title: KFs, MDI medium plus Chlorpheniramine, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Chlorpheniramine for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Cortisol, 8 Days

status: Public on May 19 2023

type: SRA

city: 海淀区

first: Jun

last: Li

state: 北京市

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

country: China

institute: Peking University

description: Targeted RNA

library_source: transcriptomic

data_processing:
Data were analysed as previously described (Teder et al., 2018). First, sequencing reads were mapped to the reference sequences (left probes plus right probes) to produce total counts of each gene. The CPM (Counts of exon model per million mapped reads) matrix was then transferred from the count matrix and used in cluster analysis, Pearson correlation analysis, and PCA analysis. All scripts was descripted in (Teder et al., 2018).
Assembly: no
Supplementary files format and content: tab-delimited text files include CPM for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
For small molecule screening, 128 compounds were collected based on functions in the signaling pathway and cell fate transition. KFs were seeded at a density of 0.5 × 104 cells per well of a 96-well plate containing KF medium. The next day, the medium was changed to MDI medium (DMEM/high glucose, 1% ITS, 0.5mM isobutylmethylxanthine, 1 μM dexamethasone) plus 2 μM compounds. After 4 days, DMEM/high glucose with 1% ITS was added to the culture for another 4 days. The negative control was KF in KF medium for 8 days. The positive control was KF in AD medium for 4 days and then AM medium for another 4 days. Cells were harvested on day 8 for PHDs-seq library preparation.
Samples with compound treatments in a 96 well-plate were washed with pre-warmed PBS. 60 μl of lysis buffer containing 50mM Tris-HCl pH8.0, 75mM KCl, 6% Ficoll PM-400, 0.15% TritonX-100, and 0.5U/μl RNaseOUT (RNaseOut should be added before use) were added to each well. The 96-well plate was then incubated on a shaker at 900 rpm for 15 minutes. 4.286 μl of cell lysate were transferred to a new 96 well PCR plate. 0.714 μl reverse transcription mix containing 40mM MgCl2, 4μM strand switching primer (TSO), 0.1mM dNTP, 8U/μl Maxima reverse transcriptase, 1x ERCC, and RNaseOUT (RNaseOut should be added before use) were added to each well, mixed and slightly centrifuged for several seconds to collect all reactants on the bottom. The 96-well PCR plate was incubated at 42°C for 2 hours with a hot lid at 105°C. 6μl of hybridization-ligation mix (0.005 μM probe mix, 1U/μl Taq DNA ligase, 1x Taq DNA ligation buffer) was added to the RT products, mixed gently, and incubated at 60°C for 60 minutes with a hot lid of 105°C. After hybridization and ligation, the products were enriched with 15 ul of enrichment mixture (2 μl Dynabeads MyOne Carboxylic Acid beads plus 13 μl capture buffer containing 30% PEG-600, 2 M, NaCl, 5 mM Tris-HCl pH7.5, 10 mM EDTA, and 0.02% Tween-20). Next, 20 μl of PCR mixture (0.25 μM PHD-seq well barcode, 0.5 mM PHD-seq plate barcode, 1 x Vazyme LAmp Master Mix) were added to the enriched hybridization-ligation products, mixed, and incubated at 94°C for 5min, followed by two cycles of 95°C for 20 s, 57°C for 30 s and 72°C for 20 s. In addition, 10 cycles of 94°C for 20 s, 65°C for 30 s, and 72°C for 20 s with a final extension at 72°C for 60 s. The PCR products were pooled together into several 1.5 ml tubes which were placed on a magnet to remove the beads. The supernatant was purified with DNA Clean & Concentrator-100 column (Zymo Research, D4029) and eluted with 150 µl of ddH2O. The library was size-selected using AMPure XP beads. 150 µl of beads were added to 150 µl of the purified PCR product, incubated for 5 min, and captured by a magnet for 3 min after which the supernatant was discarded. The beads were eluted in 25 µl of ddH2O and incubated for 1 min at room temperature. After 1 min of incubation on the magnet, the supernatant was transferred to a clean 1.5 ml tube. The 208 bp library was visualized using agarose gel electrophoresis and quantified using a Qubit™ 4 NGS Starter Kit with WiFi (Q33240).

tag: tissue

tag: cell type

value: fibroblast

tag: genotype

value: WT

tag: treatment

value: KFs with MDI medium plus Cortisol for 4 days and then medium was changed to AM medium for another 4 days.


title: TTseq-HCT116-LEO1-610-P-A

city: Wuhan

first: Yin

last: Zhinang

state: Hubei

address: Donghu road 185

institute: Wuhan University

description: TT-seq with HCT116 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens .hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: TT-seq

source_name: Isolated from the colon

growth_protocol: HCT116 (ATCC CCL-247) cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Cat# S711-001, LONSERA). HCT116 analog-sensitive CDK12 (CDK12-AS, F813G), HCT116-3A, and LEO1-HaloTag knockin cell lines were generated by CRISPR-Cas9-mediated homology-directed repair (HDR). DLD1-INTS6-dTag cells (Zheng et al., 2020) were provided by Dr. Fei Xaiver Chen and were maintained in DMEM complete medium. Drosophila S2 cells were obtained from Invitrogen (Cat# R690-07) and maintained in Schneider's medium (Thermo Scientific, Cat# 21720024). Mouse embryonic fibroblast cells (3T3 MEFs WT) were grown in DMEM with 10% FBS. All cells were cultured at 37℃ with 5% CO2. Live cells were quantified using a TC20 automated cell counter (Bio-Rad).

extract_protocol:
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.
TT-seq was performed as previously described (Gregersen et al., 2020; Schwalb et al., 2016) with some modifications. Cells were labeled in media with 400 μM 4-thiouridine (4sU) (Sigma-Aldrich, Cat# T4509) for 10 min before harvest, and total RNA was extracted with TRIzol (Invitrogen, Cat# 15596-018), the labeled RNA (100 μg) was fragmented with NaOH and spike-in with 10% S2 RNA (10 μg). After biotinylated in a 300 μL reaction (100 μg RNA, 10mM HEPES-KOH, pH 7.5, 1mM EDTA, 0.167mg/ml MTSEA-biotin-XX (Sigma-Aldrich, Cat# M9938)), enriched the biotin-labeled RNA with Streptavidin M280 beads (Invitrogen, Cat# 11206D) and eluted by 100mM DTT. RNA was purified by 1.8 x RNAClean XP beads before library preparation.

value: Isolated from the colon

tag: cell line

value: Human colon


title: 0.5 mM D-lactic acid, biol rep3

city: Irkutsk

first: Polina

last: Drozdova

state: Irkutsk region

address: Lenin str. 3

department: Institute of Biology

country: Russia

institute: Irkutsk State University

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq v2.20, and adapters were trimmed with Skewer v 0.2.2
Quality control of raw data was performed with FastQC v0.11.9 and summarized with MultiQC v1.13
The reads were aligned to the reference genome (R64-1-1 release of the S. cerevisiae genome) with hisat2 v2.2.1, sorted with samtools v1.9 and quantified with featureCounts from subread v2.0.4.
The resulting count table was further processed with the DESeq2 v1.34.0 for R v4.1.2 to compare expression levels.
All the code used is available at GitHub (https://github.com/drozdovapb/S_cerevisiae_lactate_transcriptome)
Assembly: R64-1-1 (GCA_000146045.2)
Supplementary files format and content: allSamples.featureCounts.txt is a plain text file containing raw counts obtained with the featureCounts function of the subread package.
Supplementary files format and content: normalized_counts_DESeq.csv is a plain text (comma-delimited) table with normalized counts obtained with DESeq2

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: haploid vegetative cells

growth_protocol: The yeast strain used for this work was BY4742 (MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0; Brachmann et al., 1998). It was grown in synthetic medium containing 0.67% (w/v) yeast nitrogen base, 2% (w/v) glucose, 150 mM NaCl, 20 mg/L L-histidine HCl, 100 mg/L L-leucine, 30 mg/L L-lysine HCl, and 20 mg/L uracil at 28 °C with orbital shaking (120 rpm). The addition of NaCl had the purpose of mimicking the conditions in the blood serum for further use in sensor applications.

extract_protocol:
RNA isolation was performed with the RNeasy kit according to manual (RNeasy Mini Handbook) with slight modifications. Cells were homogenized by mechanical disruption. After the addition of RLT buffer and glass beads, the samples were vortexed 3 times for 3 minutes. After each vortexing step, the samples were cooled on ice. Then the lysate was centrifuged for 2 min at maximum speed, and the supernatant was transferred to new microcentrifuge tubes, combined with the same volume of 70% ethanol and mixed by pipetting.
Sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina) and sequenced at 2 x 100 bp with a NovaSeq 6000 (Illumina).

treatment_protocol: For the experimental exposure, the overnight suspension cultures in logarithmic phase (optical density at 600 nm (OD600) in the range of 0.9–1.0) were prepared. 1.5 ml of each culture was collected by centrifugation (1700 × g for 5 minutes at room temperature) and resuspended in 3 ml of the same media or media with 0.05, 0.5, 5, or 45 mM D-lactic acid, or 45 mM of L-lactic acid. The experimental cultures were exposed in the indicated media for 3 hours, collected by centrifugation and frozen at -80 °C until the analysis.

tag: agent

value: 0.5 mM D-lactic acid

value: haploid vegetative cells

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0

tag: strain

value: exposed to the same medium with 0.5 mM D-lactic acid added for 3 hours


title: WT, rep2

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

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

department: Ophthalmology & Visual Sciences

country: USA

description:
sample 02
all.gene_counts.tsv
group_KO_Differential_Expression.tsv

data_processing:
RNA sequencing reads were aligned to the mouse genome (Ensembl release 76 primary assembly) with Spliced Transcripts Alignment to a Reference. Finally, we performed standard analysis of gene-level features using EdgeR and Limma.
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: group_KO_Differential_Expression.tsv: Differential gene expression performed comparing WT vs. SCD2KO.
Supplementary files format and content: all.gene_counts.tsv: Raw counts.

