NeuN+) and glial (NeuN-) fractions.   Chromatin fragmentation:  M1-2: 4,000 nuclei per replicate was used so that both neuronal and glial fractions of every neocortex slice sample yielded enough material for two ChIP-seq replicates. The nuclei suspension (containing 8,000 nuclei) was topped up to 1 ml using Dulbecco’s PBS (DPBS; 14190144, Life Technologies). 200 µl of 1.8M sucrose, 10 µl of 1M CaCl2, and 3 µl of 1M Mg(Ac)2 were then added sequentially. The sample was mixed gently by inverting the tube up and down and then incubated for 15 min on ice. The suspension was centrifuged at 3,000 rpm for 15 min at 4 ℃. Supernatant was carefully removed, and the pellet was resuspended in 10 µl DPBS. 0.1 µl of PIC, 0.1 µl of 100 mM PMSF and 10 µl of lysis buffer [4% Triton X-100, 100 mM tris (pH 7.5), 100 mM NaCl, and 30 mM MgCl2] were added, mixed by vortexing and then incubated at room temperature for 10 min. 1 µl of 0.1 M CaCl2 and 0.4 µl of 100 U/µl MNase (88216, Thermo Fisher Scientific) were then added, mixed by vortexing and incubated at room temperature for 10 min. 2.22 µl of 0.5 M EDTA (pH 8) was added to quench the rection. The sample was vortexed and incubated on ice for 10 min before it was centrifuged at 16,100 g for 5min. The supernatant (~20 µl, containing chromatin) was transferred to a new tube and 60 µl of IP buffer [20 mM Tris-HCl, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100] was added to obtain a total volume of ~80 µl. The solution was finally split for two ChIP-seq replicates. The chromatin was stored on ice before loaded into the MOWChIP device.  M4-5: 200 µl of sorted neuronal nuclei suspension from one neocortex slice sample was used to prepare chromatin (containing ~30,000 nuclei). 2 µl of PIC, 2 µl of 100 mM PMSF and 200 µl of lysis buffer were added, mixed by vortexing and incubated at room temperature for 10 min. 4 µl of 1 M CaCl2 and 5 µl of 100 U MNase (88216, Thermo Fisher Scientific) were added, mixed by vortexing and incubated at room temperature for 10 min. 44 µl of 0.5 M EDTA was then added, mixed by vortexing and incubated on ice for 10 min. The mixture was finally centrifuged at 16,100g for 5 min at 4 °C. Supernatant containing fragmented chromatin (~ 440 µl) was collected into a new 1.5 ml tube and placed on ice before use. 70 µl of chromatin (containing chromatin from ~4,000 nuclei) was used for each MOWChIP-seq assay for consistency with data on M1-2.  Antibody coating on IP beads:  5 µl of Dynabeads Protein A (10002D, Thermo Fisher Scientific) were used in each MOWChIP assay. Beads were washed twice with 150 µl of IP buffer [20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100] and then resuspended in 150 µl of IP buffer. An antibody that targets a specific modified histone was added to coat the beads: anti-H3K27ac (ab4729, Abcam) at 0.125 µg/assay or anti-H3K27me3 (39155, Active Motif) at 0.5 µg/assay. The bead/antibody suspension was incubated on a rotator at 4 °C overnight. Beads were then washed with IP buffer twice and resuspended in 5 µl of IP buffer for use in MOWChIP.  MOWChIP:  The MOWChIP process, including device fabrication and operation, was performed following our published protocol (Zhu, B., Hsieh, YP., Murphy, T.W. et al. MOWChIP-seq for low-input and multiplexed profiling of genome-wide histone modifications. Nat Protoc 14, 3366–3394 (2019).).
ChIP-seq libraries:  ~4,000 neuronal or glial nuclei were used to produce each ChIP-seq library and two technical replicates were generated on each neocortex slice sample. The input libraries were created using the same starting quantity of nuclei (~ 4,000 per library) with the MOWChIP step skipped. Libraries were constructed using 2S Plus DNA Library kit (10009877, IDT) and 2S CDI Adapter S1 indexing kit (10009895, IDT) following the manufacturer’s instructions. 5% (v/v) EvaGreen (31000, Biotium) was added to the amplification mixture to monitor the progress of library amplification. Amplification was stopped once an increase of 2,000 RFU was reached. Library was eluted to 10 µl of low EDTA TE buffer.  mRNA-seq:  mRNA libraries were prepared following Smart-seq2 protocol55 with minor modifications. ~7,500 neuronal nuclei (from M3) were used to generate each RNA-seq library, and each slice sample has two technical replicates. 50 μl of neuronal suspension containing about 7,500 nuclei was used for RNA extraction using RNeasy Mini kit (QIAGEN) and RNase-Free DNase Set (79254, QIAGEN). Extracted RNA was concentrated using ethanol precipitation and resuspended in 5 μl of RNase-free water. 4.6 μl of RNA solution, 2 μl of 10 μM oligo-dT primer and 2 μl of 10 mM dNTP mix were mixed, incubated at 72°C for 3 mins and then stored on ice. 11.4 μl of reverse-transcription mix (made from 1 μl of SuperScript II reverse transcriptase (200 U/μl), 0.5 μL of RNase inhibitor (40 U/μl), 4 μL of Superscript II first-strand buffer, 1 μl of DTT (100mM), 4 μl of 5 M Betaine, 0.12 μl of 1 M MgCl2, 0.2 μl of TSO (10 μM), 0.58 μl of nuclease-free water) was added to the RNA solution and incubated at 42°C for 90 min, followed by 10 cycles of (50°C for 2 min, 42°C for 2 min), and at 70°C for 15 min. 25 μl KAPA HiFi HotStart ReadyMix, 0.5 μl of 10 μM IS PCR primers, 2.5 μl of 20x Evagreen, and 4 μl of RNase-free water were then added. cDNA was amplified by incubation at 98°C for 1 min, followed by 9-11 cycles (to achieve an increase of 50-100 RFU) of (98°C for 15 s, 67°C for 30 s, 72°C for 6 min). After amplification, cDNA was purified using 0.8× SPRIselect beads. Tn5 transposase (14-17 mg/ml) was produced following a published protocol56.  Tn5 transposase and T5/T7 transposons were assembled to form Tn5 transposome using a published protocol57. Briefly, 1.5 μl of 100 μM T5 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS (a 5'-phosphorylated 19-bp mosaic end complementary oligonucleotide, IDT), while 1.5 μl of 100 μM T7 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS. 3 μl of T5-pMENTS solution and 3 μl of T7-pMENTS solution were separately incubated at 95℃ for 5 min followed by a slow ramp to 25℃ at -0.1℃/sec. 2.5 μl of T5-pMENTS solution was then mixed with 2.5 μl of Tn5 transposase (14-17 mg/ml), while 2.5 μl of T7-pMENTS solution was mixed with 2.5 μl of Tn5 transposase. T5-Tn5 solution and T7-Tn5 solution were separately incubated at 37℃ for 1 h to form T5-Tn5 transposome and T7-Tn5 transposome, respectively. 4 μl of T5-Tn5 transposome and 4 μl of T7-Tn5 transposome were mixed to form 8 μl of assembled Tn5 transposome before it was mixed with 1 μl cDNA (containing ~500 pg cDNA) and 1 μl reaction buffer (TNP92110, Lucigen). The reaction mixture was incubated at 37 ℃ for 1 h. 1 μl of 10× stop solution (TNP92110, Lucigen) was added to the reaction mixture to stop tagmentation. Two rounds of 1× SPRIselect beads cleanup were performed to purify tagmented cDNA. The tagmented cDNA was then eluted in 10 μl low EDTA TE buffer. 25 μl KAPA HiFi HotStart ReadyMix was activated at 98 ℃ for 30 sec and then mixed with 9.5 μl tagmented cDNA and 10 μl Nuclease-free water, followed by incubation at 72 ℃ for 5 min. 1.5 μl of 25 M P5 primer, 1.5 μl of 25 M P7 primer and 2.5 μl 20x Evagreen were then added. The following amplification program was used to achieve a 300-400 RFU increase: 98 ℃ for 30 s; 11-12 cycles of (98 ℃ for 10 s, 63 ℃ for 30 s, 72 ℃ for 30 s) and 72 ℃ for 1 min. Amplified library was purified with 0.8× SPRIselect beads and eluted in 8 μl low EDTA TE buffer.  Library quality control and sequencing:  Library size and concentration were measured by Tapestation (Agilent) and KAPA Library Quantification Kit (07960140001, Roche), respectively. Libraries were pooled for sequencing by Illumina HiSeq 4000 with single-end 50 nt reads or NovaSeq 6000 in S4 200 mode with paired-end 100 nt reads. Averagely, 19 million reads were generated for each ChIP-seq library, 12 million reads for each ChIP-seq input library, and 16 million reads for each RNA-seq library.
ChIP-seq, RNA-seq

treatment_protocol: All procedures were conducted in accordance with NIH guidelines and were approved by the Institutional Animal Care and Use Committee (IACUC) at Virginia Tech. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory and housed on a 12 h light/dark cycle at 23 °C with food and water ad libitum for 2 weeks before experiments.  M1-M3 were euthanized using compressed CO2 followed by cervical dislocation. Mouse brain was then isolated and cut into coronal slices with a thickness of 0.5 mm using an adult mouse brain slicer (BSMAS005-1, Zivic Instruments) on ice. Left and right neocortex sections were dissected from each slice and immediately frozen in dry ice. The dissected neocortex slice samples (a total of 18-21 slices for either left or right hemisphere of a neocortex) were stored at -80 ℃ until use.M4 and M5 were treated for the study of chemically induced seizure. 2 mg/ml kainic acid (K0133, LKT Laboratories) in sterile saline was prepared freshly. M4 was injected intraperitoneally with repeated 5 mg/kg doses of kainic acid at 30 min intervals until behavioral seizures were observed (after 2 doses). M5 (control) was injected with the same amount of sterile saline at 30 min intervals for 2 doses. M4 and M5 were euthanized by cervical dislocation and death was confirmed by bilateral thoracotomy. Mouse brain was processed to extract 0.5 mm-thick left and right coronal neocortex slices and the slice samples were stored at -80 °C until use.

value: brain


title: K8_KO_D7_061721

value: KO

value: Biol Rep 1


title: THP1, CYR61 0.5, rep1

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample11

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: all.gene_counts.tsv: Raw counts.
Supplementary files format and content: group_5ug_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 5
Supplementary files format and content: group_0.50ug_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.5
Supplementary files format and content: group_0.05ug_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.05

organism: Homo sapiens

source_name: cell line

growth_protocol: We used THP1 monocytes (ATCC TIB-202). These cells were maintained in RPMI 1640 media containing 1% L-glutamine, 1% penicillin/streptomycin, and 10% FBS.

