title: Huh7_ARID3A

value: ARID3A,   Santa Cruz, sc-398367 X

value: untreated


title: DIO_Tumor_Mouse_113

status: Public on Aug 10 2022

type: RNA

city: Chapel Hill

first: Stephen

middle: D

last: Hursting

state: North Carolina

address: 215B MHRC

country: USA

institute: University of North Carolina - Chapel Hill

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the GeneTitan Hybridization Wash and Stain Kit for WT Arrays (Affymetrix).

scan_protocol: Scanning of the Clariom S peg plate was carried out using the GeneTitan MC Instrument (Affymetrix).

data_processing: Transcriptome analysis console software (version 4.0; ThermoFisher Scientific)

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Azoxymethane-induced colon tumor

label_protocol: Total RNA was used to synthesize fragmented and labeled sense-strand cDNA and hybridized onto the Clariom S peg plate. The GeneChip® WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA, USA) was used to prepare the samples, following manufacturer’s instructions.

extract_protocol: Total RNA was isolated from colon tumor tissue via TRIzol reagent (ThermoFisher Scientific, Waltham, MA, USA) according to manufacturer’s instructions.

treatment_protocol: See methods of corresponding paper for details.

tag: tissue

value: colon tumor

tag: Sex

value: Male

tag: strain

value: FVB/N

tag: diet

value: High-fat diet (60% kcal fat)

tag: sulindac treatment

value: No sulindac


title: Heart-GFP [L6]

type: SRA

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

library_source: transcriptomic

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) using kallisto v0.46
Gene counts were tabulated with tximport.
Assembly: GRCm38.p6
Supplementary files format and content: *.txt files are tab-delimited text containing gene counts

source_name: heart

extract_protocol:
Total RNA from mouse heart and white adipose samples  was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
Libraries were prepared using the Nugen Universal Plus mRNA kit (Tecan Genomics Inc, Redwood City, CA)
RNA-Seq: single and paired-end mode to a length of 2x50 base pairs using the Illumina NovaSeq S2 platform

treatment_protocol: Mice were injected with AAV8-GFP or AAV8-F11, and fed a HFD + l-NAME diet for 7 weeks.  Tissues were collected at 15 weeks of age.

value: heart

value: M


title: M3_1

city: Beijing

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

country: China

institute: Beingjing Forestry University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq software was used to calculated the expression abundance of each gene and normalized to the expected number of fragments per kilobase of transcript sequence per million fragments mapped (FPKM).
Genome_build: The clean reads was mapped to the genome dataset of Zanthoxylum armatum obtained in FigShare database (https://doi.org/10.6084/m9.figshare.14400884.v1) (Wang et al., 2021c).
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Zanthoxylum armatum

source_name: Zanthoxylum armatum_tissue

extract_protocol:
Total RNA from four vital periods was separately extracted using FastPure Plant Total RNA Isolation Kit (Vazyme, Nanjing, China). The quantity and purity of total RNA were investigated by agarose gel electrophoresis and Nanodrop 2100 (Agilent, USA).
The twenty-four cDNA libraries, including M1_1, M1_2, M1_3, M2_1, M2_2, M2_3, M3_1, M3_2, M3_3, M4_1, M4_2, M4_3, F1_1, F1_2, F1_3, F2_1, F2_2, F2_3, F3_1, F3_2, F3_3, F4_1, F4_2 and F4_3, were constructed and sequenced using Illumina HiSeq™ 4000 platform at Novegene Bioinformatics Technology Co. Ltd (Beijing, China).

tag: plant

value: Zanthoxylum armatum DC.

value: flower

tag: floral sex differentiation stage


title: DIO_Tumor_Mouse_109


title: M2_3


title: H3K9me3_input_24h

city: Ahmedabad

first: Noopur

last: Thakur

state: Gujarat

address: Navrangpura

department: Biological and Life Sciences

country: India

institute: Ahmedabad University

description:
prostate; derived from metastatic site: bone
grade IV, adenocarcinoma

library_source: genomic

data_processing:
FastQC (v 0.11.9) was performed on Raw FastQ files for Quality Check.
Sequence read were trimmed where necessary to retain only high quality sequence. In addition, the low-quality sequence reads were excluded from the analysis. The adapter trimming was performed using Trimmomatic (Ver-0.36).
FastQ files were aligned to hg19 Reference Genome.
The paired-end reads were aligned to the Human reference genome (hg19) Feb. 2009 release downloaded from UCSC database (GRCh37/hg19). The chromosome fasta file was downloaded from the following website (http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz). The chromosome fasta file was downloaded from the following website and the Alignment was performed using BWA MEM (Ver-0.7.12).
Model-based Analysis of ChIP-Seq (MACS 2.1.1.20160309) was used to call peaks from aligned sequences with the following parameters: q value cutoff = 0.05, mfold = 5-50, bandwidth = 300 and Paired-end mode = ON.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peak.bed: Peak files in BED format.