organism: Mus musculus

source_name: primary cells

growth_protocol: We prepared macrophages from bone marrow. To isolate bone marrow from mice, we sacrificed mice using CO2 euthanasia, dissected out both tibias and femurs, and passed 8 ml of ice-cold DMEM through each bone's medullary cavity. We filtered the bone marrow aspirates through a 40 micrometer nylon mesh strainer, pelleted the cells, and re-suspended the pellet in macrophage differentiation media consisting of DMEM with 10% FBS, 10% CMG-conditioned media, 1% P/S, and 1% L-glut. We replenished differentiation media 3 days after initial plating. After differentiation for 5-6 days, macrophages were maintained in mature macrophage media consisting of DMEM with 10% FBS, 2% CMG-conditioned media, 1% P/S, and 1% L-glut.

extract_protocol:
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 quantified the quality and quantity of the RNA samples with an Agilent Bioanalyzer or 4200 Tapestation. All RNA samples (n=6) were of high quality with RNA integrity numbers ≥ 9.3. We enriched our samples for mRNA by performing polyA selection according to the manufacturer’s recommended protocol. Then, we prepared sequencing libraries with standard protocols and sequenced the samples on an Illumina NovaSeq 6000 at the McDonnell Genome Institute at Washington University School of Medicine in St. Louis.

value: primary cells

value: bone marrow-derived macrophages

value: macrophages


title: SCD2KO, rep1

institute: Washington University School of Medicine

description:
sample 04
all.gene_counts.tsv
group_KO_Differential_Expression.tsv


title: SCD2KO, rep2

description:
sample 05
all.gene_counts.tsv
group_KO_Differential_Expression.tsv


title: SCD2KO, rep3

description:
sample 06
all.gene_counts.tsv
group_KO_Differential_Expression.tsv


title: ChIPRx-HCT116-THZ531-0min-pol2

description: ChIP-seq with HCT116 cells

library_source: genomic

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens .hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: ChIP-Rx

molecule: genomic DNA

extract_protocol:
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.
ChIP-Rx experiments were performed as previously described (Li et al., 2021; Wang et al., 2021). Briefly, 1×107 human cells were spiked-in with 1-2×106 MEF cells and were fixed with 1% paraformaldehyde in PBS for 10 minutes, and quenched with 0.125 M glycine for 5 minutes. Fixed cells were used for nuclei isolation and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The chromatin was immunoprecipitated with 5 μg individual antibodies and 15 μL of pre-blocked Protein A/G beads (Santa Cruz, Cat# sc-2003). After wash for three times with wash buffer (50 mM HEPES-KOH at pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), the captured DNA was eluted and reverse-crosslinked with 200 μL of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) by incubating at 55°C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation.

tag: antibody

value: Pol II


title: KFs, MDI medium plus D4476, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus D4476 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus CX6258_HCl, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus CX6258_HCl for 4 days and then medium was changed to AM medium for another 4 days.


title: 0.5 mM D-lactic acid, biol rep1


title: 0.5 mM D-lactic acid, biol rep2


title: KFs, MDI medium plus Chidamide, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus Chidamide for 4 days and then medium was changed to AM medium for another 4 days.


title: 1022_NI-PGE_Female_Stroma

city: Indianapolis

first: Andrea

middle: Marie

last: Patterson

state: IN

address: 980 W. Walnut St.

department: Medicine

institute: Indiana University School of Medicine

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
1022_S32

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK) for quality control. The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.5) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.5.9). Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.1.5.1) with the following parameters: “-s 2 -Q 10”. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR (v.3.36.0). False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
mm10
excel table including raw counts, log2 fold change, p-values and FDR

source_name: Bone marrow

growth_protocol: Cells were utilized direct ex vivo from murine bone marrow

extract_protocol:
Qiagen RNeasy Plus Mini kit
Total RNA samples were first evaluated for their quantity and quality using Agilent Bioanalyzer 2100. All samples had good quality with RIN (RNA Integrity Number) greater than 8. 100 nanograms of total RNA was used for library preparation with the KAPA mRNA Hyperprep Kit (KK8581) (Roche) following the manufacturer’s protocol. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity. The pooled libraries were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

treatment_protocol: Cell were not treated ex vivo prior to immediate magnetic enrichment and/or FACS sorting and RNA extraction

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

tag: Sex

value: Female

value: NI-PGE


title: ChIPRx-DLD1-IAA-THZ531-pol2

description: ChIP-seq with DLD-1 cells

source_name: Isolated from Large intestine; Colon

value: Isolated from Large intestine; Colon

value: Human Large intestine; Colon

value: treated with IAA and THZ531


title: 1021_NI-Veh_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
1021_S31

value: NI-Veh


title: ChIPRx-HCT116-THZ531-15min-pol2

description: ChIP-seq with HCT116 cells

value: Isolated from the colon

value: Human colon

value: treated with THZ531 for 15 mins


title: WT, rep1

description:
sample 01
all.gene_counts.tsv
group_KO_Differential_Expression.tsv

value: primary cells

value: bone marrow-derived macrophages

value: macrophages

value: WT


title: ChIPRx-DLD1-IAA-THZ531-LEO1

description: ChIP-seq with DLD-1 cells


title: ChIPRx-DLD1-IAA-DMSO-pol2

description: ChIP-seq with DLD-1 cells

value: treated with IAA

value: Pol II


title: KFs, MDI medium plus CHIR_99021, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus CHIR_99021 for 4 days and then medium was changed to AM medium for another 4 days.


title: 0.05 mM D-lactic acid, biol rep2

value: 0.05 mM D-lactic acid

value: haploid vegetative cells

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0

value: exposed to the same medium with 0.05 mM D-lactic acid added for 3 hours


title: KFs, MDI medium plus CHX, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus CHX for 4 days and then medium was changed to AM medium for another 4 days.


title: WT, rep3

description:
sample 03
all.gene_counts.tsv
group_KO_Differential_Expression.tsv


title: 793_EP4_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
793_S30

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: Female


title: 792_EP3_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
792_S29


title: 0.05 mM D-lactic acid, biol rep1


title: 791_PGE_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
791_S28

value: PGE


title: ChIPRx-DLD1-IAA-DMSO-LEO1

description: ChIP-seq with DLD-1 cells

value: Isolated from Large intestine; Colon

value: Human Large intestine; Colon


title: control, biol rep3

value: parallel control (see medium composition in treatment conditions)


title: KFs, MDI medium plus CEP33779, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus CEP33779 for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus C59, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus C59 for 4 days and then medium was changed to AM medium for another 4 days.


title: 790_Veh_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
790_S27

value: Veh


title: iPSCM_LRRC10_1

city: Utrecht

first: Phong

middle: Dang

last: Nguyen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data (fastq file) was demultiplexed and analyzed with 10X Genomics Cell Ranger software v 7.0.0 using the standard default settings. A custom reference was generated by adding the mCherry locus to the prebuilt Cell Ranger human reference.
Assembly: GRChg38
Supplementary files format and content: matrix.mtx of UMI counts where cells are columns and genes are rows; barcode.tsv: list of 12bp barcodes corresponding to the columns of matrix; features.tsv: list of gene names corresponding to the rows of the matrix.

growth_protocol: Spontaneously beating hiPSC-CMs at day 20 of differentiation were dissociated and frozen and subsequently thawed into 96-well Black/Clear tissue culture treated plate (Falcon)  LI-BPEL medium.

extract_protocol:
Cells were trypsinized.
Single cell gene expression libraries were generated on the 10X Genomics Chromium platform using the Chromium Next GEM Single Cell 3’ Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit (10X Genomics) according to the manufacturer’s protocol.

treatment_protocol: hiPSC-CMs were transfected 5 days after thawing with LRRC10-mCherry mRNA using Lipofectamine Stem Transfection Reagent (Thermofisher Scientific) according to the manufacturer’s instructions. 24h before transfection, culture medium was switched from LI-BPEL medium to a modified version (mBEL medium) to improve transfection efficiency. hiPSC-CMs transfected with LRRC10 mRNA were collected at day 2 after transfection.

value: LUMC0020iCTRL-06 hiPSC cell line

value: iPS cardiomyocytes

value: LRRC10-mCherry transfected


title: KFs, MDI medium plus CPI_455_HCl, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus CPI_455_HCl for 4 days and then medium was changed to AM medium for another 4 days.


title: control, biol rep1

value: haploid vegetative cells

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0


title: KFs, MDI medium plus Bexarotene, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Bexarotene for 4 days and then medium was changed to AM medium for another 4 days.


title: 20_3000-T00-PBM_7, Control, snATACseq

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

description:
3000-T00
COVID19_scATAC_integration.tar

data_processing:
Reads of snATAC-seq experiments were aligned to the GRCh38 (hg38) human reference genome using cellranger-atac software (10x Genomics; version 2.0). The resulting fragment files were processed using ArchR [PMID: 33633365].
Assembly: hg38
Supplementary files format and content: tar file contains the integrated data of all samples

source_name: PBMC

extract_protocol:
Followed the 10X Genomics Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing protocol
Followed the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (10x Genomics, Pleasanton, CA).
Single Cell Multiome ATAC + Gene Expression

value: PBMC

tag: disease state

value: Control

tag: timepoint

tag: age

value: Male

tag: fraction

value: Nuclear DNA


title: KFs, MDI medium plus Blebbistatin, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Blebbistatin for 4 days and then medium was changed to AM medium for another 4 days.