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
We determined total RNA integrity using an Agilent Bioanalyzer or 4200 Tapestation. Using 500 ng - 1 ug of starting total RNA, we removed ribosomal RNA using an RNase-H method using RiboErase kits (Kapa Biosystems). We fragmented mRNA in reverse transcriptase buffer and heated samples to 94 degrees for 8 minutes. We reverse transcribed mRNA to cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. We performed a second strand reaction to yield ds-cDNA. We blunt ended the cDNA, added an A base to the 3' ends, and then ligated Illumina sequencing adapters to the ends. We amplified the ligated fragments for 12-15 cycles using primers incorporating unique dual index tags. We sequenced fragments on an Illumina NovaSeq 6000 using paired end reads extending 150 bases.

treatment_protocol: We treated THP1 cells with recombinant human CYR61 (PeproTech 120-25): 0.00, 0.05, 0.50, and 5.00 μg/ml for 24 hr.

value: cell line

tag: cell line

value: monocytes

value: CYR61, 0.5 ug/ml


title: THP1, CYR61 0.5, rep2

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample12


title: C57_MA_TCR_ASC1350A7

description: 10x Genomics


title: M1-Right-01-Neuron-H3K27me3-R2


title: THP1, CYR61 0.05, rep5

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample10


title: Camellia-seq-lineage_LL653-E1-P2-CC_rep2

value: CC


title: K8_KO_D3_061721


title: M1-Right-01-Neuron-H3K27me3-R1


title: THP1, CYR61 0.05, rep4

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample09


title: K8_WT_D3_061721


title: THP1, CYR61 0.05, rep3

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample08


title: M1-Right-01-Glia-H3K27me3-R2


title: M1-Right-03-Glia-H3K27me3-R2


title: THP1, CYR61 0.05, rep2

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample07


title: K8_KO_D1_061721


title: Camellia-seq-lineage_LL653-E1-P1-TC


title: Camellia-seq-lineage_LL653-E1-P1-RC_rep2


title: Camellia-seq-lineage_LL653-E1-P1-TC_rep2


title: Camellia-seq-lineage_LL653-E1-P2-RC


title: K8_KO_D0_061721


title: THP1, CYR61 0.05, rep1

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample06


title: M1-Left-19-Neuron-H3K27me3-R1


title: Camellia-seq-lineage_LL653-E1-P1-RC


title: M1-Left-19-Neuron-H3K27me3-R2


title: M1-Left-19-Glia-H3K27me3-R2


title: Camellia-seq-lineage_LL653-E1-P1-CC_rep2


title: THP1, control, rep4

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample04

value: control


title: Camellia-seq-lineage_LL653-E1-P2-CC


title: K8_WT_D7_061721


title: THP1, control, rep5

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample05


title: M1-Right-01-Glia-H3K27me3-R1


title: K8_WT_D7_080321

value: Biol Rep 3


title: THP1, control, rep3

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample03


title: K8_KO_D3_080321


title: K8_WT_D1_061721


title: Bulk_DARLIN_v2_TC-DNA-LL675

source_name: Granulocyte

value: Granulocyte


title: M1-Left-18-Neuron-H3K27me3-R2


title: M1-Left-18-Neuron-H3K27me3-R1


title: K8_WT_D3_080321


title: THP1, control, rep1

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample01


title: Bulk_DARLIN_v2_TC-DNA-LL638


title: Bulk_DARLIN_v2_TC-DNA-LL646


title: M1-Left-18-Glia-H3K27me3-R1


title: CRC org-shHILPS rep3

city: Chapel Hill

first: Donghai

last: Wang

state: North Carolina

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina-Chapel Hill (UNC)

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-shGFP-3_R1.fq.gz

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to hg38 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Assembly: hg38
Supplementary files format and content: excel files include counts of samples

source_name: colorectal cancer organoids

growth_protocol: NCM460, RKO and MDA-MB-231 cells were purchased from American Type Culture Collection (ATCC). All these cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (Hyclone). Human ESC H9 (also named WA09) were cultured on Matrigel (Corning)-coated plates in mTesR1 (STEMCELL Technologies) with 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara Bio) following the manufacturer’s instruction and subjected to quality control to inspect RNA integrity by Agilent Bioanalyzer 2100 (Agilent Technologies). RNAs were further purified by RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN).
RNA libraries were constructed using VAHTS Total RNA-Seq (H/M/R) Library PrepKit for Illumina (Vazyme) following manufacturer's protocol.

treatment_protocol: Cells under hypoxia culture were placed in the Hypoxia Incubated Workstation (Ruskinn) and flushed with a gas mixture of 1% O2, 5% CO2, and balanced N2.

value: colorectal cancer organoids

value: HILPS knockdown

value: 1percent O2 shHILPS


title: K8_WT_D0_061721

value: Alveolar epithelial cells

value: WT


title: CRC org-shHILPS rep2

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-shGFP-2_R1.fq.gz


title: K8_KO_D7_080321


title: Bulk_DARLIN_v2_TC-DNA-LL584

value: TC


title: Bulk_DARLIN_v2_TC-DNA-LL591


title: Camellia-seq-lineage_LL653-E1-P1-CC

value: FetalLiver-HSC


title: M1-Left-19-Glia-H3K27me3-R1

value: brain


title: CRC org-shHILPS rep1

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-shGFP-1_R1.fq.gz


title: K8_KO_D0_080321

value: KO


title: Bulk_DARLIN_v2_TC-DNA-LL583


title: THP1, control, rep2

description:
all.gene_counts.tsv
group_5ug_Differential_Expression.tsv
group_0.50ug_Differential_Expression.tsv
group_0.05ug_Differential_Expression.tsv
sample02


title: M1-Left-17-Glia-H3K27me3-R2


title: K8_WT_D0_080321


title: M1-Left-17-Glia-H3K27me3-R1


title: K8_KO_D1_080321


title: Bulk_DARLIN_v2_RC-DNA-LL675

value: RC


title: M1-Left-16-Neuron-H3K27me3-R2


title: CRC org-shGFP rep2

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-sh2-2_R1.fq.gz

value: 1percent O2 shGFP


title: M1-Left-17-Neuron-H3K27me3-R2

description: MOWChIP-seq data. Name format: Mouse number-Left/right hemisphere-Slice number-Neuron/glia-Marker-Replicate number


title: K8_KO_D7_071421

value: Biol Rep 2


title: CRC org-shGFP rep3

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-sh2-3_R1.fq.gz


title: M1-Left-17-Neuron-H3K27me3-R1


title: CRC org-shGFP rep1

description:
RNA-seq
CRC_sh2_vs_shGFP_diffexpr-results.csv
CRC-sh2-1_R1.fq.gz


title: Bulk_DARLIN_v2_RC-DNA-LL646


title: M1-Left-16-Neuron-H3K27me3-R1


title: H9-shHILPS#2 rep3

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-3-3_R1.fq.gz

value: embryonic stem cell

value: 1percent O2 shHILPS#2


title: K8_KO_D3_071421


title: K8_WT_D7_071421


title: M1-Left-16-Glia-H3K27me3-R1


title: K8_WT_D1_080321


title: K8_WT_D3_071421


title: H9-shHILPS#2 rep2

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-3-2_R1.fq.gz


title: M1-Left-15-Neuron-H3K27me3-R2


title: Bulk_DARLIN_v2_RC-DNA-LL584


title: H9-shHILPS#2 rep1

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-3-1_R1.fq.gz


title: M1-Left-15-Neuron-H3K27me3-R1


title: K8_KO_D1_071421


title: Bulk_DARLIN_v2_RC-DNA-LL583


title: H9-shHILPS#1 rep3

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-2-3_R1.fq.gz

value: 1percent O2 shHILPS#1


title: K8_WT_D1_071421


title: M1-Left-15-Glia-H3K27me3-R2


title: Bulk_DARLIN_v2_CC-DNA-LL675

value: CC


title: H9-shHILPS#1 rep2

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-2-2_R1.fq.gz


title: K8_KO_D0_071421


title: Bulk_DARLIN_v2_RC-DNA-LL638

value: Granulocyte


title: M1-Left-15-Glia-H3K27me3-R1


title: Bulk_DARLIN_v2_CC-DNA-LL638


title: H9-shHILPS#1 rep1

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shHILPS-2-1_R1.fq.gz


title: Bulk_DARLIN_v2_CC-DNA-LL646


title: Bulk_DARLIN_v2_RC-DNA-LL591


title: BMDMs, CYR61-0.5, rep3

description:
sample_11
Primary cells

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: group_CYR61_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

source_name: bone marrow-derived macrophages

growth_protocol: We isolated bone marrow from the tibias and femurs of C57BL/6J mice (2-5 months old). Bone marrow cells were incubated for 5-6 days in macrophage differentiation media: DMEM + 10% FBS + 10% CMG-conditioned media + 1% penicillin/streptomycin + 1% L-glutamine. After differentiation, macrophages were switched to mature macrophage media: DMEM + 10% FBS + 2% CMG-conditioned media + 1% penicillin/streptomycin + 1% L-glutamine.

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (Ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: We treated macrophages with 0.00 or 0.50 ug/ml CYR61 (PeproTech 120-25) for 24 hrs.

value: bone marrow-derived macrophages

value: CYR61, 0.5 ug/ml


title: BMDMs, CYR61-0.5, rep4

description:
sample_12
Primary cells


title: BMDMs, CYR61-0.5, rep2

description:
sample_10
Primary cells


title: H9-shGFP rep2

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shGFP-2_R1.fq.gz


title: Bulk_DARLIN_v2_CC-DNA-LL591


title: M1-Left-14-Neuron-H3K27me3-R2


title: M1-Left-14-Glia-H3K27me3-R2


title: H9-shGFP rep3

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shGFP-3_R1.fq.gz


title: Bulk_DARLIN_v2_CC-DNA-LL584


title: M1-Left-14-Neuron-H3K27me3-R1


title: H9-shGFP rep1

description:
RNA-seq
H9_sh2_vs_vehicle_diffexpr-results.csv
H9-H-shGFP-1_R1.fq.gz


title: Bulk_DARLIN_v2_CC-DNA-LL583


title: 231-3819-H rep3

description:
RNA-seq
231.xls
231-3819-H-3

value: breast cancer cell

value: HIF1Beta knockdown

value: 1percent O2 shHIF1Beta


title: Blood_migration_induced_at_E10_LL715RH-mono

source_name: RightArm-mono

value: RightArm-mono

value: TC


title: BMDMs, control, rep7

description:
sample_07
Primary cells

value: control


title: M1-Left-14-Glia-H3K27me3-R1

value: brain


title: M1-Left-13-Neuron-H3K27me3-R2


title: 231-3819-H rep2

description:
RNA-seq
231.xls
231-3819-H-2


title: BMDMs, control, rep6

description:
sample_06
Primary cells


title: 231-3819-H rep1

description:
RNA-seq
231.xls
231-3819-H-1


title: M1-Left-13-Neuron-H3K27me3-R1


title: BMDMs, control, rep5

description:
sample_05
Primary cells


title: M1-Left-13-Glia-H3K27me3-R2


title: BMDMs, CYR61-0.5, rep1

description:
sample_09
Primary cells


title: Blood_migration_induced_at_E10_LL715RH-Mega

source_name: RightArm-Mega

value: RightArm-Mega


title: BMDMs, control, rep4

description:
sample_04
Primary cells


title: BMDMs, control, rep3

description:
sample_03
Primary cells


title: Blood_migration_induced_at_E10_LL715RH-LT-HSCs

source_name: RightArm-LT-HSCs

value: RightArm-LT-HSCs


title: M1-Left-12-Neuron-H3K27me3-R2


title: M1-Left-12-Neuron-H3K27me3-R1


title: 231-3810-H rep3

description:
RNA-seq
231.xls
231-3810-H-3

value: HIF1alpha knockdown

value: 1percent O2 shHIF1alpha


title: Blood_migration_induced_at_E10_LL715RH-MPP3-4


title: M5-Neuron-Input

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2. Uniquely mapped reads were filtered for known blacklisted genome regions using Samtools and bedtools to remove ChIP-seq artifacts.
Reads were extended by 100 bp on either ends
Sample was normalized and input subtracted. The reference genome was then divided into 100-bp bins and ChIP-seq signal for each bin was counted for both ChIP and input samples.
Sample was converted to BigWig format
Assembly: mm10
Supplementary files format and content: Normalized ChIP-seq and RNA-seq signal in BigWig format.