molecule: genomic DNA

organism: Homo sapiens

source_name: PC-3 Cells

growth_protocol: PC-3 cells were routinely maintained and subcultured in RPMI-1640 medium (Himedia, Cat# AT028) supplemented with 10% FBS (Gibco, Cat# 10270106) and 1% Antibiotic-Antimycotic (Himedia, Cat# A002A) in 5% CO2 atmosphere.

extract_protocol:
TGF-β1 stimulated cells were treated with Formaldehyde to a final concentration of 1% to crosslink Proteins to DNA for 10 minutes at room temperature. Glycine was added at a final concentration of 125mM to quench the formaldehyde. Cells were washed twice with Phosphate Buffered Saline, scraped and centrifuged. The cell pellet was resuspended in ChIP lysis buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1 mM EDTA pH8, 1% Triton X-100, 0.1% Sodium Deoxycholate, 0.1% SDS and Protease Inhibitors). Cell were lysed and sonicated using Diagenode Bioruptor Pico under 30 seconds ON and 30 seconds OFF for 30 cycles condition to generate DNA-Protein Complex fragments. 50uL of chromatin was removed to serve as input sample and rest of the chromatin was immunoprecipitated using ChIP-grade H3K9me3 Antibody (Santa Cruz, Cat# sc-130356). The immunoprecipitated chromatin was purified using Protein G Sepharose beads and washed once in low salt wash buffer, once in high salt wash buffer and once in LiCl wash buffer. DNA was eluted using elution buffer and treated with 5M NaCl to reverse cross-link followed by treatment with RNaseA (Invitrogen, Cat# 12091021) and Proteinase K (Sigma-Aldrich, Cat#P2308). DNA was purified using PCR Purification kit (Himedia, Cat# MB512) and was stored at -20℃ until further use.
Libraries for ChIP sequencing were prepared using NEBNext® Ultra II DNA Library preparation kit (Cat# E7645). In brief, ChIP DNA and the Input DNA were subjected to various enzymatic steps for repair the ends and tailing with dA-tail followed by ligation of adapter sequences. These adapter ligated fragments were then size selected using SPRI beads. Next, the size selected fragments were indexed during limited cycle PCR to generate final libraries for paired-end sequencing.

treatment_protocol: TGF-β1 (Abcam, Cat# AB50036) was reconstituted in 10mM Citric Acid (pH 3.0). 10^5 PC-3 cells were seeded into T-25 Flask and incubated at 37℃ in 5% CO2 atmosphere till 70% confluency was achieved. Cells were serum-starved for 24hrs. Serum-starved cells were then stimulated with TGF-β (5ng/mL) for 6Hrs and 24Hrs. Untreated cells were used as Control.

tag: cell line

tag: cell type

value: Prostate cancer cells

tag: treatment

value: Treated with TGF-beta1 for 24hrs

tag: chip antibody


title: H3K9me3_input_6h

value: Treated with TGF-beta1 for 6hrs


title: DIO_Tumor_Mouse_107


title: Heart-GFP [L2]


title: Heart-GFP [L5]


title: M2_2


title: DIO_Tumor_Mouse_101


title: Heart-GFP [L9]


title: DIO_Tumor_Mouse_96


title: H3K9me3_input_control

value: Control


title: Heart-GFP [L1]


title: M2_1


title: H3K9me3_24h

value: H3K9me3 (Santa Cruz, sc-130356)


title: H3K9me3_6h


title: M1_3


title: Control_Tumor_Mouse_32

value: Low-fat diet (10% kcal fat)


title: SC7

city: Creteil

first: Celine

last: Colnot

state: Val de Marne

address: 8 rue du Général Sarrail

department: INSERM U955, IMRB

country: France

institute: Univ Paris Est Créteil, INSERM

data_processing:
Fastq files were processed with the CellRanger pipeline with the default’s parameters
Reads were align against the mm10 reference genome
Filtered features barcodes matrices were used to perform data analysis
Data processing were performed using Seurat v4.0.1 with the following parameters: Cells expressing between 100 and 8000 genes and expressing less that 10% of mitochondrial gene were retained for analysis, genes expressed in less than 3 cells were not taken into account. 25 first principal component were used for the dimensional reduction.
Genome_build: mm10
Supplementary_files_format_and_content: filtered raw count, barcodes and features names

source_name: Prx1-derived cells isolated from periosteum at day 3 post-fracture

growth_protocol: Cells were isolated from periosteum by explant culture and grown until 80% of confluence in culture medium (aMEM supplemented with 20% FBS, 1% penicilin/streptomycin and bFGF at 10ng/mL) at 33°C.

extract_protocol:
all lived cells were used for sequencing
Libraries were generated using Chromium Single Cell 3’Library & Gel Bead Kit v.2 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1000 cells/µL in PBS+0,04% FBS and 20 000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR.