title: 20_2800-T00-PBM_7, Control, snATACseq

description:
2800-T00
COVID19_scATAC_integration.tar


title: 20_2773-T00-PBM_7, Control, snATACseq

description:
2773-T00
COVID19_scATAC_integration.tar


title: 787_NI-PGE_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
787_S24

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: NI-PGE


title: 0.05 mM D-lactic acid, biol rep3

value: 0.05 mM D-lactic acid

value: exposed to the same medium with 0.05 mM D-lactic acid added for 3 hours


title: LC10_Smad4_iBECs_MUT-3

city: New Orleans

first: Xingyan

last: Zhou

address: 6823 St Charles Ave

institute: Tulane University

description: Raw counts

data_processing:
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated spreadsheet file with raw counts for every gene for every sample.

source_name: Endothelial cells

extract_protocol:
Whole brain tissue was digested using a Neural Tissue Dissociation Kit (P) (Milteni, 130-092-628) following the manufacture instructions. Brain endothelial cells were purified using dynabeads (Invitrogen 11035) coated with platelet endothelial cell adhesion molecule (PECAM) antibody (BD, 553370), followed by immediate RNA or protein extraction. RNA was extracted using Thermo Fisher GeneJET RNA Purification Kit (Thermo, K0732).
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 1 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).

treatment_protocol: Tamoxifen (300µg) was adminstered to new born pups at postnatal days 1,2 and 3 for Smad4 and Eng models;  Tamoxifen (100µg) was adminstered to Alk1 pups at postnatal days 4. IgG or LC10 (Ang2 inhibitor) (30ug) were administered at P2 and P4 in Smad4-HHT mouse model.

value: Brain

value: Endothelial

value: Postnatal day 7

value: Smad4f/f; Cdh5-CreERT2


title: KFs, MDI medium plus Berberine, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus Berberine for 4 days and then medium was changed to AM medium for another 4 days.


title: 20_2654-T35-PBM_7, SARS-CoV-2, snATACseq

description:
2654-T35
COVID19_scATAC_integration.tar

value: PBMC

value: SARS-CoV-2 infection

value: Male


title: 786_NI-Veh_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
786_S23

value: NI-Veh


title: KFs, MDI medium plus Belinostat, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Belinostat for 4 days and then medium was changed to AM medium for another 4 days.


title: LC10_Smad4_iBECs_MUT-2

description: Raw counts


title: 20_2624-T32-PBM_7, SARS-CoV-2, snATACseq

description:
2624-T32
COVID19_scATAC_integration.tar

value: Nuclear DNA


title: LC10_Smad4_iBECs_MUT-1

description: Raw counts


title: IgG_Smad4_iBECs_MUT-3

description: Raw counts


title: 785_Miso_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
785_S22

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: Miso


title: control, biol rep2

value: haploid vegetative cells

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0

value: parallel control (see medium composition in treatment conditions)


title: KFs, MDI medium plus BMP4, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus BMP4 for 4 days and then medium was changed to AM medium for another 4 days.


title: 20_2557-T32-PBM_7, SARS-CoV-2, snATACseq

description:
2557-T32
COVID19_scATAC_integration.tar


title: 789_Miso_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
789_S26

value: Female


title: KFs, MDI medium plus Baricitinib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus Baricitinib for 4 days and then medium was changed to AM medium for another 4 days.


title: 784_EP3+4_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
784_S21

value: Male


title: IgG_Smad4_iBECs_MUT-2

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 7

value: Smad4f/f; Cdh5-CreERT2


title: KFs, MDI medium plus BI_9564, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus BI_9564 for 4 days and then medium was changed to AM medium for another 4 days.


title: IgG_Smad4_iBECs_MUT-1

description: Raw counts


title: 782_EP3_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
782_S19

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma


title: 20_2528-T42-PBM_7, SARS-CoV-2, snATACseq

description:
2528-T42
COVID19_scATAC_integration.tar

value: PBMC

value: SARS-CoV-2 infection

value: Nuclear DNA


title: 783_EP4_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
783_S20


title: KFs, MDI medium plus BIO, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus BIO for 4 days and then medium was changed to AM medium for another 4 days.


title: 20_1855-T49-PBM_7, SARS-CoV-2, snATACseq

description:
1855-T49
COVID19_scATAC_integration.tar


title: KFs, MDI medium plus BI4394, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus BI4394 for 4 days and then medium was changed to AM medium for another 4 days.


title: IgG_Smad4_iBECs_WT-2

description: Raw counts


title: IgG_Smad4_iBECs_WT-1

description: Raw counts


title: KFs, MDI medium plus BI9564, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus BI9564 for 4 days and then medium was changed to AM medium for another 4 days.


title: 780_Veh_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
780_S17

value: Male

value: Veh


title: IgG_Smad4_iBECs_WT-3

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 7


title: 730_NI-PGE_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
730_S16

value: NI-PGE


title: ChIPRx-DLD1-IAA-PAF1

description: ChIP-seq with DLD-1 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples

extract_protocol:
ChIP-Rx experiments were performed as previously described (Li et al., 2021; Wang et al., 2021). Briefly, 1×10^7 human cells were spiked-in with 1-2×10^6 MEF cells and were fixed with 1% paraformaldehyde in PBS for 10 minutes, and quenched with 0.125 M glycine for 5 minutes. Fixed cells were used for nuclei isolation and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The chromatin was immunoprecipitated with 5 μg individual antibodies and 15 μL of pre-blocked Protein A/G beads (Santa Cruz, Cat# sc-2003). After wash for three times with wash buffer (50 mM HEPES-KOH at pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), the captured DNA was eluted and reverse-crosslinked with 200 μL of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) by incubating at 55°C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation.
library strategy: ChIP-seq-Rx
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.

value: Large intestine; Colon

value: IAA for 6 hours

tag: chip antibody


title: KFs, MDI medium plus Alvimopan_dihydrate, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus Alvimopan_dihydrate for 4 days and then medium was changed to AM medium for another 4 days.


title: 729_NI-Veh_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
729_S15

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: NI-Veh


title: KFs, MDI medium plus Alfacalcidol, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus Alfacalcidol for 4 days and then medium was changed to AM medium for another 4 days.


title: Eng_iBECs_MUT-4

description: Raw counts

value: Engf/f; Cdh5-CreERT2


title: ChIPRx-DLD1-IAA-PolII

description: ChIP-seq with DLD-1 cells

value: Pol II


title: 781_PGE_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
781_S18

value: Male

value: PGE


title: ChIPRx-DLD1-DMSO-PolII

description: ChIP-seq with DLD-1 cells

value: DMSO for 6 hours


title: ChIPRx-DLD1-IAA-LEO1

description: ChIP-seq with DLD-1 cells


title: ChIPRx-DLD1-DMSO-PAF1

description: ChIP-seq with DLD-1 cells


title: KFs, MDI medium plus Adavosertib, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Adavosertib for 4 days and then medium was changed to AM medium for another 4 days.


title: 788_EP3+4_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
788_S25

value: Female


title: Eng_iBECs_MUT-2

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 7


title: KFs, MDI medium plus AcitvinA, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: WT

value: KFs with MDI medium plus AcitvinA for 4 days and then medium was changed to AM medium for another 4 days.


title: KFs, MDI medium plus Apalutamide, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus Apalutamide for 4 days and then medium was changed to AM medium for another 4 days.


title: Eng_iBECs_MUT-5

description: Raw counts


title: Eng_iBECs_MUT-1

description: Raw counts


title: ChIPRx-HCT116-3XFlag-PROTAC-PolII-rep2

description: ChIP-seq with HCT116 cells

value: colon

value: HaloPROTAC for 6 hours


title: Eng_iBECs_WT-5

description: Raw counts

value: Engf/f


title: KFs, MDI medium plus AM580, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: KFs with MDI medium plus AM580 for 4 days and then medium was changed to AM medium for another 4 days.


title: 726_PGE_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
726_S12

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: Male


title: 727_EP3_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
727_S13


title: ChIPRx-DLD1-DMSO-LEO1

description: ChIP-seq with DLD-1 cells

value: Large intestine; Colon

value: DMSO for 6 hours


title: 725_Veh_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
725_S11

value: Veh


title: KFs, AD medium, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus AD for 4 days and then medium was changed to AM medium for another 4 days.


title: 724_Miso_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
724_S10

value: Miso


title: Eng_iBECs_MUT-3

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 7

value: Engf/f; Cdh5-CreERT2


title: Eng_iBECs_WT-4

description: Raw counts

value: Engf/f


title: 728_EP4_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
728_S14


title: KFs, MDI medium plus ABT869, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: WT

value: KFs with MDI medium plus ABT869 for 4 days and then medium was changed to AM medium for another 4 days.


title: Eng_iBECs_WT-3

description: Raw counts


title: ChIPRx-HCT116-3XFlag-DMSO-PolII-rep1

description: ChIP-seq with HCT116 cells

value: colon

value: Pol II


title: KFs, MDI medium plus A8301, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: KFs with MDI medium plus A8301 for 4 days and then medium was changed to AM medium for another 4 days.


title: 722_NI-Veh_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
722_S8

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: Female

value: NI-Veh


title: KFs, MDI medium plus A769662, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with MDI medium plus A769662 for 4 days and then medium was changed to AM medium for another 4 days.


title: Eng_iBECs_WT-2

description: Raw counts

value: Brain

value: Endothelial


title: 721_NI-PGE_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
721_S7

value: NI-PGE


title: 723_EP3+4_Male_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
723_S9

value: Male


title: KFs, MDI medium plus 8_bromo_cAMP_, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with MDI medium plus 8_bromo_cAMP_ for 4 days and then medium was changed to AM medium for another 4 days.


title: ChIPRx-HCT116-CDK12as--PP1-PAF1

description: ChIP-seq with HCT116 cells

value: 1-NA-PP1 for 6 hours


title: ChIPRx-HCT116-3XFlag-DMSO-PolII-rep2

description: ChIP-seq with HCT116 cells

value: colon

value: DMSO for 6 hours


title: KFs, MDI medium plus 5_aza_dC, 8 Days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with MDI medium plus 5_aza_dC for 4 days and then medium was changed to AM medium for another 4 days.