title: M1-Left-12-Glia-H3K27me3-R1


title: BMDMs, control, rep2

description:
sample_02
Primary cells


title: M1-Left-13-Glia-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715RH-B

source_name: RightArm-B

value: RightArm-B


title: M1-Left-11-Neuron-H3K27me3-R2


title: M1-Left-12-Glia-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715RH-ery

source_name: RightArm-ery

value: RightArm-ery


title: Blood_migration_induced_at_E10_LL715RF-mono

source_name: RightLeg-mono

value: RightLeg-mono


title: Blood_migration_induced_at_E10_LL715RH-Gr

source_name: RightArm-Gr

value: RightArm-Gr


title: Blood_migration_induced_at_E10_LL715RF-ery

source_name: RightLeg-ery

value: RightLeg-ery


title: 231-3810-H rep1

description:
RNA-seq
231.xls
231-3810-H-1


title: M4-Neuron-Input


title: BMDMs, control, rep1

description:
sample_01
Primary cells

value: bone marrow-derived macrophages


title: M5-Right-19-Neuron-H3K27me3-R2


title: M5-Right-19-Neuron-H3K27me3-R1


title: M1-Left-11-Neuron-H3K27me3-R1


title: M1-Left-11-Glia-H3K27me3-R2


title: M1-Left-11-Glia-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715RF-ST-HSCs

source_name: RightLeg-ST-HSCs

value: RightLeg-ST-HSCs


title: Blood_migration_induced_at_E10_LL715RH-ST-HSCs

source_name: RightArm-ST-HSCs

value: RightArm-ST-HSCs


title: Blood_migration_induced_at_E10_LL715RF-Mega

source_name: RightLeg-Mega

value: RightLeg-Mega


title: 231-3810-H rep2

description:
RNA-seq
231.xls
231-3810-H-2

value: breast cancer cell


title: M5-Right-19-Neuron-H3K27ac-R2


title: Blood_migration_induced_at_E10_LL715RF-MPP3-4

value: TC


title: RKO-3819-H rep2

description:
RNA-seq
RKO.xls
RKO-3819-H-2

source_name: RKO

value: RKO

value: colorectal cancer cell

value: HIF1Beta knockdown

value: 1percent O2 shHIF1Beta


title: M5-Right-18-Neuron-H3K27me3-R2

source_name: C57BL/6J brain

value: brain


title: Blood_migration_induced_at_E10_LL715RF-Gr-rep3


title: RKO-3819-H rep1

description:
RNA-seq
RKO.xls
RKO-3819-H-1


title: M1-Left-10-Neuron-H3K27me3-R1


title: M5-Right-19-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715RF-LT-HSCs

source_name: RightLeg-LT-HSCs

value: RightLeg-LT-HSCs


title: RKO-3819-H rep3

description:
RNA-seq
RKO.xls
RKO-3819-H-3


title: M1-Left-10-Glia-H3K27me3-R2


title: M1-Left-10-Neuron-H3K27me3-R2


title: M1-Left-10-Glia-H3K27me3-R1


title: RKO-3810-H rep3

description:
RNA-seq
RKO.xls
RKO-3810-H-3

value: HIF1alpha knockdown

value: 1percent O2 shHIF1alpha


title: RKO-3810-H rep2

description:
RNA-seq
RKO.xls
RKO-3810-H-2


title: M5-Right-18-Neuron-H3K27ac-R2


title: RKO-3810-H rep1

description:
RNA-seq
RKO.xls
RKO-3810-H-1


title: M5-Right-18-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715RF-Gr-rep2


title: M1-Left-09-Neuron-H3K27me3-R1


title: M1-Left-09-Neuron-H3K27me3-R2


title: M5-Right-17-Neuron-H3K27me3-R2


title: M1-Left-09-Glia-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715RF-B-rep1


title: Blood_migration_induced_at_E10_LL715RF-B-rep3


title: Blood_migration_induced_at_E10_LL715RF-B-rep2


title: M5-Right-18-Neuron-H3K27me3-R1


title: M5-Right-17-Neuron-H3K27ac-R2


title: M1-Left-09-Glia-H3K27me3-R1


title: M5-Right-17-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715LH-mono

source_name: LeftArm-mono

value: LeftArm-mono


title: Blood_migration_induced_at_E10_LL715LH-ery

source_name: LeftArm-ery

value: LeftArm-ery


title: M1-Left-08-Neuron-H3K27me3-R1


title: M1-Left-08-Glia-H3K27me3-R1


title: M5-Right-16-Neuron-H3K27me3-R2


title: M1-Left-08-Glia-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715LH-Mega

source_name: LeftArm-Mega

value: LeftArm-Mega


title: M5-Right-16-Neuron-H3K27me3-R1


title: M5-Right-16-Neuron-H3K27ac-R2


title: NCM460-3819-H rep3

description:
RNA-seq
NCM460.xls
NCM460-3819-H-3

value: colon epithelial cell


title: Blood_migration_induced_at_E10_LL715LH-ST-HSCs

source_name: LeftArm-ST-HSCs

value: LeftArm-ST-HSCs


title: M1-Left-07-Neuron-H3K27me3-R2


title: NCM460-3819-H rep2

description:
RNA-seq
NCM460.xls
NCM460-3819-H-2


title: Blood_migration_induced_at_E10_LL715RF-Gr-rep1


title: Blood_migration_induced_at_E10_LL715LH-MPP3-4


title: M5-Right-16-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715LH-LT-HSCs

source_name: LeftArm-LT-HSCs

value: LeftArm-LT-HSCs


title: M1-Left-07-Neuron-H3K27me3-R1


title: NCM460-3819-H rep1

description:
RNA-seq
NCM460.xls
NCM460-3819-H-1


title: M1-Left-08-Neuron-H3K27me3-R2


title: M1-Left-07-Glia-H3K27me3-R2


title: M5-Right-17-Neuron-H3K27me3-R1


title: M5-Right-15-Neuron-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715LH-B

source_name: LeftArm-B

value: LeftArm-B


title: M1-Left-07-Glia-H3K27me3-R1


title: M5-Right-15-Neuron-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715LH-Gr

source_name: LeftArm-Gr

value: LeftArm-Gr


title: NCM460-3810-H rep3

description:
RNA-seq
NCM460.xls
NCM460-3810-H-3


title: NCM460-3810-H rep2

description:
RNA-seq
NCM460.xls
NCM460-3810-H-2


title: M1-Left-05-Neuron-H3K27me3-R2


title: M5-Right-15-Neuron-H3K27ac-R2


title: Blood_migration_induced_at_E10_LL715LF-ery

source_name: LeftLeg-ery

value: LeftLeg-ery

value: TC


title: NCM460-3810-H rep1

description:
RNA-seq
NCM460.xls
NCM460-3810-H-1


title: Blood_migration_induced_at_E10_LL715LF-mono

source_name: LeftLeg-mono

value: LeftLeg-mono


title: M1-Left-05-Glia-H3K27me3-R2


title: M5-Right-14-Neuron-H3K27me3-R1


title: M5-Right-15-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715LF-Mega

source_name: LeftLeg-Mega

value: LeftLeg-Mega


title: M1-Left-05-Glia-H3K27me3-R1


title: M5-Right-14-Neuron-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715LF-ST-HSCs

source_name: LeftLeg-ST-HSCs

value: LeftLeg-ST-HSCs


title: Blood_migration_induced_at_E10_LL715LF-LT-HSCs

source_name: LeftLeg-LT-HSCs

value: LeftLeg-LT-HSCs


title: M1-Left-04-Neuron-H3K27me3-R2

value: brain


title: M1-Left-04-Neuron-H3K27me3-R1


title: M5-Right-14-Neuron-H3K27ac-R1


title: M5-Right-13-Neuron-H3K27me3-R2


title: M5-Right-14-Neuron-H3K27ac-R2


title: M5-Right-13-Neuron-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715LF-MPP3-4


title: Blood_migration_induced_at_E10_LL715LF-Gr-rep3


title: M1-Left-04-Glia-H3K27me3-R2


title: M1-Left-04-Glia-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715LF-Gr-rep2


title: M5-Right-13-Neuron-H3K27ac-R2


title: H9-3819-H rep3

description:
RNA-seq
H9.xls
H9-3819-H-3

value: embryonic stem cell

value: HIF1Beta knockdown

value: 1percent O2 shHIF1Beta


title: M1-Left-05-Neuron-H3K27me3-R1


title: H9-3819-H rep2

description:
RNA-seq
H9.xls
H9-3819-H-2


title: M5-Right-13-Neuron-H3K27ac-R1


title: Blood_migration_induced_at_E10_LL715LF-Gr-rep1


title: M1-Left-03-Neuron-H3K27me3-R1


title: Blood_migration_induced_at_E10_LL715LF-B-rep3


title: H9-3819-H rep1

description:
RNA-seq
H9.xls
H9-3819-H-1


title: Blood_migration_induced_at_E10_LL715LF-B-rep2


title: H9-3810-H rep3

description:
RNA-seq
H9.xls
H9-3810-H-3

value: HIF1alpha knockdown

value: 1percent O2 shHIF1alpha


title: M1-Left-03-Glia-H3K27me3-R2


title: M5-Right-12-Neuron-H3K27me3-R2


title: Blood_migration_induced_at_E10_LL715LF-B-rep1


title: M5-Right-12-Neuron-H3K27ac-R2


title: H9-3810-H rep2

description:
RNA-seq
H9.xls
H9-3810-H-2


title: H9-3810-H rep1

description:
RNA-seq
H9.xls
H9-3810-H-1


title: M1-Left-03-Neuron-H3K27me3-R2


title: M5-Right-12-Neuron-H3K27me3-R1


title: M1-Left-02-Glia-H3K27me3-R2


title: M5-Right-12-Neuron-H3K27ac-R1


title: M1-Left-03-Glia-H3K27me3-R1


title: M1-Left-01-Neuron-H3K27me3-R1


title: M5-Right-11-Neuron-H3K27ac-R1


title: M1-Left-02-Glia-H3K27me3-R1


title: M5-Right-11-Neuron-H3K27me3-R2


title: 963LP

city: Vancouver

first: Yen-Yi

state: British Columbia

address: 2660 Oak St

country: Canada

institute: University of British Columbia

data_processing:
Raw sequencing reads were pre-processed to remove llumina Truseq adapters and polyA/polyT sequences using Cutadapt version 2.3
Trimmed reads were aligned against mouse genome version mm10 and Ensembl gene annotations version 84 using STAR version 2.7.0d_0221 (RRID:SCR_004463)38, and alignment parameters from ENCODE long RNA-seq pipeline (https://github.com/ENCODE-DCC/long-rna-seq-pipeline).
Gene level estimated counts and transcripts per million (TPM) were obtained using RSEM version 1.3.139. FastQC version 0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; RRID: SCR_014583) and MultiQC version 1.8 were used to assess the quality of trimmed reads and alignment to genome/transcriptome
Assembly: hg38
Supplementary files format and content: tab-delimited files include normalized read counts for each sample

source_name: prostate cancer

extract_protocol:
Total RNA was extracted from cells using a GenElute RNA purification kit (Sigma-Aldrich, RTN70). RNA purity and concentration were assessed using a NanoDrop spectrophotometer (Thermo Fisher). Aliquots of 1 ug of total RNA were reverse transcribed using qScript cDNA synthesis kit (Quantabio, 95047-500) according to the manufacturer’s protocol. qRT-PCR analyses were performed using LightCycler® 480 SYBR Green I Master RT-PCR kits (ROCHE) on a Bio-Rad CFX Connect Real-Time system (Bio-Rad, CFX Connect Real-Time System). Expression levels were normalized to GAPDH.
PolyA RNA was isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module, and bar-coded libraries were constructed using the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA). Libraries were pooled and sequenced single-end (1X75) on an Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).