treatment_protocol: no injury or d3 post-tibial fracture

value: Periosteum

tag: day post-injury


title: H3K9me3_control


title: SC6

source_name: Prx1-derived cells isolated from uninjured periosteum


title: M1_1


title: M1_2


title: Control_Tumor_Mouse_27


title: Control_Tumor_Mouse_26


title: S7-CARLOS-2

status: Public on Aug 09 2022

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality reads were trimmed or removed. The high quality reads were then mapped to Vitis_vinifera.12X using STAR 2.7.6a
Fragments Per Kilobase of exon per Megabase of library size (FPKM), Transcript Per Million (TPM) and extimated read counts were calculated using RSEM 1.3.3
Assembly: Vitis_vinifera
Supplementary files format and content: tab-delimited text files include  expected_count,  TPM,  and FPKM values for each Sample

organism: Vitis rotundifolia

source_name: Berry

extract_protocol:
RNA was extracted from two different cultivars of muscadine grapes, ‘Carlos’ and ‘Noble’. Grape berries from the last three developmental stages, namely bunch closure, veraison, and maturity (harvest), were collected from the research station (Citra) at University of Florida. Total RNA was isolated from each of the developmental stages using TRIZOL (Ambion, Life Technologies) followed by DNase treatment (Turbo DNA free, Thermo-Fisher).
RNA-seq libraries were constructed at the ICBR Gene Expression & Genotyping Core Lab using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s recommendations.
A total of 1000 ng samples of high-quality total RNA (RNA Integrity Number, RIN ≥ 7) was used and followed by RNA library preparation with NEBNext Ultra II Directional Lib Prep (New England Biolabs, Ipswich, MA, USA, catalog #E7760) according to the manufacturer's user guide.

value: Berry

tag: genotype

value: Carlos

tag: developmental stage

value: Berry E-L 38


title: S7-CARLOS-3


title: S7-CARLOS-1


title: S6-CARLOS-3

value: Berry E-L 35


title: S7-NOB-1

value: Noble


title: S7-NOB-3


title: S6-CARLOS-1


title: S7-NOB-2


title: S6-CARLOS-2


title: S6-NOB-3


title: Control_Tumor_Mouse_30

value: colon tumor

value: Male

value: FVB/N

value: No sulindac


title: Control_Tumor_Mouse_17


title: S5-CARLOS-2

value: Berry E-L 32


title: S6-NOB-2


title: S6-NOB-1


title: S5-CARLOS-1


title: S5-NOB-3


title: S5-NOB-2


title: S5-NOB-1


title: Control_Tumor_Mouse_20


title: C6F5UE-C6F(L)V-induced MEFs, scRNA-seq

first: yunfei

last: bai

address: No.5 Yiheyuan road

institute: Peking University

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using an in-house pipeline. Briefly, after filtering all read one sequences lacking a poly T tail, cell barcodes and UMI were extracted. Adapters and poly-A tails were trimmed (fastp V1) before aligning read two to GRCm38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2).
Reads with the same cell barcode, UMI, and gene were grouped to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis.
Cell type identification and clustering analysis using the Seurat program. The Seurat program (http://satijalab.org/seurat/, R package,v.4.0.4) was applied for analysis of RNA-seq data. UMI count tables were loaded into R using the read.table function. We then set the parameter resolution to 0.6 for the FindClusters function for clustering analyses.
Assembly: GRCm38
Supplementary files format and content: Tab-separated matrix file reporting counts.

source_name: primary cells

extract_protocol:
Single-cell suspensions were prepared in PBS (HyClone) at a density of 1×10^5 cells/mL and loaded onto microfluidic devices.
The GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies) was used to create single-cell RNA-seq libraries according to the Singleron GEXSCOPE® procedure (Singleron Biotechnologies). Individual libraries were diluted to a concentration of 4 nM before they were pooled for sequencing. Pooled libraries were sequenced with 150 bp paired end reads on an Illumina sequencer.

treatment_protocol: The medium was switched to XEN chemical reprogramming medium (CRM): KnockOut DMEM supplemented with 10% KnockOut Serum Replacement (KSR), 10% FBS, 1% GlutaMAX, 1% NEAAs, 0.055 mM 2-mercaptoethanol, 1% penicillin-streptomycin (Invitrogen), and 50 ng/ml basic fibroblast growth factor (bFGF) the next day (day 0); with induction by the small molecule cocktail C6F5UE (20 µM CHIR99021, 10 µM 616452, 50 µM Forskolin, 1 µM CH55, 0.05 µM UNC0638, and 5 µM EPZ004777). On day 4, the medium was switched to hepatocyte culture medium (HCM): DMEM/F-12 supplemented with 10% FBS, 1% ITS (insulin-transferrin-selenium) premix (Sigma), 1 µM dexamethasone (Sigma), 10 mM nicotinamide (Sigma), 1% GlutaMAX, 1% penicillin-streptomycin (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech), 20 ng/ml hepatocyte growth factor (Peprotech), and 20 ng/ml epidermal growth factor (Peprotech); plus 20 µM CHIR99021, 10 µM 616452, and 50µM Forskolin (C6F#H) for the first 4 days, then reduced to 3 µM CHIR99021, 2 µM 616452, and 2 µM Forskolin (C6F#L) for subsequent induction, with 50 µg/ml Vitamin C.