title: ChIPRx-HCT116-CDK12as-DMSO-PolII

description: ChIP-seq with HCT116 cells

value: Pol II


title: Eng_iBECs_WT-1

description: Raw counts

value: Postnatal day 7

value: Engf/f


title: KFs, KF medium, 8 days, rep4

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

extract_protocol:
KFs were seeded at a density of 5000 cells per well of a 96-well plate containing KF medium. The next day, KFs were incubated in AD medium (DMEM/high glucose, 1% ITS, 0.5mM isobutylmethylxanthine, 0.1 μM cortisol, 1 μM dexamethasone, 0.2 nM triiodothyronine, 1 μM rosiglitazone) for adipocyte fate transition or  KF medium as control. After 4 days, the AD medium was changed to an AM medium (DMEM/high glucose, 1% ITS, 0.1 μM cortisol, 0.2 nM triiodothyronine) for adipocyte cell fate maintenance for another 8 days. The AM medium was changed every 4 days. Meanwhile, KF medium was was changed every 4 days. Cells were harvested on day 12 for PHDs-seq.
Samples in a 96 well-plate were washed with pre-warmed PBS. 60 μl of lysis buffer containing 50mM Tris-HCl pH8.0, 75mM KCl, 6% Ficoll PM-400, 0.15% TritonX-100, and 0.5U/μl RNaseOUT (RNaseOut should be added before use) were added to each well. The 96-well plate was then incubated on a shaker at 900 rpm for 15 minutes. 4.286 μl of cell lysate were transferred to a new 96 well PCR plate. 0.714 μl reverse transcription mix containing 40mM MgCl2, 4μM strand switching primer (TSO), 0.1mM dNTP, 8U/μl Maxima reverse transcriptase, 1x ERCC, and RNaseOUT (RNaseOut should be added before use) were added to each well, mixed and slightly centrifuged for several seconds to collect all reactants on the bottom. The 96-well PCR plate was incubated at 42°C for 2 hours with a hot lid at 105°C. 6μl of hybridization-ligation mix (0.005 μM probe mix, 1U/μl Taq DNA ligase, 1x Taq DNA ligation buffer) was added to the RT products, mixed gently, and incubated at 60°C for 60 minutes with a hot lid of 105°C. After hybridization and ligation, the products were enriched with 15 ul of enrichment mixture (2 μl Dynabeads MyOne Carboxylic Acid beads plus 13 μl capture buffer containing 30% PEG-600, 2 M, NaCl, 5 mM Tris-HCl pH7.5, 10 mM EDTA, and 0.02% Tween-20). Next, 20 μl of PCR mixture (0.25 μM PHD-seq well barcode, 0.5 mM PHD-seq plate barcode, 1 x Vazyme LAmp Master Mix) were added to the enriched hybridization-ligation products, mixed, and incubated at 94°C for 5min, followed by two cycles of 95°C for 20 s, 57°C for 30 s and 72°C for 20 s. In addition, 10 cycles of 94°C for 20 s, 65°C for 30 s, and 72°C for 20 s with a final extension at 72°C for 60 s. The PCR products were pooled together into several 1.5 ml tubes which were placed on a magnet to remove the beads. The supernatant was purified with DNA Clean & Concentrator-100 column (Zymo Research, D4029) and eluted with 150 µl of ddH2O. The library was size-selected using AMPure XP beads. 150 µl of beads were added to 150 µl of the purified PCR product, incubated for 5 min, and captured by a magnet for 3 min after which the supernatant was discarded. The beads were eluted in 25 µl of ddH2O and incubated for 1 min at room temperature. After 1 min of incubation on the magnet, the supernatant was transferred to a clean 1.5 ml tube. The 208 bp library was visualized using agarose gel electrophoresis and quantified using a Qubit™ 4 NGS Starter Kit with WiFi (Q33240).

value: KFs with KF medium for 8 days.


title: ChIPRx-HCT116-CDK12as-PP1-LEO1

description: ChIP-seq with HCT116 cells


title: 720_Miso_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
720_S6

value: Bone marrow

value: Primary bone marrow stroma cells

value: BM Stroma

value: Female

value: Miso


title: 718_EP4_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
718_S4


title: Alk1_iBECs_MUT-4

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 6

value: Alk1f/f; Cdh5-CreERT2


title: Alk1_iBECs_MUT-3

description: Raw counts


title: Alk1_iBECs_MUT-5

description: Raw counts


title: ChIPRx-HCT116-3XFlag-PROTAC-PolII-rep1

description: ChIP-seq with HCT116 cells

value: colon

value: HaloPROTAC for 6 hours


title: KFs, KF medium, 8 days, rep3

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT


title: 717_EP3_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
717_S3


title: ChIPRx-HCT116-CDK12as-DMSO-LEO1

description: ChIP-seq with HCT116 cells

value: DMSO for 6 hours


title: ChIPRx-HCT116-CDK12as-DMSO-PAF1

description: ChIP-seq with HCT116 cells


title: Alk1_iBECs_MUT-2

description: Raw counts


title: KFs, KF medium, 8 days, rep2

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA


title: ChIPRx-HCT116-CDK12as-PPI-PolII

description: ChIP-seq with HCT116 cells

value: 1-NA-PP1 for 6 hours

value: Pol II


title: ChIPRx-HCT116-LEO1-FL-PROTAC

description: ChIP-seq with HCT116 cells


title: 716_PGE_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
716_S2

value: Bone marrow

value: PGE


title: KFs, KF medium, 8 days, rep1

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with KF medium for 8 days.


title: Alk1_iBECs_MUT-1

description: Raw counts


title: 715_Veh_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
715_S1

value: Primary bone marrow stroma cells

value: BM Stroma

value: Female

value: Veh


title: KFs, AD medium 4 days then AM 4 days, rep4

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with AD medium for 4 days and then medium was changed to AM medium for another 4 days.


title: 957_Veh_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
957_Veh_S32

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK) for quality control. The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.5) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genome was assessed using bamutils (from ngsutils v.0.5.9). Uniquely mapped reads were used to quantify the gene level expression employing featureCounts (subread v.1.5.1) with the following parameters: “-s 0 -Q 10”. The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR (v.3.36.0). False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
mm10
excel table including raw counts, log2 fold change, p-values and FDR

extract_protocol:
Qiagen RNeasy Plus Micro kit
Total RNA samples were first evaluated for their quantity and quality using Agilent Bioanalyzer 2100. All samples had good quality with RIN (RNA Integrity Number) greater than 7. One nanograms of total RNA was used for library preparation with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA) and the Nextera XT DNA Lib Kit (Illumina, San Diego, CA) following the manufacturer’s protocol. Each resulting uniquely dual-indexed library was quantified and quality accessed by Qubit and Agilent TapeStation, and multiple libraries were pooled in equal molarity. The pooled libraries were sequenced with 2×100bp paired-end configuration on an Illumina NovaSeq 6000 sequencer using the v1.5 reagent kit.

value: Primary bone marrow hematopoietic stem cells (HSCs)

value: HSC


title: Alk1_iBECs_WT-5

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 6


title: Alk1_iBECs_WT-4

description: Raw counts


title: KFs, AD medium 4 days then AM 4 days, rep3

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT


title: Alk1_iBECs_WT-3

description: Raw counts


title: KFs, AD medium 4 days then AM 4 days, rep2

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA


title: Alk1_iBECs_WT-2

description: Raw counts


title: 955_EP4_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
955_EP4_S30


title: KFs, AD medium 4 days then AM 4 days, rep1

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA


title: 954_EP3+4_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
954_EP3-EP4_S29


title: 719_EP3+4_Female_Stroma

description:
ILMN_1369_Patterson_mRNA32_May2022_processedData.xlsx
719_S5


title: Alk1_iBECs_WT-1

description: Raw counts


title: ChIPRx-HCT116-LEO1-540-666-PROTAC-rep1

description: ChIP-seq with HCT116 cells

value: colon

value: HaloPROTAC for 6 hours

value: Pol II


title: ChIPRx-HCT116-LEO1-540-666-PROTAC-rep2

description: ChIP-seq with HCT116 cells


title: Proseq-HCT116-LEO1-FL-HALOPROTAC3-Group540-666

description: Pro-seq with HCT116 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: PRO-seq

extract_protocol:
PRO-seq was performed as previously reported (Judd et al., 2020; Li et al., 2021; Liang et al., 2018) and PRO-seq libraries were sequenced on a NovaSeq 6000 platform.
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.