value: prostate cancer

tag: age

tag: collection date

tag: geo loc_name

value: Canada:British Columbia, Vancouver

tag: biomaterial provider

value: Vancouver Prostate Centre:2660 Oak Street, Vancouver, BC, V6H3Z6

tag: Sex

value: male


title: 997RP

tag: tissue


title: 974LP


title: M1-Left-01-Neuron-H3K27me3-R2

tag: strain


title: M5-Right-11-Neuron-H3K27me3-R1


title: 972


title: 945RP


title: 917LP


title: 964RP


title: M5-Right-10-Neuron-H3K27me3-R2


title: M5-Right-11-Neuron-H3K27ac-R2


title: M1-Left-01-Glia-H3K27me3-R1


title: 961RP


title: M1-Left-01-Glia-H3K27me3-R2


title: 912LT


title: M5-Right-10-Neuron-H3K27me3-R1


title: 890LP


title: IC-ATGR1, rep2

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
ORGATR8D22.2
counts_ATGR.txt

data_processing:
The paired FASTQ files from each sample were preprocessed using fastp 0.23.2, which performs trimming, adapter removal, and filtering. Reads are then psuedoalligned against the hg38 transcriptome with kallisto 0.46.0 to quantify transcript abundances. The R package tximport estimates and outputs gene counts from these abundances.
Assembly: hg38
Supplementary files format and content: tab-separated matrix of raw counts

source_name: iPSC

extract_protocol:
Total RNA was extracted from 4-6 organoids derived from ACE-/- (clone AC1), AGTR1-/- (clone AT1) and Isogenic Control (IC-ACE and IC-AGTR1) iPSC lines using the Quick-RNA MiniPrep kit (Zymo Research, R1054) per the manufacturer instructions. RNA samples from organoids derived from n=3 independent differentiation experiments from each line were quantified using Qubit® RNA BR Assay kit. Normalized in nuclease free water to 8 ng/uL and run on Agilent Fragment Analyzer for peak analysis. RQN values averaged 8.6 with a range of 7.4-9.9. 28S/18S ratio averaged 1.85 with a range of 1.6 to 2.2.
100 ng of RNA were prepared into libraries following Illumina Stranded Total RNA Prep with Ribo-Zero Plus protocol with all recommended reagents. Final library amplification step used 2.5 uL index anchors and 14 PCR cycles. Individual libraries were quantified using Qubit® dsDNA HS assay and run on the Agilent Fragment Analyzer for library bp size. Libraries were pooled using the percent range adjusted concentration of fragments 175-650 bp. Library pool was run on 1.5% Bio-Rad Certified Low Range Ultra Agarose for size selection greater than 150 bp. DNA library was purified following MinElute Gel Extraction Kit Protocol.

value: iPSC


title: IC-ATGR1, rep1

description:
ORGATR8D22.1
counts_ATGR.txt


title: M5-Right-10-Neuron-H3K27ac-R1


title: M5-Right-10-Neuron-H3K27ac-R2


title: M5-Right-09-Neuron-H3K27me3-R1


title: AT1, rep3

description:
ORGATR27D22.3
counts_ATGR.txt


title: AT1, rep1

description:
ORGATR27D22.1
counts_ATGR.txt


title: AT1, rep2

description:
ORGATR27D22.2
counts_ATGR.txt


title: M5-Right-09-Neuron-H3K27ac-R2


title: M5-Right-09-Neuron-H3K27ac-R1


title: M5-Right-08-Neuron-H3K27me3-R1


title: 867RP


title: M5-Right-08-Neuron-H3K27me3-R2


title: 761RT


title: 731LT


title: IC-ACE, rep2

description:
ORGACENHSKD22_08
counts_ACE.txt

value: ACE+/+


title: 703LP


title: 946


title: M5-Right-09-Neuron-H3K27me3-R2


title: IC-ACE, rep1

description:
ORGACENHSKD22_07
counts_ACE.txt


title: AC1, rep3

description:
ORGACEC9_06
counts_ACE.txt

value: ACE-/-


title: AC1, rep1

description:
ORGACEC9_02
counts_ACE.txt


title: M5-Right-08-Neuron-H3K27ac-R2


title: AC1, rep2

description:
ORGACEC9_04
counts_ACE.txt


title: 702LP


title: K562_library2_rep3_2_gRNA amplification

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep3_2)

data_processing:
(Sample 28-40) All 10x scRNA-seq datasets were processed with the Cell Ranger (v3.0.2) pipeline (https://www.10xgenomics.com/) and were mapped to the Homo sapiens genome (Ensembl GRCh38.p12).
Libraries of gRNA amplification were separately indexed and sequenced as spike-ins alongside the scRNA-seq libraries. UMI and cell-barcode assignments were made for each read by processing these samples with the Cell Ranger (v3.0.2) 'count' tools. Then, we combined the output bam files and the whitelist of guides sequence in our libraries to obtain the cell-barcode and guide pairwise using 'get_barcodes.py' (Hill et al., 2018) with parameters: "--search_seq TTGTGGAAAGGACGAAACACCG --all_reads --barcode_length 20 --no_swalign --chimeric_threshold 0.2". The similar chimeric sequences and reads unassigned to a gRNA were removed. Cell barcodes detected in the gRNA amplification libraries were then matched with cell-barcodes detected in the regular 10x scRNA-seq libraries. We take all whitelist sequences that have at least one UMI counts and account for over 7.5% of the whitelist reads assigned to a given cell using 'preprocess_cfg.R' tools (Hill et al., 2018).
Assembly: Ensembl GRCh38.p12
Supplementary files format and content: gRNA sequence list

source_name: K562 cell line

growth_protocol: Human erythroleukemia cell line K562 was maintained in RPMI1640 supplemented with 10% FBS (Gibco, Carlsbad, CA, USA).

extract_protocol: The enriched PCR procedure was performed as described previously(Hill et al., 2018) with the following modifications. A heminested PCR starting from 40 ng of full-length cDNA was used to enrich for gRNA barcodes. Q5 High-Fidelity DNA Polymerase (New England BioLabs) was used for PCR amplification according to the following PCR protocol: (1) 98°C for 45 s, (2) 98°C for 15 s, 65°C for 20 s, then 72°C for 60 s (14-16 cycles). PCRs were cleaned with Zymo DNA Clean & Concentrator-5 columns (Zymo, Orange County, CA, USA) and 15 µl of a 1:2 dilution of the first PCR and 1:2 dilution of the second PCR were carried in each reaction. Then fragments of length 400-500 bp were selected using 8% TBE gel.

treatment_protocol: gRNAs were connected to the tandem double gRNA expression plasmid (pLV-hEF1a-EGFP-2A-Puro-U6-gRNA1-7sK-gRNA2) to obtain the gRNA libraries expressing EGFP green fluorescence. 3×106 of K562 cells in 7.5 ml media plus 8 µg/ml polybrene were transduced, with either of the gRNA-EGFP (MOI ~4) or Cas9-mCherry (MOI ~50) expressing viruses that had been packaged singly. At 72 hours post-infection, gRNA-EGFP+/Cas9-mCherry+ cells were collected by flow-cytometry and subjected to Single-cell RNA-seq.

tag: treatment

value: tranduced with a CRISPR KO library 2(molncRNA(-/-)+IC gRNA)

value: K562 cell line


title: 650RP


title: 689RT


title: M5-Right-07-Neuron-H3K27me3-R2

source_name: C57BL/6J brain


title: K562_library2_rep3_1_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep3_1)


title: M5-Right-07-Neuron-H3K27ac-R2


title: M5-Right-07-Neuron-H3K27me3-R1


title: 647RP


title: 686RP


title: K562_library1_rep3_3_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep3_3)

value: tranduced with a CRISPR KO library 1(molncRNA(-)+IC gRNA)


title: 639LP


title: M5-Right-08-Neuron-H3K27ac-R1


title: M5-Right-06-Neuron-H3K27me3-R2


title: K562_library1_rep3_2_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep3_2)


title: 627RT


title: K562_library1_rep3_1_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep3_1)


title: 611LT


title: K562_library2_rep2_4_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep2_4)


title: K562_library2_rep2_3_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep2_3)


title: M5-Right-06-Neuron-H3K27ac-R2

description: MOWChIP-seq data. Name format: Mouse number-Left/right hemisphere-Slice number-Neuron/glia-Marker-Replicate number


title: 601RP


title: 597RP


title: K562_library2_rep2_2_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep2_2)


title: M5-Right-06-Neuron-H3K27ac-R1


title: 585LP


title: K562_library1_rep2_4_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep2_4)


title: 569LP


title: M5-Right-05-Neuron-H3K27ac-R2


title: K562_library2_rep2_1_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library2_rep2_1)


title: K562_library1_rep2_3_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep2_3)


title: M5-Right-05-Neuron-H3K27me3-R1


title: M5-Right-05-Neuron-H3K27me3-R2


title: 537RP


title: K562_library1_rep2_2_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep2_2)


title: M5-Right-05-Neuron-H3K27ac-R1


title: 536RP


title: M5-Right-04-Neuron-H3K27me3-R1


title: M5-Right-06-Neuron-H3K27me3-R1


title: K562_library2_rep3_2

description: replicate 3, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 2

extract_protocol: The libraries were prepared using a Single Cell 3' Library Gel Bead kit V3 following the manufacturer's instructions.