title: Proseq-HCT116-LEO1-FL-HALOPROTAC3-Group3PA

description: Pro-seq with HCT116 cells


address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

data_processing:
Data were analysed as previously described (Teder et al., 2018). First, sequencing reads were mapped to the reference sequences (left probes plus right probes) to produce total counts of each gene. The CPM (Counts of exon model per million mapped reads) matrix was then transferred from the count matrix and used in cluster analysis, Pearson correlation analysis, and PCA analysis. All scripts was descripted in (Teder et al., 2018).
Assembly: no
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

extract_protocol:
KFs were seeded at a density of 5000 cells per well of a 96-well plate containing KF medium. The next day, KFs were incubated in AD medium (DMEM/high glucose, 1% ITS, 0.5mM isobutylmethylxanthine, 0.1 μM cortisol, 1 μM dexamethasone, 0.2 nM triiodothyronine, 1 μM rosiglitazone) for adipocyte fate transition (Posi) or  KF medium as negative control. After 4 days, the AD medium was changed to an AM medium (DMEM/high glucose, 1% ITS, 0.1 μM cortisol, 0.2 nM triiodothyronine) for adipocyte cell fate maintenance for another 1 or 4 days. KF medium was changed for another 1 or 4 days. Cells were harvested on day 5 and day 8 for PHDs-seq.
Samples in a 96 well-plate were washed with pre-warmed PBS. 60 μl of lysis buffer containing 50mM Tris-HCl pH8.0, 75mM KCl, 6% Ficoll PM-400, 0.15% TritonX-100, and 0.5U/μl RNaseOUT (RNaseOut should be added before use) were added to each well. The 96-well plate was then incubated on a shaker at 900 rpm for 15 minutes. 4.286 μl of cell lysate were transferred to a new 96 well PCR plate. 0.714 μl reverse transcription mix containing 40mM MgCl2, 4μM strand switching primer (TSO), 0.1mM dNTP, 8U/μl Maxima reverse transcriptase, 1x ERCC, and RNaseOUT (RNaseOut should be added before use) were added to each well, mixed and slightly centrifuged for several seconds to collect all reactants on the bottom. The 96-well PCR plate was incubated at 42°C for 2 hours with a hot lid at 105°C. 6μl of hybridization-ligation mix (0.005 μM probe mix, 1U/μl Taq DNA ligase, 1x Taq DNA ligation buffer) was added to the RT products, mixed gently, and incubated at 60°C for 60 minutes with a hot lid of 105°C. After hybridization and ligation, the products were enriched with 15 ul of enrichment mixture (2 μl Dynabeads MyOne Carboxylic Acid beads plus 13 μl capture buffer containing 30% PEG-600, 2 M, NaCl, 5 mM Tris-HCl pH7.5, 10 mM EDTA, and 0.02% Tween-20). Next, 20 μl of PCR mixture (0.25 μM PHD-seq well barcode, 0.5 mM PHD-seq plate barcode, 1 x Vazyme LAmp Master Mix) were added to the enriched hybridization-ligation products, mixed, and incubated at 94°C for 5min, followed by two cycles of 95°C for 20 s, 57°C for 30 s and 72°C for 20 s. In addition, 10 cycles of 94°C for 20 s, 65°C for 30 s, and 72°C for 20 s with a final extension at 72°C for 60 s. The PCR products were pooled together into several 1.5 ml tubes which were placed on a magnet to remove the beads. The supernatant was purified with DNA Clean & Concentrator-100 column (Zymo Research, D4029) and eluted with 150 µl of ddH2O. The library was size-selected using AMPure XP beads. 150 µl of beads were added to 150 µl of the purified PCR product, incubated for 5 min, and captured by a magnet for 3 min after which the supernatant was discarded. The beads were eluted in 25 µl of ddH2O and incubated for 1 min at room temperature. After 1 min of incubation on the magnet, the supernatant was transferred to a clean 1.5 ml tube. The 208 bp library was visualized using agarose gel electrophoresis and quantified using a Qubit™ 4 NGS Starter Kit with WiFi (Q33240).

value: KFs with AD medium for 4 days and then medium was changed to AM medium for another 4 days


title: 953_Miso_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
953_Miso_S28

value: Bone marrow

value: Miso


title: Smad4_iBECs_MUT-5

description: Raw counts

value: Postnatal day 7

value: Smad4f/f; Cdh5-CreERT2


address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA


title: 952_Veh_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
952_Veh_S27

value: Male

value: Veh


title: 951_EP3_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
951_EP3_S26

value: Primary bone marrow hematopoietic stem cells (HSCs)

value: HSC


title: Smad4_iBECs_MUT-4

description: Raw counts

value: Brain

value: Endothelial


title: Proseq-HCT116-LEO1-3PA-HALOPROTAC3-Group3PA

description: Pro-seq with HCT116 cells


title: KFs, AD medium 5 days

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: KFs with AD medium for 5 days.


title: Smad4_iBECs_MUT-3

description: Raw counts


title: KFs, KF medium, 8 days, rep2

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: fibroblast

value: WT

value: KFs with KF medium for 8 days.


title: 956_EP3_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
956_EP3_S31

value: Female


title: 950_EP4_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
950_EP4_S25


title: Smad4_iBECs_MUT-2

description: Raw counts


title: TTseq-HCT116-LEO1-FL-HaloPROTAC3-rep2

description: TT-seq with HCT116 cells

data_processing:
ChIP-Rx reads were aligned to the Human reference genome GRCh38/hg38 and Mouse reference genome GRCm38/mm10 with Bowtie2 (Langmead and Salzberg, 2012), allowing only uniquely mapping reads with up to two mismatches. The aligned human reads were normalized using the aligned mouse reads. The human BAM files were normalized and converted to bigwig files using Samtools (Li et al., 2009; Orlando et al., 2014). ChIP Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters (Zhang et al. 2008). Heatmaps and metaplots were made for the indicated windows using the average coverage (r.p.m.) using Deeptools 2.0 (Ramirez et al., 2016). Ngsplot was used to calculate the ratio of PAF1C occupancy to Pol II coverage.
PRO-seq reads were aligned to the human hg38 and Drosophila dm6 genome using Bowtie2. The resulting reads were normalized to spiked-in Drosophila reads and converted to bigwig files for visualization in the UCSC Genome Browser. Heatmaps and metaplots were made for the indicated windows using the average coverage using Deeptools 2.0 (Ramirez et al., 2016).
TT-seq reads were aligned to the Human reference genome GRCh38/hg38 or Drosophila reference genome BDGP Release 6/dm6 with Bowtie2 (Langmead and Salzberg, 2012). The aligned human reads were normalized using the aligned Drosophila reads. The human BAM files were normalized and converted to bigwig files using Deeptools 2.0 (Ramirez et al., 2016). Heatmaps, metaplots, and boxplots were made for the indicated windows using the average coverage.
Assembly: Homo sapiens hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: TT-seq

extract_protocol:
TT-seq was performed as previously described (Gregersen et al., 2020; Schwalb et al., 2016) with some modifications. Cells were labeled in media with 400 μM 4-thiouridine (4sU) (Sigma-Aldrich, Cat# T4509) for 10 min before harvest, and total RNA was extracted with TRIzol (Invitrogen, Cat# 15596-018), the labeled RNA (100 μg) was fragmented with NaOH and spike-in with 10% S2 RNA (10 μg). After biotinylated in a 300 μL reaction (100 μg RNA, 10mM HEPES-KOH, pH 7.5, 1mM EDTA, 0.167mg/ml MTSEA-biotin-XX (Sigma-Aldrich, Cat# M9938)), enriched the biotin-labeled RNA with Streptavidin M280 beads (Invitrogen, Cat# 11206D) and eluted by 100mM DTT. RNA was purified by 1.8 x RNAClean XP beads before library preparation.
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.

value: colon

value: HaloPROTAC for 6 hours


title: KFs, KF medium, 8 days, rep1

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA


title: TTseq-HCT116-LEO1-FL-HaloPROTAC3-rep1

description: TT-seq with HCT116 cells


title: Proseq-HCT116-LEO1-540-666-HALOPROTAC3-Group540-666

description: Pro-seq with HCT116 cells


title: KFs, KF medium, 5 days, rep2

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: KFs with KF medium for 5 days.


title: 949_EP3+4_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
949_EP3-EP4_S24

value: Bone marrow


title: 948_Miso_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
948_Miso_S23

value: Miso


title: Smad4_iBECs_WT-5

description: Raw counts

value: Postnatal day 7


title: Corpus_T_PID00165

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description:
We analyzed single-cells, which were sorted to 384-wells in total. read1 = cell barcode (1-15), UMI (16-23), read2 = transcript
04_export_counts_dataset2.csv
04_export_meta_data_dataset2.csv

data_processing:
BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.20.0.422) with demultiplexing pool barcodes.
We trimmed read2 length to 62 nucleotides by using FASTX-Toolkit (version 0.0.14).
Data for Quartz-Seq2 was processed by Drop-seq tools (version 2.4.1) and correct_bacode program (https://github.com/rikenbit/correct_barcode) to convert fastq files to digital expression matrix.
Transcript reads were mapped to GRCm39 reference genomes using STAR2.7.8a.
dataset1 [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript], dataset2 [read1 = cell barcode (1-15), UMI (15-23), read2 = transcript]
Assembly: Gencode Release M27 (GRCm39 primary genome assembly)
Supplementary files format and content: tab-delimited text files include UMI counts for each gene for each cell

source_name: corpus gastric units

extract_protocol:
For single-cell RNA-seq analysis of dataset1 and dataset2, we performed Quartz-Seq2 as reported previously [Sasagawa et al., Genome Biology 19:29(2018), https://doi.org/10.1186/s13059-018-1407-3].
For the Quartz-Seq2 method, single-cell was aliquoted into the wells of a 384-well PCR plate with cell-sorter. These plates contain reverse transcription primers with different cell-barcodes in each well. For dataset1 and dataset2, v3.1 RT primers and v3.2a RT primers are used, respectively. In dataset1, ERCC spike mix I was included in the lysis buffer of the 384-well PCR plate. The collected single-cell lysis plates were stored at -80 ºC until the next whole-transcript amplification steps. The whole-transcript amplification steps and sequence library preparation were performed as described in previous paper [Sasagawa et al., Genome Biology 19:29(2018), https://doi.org/10.1186/s13059-018-1407-3]. The sequence library DNA was analyzed by the Agilent High Sensitivity DNA Kit (Agilent) and QuantiFluor® dsDNA System (Promega) to measure the exact DNA size length and DNA concentration. The sequence library DNA was then analyzed with NextSeq500 HOP 75 cycles kit v2.5.

treatment_protocol: In this project, two types of cell suspensions (dataset1, dataset2) were prepared from the mouse stomach. In dataset1, single-cells were isolated from a tissue containing both corpus and antrum gastric units. In dataset2, single-cells were isolated from the corpus gastric units. For both datasets, cell suspensions from three mice were prepared and designated as biological replicate1 and biological replicate2, respectively. Cell suspensions of dataset1 were stained with ToPro3 dye in order to remove dead cells by cell-soring using MoFlo Astrios EQ cell sorter. Cell suspensions of dataset2 were stained with Hoechst33342 and ToPro3 dyes in order to remove dead cells and cellular debris by cell-sorting. Isolated single-cells were analyzed by single-cell RNA-seq method.