title: M5-Right-04-Neuron-H3K27ac-R2


title: 518LP


title: K562_library2_rep3_1

description: replicate 3, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 1


title: 482RT


title: M5-Right-04-Neuron-H3K27ac-R1


title: 481RP


title: M5-Right-03-Neuron-H3K27me3-R1


title: 452LP


title: K562_library1_rep2_1_gRNA amplification

description: gRNA amplification library for 10X cDNA samples (K562_library1_rep2_1)


title: 531RP


title: 445RT


title: M5-Right-03-Neuron-H3K27ac-R2


title: 422RP


title: 427LT


title: 420LP


title: K562_library2_rep2_1

description: replicate 2, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 1


title: M5-Right-04-Neuron-H3K27me3-R2


title: M5-Right-02-Neuron-H3K27ac-R2


title: 419LP


title: K562_library1_rep2_4

description: replicate 2, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 4


title: 494LP


title: M5-Right-03-Neuron-H3K27me3-R2


title: M5-Right-02-Neuron-H3K27me3-R1


title: M5-Right-02-Neuron-H3K27me3-R2


title: K562_library1_rep3_2

description: replicate 3, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 2


title: M5-Right-03-Neuron-H3K27ac-R1


title: 412RP


title: K562_library1_rep3_3

description: replicate 3, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 3


title: K562_library1_rep3_1

description: replicate 3, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 1


title: K562_library1_rep2_3

description: replicate 2, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 3


title: K562_library2_rep2_4

description: replicate 2, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 4


title: M5-Right-02-Neuron-H3K27ac-R1


title: M5-Right-01-Neuron-H3K27me3-R2


title: K562_library1_rep2_2

description: replicate 2, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 2


title: M5-Right-07-Neuron-H3K27ac-R1

description: MOWChIP-seq data. Name format: Mouse number-Left/right hemisphere-Slice number-Neuron/glia-Marker-Replicate number


title: 404LT


title: 399RT


title: K562_library2_rep2_2

description: replicate 2, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 2


title: M5-Right-01-Neuron-H3K27ac-R2


title: M5-Right-01-Neuron-H3K27me3-R1


title: 332RP


title: 6Z-3

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: UBE2Z siRNAs replicate 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg38 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for all 116 samples

source_name: human HEK293T cells treated with siRNAs

extract_protocol:
Cells were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from from human HEK293T cells treated with siRNAs targetingUBA1 and E2 ubiquitin-conjugating enzymes compared to control treatment with non-targeting (NT) siRNAs
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: UBE2Z siRNAs


title: 308LT2


title: 6Z-2

description: UBE2Z siRNAs replicate 2


title: 6Z-1

description: UBE2Z siRNAs replicate 1


title: M4-Right-21-Neuron-H3K27me3-R1

value: brain


title: 6W-3

description: UBE2W siRNAs replicate 3

value: UBE2W siRNAs


title: 278RP


title: M4-Right-21-Neuron-H3K27ac-R2


title: 274LP


title: 261RP


title: 6W-1

description: UBE2W siRNAs replicate 1


title: 6V-2

description: UBE2V1+2 siRNAs replicate 2

value: UBE2V1+2 siRNAs


title: 6V-3

description: UBE2V1+2 siRNAs replicate 3


title: M4-Right-21-Neuron-H3K27me3-R2


title: M4-Right-20-Neuron-H3K27me3-R2


title: 239LP


title: K562_library1_rep2_1

description: replicate 2, scRNA-seq with molncRNA(-) and internal control gRNAs, 10X lane 1


title: M4-Right-20-Neuron-H3K27ac-R2


title: M4-Right-21-Neuron-H3K27ac-R1


title: 243LP


title: 1151LP


title: 6V-1

description: UBE2V1+2 siRNAs replicate 1


title: M4-Right-20-Neuron-H3K27ac-R1


title: 1137LT


title: M4-Right-19-Neuron-H3K27me3-R2


title: M5-Right-01-Neuron-H3K27ac-R1


title: M4-Right-20-Neuron-H3K27me3-R1


title: 6T-3

description: UBE2T siRNAs replicate 3

value: UBE2T siRNAs


title: 6W-2

description: UBE2W siRNAs replicate 2


title: 6T-2

description: UBE2T siRNAs replicate 2


title: 1136RP


title: 6NT-4

description: control siRNAs replicate 4

value: control siRNAs


title: 1135RP


title: 1128LP


title: 6T-1

description: UBE2T siRNAs replicate 1


title: M4-Right-19-Neuron-H3K27ac-R1


title: 242LP


title: M4-Right-19-Neuron-H3K27ac-R2


title: 6NT-2

description: control siRNAs replicate 2


title: M4-Right-18-Neuron-H3K27me3-R2


title: 1117_RP


title: 1123_2


title: M4-Right-18-Neuron-H3K27ac-R2


title: M4-Right-18-Neuron-H3K27me3-R1


title: 1117RP_GSC


title: 5S-3

description: UBE2S siRNAs replicate 3

value: UBE2S siRNAs


title: 5S-2

description: UBE2S siRNAs replicate 2


title: M4-Right-18-Neuron-H3K27ac-R1


title: M4-Right-19-Neuron-H3K27me3-R1


title: M4-Right-17-Neuron-H3K27me3-R2


title: 1113R-LN

source_name: lymph node metastasis (prostate cancer origin)


title: M4-Right-17-Neuron-H3K27me3-R1


title: 5R-3

description: UBE2R2 siRNAs replicate 3

value: UBE2R2 siRNAs


title: 1111RP

value: prostate cancer

value: Canada:British Columbia, Vancouver


title: M4-Right-17-Neuron-H3K27ac-R2


title: 1108LP

value: Vancouver Prostate Centre:2660 Oak Street, Vancouver, BC, V6H3Z6

value: male


title: 6NT-3

description: control siRNAs replicate 3


title: M4-Right-17-Neuron-H3K27ac-R1


title: 5R-1

description: UBE2R2 siRNAs replicate 1


title: 1101RT


title: 5S-1

description: UBE2S siRNAs replicate 1


title: 5QL-2

description: UBE2QL1 siRNAs replicate 2

value: UBE2QL1 siRNAs


title: 5QL-3

description: UBE2QL1 siRNAs replicate 3


title: 1113RP


title: 5R-2

description: UBE2R2 siRNAs replicate 2


title: 5QL-1

description: UBE2QL1 siRNAs replicate 1


title: M4-Right-16-Neuron-H3K27ac-R2


title: M4-Right-16-Neuron-H3K27me3-R2


title: M4-Right-16-Neuron-H3K27ac-R1


title: 1095LP


title: M4-Right-15-Neuron-H3K27me3-R2


title: 5Q-2

description: UBE2Q1+2 siRNAs replicate 2

value: UBE2Q1+2 siRNAs


title: 1104RT


title: M4-Right-15-Neuron-H3K27me3-R1


title: 5Q-3

description: UBE2Q1+2 siRNAs replicate 3


title: 1078LP


title: 1067RT


title: M4-Right-15-Neuron-H3K27ac-R2


title: M4-Right-15-Neuron-H3K27ac-R1


title: 5NT-4

description: control siRNAs replicate 4


title: 1085LT


title: 1086RP


title: 1065RP-LN

value: lymph node metastasis (prostate cancer origin)


title: 5NT-3

description: control siRNAs replicate 3


title: K562_library2_rep2_3

description: replicate 2, scRNA-seq with molncRNA(-/-) and internal control gRNAs, 10X lane 3

value: tranduced with a CRISPR KO library 2(molncRNA(-/-)+IC gRNA)

value: K562 cell line


title: 5NT-2

description: control siRNAs replicate 2


title: M4-Right-14-Neuron-H3K27me3-R2


title: 1056LP


title: M4-Right-14-Neuron-H3K27me3-R1


title: 1053RT


title: 5Q-1

description: UBE2Q1+2 siRNAs replicate 1


title: M4-Right-16-Neuron-H3K27me3-R1


title: 1046LP


title: 302LP


title: 4N-3

description: UBE2N siRNAs replicate 3

value: UBE2N siRNAs


title: M4-Right-14-Neuron-H3K27ac-R2

value: brain


title: 5NT-1

description: control siRNAs replicate 1


title: M4-Right-14-Neuron-H3K27ac-R1


title: 1084LP


title: M4-Right-13-Neuron-H3K27me3-R2


title: 4N-2

description: UBE2N siRNAs replicate 2


title: 4N-1

description: UBE2N siRNAs replicate 1


title: 1039LP


title: 1036LP


title: 1062LT


title: 4M-2

description: UBE2M siRNAs replicate 2

value: UBE2M siRNAs


title: 4M-3

description: UBE2M siRNAs replicate 3


title: M4-Right-13-Neuron-H3K27me3-R1


title: 1022_1

value: missing


title: M4-Right-13-Neuron-H3K27ac-R2


title: M4-Right-12-Neuron-H3K27me3-R2


title: 4M-1

description: UBE2M siRNAs replicate 1


title: M4-Right-13-Neuron-H3K27ac-R1


title: 6NT-1

description: control siRNAs replicate 1


title: 4L6-3

description: UBE2L6 siRNAs replicate 3

value: UBE2L6 siRNAs


title: 1011RT


title: M4-Right-12-Neuron-H3K27me3-R1


title: 4L6-2

description: UBE2L6 siRNAs replicate 2


title: 4L6-1

description: UBE2L6 siRNAs replicate 1


title: 1007RT


title: 1045LP


title: M4-Right-12-Neuron-H3K27ac-R2


title: 4L3-2

description: UBE2L3 siRNAs replicate 2

value: UBE2L3 siRNAs


title: Hb3+ 1.5 hr 3 [5958-NP-23]

city: Nashville

first: James

last: West

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: mm10
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)
Supplementary files format and content: Additional columns include gene chromosomal position, gene symbol, gene name, gene biotype, and source

source_name: Pulmonary microvascular endothelial cells

growth_protocol: 6-well plates coated with 0.1% gelatin, cultured in ECGM-MV2+5%FBS (Promocell)

extract_protocol:
RNEasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with diH2O, Hb2+ (1 mg/mL), Hb3+ (1 mg/mL), or hemin (60uM) for 30 min or 1.5 hours


title: M4-Right-12-Neuron-H3K27ac-R1


title: 4L3-3

description: UBE2L3 siRNAs replicate 3


title: Hb2+ 1.5 hr 3 [5958-NP-22]

value: Pulmonary microvascular endothelial cells


title: 4L3-1

description: UBE2L3 siRNAs replicate 1


title: M4-Right-11-Neuron-H3K27me3-R2


title: Hemin 1.5 hr 3 [5958-NP-24]

value: Hemin 1.5 hr


title: M4-Right-11-Neuron-H3K27me3-R1


title: Ctrl 1.5 hr 3 [5958-NP-21]

value: Ctrl 1.5 hr


title: Hemin 30 min 3 [5958-NP-20]

value: Hemin 30 min


title: 4NT-4

description: control siRNAs replicate 4

value: control siRNAs


title: 1015LP

value: prostate cancer

value: Canada:British Columbia, Vancouver

value: Vancouver Prostate Centre:2660 Oak Street, Vancouver, BC, V6H3Z6

value: male


title: 4NT-3

description: control siRNAs replicate 3


title: M4-Right-11-Neuron-H3K27ac-R2


title: 4NT-2

description: control siRNAs replicate 2


title: 4NT-1

description: control siRNAs replicate 1


title: Hb3+ 30 min 3 [5958-NP-19]

value: Hb3+ 30 min


title: M4-Right-11-Neuron-H3K27ac-R1


title: Hemin 1.5 hr 2 [5958-NP-16]


title: M4-Right-10-Neuron-H3K27me3-R2


title: Hb2+ 30 min 3 [5958-NP-18]

value: Hb2+ 30 min


title: M4-Right-10-Neuron-H3K27me3-R1


title: 3K-2

description: UBE2K siRNAs replicate 2

value: UBE2K siRNAs


title: Ctrl 30 min 3 [5958-NP-17]

value: Ctrl 30 min


title: 3K-3

description: UBE2K siRNAs replicate 3


title: M4-Right-10-Neuron-H3K27ac-R1

value: brain


title: M4-Right-09-Neuron-H3K27me3-R2


title: 3K-1

description: UBE2K siRNAs replicate 1


title: 3J2-3

description: UBE2J2 siRNAs replicate 3

value: UBE2J2 siRNAs


title: Hb3+ 1.5 hr 2 [5958-NP-15]


title: M4-Right-09-Neuron-H3K27me3-R1


title: Hb2+ 1.5 hr 2 [5958-NP-14]


title: M4-Right-09-Neuron-H3K27ac-R2


title: M4-Right-09-Neuron-H3K27ac-R1


title: M4-Right-08-Neuron-H3K27me3-R2


title: 3J1-3

description: UBE2J1 siRNAs replicate 3

value: UBE2J1 siRNAs


title: Ctrl 1.5 hr 2 [5958-NP-13]


title: Hb2+ 30 min 2 [5958-NP-10]


title: 3J2-2

description: UBE2J2 siRNAs replicate 2


title: Hemin 30 min 2 [5958-NP-12]


title: 3J2-1

description: UBE2J2 siRNAs replicate 1


title: Hb3+ 30 min 2 [5958-NP-11]


title: Ctrl 30 min 2 [5958-NP-9]


title: 3J1-1

description: UBE2J1 siRNAs replicate 1


title: M4-Right-08-Neuron-H3K27me3-R1


title: 3J1-2

description: UBE2J1 siRNAs replicate 2


title: 3I-3

description: UBE2I siRNAs replicate 3

value: UBE2I siRNAs


title: M4-Right-08-Neuron-H3K27ac-R1


title: M4-Right-10-Neuron-H3K27ac-R2


title: Hb3+ 1.5 hr 1 [5958-NP-7]

value: Pulmonary microvascular endothelial cells


title: 3I-2

description: UBE2I siRNAs replicate 2


title: Hemin 1.5 hr 1 [5958-NP-8]

value: Hemin 1.5 hr


title: M4-Right-08-Neuron-H3K27ac-R2


title: M4-Right-07-Neuron-H3K27me3-R2


title: Hb2+ 1.5 hr 1 [5958-NP-6]


title: 3NT-4

description: control siRNAs replicate 4


title: 3I-1

description: UBE2I siRNAs replicate 1


title: Ctrl 1.5 hr 1 [5958-NP-5]

value: Ctrl 1.5 hr


title: M4-Right-07-Neuron-H3K27ac-R2


title: 3NT-3

description: control siRNAs replicate 3


title: M4-Right-06-Neuron-H3K27me3-R2


title: M4-Right-07-Neuron-H3K27ac-R1


title: Hb3+ 30 min 1 [5958-NP-3]


title: M4-Right-06-Neuron-H3K27me3-R1


title: M4-Right-06-Neuron-H3K27ac-R2


title: 3NT-1

description: control siRNAs replicate 1


title: 3NT-2

description: control siRNAs replicate 2


title: Hb2+ 30 min 1 [5958-NP-2]


title: 2H-3

description: UBE2H siRNAs replicate 3

value: UBE2H siRNAs


title: Hemin 30 min 1 [5958-NP-4]

value: Hemin 30 min


title: M4-Right-07-Neuron-H3K27me3-R1


title: 2H-1

description: UBE2H siRNAs replicate 1


title: M4-Right-05-Neuron-H3K27me3-R2


title: T98g.mRNA

city: Jerusalem

first: Yifat

last: Edrei

address: Ein Karem Cmpus

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Library strategy: STARR-seq
DNA and cDNA samples were sequenced using the Illumina HiSeq2500 device, 125bp paired-end protocol. Technical and biological replications performed using illumina MiSeq, 250bp paired-end
Alignment with the hg19 reference genome was performed on the first 40 bp from both sides of the DNA segments, using Bowtie2
Reads with mapping quality value above 40 aligned with the probe targets were considered for further analyses. Each of the captured genomic segments was given a unique ID according to genomic location and indicated the total number of DNA and RNA reads
Genome_build: hg19
Supplementary_files_format_and_content: text

source_name: post-methylation cDNA

growth_protocol: Human GBM T98G/U87 cells were cultured in minimum essential medium-Eagle (Biological Industries), supplemented with 10% heat-inactivated FBS #04-127-1A (Biological Industries), 1% penicillin/streptomycin P/S # 03-031-1B (Biological Industries), 1% L-glutamine #03-020-1C (Biological Industries;), 1% nonessential amino acids, #01-340-1B (Biological Industries) and 1% sodium pyruvate #03-042-1B (Biological Industries), at 37°C and 5% CO2.

extract_protocol:
Plasmid DNA was extracted from 2.5x10e7 cells, 24 h post-transfection. Cells were rinsed twice with PBS pH 7.4, using the NucleoSpin Plasmid EasyPure kit #740727250 (Macherey-Nagel), according to the manufacturer’s protocol. Total RNA was extracted from 2.5x10e7 cells 24h post-transfection using GENEZOL reagent # GZR200 (Geneaid), according to the manufacturer’s protocol. The polyA+ RNA fraction was isolated using Dynabeads Oligo-(dT)25 #61002 (Thermo scientific), scaling up the manufacturer’s protocol 5-fold per tube, and treated with 10 U turboDNase #AM2238 (Invitrogen) at 20 ng/µl 37°C, for 1 h. Two reactions of 50 µl each, were  pooled  and subjected  to  RNeasy  MinElute clean  up kit  #74204 reaction  (Qiagen)  to inactivate turbo DNase and concentrate the  polyA+ RNA.
First  strand  cDNA  synthesis  was  performed  with  1-1.5 µg polyA+ RNA  in a total  of  four  reactions, 20 µl each, using the  Verso cDNA Synthesis Kit #AB1453B (Thermo scientific ) according to the manufacturer’s protocol, with  a  reporter-RNA  specific primer (5’-CAAACTCATCAATGTATCTTATCATG-3’). cDNA (50 ng) was first amplified by PCR, at 98°C for 3 min, followed by 15 cycles at 95°C for 20s each, 65°C for 15s, 72°C for 30s. Final extension was performed at 72°C for 2 min, using the Hifi Hot Start Ready Mix (KAPA), with reporter-specific primers. Forward primer: 5’-GGCCAGCTGTTGGGGTG*T*C*C*A*C-3’ which spans the splice junction of the synthetic intron, and reverse primer: 5’-CTTATCATGTCTGCTCGA*A*G*C-3’, where “*” indicates phosphorothioate bonds. In total, 16-20 reactions were performed. The amplified products were purified with 0.8 x Agencourt AMPureXP DNA beads and eluted in 20 µl nuclease- free water. The resultant purified products served as a template for a second PCR performed under the following conditions: 95°C for 3 min, 12 cycles of 98°C for 15s, 65°C for 30s, 72°C for 30s. Final extension was performed at 72°C for 2 min, with forward Ilumina universal primer: 5’-TAGAGCATGCACCGGTAATGATACGGCGACCACCGAGATCT-3’ and reverse Indexed Ilumina primer: 5’-GGCCGAATTCGTCGACCAAGCAGAAGACGGCATACGAGAT-3’. PCR products were purified with 0.8 x Agencourt AMPureXP DNA beads, eluted in 10 μl nuclease-free water, and pooled.

treatment_protocol: The pGL3-promoter vector (Promega, GenBank accession number U47298) was modified by replacing the sequence between SacI and AfeI with a synthetic sequence 33 and then insertion of the capture library fragments (between AgeI-HF and SalI-HF). Sample #AK100 capture library was selected for this construction. 20 µg of the plasmid DNA were transfected into 2x10e6 cells at 70-80% confluence, using the Lipofectamine 3000 transfection kit #L3000-015 (Invitrogen), according to the manufacturer’s protocol. In each experiment, 5x10e7 cells were transfected and incubated at 37°C, for 24 h.

value: Bisulfite

tag: sequenced molecule

value: post-methylation cDNA


title: 2G2-3

description: UBE2G2 siRNAs replicate 3

value: UBE2G2 siRNAs


title: M4-Right-05-Neuron-H3K27me3-R1


title: Ctrl 30 min 1 [5958-NP-1]


title: 2H-2

description: UBE2H siRNAs replicate 2


title: M4-Right-06-Neuron-H3K27ac-R1


title: 2G2-1

description: UBE2G2 siRNAs replicate 1


title: D6_c.808C>T_rep2 [P6_2]

city: BEIJING

first: QINGYUAN

last: LIU

state: BEIJING

address: QINGHUAYUAN street，HAIDIAN distribute

institute: Tsinghua University

data_processing:
For RNA-seq data, sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trim galore (v0.6.4).
Reads were mapped to human genome 38 using hisat2 (v2.2.0).
Gene count and TPM value were calculated by Stringtie (v2.1.4).
Assembly: hg38
Supplementary files format and content: The tab-delimited text files include raw counts for each sample.

extract_protocol:
Total RNA was extracted using the TRIzol® Reagent (Life Technologies).
For RNA-seq of WT DAZL and c.808C>T DAZL hPGCLCs at two time points, libraries were constructed by Genewiz. For RNA-seq of H9, libraries were constructed using VAHTS mRNA-seq v2 Library Prep Kit (Vazyme NR611-02).

tag: cell type

value: hPGCLCs derived from hESCs

value: c.808C>T DAZL

value: overexpression of c.808C>T DAZL during differentiation


title: D4_c.808C>T_rep2 [P4_2]


title: AK178

data_processing:
Methyl-seq-captured libraries were sequenced using a Hiseq2500 device (Illumina), by applying paired-end 125bp reads.
Sequence alignment and DNA methylation calling were performed using Bismark V0.15.0 software against the hg19 reference genome.
Sites that were covered by less than 100 reads were excluded from the analyses.
Sites that reported in less than eight of the tumors were excluded from the analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bismark coverage

source_name: adult glioblastoma tumour

extract_protocol:
Enrichment libraries of GBM-targeted regulatory DNA segments were constructed using the SureSelect Methyl-Seq protocol #G9651A using one microgram genomic DNA per reaction. Quality and size distribution of the bisulfite-converted captured  segments were verified by TapeStation nucleic acids system (Agilent) assessments. Target enrichment efficiency and coverage was evaluated via sequencing of  the bisulfite-converted libraries.
Variable regulatory regions were defined as the regions carrying H3K4me1 marks in all tumors, and also H3K27ac in at least 25% of the tumors, but not in at least other 25% of the tumors. RNA probes were designed to target all methylation sites within these regions, utilizing the SureDesign tool (https://earray.chem.agilent.com/suredesign/). Probe duplication was applied in cases (n=8,652) of >5 CpG sites within the 120 bp span of the probes. Repetitive regions were identified by BLAT and excluded from the design. Custom-designed biotinylated RNA probes were ordered from Agilent Technologies (https://www.agilent.com).