value: corpus gastric units

value: adult stomach

value: Mixture of cell types from adult stomach

value: Male

tag: collected cell_by_using_cell-sorter


title: 946_EP3+4_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
946_EP3-EP4_S21

value: Primary bone marrow hematopoietic stem cells (HSCs)

value: HSC


title: Smad4_iBECs_WT-4

description: Raw counts

value: Brain

value: Endothelial


title: Proseq-HCT116-CDK12as-DMSO

description: Pro-seq with HCT116 cells

value: DMSO for 6 hours


title: KFs, KF medium, 5 days, rep1

address: 北京市海淀区颐和园路5号北京大学王克桢楼207

description: Targeted RNA

value: skin

value: fibroblast

value: WT


title: 945_EP4_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
945_EP4_S20

value: Female


title: FXS-iPS848_dCas9-gNHG3_36d_rep2

city: Boston

first: Hun-Goo

last: Lee

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Mass General Hospital

data_processing:
Preprocessing for the raw fastq files including adaptor sequence removal was performed by Trim Galore v0.4.1 software
Preprocessed fastq files were aligned to hg19 genome by TopHat v2.0.10 with the following parameters: --read-edit-dist 3 --read-mismatches 3 --read-gap-length 3 --b2-very-sensitive --mate-inner-dist 100 --mate-std-dev 100
DEseq2 (Love et al., 2014), featureCounts (Liao et al., 2014), and enhancedVolcano were used for analyzing the differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig coverage files were generated by using bamCoverage software with the parameter --normalizeUsingRPKM
Supplementary_files_format_and_content: Differentially Expressed gene analysis result table was generated by DEseq2 software

source_name: human iPSC

growth_protocol: hiPSCs were grown in mTeSR media.

extract_protocol:
Total RNA was extracted by RNAzol and isopropanol precipitation. Poly(A) tailed mRNAs were purified by using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490)
RNAseq libraries were constructed by using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760S) by following the protocols from the manufacturer.

treatment_protocol: Catalytically dead Cas9 (pGH125 dCas9-Blast) was introduced by lentivirus with the Blasticidin selection. Guide RNA for FMR1 5' UTR unique site, named as gNHG3, or scrambled gRNA (gScr) was introduced by lentivirus with the puromycin selection. pgRNA-modified plasmid was used as a backbone.

value: iPSCs

value: FXS full-mutation

value: dCas9+gNHG3 introduced

value: Fragile X syndrome


title: FXS-iPS848_dCas9-gNHG3_36d_rep1


title: Smad4_iBECs_WT-2

description: Raw counts

value: Postnatal day 7


title: Corpus_T_PID00163

value: corpus gastric units

value: adult stomach


title: 944_EP3_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
944_EP3_S19

value: Bone marrow


title: Smad4_iBECs_WT-3

description: Raw counts


title: Smad4_iBECs_WT-1

description: Raw counts


title: FXS-iPS848_dCas9-gScr_36d_rep2

value: dCas9+gScr introduced


title: Corpus_T_PID00162

value: Mixture of cell types from adult stomach

value: Male


title: Corpus_T_PID00164


title: Corpus_T_PID00159


title: 947_Miso_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
947_Miso_S22

value: Primary bone marrow hematopoietic stem cells (HSCs)

value: HSC

value: Miso


title: 942_Miso_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
942_Miso_S17


title: TTseq-HCT116-LEO1-3PA-HaloPROTAC3-rep2

description: TT-seq with HCT116 cells

value: colon

value: HaloPROTAC for 6 hours


title: TTseq-HCT116-LEO1-3PA-HaloPROTAC3-rep1

description: TT-seq with HCT116 cells


title: Corpus_T_PID00158

value: WT


title: B13F14

city: Shanghai

first: Qi

last: Ai

address: 197 Ruijin Second Road, Shanghai

department: General Surgery

institute: Shanghai Jiaotong University

description: 10x Genomics

data_processing:
The Cell Ranger- mkfastq subroutine was used to convert the sequencing data of BCL format into FastQ format. Using FastQC software to analyze the quality control of preprocessed data.
Using FastQC software to analyze the quality control of preprocessed data. Cell Ranger- VDJ subroutine was used to assemble the V (D) J region sequence of TCR gene of every single cell.
IMGT database (https://support.10xgenomics.com/single-cellvdj) and VDJ database (https://vdjdb.cdr3.net/) were used to analyze the results, and Loupe V (D) J Browser was used for the visualization of analysis results.
Assembly: hg38
Supplementary files format and content: fasta DNA sequences, and csv values files

source_name: Pancreas

extract_protocol:
The qualified cells are washed and re-suspended to prepare suitable cell concentration at 700~1200 cells/ml for computer operation of 10X Genomics Chromium™ system.
10X genomics Single Cell Sequencing
Using 10X Genomics Chromium™ system, gel Bead with sequence tags, sorted T cells and reagent premixed liquid and oil were loaded into their respective injection channels, a “double cross” cross system was formed through the microfluidic channel network to finally emerge a single cell micro-reaction system GEMs wrapped by oil droplets. The single cell was isolated by gel beads, and then the mRNA molecule was released by cell cleavage and reverse-transcribed into cDNA by the polyT primer. The V (D) J region was amplified by a pair of primers near the 5-terminal UTR region of the V (D) J region and the gene C region. During the amplification process, the unique molecular tag (UMI) of the cell marker and transcript marker were introduced, and the amplified products were digested with restriction endonuclease to produce the second generation sequencing library. Finally, the high-throughput sequencing is carried out by using the double-ended sequencing mode of Illumina platform.

value: Pancreas

value: human tumor infiltrating lymphocytes

value: sorted T cells


title: 941_EP3+4_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
941_EP3-EP4_S16


title: 20_2266-T32-PBM_7, SARS-CoV-2, snATACseq

description:
2266-T32
COVID19_scATAC_integration.tar

value: PBMC

value: SARS-CoV-2 infection

value: Nuclear DNA


title: B13F4

description: 10x Genomics


title: Corpus_K_PID00171

value: corpus gastric units

value: adult stomach


title: 940_EP4_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
940_EP4_S15

value: Bone marrow


title: Corpus_K_PID00170

value: Mixture of cell types from adult stomach


title: B13F1

description: 10x Genomics


title: 943_Veh_Female_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
943_Veh_S18

value: Female

value: Veh


title: UA44 strain, P0 generation, HB101 diet, rep3

city: Tuscaloosa

first: Guy

last: Caldwell

state: AL

address: 300 Hackberry Lane

department: Biological Sciences

institute: The University of Alabama

data_processing:
Raw reads were filtered to remove adapters or low quality reads
HISAT2, version 2.1.0-beta, with a parameter of "mismatch=2" was used to map filtered sequenced reads to the reference genome.
HTSeq, version 0.6.1, with a parameter of "-m union" was used to quantify reads.
Differentially expressed genes were extracted using DESeq, version 1.10.1.
Assembly: PRJNA13758.WBPS13
Supplementary files format and content: 2 tab-delimited text files with significant differentially expressed genes each for P0 and F3 generations.
Supplementary files format and content: 2 tab-delimited text files with all differential analysis results each for P0 and F3 generations.
Supplementary files format and content: 2 tab-delimited text files with readcounts for each gene each for P0 and F3 generations.
Supplementary files format and content: tab-delimited text file with FPKM values.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were grown on large NGM plates seeded with either OP50 or HB101 E.coli and grown at 20°C.

extract_protocol:
RNA was extracred by freezing and thawing samples in 500μL of Trizol 7 times, then vortexed and iced 7 times. Phases were separated with 100 μL choloform. After separation, the aqueous phase was added to an equal volume of 70% ethanol and subjected to the protocol outlined in the Qiagen RNeasy Micro Kit. RNA was eluted with 35μL of RNase-free water.
mRNA was enriched using oligo(dT) beads and then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. Then, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I. The final cDNA library was ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

value: whole animal

tag: generation

tag: developmental stage

value: Day 6 post hatching

tag: biological replicate

value: a-synuclein overexpression

value: HB101 diet


title: 938_Veh_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
938_Veh_S13

tag: tissue

value: Primary bone marrow hematopoietic stem cells (HSCs)

tag: cell type

value: HSC

value: Male


title: mid-old fibroblasts (P27), HDF-mid2

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

data_processing:
instrument model: MGIsea-2000
MGI DNBSEQ-G400 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.4) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Assembly: hg19
Supplementary files format and content: count (RPKM)

extract_protocol:
RNA was harvested using NucleoSpin RNA, Mini kit (MN). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacturer's protocols.