tag: gender

value: f

tag: subtype

value: glioblastoma


title: M4-Right-05-Neuron-H3K27ac-R1

value: brain


title: D4_c.808C>T_rep1 [P4_1]


title: T98g.mDNA

source_name: post-methylation genomic DNA

value: post-methylation genomic DNA


title: D6_WT_rep1 [W6_1]

value: WT DAZL

value: overexpression of WT DAZL during differentiation


title: M4-Right-04-Neuron-H3K27me3-R1


title: T98g.RNA

source_name: cDNA

value: cDNA


title: D6_c.808C>T_rep1 [P6_1]


title: 2G1-2

description: UBE2G1 siRNAs replicate 2

value: UBE2G1 siRNAs


title: D6_WT_rep2 [W6_2]


title: 2G1-1

description: UBE2G1 siRNAs replicate 1


title: M4-Right-04-Neuron-H3K27ac-R1


title: AK089

value: m


title: M4-Right-04-Neuron-H3K27ac-R2


title: T98g.DNA

source_name: genomic DNA

value: genomic DNA


title: 2G2-2

description: UBE2G2 siRNAs replicate 2


title: 2G1-3

description: UBE2G1 siRNAs replicate 3


title: M4-Right-05-Neuron-H3K27ac-R2


title: AK216


title: M4-Right-04-Neuron-H3K27me3-R2


title: AK053


title: AK158


title: D4_WT_rep2 [W4_2]


title: M4-Right-03-Neuron-H3K27me3-R2


title: AK173


title: M4-Right-03-Neuron-H3K27me3-R1


title: 2F-2

description: UBE2F siRNAs replicate 2

value: UBE2F siRNAs


title: AK100


title: 2cell embryo 46 Mutant scBS-seq

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

data_processing:
A total of 96 scBS-seq libraries were processed for analysis. The first 6 bp containing the N portion of the random primers, adapters and bases called with poor quality (Phred score <20) were removed using Trim Galore version 0.4.4 (Krueger, 2017) in single-end mode. Only the good quality reads were used for the alignment to the Genome Reference Consortium mouse genome build 39 (GRCm39) using Bismark version 0.18.2 (Krueger & Andrews, 2011) with single-end and non-directional mode followed by deduplication and methylation calling using Bismark functions. The MII scBS-seq libraries having a mapping efficiency <10% or fewer than 500,000 CpGs covered were removed (Supp. Table S20-21). To investigate a possible somatic cell DNA contamination in MII oocytes, we compared the global CpG methylation rates with the methylation of X-chromosome CpG islands, removing the samples with X-chromosome CpG island mean methylation > 12 % (Fig. S5a-c; Castillo-Fernandez et al. 2020); there was no difference in the proportion of oocytes excluded on this basis between Padi6P620A/P620A and control. In total, out of 44 MII oocytes, we kept 10 cells for downstream analysis. The embryos scBS-seq libraries having fewer than 100,000 reads were removed. In total, out of 44 embryos, we kept for 29 the downstream analysis (Fig. S5d,e). The methylation profile for each feature was calculated by the Bisulfite methylation pipeline implemented in SeqMonk.
Assembly: mm39
Supplementary files format and content: Bismark coverage file

source_name: embryo

growth_protocol: For the experiment, males of 8-12 weeks of age and females of 4-8 weeks of age were used. The day before the start of the experiment, the males were separated. On day 1, at 2 pm, intraperitoneal injections of pregnant mare serum gonadotropin (PMSG) were given to the females. After approximately 52 hours, the same females received intraperitoneal injections of human chorionic gonadotropin (hCG). Male was sacrificed approximately 12 hours after the female hCG injection. The cauda epididymis and vasa deferentia were dissected and the spermatozoa were collected in the human tubal fluid medium (HTF) (EmbryoMax® HTF MR-070-D). Spermatozoa were counted and incubated at 37°C within a humidified atmosphere of 5% CO2 in air. Females were sacrificed approximately 13 hours after the hCG injection. Ampullae were placed in hyaluronidase 1mg/ml (H6254-500MG) drops to break down the oocyte-cumulus complex and collect MII oocyte. The oocytes were moved to the HTF medium and a 2x106 sperm/ml concentration of spermatozoa were added. After 4 - 6 hours of incubation at 37°C within a humidified atmosphere of 5% CO2 in air, the fertilised oocytes were washed, to remove the spermatozoa e debris, transferred in KSOM medium and incubated overnight at 37°C within a humidified atmosphere of 5% CO2 in air. The embryos' status was evaluated in the morning and the next 120 hours.

extract_protocol:
MII oocytes and 2-cell embryos were collected as described before. For 2-cell embryos, the zona pellucida was removed with Tyrode’s solution (SIGMA-ALDRICH), the blastomeres were separated and the polar body was discarded. Then single oocytes and blastomeres were picked and put into a lysis buffer (Buffer RLT Plus Qiagen). DNA and RNA from lysate were separated using the G&T protocol (Angermueller et al. 2016). The magnetic beads (MyOne C1, Life Technologies) were washed and then annealed to oligo dTs. These were used to capture polyadenylated mRNA from individual cell lysate. The supernatant containing the DNA was transferred to a new tube and the beads washed three times in 1xFSS buffer (Superscript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma) and 0.4 U/μl of RNAsin (Promega) to remove all DNA residue. Each washing solution was added to the DNA tube to maximise recovery.
The scBS-seq libraries were generated as described (Clark et al., 2017). The DNA was purified from the lysated using a 0.9:1 ratio of Ampure XP Beads (Beckman Coulter) and eluted into 10 μl of water. DNA purified from single cells was treated with the EZ Methylation Direct Kit (Zymo) for bisulfite-conversion following the manufacturer's instructions. First-strand synthesis was performed in five rounds. Initially, the bisulfite-treated DNA was mixed with 40 μl first-strand synthesis mastermix (1 × Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT)) and heated to 65 °C for 2 min and cooled on ice, followed by the addition of 50U of Klenow exo- and incubation at 37 °C for 30 minutes after slowly ramping from 4 °C. This process was repeated four more times with additional reaction mixture added each time, and the final round was incubated for 90 minutes at 37 °C. Exonuclease digestion was carried out by adding 20U of exonuclease I (NEB) in a total volume of 100 μl, at 37 °C for 1 h. The resulting samples were purified using AMPure XP beads with a 0.8:1 ratio. The beads were mixed with 50 μl second-strand master mix (1× Blue Buffer (Enzymatics), 0.4 mM dNTP mix (Roche), 0.4 μM 6NF oligo (IDT). The mixture was heated to 98 °C for 1 min and cooled on ice. Then, 50U of Klenow exo- (Enzymatics) were added. The mixture was incubated on a thermocycler at 37 °C for 90 min after slowly ramping from 4 °C. The resulting samples were purified using a 0.8:1 ratio of AMPure XP beads, and libraries were amplified using a 50 μl PCR mastermix (1× KAPA HiFi Readymix, 0.2 μM PE1.0 primer, 0.2 μM iTAG index primer) The amplification process involved a 2 min step at 95 °C, followed by 14 cycles of 80 s at 94 °C, 30 s at 65 °C, and 30 s at 72 °C, with a final extension for 3 min at 72 °C. Finally, the scBS-seq libraries were subjected to purification using a 0.7:1 ratio of AMPure XP beads. After purification, the libraries were eluted in 15 µl of water, pooled together, and sequenced. The sequencing process involved the generation of pools of 48 libraries, which were sequenced on an Illumina HiSeq 2500 platform. On average, the libraries were sequenced to generate 13.0 million paired-end reads with a read-length of 75 bp.

value: embryo


title: M4-Right-03-Neuron-H3K27ac-R2


title: AK156


title: AK183


title: 2cell embryo 45 Mutant scBS-seq


title: 2F-3

description: UBE2F siRNAs replicate 3


title: D4_WT_rep1 [W4_1]


title: Negative control8 48 Negative scBS-seq

source_name: control

value: control


title: Negative control7 47 Negative scBS-seq


title: 2F-1

description: UBE2F siRNAs replicate 1


title: 2cell embryo 44 Mutant scBS-seq


title: AK149


title: M4-Right-03-Neuron-H3K27ac-R1


title: 2cell embryo 43 Mutant scBS-seq


title: M4-Right-02-Neuron-H3K27me3-R2


title: AK142


title: 2NT-1

description: control siRNAs replicate 1

value: control siRNAs


title: M4-Right-02-Neuron-H3K27me3-R1


title: M4-Right-02-Neuron-H3K27ac-R2


title: 2cell embryo 42 Mutant scBS-seq


title: 2NT-4

description: control siRNAs replicate 4


title: 2NT-3

description: control siRNAs replicate 3


title: 2cell embryo 41 Mutant scBS-seq


title: AK153

value: MES


title: M4-Right-02-Neuron-H3K27ac-R1


title: 1E-2

description: UBE2E1+2 siRNAs replicate 2

value: UBE2E1+2 siRNAs


title: 2cell embryo 39 Mutant scBS-seq


title: 2NT-2

description: control siRNAs replicate 2


title: AK139


title: AK091


title: 2cell embryo 38 Mutant scBS-seq


title: 1D-3

description: UBE2D1+2+3 siRNAs replicate 3

value: UBE2D1+2+3 siRNAs


title: AK071

value: f


title: M4-Right-01-Neuron-H3K27me3-R1


title: M4-Right-01-Neuron-H3K27ac-R2


title: AK003

value: glioblastoma


title: M4-Right-01-Neuron-H3K27ac-R1

value: brain


title: 1D-1

description: UBE2D1+2+3 siRNAs replicate 1


title: 2cell embryo 36 Mutant scBS-seq


title: AK055


title: AK030


title: 1E-3

description: UBE2E1+2 siRNAs replicate 3


title: 1C-3

description: UBE2C siRNAs replicate 3

value: UBE2C siRNAs


title: EV miRNA, primary hepatocytes, HFHC diet, biol rep 3

city: Guangzhou

first: Shen

last: Chen

state: Guangdong Sheng

address: No.74 Zhongshan Road 2, Guangzhou

institute: Sun Yat-sen University

description: miRNA contents in EVs isolated from primary hepatocytes of HFHC diet-fed ApoE-/- mice

data_processing:
The raw sequencing data are called raw tags. The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: processed data files include FPKM values for each Sample

source_name: not applicable

extract_protocol:
The miRNA in primary hepatocytes derived EVs were extracted by SeraMir exosome RNA kit (SBI, USA). 1 μg total RNA for each sample was used for library construction.
Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, Takara) were excised and recovered. Then the 18–30 nt small RNAs were ligated to a 5′-adaptor and a 3′-adaptor. The adapter ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 100~120 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe).