value: skin

value: mid-old fibroblasts (P27)


title: Old fibroblasts (P57), HDF-Old2

value: Old fibroblasts (P57)


title: Old fibroblasts (P57), HDF-Old1


title: Young fibroblasts (P8), HDF-Young2

value: Young fibroblasts (P8)


title: mid-old fibroblasts (P27), HDF-mid1


title: Corpus_K_PID00169

value: corpus gastric units

tag: genotype

value: WT


title: FXS-iPS848_dCas9-gScr_36d_rep1

value: iPSCs

value: FXS full-mutation

tag: treatment

value: dCas9+gScr introduced

value: Fragile X syndrome


title: Young fibroblasts (P8), HDF-Young1


title: UA44 strain, P0 generation, HB101 diet, rep2

value: whole animal


title: mid-old fibroblasts co-cultured with young fibroblasts, cocul_Y2

value: Mid-old fibroblasts

value: co-cultured with young fibroblasts


title: TKN_Atf3-WT_5

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were align to the mm39 reference genome using STAR and default parameters
Ensmebl v104 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method and differential gene expression conducted using LIMMA.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include VOOM adjusted cpms values for each Sample

source_name: Lung

growth_protocol: ARIES protocol #806345

extract_protocol:
PureLink™ RNA Micro Kit
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina®

treatment_protocol: ARIES protocol #806345; all animals received intranasal administration of PR8 H1N1 influenza virus

value: Lung

value: F


title: TKN_Atf3-WT_4


title: UA44 strain, P0 generation, HB101 diet, rep1

value: Day 6 post hatching

value: a-synuclein overexpression

value: HB101 diet


title: Corpus_K_PID00167

tag: cell line

value: adult stomach

value: Mixture of cell types from adult stomach

value: Male


title: mid-old fibroblasts co-cultured with young fibroblasts, cocul_Y1

value: skin


title: UA44 strain, F3 generation, HB101 diet, rep3

tag: strain


title: 939_EP3_Male_HSC

description:
ILMN_1360_Patterson_mRNAseq20_May2022_processedData.xlsx
939_EP3_S14

value: Bone marrow

value: Primary bone marrow hematopoietic stem cells (HSCs)

value: HSC


title: UA44 strain, F3 generation, HB101 diet, rep2


title: adult_stomach_tube2_p31

description:
We analyzed single-cells, which were sorted to 384-wells in total. read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.
04_export_counts_dataset1.csv
04_export_meta_data_dataset1.csv

source_name: corpus and antrum gastric units

value: corpus and antrum gastric units

value: WT


title: mid-old fibroblasts co-cultured with mid-old fibroblasts, cocul_M2

value: co-cultured with mid-old fibroblasts


title: Corpus_K_PID00166

value: corpus gastric units


title: TKN_Atf3-WT_2


title: mid-old fibroblasts co-cultured with mid-old fibroblasts, cocul_M1

value: Mid-old fibroblasts


title: UA44 strain, F3 generation, HB101 diet, rep1

value: whole animal


title: UA44 strain, F3 generation, OP50 diet, rep3

value: OP50 diet


title: Corpus_K_PID00168


title: Smad4_iBECs_MUT-1

description: Raw counts

value: Brain

value: Endothelial

value: Postnatal day 7

value: Smad4f/f; Cdh5-CreERT2


title: adult_stomach_tube2_p29

value: adult stomach

value: Mixture of cell types from adult stomach


title: UA44 strain, F3 generation, OP50 diet, rep2

value: Day 6 post hatching

value: a-synuclein overexpression


title: D3- Dro141TX

city: College Park

first: Madhu

last: Kappagantu

state: MD

address: 4291 Fieldhouse drive

institute: University of Maryland

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed reads were mapped to Nicotiana benthamiana genome Niben 1.0.1 and unmapped reads are collected (match score =1, mismatch cost =2, insertion cost =3, deletion cost =3, length fraction =0.5, similarity fraction =0.8, global alignment =No)
Read not matched with Nicotiana benthamiana genome (Niben1.0.1) were mapped to Solanum lycopersicum genome (SL3.0) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: SL3.0
Supplementary files format and content: Excel file include RPKM values for all six samples

organism: Nicotiana benthamiana

source_name: Scion Leaf

growth_protocol: 2 to 3 week old tomato rootstock seedlings of Maxifort and DRO141TX were grafted to similarly cut 3-5 week old N. benthamiana scions. Grafted plants were maintained under a humidity dome for one week before being transferred to a growth chambers at 25°C under a 12 hr light cycle

extract_protocol:
RNA was isolated from scion leaves using Rneasy plant mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEB NEXT ultra Prep Kit following manufacturer's protocols.

treatment_protocol:
Scion transcripts of Nicotiana benthamiana grafted to Maxifort and Dro141TX were compared
Unmapped reads to Nicotiana benthamiana genome were mapped to Solanum lycopersicum genome (SL3.0) to identify graft transmissible transcripts from rootstock to scion

value: Scion Leaf

value: Grafted to tomato rootstock

tag: tomato rootstock


title: TKN_Atf3-KO_1

value: Lung

tag: Sex

value: F


title: adult_stomach_tube2_p30

value: corpus and antrum gastric units

value: WT

value: Male


title: adult_stomach_tube1_p25


title: D1- Dro141TX


title: TKN_Atf3-WT_1

value: M


title: TKN_Atf3-KO_2


title: D2- Dro141TX


title: TKN_Atf3-KO_5


title: M3- Maxifort

value: Maxifort


title: adult_stomach_tube1_p24


title: UA44 strain, P0 generation, OP50 diet, rep3

value: whole animal

value: OP50 diet


title: adult_stomach_tube1_p23


title: UA44 strain, F3 generation, OP50 diet, rep1


title: Epi cysts

city: Leiden

first: Christian

last: Schröter

state: Zuid-Holland

address: Einsteinweg 55

department: Cell Systems and Drug Safety

institute: Leiden University, Leiden Academic Centre for Drug Research

data_processing:
Genome alignment, counting and cell calling was performed with default parameters with Cellranger v4.0.0
Assembly: mm10, provided with CellRanger v4.0.0
Supplementary files format and content: matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx

source_name: mESCs

growth_protocol: Cysts of Epi cells were made according to Bedzhov and Zernicka-Goetz (Cell, 2014) with minor modifications. iGATA ESCs were detached, resuspended in growth factor-reduced matrigel (Corning) and plated as 25 µl drops on µ-slides (Ibidi). The slides were incubated at 37ºC to allow the matrigel to solidify and then filled with prewarmed 2i + LIF medium. 2i + LIF was changed to N2B27 after one day, and cells were grown for another three days before extraction from matrigel, dissociation of cysts, and generation of single cell transcriptomes

extract_protocol:
Cysts were recovered from matrigel by incubation in recovery solution (Corning) for 20 min on ice. Cysts were then gently spun down, resuspended in 1 ml Accutase and incubated at 37ºC for 10 min, followed by mechanical dissociation by pipetting and further incubation in Accutase for 5 min. Next, cells were spun down, washed in PBS, and resuspended in a small volume of PBS + 0.5% BSA. To remove residual matrigel, dissociated cells were washed once with recovery solution and twice with ice-cold PBS, followed by resuspending in a small volume of PBS + 0.5% BSA. Single cells were counted, and mixed with H2O and RT master mix (10x Genomics) to obtain a cell density required for targeting 1000 cells. Cell suspensions were loaded on a Chromium Controller (10x Genomics) to partition cells with gel beads in emulsion.
Reverse transcription, cDNA recovery and amplification, and sequencing library construction were performed according to 10x Genomics ChromiumNextGEMSingleCell_v3.1_Rev_D protocol with Chromium Next GEM Single Cell 3ʹ GEM and Library & Gel Bead Kit v3.1. We chose 12 PCR cycles for cDNA amplification, and 13 PCR cycles for index PCR. Concentration and insert size of sequencing libraries were determined with a BioAnalyzer High Sensitivity DNA Assay (Agilent)

value: Epi cysts


title: VE cysts

growth_protocol: VE cysts were generated from pure cultures of PrE cells that were differentiated as follows: iGATA mESCs (clone C6) were induced with 0.5 µg/ml doxycycline in 2i + LIF for 8 hours, followed by another 16 hours of doxycycline treatment in N2B27 supplemented with 10 ng/ml FGF4 and 1 µg/ml heparin. To generate VE cysts, these cells were dissociated with Accutase and re-seeded onto gelatin-coated dishes at a density of 30,000 cells/cm2 in N2B27 medium supplemented with 10 ng/ml FGF4 and 1 µg/ml heparin, and cultured for 3 days.

extract_protocol:
Approximately 200 VE cysts were manually picked under a dissection microscope for further processing. We selected round cysts, and excluded structures that contained a large number of dead cells, or that were unusually big or small. We also excluded structures that contained a clearly visible core of putative Epi-like cells, which likely arise from insufficiently induced cells. VE cysts were gently spun down, resuspended in 1 ml Accutase and incubated at 37oC for 10 min, followed by mechanical dissociation by pipetting and further incubation in Accutase for 5 min. Next, cells were spun down, washed in PBS, and resuspended in a small volume of PBS + 0.5% BSA (Sigma).
Single cells were counted, and mixed with H2O and RT master mix (10x Genomics) to obtain a cell density required for targeting 1000 cells. Cell suspensions were loaded on a Chromium Controller (10x Genomics) to partition cells with gel beads in emulsion.
Reverse transcription, cDNA recovery and amplification, and sequencing library construction were performed according to 10x Genomics ChromiumNextGEMSingleCell_v3.1_Rev_D protocol with Chromium Next GEM Single Cell 3ʹ GEM and Library & Gel Bead Kit v3.1. We chose 12 PCR cycles for cDNA amplification, and 13 PCR cycles for index PCR. Concentration and insert size of sequencing libraries were determined with a BioAnalyzer High Sensitivity DNA Assay (Agilent)

value: VE cysts


title: UA44 strain, P0 generation, OP50 diet, rep2


title: SAS_ASC

city: Taoyuan

first: Chi-Sheng

last: Wu

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

data_processing:
Illumina BaseSpace RNA-seq Aligment V1.1.0
Genome_build: UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read counts values for each Sample

source_name: SAS cell

growth_protocol: SAS_con and SAS_ASC cell lines were maintained in DMEM containing 10% FBS, G418 (200 μg/ml), and puromycin (2 μg/ml)

extract_protocol:
Total RNA extraction was using TRIZOL reagent (Invitrogen)
Library construction was using TruseqRNA Library Prep Kit v2 (Illumina)

value: SAS cell

value: oral cancer cell line

tag: vector

value: SAS overexpression


title: UA44 strain, P0 generation, OP50 diet, rep1

value: Day 6 post hatching

value: a-synuclein overexpression


title: M2- Maxifort

value: Scion Leaf

value: Grafted to tomato rootstock


title: BELAs

growth_protocol: BELAs were generated by inducing iGATA ESCs (clone C6) with 0.5 µg/ml doxycycline in 2i + LIF for 8 hours, followed by a media change to N2B27 for 16 hours. Cells were then seeded at a density of 30,000 cells/cm2 in N2B27 on dishes that had been coated with 0.1% gelatin in PBS for 30 minutes. Floating aggregates were collected for further processing after three days.