value: not applicable

value: primary hepatocyte

value: ApoE KO

value: HFHC diet


title: 2cell embryo 40 Mutant scBS-seq


title: AK231

value: m

value: IDH


title: 2cell embryo 35 Mutant scBS-seq


title: 2cell embryo 34 Mutant scBS-seq


title: 1C-2

description: UBE2C siRNAs replicate 2


title: EV miRNA, primary hepatocytes, HFHC diet, biol rep 1


title: 1E-1

description: UBE2E1+2 siRNAs replicate 1


title: M4-Right-01-Neuron-H3K27me3-R2


title: 1C-1

description: UBE2C siRNAs replicate 1


title: EV miRNA, primary hepatocytes, Chow diet, biol rep 3

description: miRNA contents in EVs isolated from primary hepatocytes of chow diet-fed ApoE-/- mice

value: chow diet


title: 1AB-3

description: UBE2A+B siRNAs replicate 3

value: UBE2A+B siRNAs


title: AK199


title: 2cell embryo 33 Mutant scBS-seq

value: embryo


title: 2cell embryo 37 Mutant scBS-seq


title: 2cell embryo 32 Mutant scBS-seq


title: 1AB-2

description: UBE2A+B siRNAs replicate 2


title: AK124


title: 1D-2

description: UBE2D1+2+3 siRNAs replicate 2


title: EV miRNA, primary hepatocytes, HFHC diet, biol rep 2


title: 2cell embryo 30 Mutant scBS-seq


title: AK068


title: 1NT-4

description: control siRNAs replicate 4

value: control siRNAs


title: 2cell embryo 29 Mutant scBS-seq


title: 2cell embryo 28 Mutant scBS-seq


title: S228Erep2

city: wuhan

first: Yu

last: Qi

state: Hubei

address: xujiapeng

department: College of life sciences

institute: Hubei university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to sacCer3 whole genome using bowtie v0.12.2 with parameters -q -p 5 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: sacCer3

organism: Saccharomyces cerevisiae S288C

growth_protocol: Cells were grown in YPD until mid-log phase

extract_protocol:
Lysates were clarified from sonicated yeast cell pellets and histone-DNA complexes were isolated with antibody against  H3 (ab1791, Abcam),H3K4me3 (Abclonal; A2357),FLAG (F1804-1MG; Sigma-Aldrich),Rpd3 (sc-514160; Santa Cruz Biotechnology)
Libraries were prepared using the HTP KAPA kit

treatment_protocol: No treatment

value: Set1 S228E


title: 1NT-3

description: control siRNAs replicate 3


title: EDTA plasma, control, rep12

type: RNA

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
RT-qPCR miRNA data was normalized to UniSp4 spike in Cq-values.
Delta Cq-values are provided in the "Matrix normalized" Sheet.

label: SYBR Green

source_name: EDTA plasma

label_protocol: cDNA was synthesized using the Universal cDNA Synthesis Kit II using reaction conditions provided by the manufacturer (Exiqon, Denmark). In total, 2 µL of total RNA were used as input per 10 µL reverse transcription (RT) reaction mix. Cel-miR-39-3p was added to each RT reaction to monitor RT efficiency. PCR amplification was performed in a 384-well plate format using custom Pick&Mix plates (Exiqon, Denmark) in a Roche LC480 II instrument (Roche, Germany) and EXiLENT SYBR Green mastermix (Exiqon, Denmark) with the following settings: 95°C for 10 min, 45 cycles of 95°C for 10 s and 60°C for 60 s, followed by melting curve analysis. Cycle of quantification values (Cq-values) were determined using the second derivative method as provided by the Roche LC480 software. Data quality was assessed by visual inspection of spike-in control data. Hemolysis was assessed in all samples using the ratio of miR-23a-3p versus miR-451a and applying a cut-off of >7 to the ratio for calling a sample hemolytic.

growth_protocol: Twelve adolescents aged 15.0–17.9 years, 7 males and 5 females, with a long-term T1D duration of at least 8 years (8.0-15.0 years) were included in this case-control study. These individuals were followed regularly at the Queen Silvia Children’s Hospital in Gothenburg, Sweden. They were identified from the Swedish Pediatric Diabetes Quality Registry (SWEDIABKIDS). The control group, comprised 12 age-matched healthy adolescents, 15.0–17.5 years, 6 females and 6 males, living in the Gothenburg area. The current study commenced in April 2019, and was completed by October 2019.

extract_protocol: Total RNA extraction from 200 µL plasma samples was performed using the miRNeasy Mini Kit (Qiagen, Germany)12. Plasma was thawed on ice and centrifuged at 12,000×g for 5 min to remove any cellular debris. For sample lysis, 200 µL of plasma were mixed with 1000 µL Qiazol to which 1 µL spike-in controls had been added (Exiqon, Denmark). Following incubation at room temperature for 10 min, 200 µL chloroform were added to the lysates. After centrifugation at 12,000×g for 15 min at 4°C, 650 µL of the upper aqueous phase were obtained and mixed with 7 µL glycogen (50 mg/mL) to enhance precipitation. The aqueous phase was then transferred to a miRNeasy mini column, and RNA was precipitated by adding 750 µL ethanol. Washing with RPE and RWT buffer was performed in a QiaCube liquid handling robot (Qiagen, Germany). In the last step, total RNA was eluted in 30 µL nuclease free water and stored at -80°C until further analysis.

tag: group

value: Control

value: F


title: S228Erep1


title: EDTA plasma, control, rep11

value: M


title: 2cell embryo 27 Mutant scBS-seq


title: EDTA plasma, control, rep10


title: 1NT-2

description: control siRNAs replicate 2


title: AK076

value: glioblastoma


title: EV miRNA, primary hepatocytes, Chow diet, biol rep 2


title: S228Arep3

value: Set1 S228A


title: EDTA plasma, control, rep9


title: 2cell embryo 31 Mutant scBS-seq


title: 2cell embryo 26 Mutant scBS-seq


title: S228Arep2


title: 2cell embryo 25 Mutant scBS-seq


title: 1AB-1

description: UBE2A+B siRNAs replicate 1


title: UBA1siRNA_4

description: UBA1 siRNAs replicate 4

value: UBA1 siRNAs


title: EDTA plasma, control, rep8


title: EV miRNA, primary hepatocytes, Chow diet, biol rep 1

value: not applicable


title: AK066


title: S228Erep3


title: Negative control 624 Negative scBS-seq

value: control


title: EDTA plasma, control, rep7


title: Negative control5 23 Negative scBS-seq


title: UBA1siRNA_3

description: UBA1 siRNAs replicate 3


title: WTrep3

value: WT Control


title: UBA1siRNA_2

description: UBA1 siRNAs replicate 2


title: EDTA plasma, control, rep6


title: WTrep2


title: 2cell embryo 22 wild-type scBS-seq


title: UBA1siRNA_1

description: UBA1 siRNAs replicate 1


title: WTrep1


title: 1NT-1

description: control siRNAs replicate 1


title: EDTA plasma, control, rep5


title: 2cell embryo 21 wild-type scBS-seq


title: NTsiRNA_4

description: control siRNAs replicate 4


title: 2cell embryo 20 wild-type scBS-seq


title: EDTA plasma, control, rep4


title: EDTA plasma, control, rep3


title: NTsiRNA_3

description: control siRNAs replicate 3


title: EDTA plasma, control, rep2


title: EDTA plasma, control, rep1


title: 2cell embryo 19 wild-type scBS-seq


title: EDTA plasma, T1D, rep12


title: 2cell embryo 17 wild-type scBS-seq


title: E2siRNAcombo_HS_2

description: E2combo siRNAs + heat shock replicate 2

value: E2combo siRNAs + heat shock


title: E2siRNAcombo_HS_1

description: E2combo siRNAs + heat shock replicate 1


title: EDTA plasma, T1D, rep11


title: 2cell embryo 15 wild-type scBS-seq


title: EDTA plasma, T1D, rep9


title: NTsiRNA_2

description: control siRNAs replicate 2


title: CTRLsiRNA_HS_3

description: control siRNAs + heat shock replicate 3

value: control siRNAs + heat shock


title: CTRLsiRNA_HS_2

description: control siRNAs + heat shock replicate 2


title: 2cell embryo 18 wild-type scBS-seq


title: EDTA plasma, T1D, rep8


title: 2cell embryo 13 wild-type scBS-seq


title: CTRLsiRNA_HS_1

description: control siRNAs + heat shock replicate 1


title: 2cell embryo 14 wild-type scBS-seq


title: 2cell embryo 12 wild-type scBS-seq


title: 2cell embryo 16 wild-type scBS-seq


title: E2siRNAcombo_HS_3

description: E2combo siRNAs + heat shock replicate 3


title: EDTA plasma, T1D, rep7


title: CD43 cell GSK343 rep3

type: genomic

city: London

first: Frederick

middle: Andrew

last: Dick

state: ON

address: 790 Commissioners Road E

department: Pathology

institute: Western University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation 285k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: CD43-3 GSK

label_protocol: Standard Illumina protocol

growth_protocol: To separate CD43- from CD43+ cells, washed splenic lymphocytes (5e7) were resuspended in 450 µL FACS buffer and stained with 50 µL CD43 microbeads on ice for 30 min. Cells were washed once, resuspended in 500 µL FACS buffer and passed through an LD column in a VarioMACS separator as per manufacturer’s recommendation. CD43 microbead-labelled non-B cells were eluted from the column by applying the plunger. Purified B cells in the flow-through were incubated in RPMI-1640  supplemented with 10% (v/v) FBS, 55 µM 2-ME, 2 mM L-glutamine, penicillin and streptomycin plus 2 ng/mL IL-4 and BAFF at 37 °C in 5% CO2.

extract_protocol: Genomic DNA was extracted using Monarch genomic DNA purification kit

treatment_protocol: CD43- or CD43+ cells were treated with DMSO or 1 uM GSK343 for 48 hours


title: CD43 cell DMSO rep3

source_name: CD43-3 DMSO


title: B cell GSK343 rep3

source_name: B3 GSK


title: E2siRNAcombo_2

description: E2combo siRNAs replicate 2

value: E2combo siRNAs


title: 2cell embryo 10 wild-type scBS-seq


title: CD43 cell DMSO rep2

source_name: CD43-2 DMSO


title: CD43 cell GSK343 rep2

source_name: CD43-2 GSK


title: EDTA plasma, T1D, rep4


title: 2cell embryo 11 wild-type scBS-seq


title: Case 35: Giant cell tumor of the bone

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description: Giant cell tumor of the bone

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
Average Beta

label: Cy3 and Cy5

source_name: Giant cell tumor of the bone

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE


title: EDTA plasma, T1D, rep3


title: E2siRNAcombo_3

description: E2combo siRNAs replicate 3

source_name: human HEK293T cells treated with siRNAs


title: E2siRNAcombo_1

description: E2combo siRNAs replicate 1


title: CTRLsiRNA_3

description: control siRNAs replicate 3


title: EDTA plasma, T1D, rep6


title: EDTA plasma, T1D, rep10


title: EDTA plasma, T1D, rep5


title: Case 34: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: B cell GSK343 rep2

source_name: B2 GSK


title: 2cell embryo 9 wild-type scBS-seq

tag: genotype


title: Case 33: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: 2cell embryo 7 wild-type scBS-seq


title: 2cell embryo 6 wild-type scBS-seq


title: 2cell embryo 8 wild-type scBS-seq


title: B cell DMSO rep3

source_name: B3 DMSO


title: CTRLsiRNA_2

description: control siRNAs replicate 2


title: Case 31: Giant cell tumor of the bone

description: Giant cell tumor of the bone


title: CD43 cell GSK343 rep1

source_name: CD43-1 GSK


title: HUVEC, CYR61-5, rep4

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: Ensembl release 101 primary assembly
Supplementary files format and content: group_CYR61_0.05_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.05.
Supplementary files format and content: group_CYR61_0.5_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 0.5.
Supplementary files format and content: group_CYR61_5_Differential_Expression.tsv: Differential gene expression performed comparing control vs. CYR61 5.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

growth_protocol: We used primary human umbilical vein endothelial cells (HUVECs) from ATCC (PCS-100-010). These cells were maintained according to the manufacturer's recommended instructions.

extract_protocol:
After incubation, we washed cells twice with PBS, then used TRIzol (Ambion) and RNeasy Plus Mini Kit (Qiagen) to extract RNA following the manufacturer's recommended protocol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: We treated HUVECs with recombinant human CYR61 (PeproTech 120-25): 0.00, 0.05, 0.50, and 5.00 μg/ml for 24 hr.

value: CYR61, 5 ug/ml