extract_protocol:
Approximately 200 BELAs were manually picked under a dissection microscope for further processing. We selected round structures, and excluded those that contained a large number of dead cells, or that were unusually big or small. BELAs were gently spun down, resuspended in 1 ml Accutase and incubated at 37oC for 10 min, followed by mechanical dissociation by pipetting and further incubation in Accutase for 5 min. Next, cells were spun down, washed in PBS, and resuspended in a small volume of PBS + 0.5% BSA (Sigma).
Single cells were counted, and mixed with H2O and RT master mix (10x Genomics) to obtain a cell density required for targeting 1000 cells. Cell suspensions were loaded on a Chromium Controller (10x Genomics) to partition cells with gel beads in emulsion.
Reverse transcription, cDNA recovery and amplification, and sequencing library construction were performed according to 10x Genomics ChromiumNextGEMSingleCell_v3.1_Rev_D protocol with Chromium Next GEM Single Cell 3ʹ GEM and Library & Gel Bead Kit v3.1. We chose 12 PCR cycles for cDNA amplification, and 13 PCR cycles for index PCR. Concentration and insert size of sequencing libraries were determined with a BioAnalyzer High Sensitivity DNA Assay (Agilent).

value: bilayered embryo-like aggregates (BELAs)


title: M1- Maxifort


title: Cited2_KO3

status: Public on May 18 2023

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Assembly: rn6
Supplementary files format and content:  Genes.tsv, Barcodes.tsv, Matrix.mtx

organism: Rattus

source_name: rat 18.5 uterine-placental interface

extract_protocol: Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.

value: gestational day 18.5

value: Cited2 mutant


title: SAS_con

value: control


title: Cited2_KO2


title: Cited2_WT3

value: wildtype


title: Cited2_WT2


title: Cited2_KO1


title: Cited2_WT1


title: Exposure to KDP20 (Day5) [D5-8]

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

data_processing:
Quality of raw sequence data was checked via the FastQC and adapter or low quality bases were trimmed with TrimGalore
After trimming, the reads were aligned to the mouse reference genome (mm10) using the STAR aligner
Expression levels of mRNAs were quantified using the HTSeq
Assembly: mm10
Supplementary files format and content: counts for each Sample

source_name: nasal

growth_protocol: C57BL/6 (6 weeks, male) Mice were kept in sanitary ventilated animal rooms with a controlled temperature (25 ± 1 °C) and regular light cycle (12 h light: 12 h dark)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: nasal

value: male

value: mouse nasal epithlium

value: Exposure to KDP20 (Day5)


title: Exposure to KDP20 (Day10) [KDEP-20-2-D10]

value: Exposure to KDP20 (Day10)


title: Exposure to KDP20 (Day5) [D5-5]


title: Exposure to KDP20 (Day10) [KDEP-20-5-D10]


title: Exposure to KDP20 (Day5) [D5-7]


title: Exposure to KDP20 (Day10) [KDEP-20-3-D10]


title: Exposure to KDP20 (Day10) [KDEP-20-1-D10]


title: Exposure to KDP20 (Day5) [D5-6]


title: PBS-vehicle [Nor-5-D10]

value: PBS-vehicle


title: PBS-vehicle [Nor-4-D10]


title: PBS-vehicle [Nor-6-D10]


title: PBS-vehicle [Nor-2-D10]


title: 12E_M_3059

city: La Jolla

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 12E_M_3050

tag: age


title: 12E_M_3053


title: 12E_M_3051


title: 12E_M_3060


title: 12E_M_3055


title: 12E_M_3054


title: 12E_M_3058


title: 12E_M_3061


title: 12E_M_3057


title: 12E_M_3062


title: 12E_M_3048


title: 12E_M_3056


title: 12E_M_3063


title: Proseq-HCT116-CDK12as-1-NA-PP1

city: Wuhan

first: Yin

last: Zhinang

address: Donghu road 185

institute: Wuhan University

description: Pro-seq with HCT116 cells

source_name: Isolated from the colon

extract_protocol:
PRO-seq was performed as previously reported (Judd et al., 2020; Li et al., 2021; Liang et al., 2018) and PRO-seq libraries were sequenced on a NovaSeq 6000 platform.
Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.

value: colon

value: 1-NA-PP1 for 6 hours


title: 12E_M_3046

first: Joseph


title: 12E_M_3044


title: 12E_M_3041


title: 12E_M_3043


title: 12E_M_3045


title: 12E_M_3040


title: 12E_M_3042


title: 12E_M_3038


title: 12E_M_3036


title: 12E_M_3047


title: 12E_M_3037


title: 12E_M_3035


title: 12E_M_3052


title: 12E_M_3049


title: 12E_M_3030


title: 12E_M_3025


title: 12E_M_3034


title: 12E_M_3031


title: 12E_M_3026


title: 12E_M_3024


title: 12E_M_3023


title: 12E_M_3022


title: 12E_M_3032


title: 12E_M_3021


title: 12E_M_3017


title: 12E_M_3016


title: 12E_M_3015


title: 12E_M_3020


title: 12E_M_3039


title: 12E_M_3013


title: 12E_M_3027


title: 12E_M_3018


title: 12E_M_3019


title: 12E_M_3012


title: 12E_M_3011


title: 12E_M_3010


title: 12E_M_3009


title: 12E_M_3008


title: 12E_M_3014


title: 12E_M_3029


title: 12E_M_3033


title: 12E_M_3007


title: 12E_M_3006


title: 12E_M_3028


title: 12E_M_3004


title: 12E_M_3005


title: 12E_M_3002


title: 12E_M_3001


title: 12E_M_3003


title: 12E_M_2936


title: 12E_M_2935


title: 12E_M_2932


title: 12E_M_2930


title: 12E_M_2926


title: 12E_M_2928


title: 12E_M_2925


title: 12E_M_2934


title: 12E_M_2931


title: 12E_M_2924


title: 12E_M_2929


title: 12E_M_2922


title: 12E_M_2920


title: 12E_M_2921


title: 12E_M_2918


title: 12E_M_2916


title: 12E_M_2919


title: 12E_M_2923


title: 12E_M_2917


title: 12E_M_2915


title: 12E_M_2927


title: 12E_M_2914


title: 12E_M_2911


title: 12E_M_2912


title: 12E_M_2913


title: 12E_M_2905


title: 12E_M_2904


title: 12E_M_2903


title: 12E_M_2908


title: 12E_M_2906


title: 12E_M_2897


title: 12E_M_2899


title: 12E_M_2894


title: 12E_M_2900


title: 12E_M_2891


title: 12E_M_2890


title: 12E_M_2901


title: 12E_M_2892


title: 12E_M_2889


title: 12E_M_2898


title: 12E_M_2888


title: 12E_M_2893


title: 12E_M_2887


title: 12E_M_2886


title: 12E_M_2909


title: 12E_M_2910


title: 12E_M_2907


title: 12E_M_2902


title: 12E_M_2895


title: 12E_M_2896


title: 12E_M_2885


title: 12E_M_2879


title: 12E_M_2884


title: 12E_M_2882


title: 12E_M_2880


title: 12E_M_2881


title: 12E_M_2878


title: 12E_M_2682


title: 12E_M_2874


title: 12E_M_2674


title: 12E_M_2676


title: 12E_M_2678


title: 12E_M_2680


title: 12E_M_2672


title: 12E_M_2671


title: 12E_M_2675


title: 12E_M_2876


title: 12E_M_2677


title: 12E_M_2668


title: 12E_M_2669


title: 12E_M_2667


title: 12E_M_2670


title: 12E_M_2875


title: 12E_M_2663


title: 12E_M_2662


title: 12E_M_2681


title: 12E_M_2873


title: 12E_M_2666


title: 12E_M_2664


title: 12E_M_2665


title: 12E_M_2679


title: 12E_M_2661


title: 12E_M_2660


title: 12E_M_2659


title: 12E_M_2656


title: 12E_M_2657


title: 12E_M_2673


title: 12E_M_2658


title: 12E_M_2653


title: 12E_M_2654


title: 12E_M_2652


title: 12E_M_2651


title: 12E_M_2655


title: 12E_M_2650


title: 12E_M_2649


title: 12E_M_2647


title: 12E_M_2646


title: 12E_M_2645


title: 12E_M_2643


title: 12E_M_2641


title: 12E_M_2640


title: 12E_M_2642


title: 12E_M_2639


title: 12E_M_2644


title: 12E_M_2636


title: 12E_M_2634


title: 12E_M_2638


title: 12E_M_2635


title: 12E_M_2632


title: 12E_M_2633


title: 12E_M_2637


title: 12E_M_2631


title: 12E_M_2627


title: 12E_M_2626


title: 12E_M_2628


title: 12E_M_2648


title: 12E_M_2630


title: 12E_M_2625


title: 12E_M_2621


title: 12E_M_2624


title: 12E_M_2623


title: 12E_M_2622


title: 12E_M_2554


title: 12E_M_2619


title: 12E_M_2553


title: 12E_M_2549


title: 12E_M_2551


title: 12E_M_2629


title: 12E_M_2548


title: 12E_M_2550


title: 12E_M_2552


title: 12E_M_2543


title: 12E_M_2544


title: 12E_M_2547


title: 12E_M_2546


title: 12E_M_2545


title: 12E_M_2541


title: 12E_M_2539


title: 12E_M_2542


title: 12E_M_2540


title: 12E_M_2620


title: 12E_M_2532


title: 12E_M_2534


title: 12E_M_2533


title: 12E_M_2535


title: 12E_M_2537


title: 12E_M_2538


title: 12E_M_2531


title: 12E_M_2526


title: 12E_M_2528


title: 12E_M_2529


title: 12E_M_2527


title: 12E_M_2523