value: Embryonic

value: Fibroblast-hepatocyte

value: WT


title: C6F5UE-C6F(L)V 1

description:
gene_FPKM 3.xlsx
gene_Count 3.xlsx

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
HISAT2 software is used to quickly and accurately compare Clean Reads with reference genomes to determine where the Reads are positioned.
Assembly: GRCm38 (mm10)
Supplementary files format and content: xlsx files include RPKM values for each Sample
Supplementary files format and content: xlsx files include Gene count values for each Sample

extract_protocol:
RNA extraction and genomic DNA removal were completed using a RaPure Total RNA Micro Kit (Magen) and DNase I after cells were digested with trypsin-EDTA.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: C6F5UE-C6F(L)V 2

description:
gene_FPKM 3.xlsx
gene_Count 3.xlsx


title: NSF-CiHeps 1

description:
gene_FPKM 1.xlsx
gene_Count 1.xlsx

value: Neonatal skin


title: NSF-CiHeps 2

description:
gene_FPKM 1.xlsx
gene_Count 1.xlsx


title: NSF-CiHeps 3

description:
gene_FPKM 1.xlsx
gene_Count 1.xlsx


title: pHeps 1

description:
gene_FPKM 3.xlsx
gene_Count 3.xlsx

treatment_protocol: Isolated and cultured for 2 days

value: liver

value: Hepatocyte


title: C6F5UE-C6F(L)V 3

description:
gene_FPKM 3.xlsx
gene_Count 3.xlsx


title: C6F(L) 3

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx

treatment_protocol: hepatocyte culture medium (HCM): DMEM/F-12 supplemented with 10% FBS, 1% ITS (insulin-transferrin-selenium) premix (Sigma), 1 µM dexamethasone (Sigma), 10 mM nicotinamide (Sigma), 1% GlutaMAX, 1% penicillin-streptomycin (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech), 20 ng/ml hepatocyte growth factor (Peprotech), and 20 ng/ml epidermal growth factor (Peprotech); plus 20 µM CHIR99021, 10 µM 616452, and 50µM Forskolin (C6F#H) for the first 4 days, then reduced to 3 µM CHIR99021, 2 µM 616452, and 2 µM Forskolin (C6F#L) for subsequent induction

value: Fibroblast


title: pHeps 2

description:
gene_FPKM 3.xlsx
gene_Count 3.xlsx


title: C6FAE-C6F(L) 4

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx

treatment_protocol: The medium was switched to XEN chemical reprogramming medium (CRM): KnockOut DMEM supplemented with 10% KnockOut Serum Replacement (KSR), 10% FBS, 1% GlutaMAX, 1% NEAAs, 0.055 mM 2-mercaptoethanol, 1% penicillin-streptomycin (Invitrogen), and 50 ng/ml basic fibroblast growth factor (bFGF) the next day (day 0); with induction by the small molecule cocktail C6FAE (20 µM CHIR99021, 10 µM 616452, 50 µM Forskolin, 0.05 µM AM580, and 5 µM EPZ004777). On day 4, the medium was switched to hepatocyte culture medium (HCM): DMEM/F-12 supplemented with 10% FBS, 1% ITS (insulin-transferrin-selenium) premix (Sigma), 1 µM dexamethasone (Sigma), 10 mM nicotinamide (Sigma), 1% GlutaMAX, 1% penicillin-streptomycin (Invitrogen), 10 ng/ml fibroblast growth factor 4 (Peprotech), 20 ng/ml hepatocyte growth factor (Peprotech), and 20 ng/ml epidermal growth factor (Peprotech); plus 20 µM CHIR99021, 10 µM 616452, and 50µM Forskolin (C6F#H) for the first 4 days, then reduced to 3 µM CHIR99021, 2 µM 616452, and 2 µM Forskolin (C6F#L) for subsequent induction.


title: C6FAE-C6F(L) 3

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: S5-CARLOS-3

value: Berry


title: C6FAE-C6F(L) 2

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: C6F(L) 2

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: C6F(L) 1

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: C6FAE 2

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx

treatment_protocol: XEN chemical reprogramming medium (CRM): KnockOut DMEM supplemented with 10% KnockOut Serum Replacement (KSR), 10% FBS, 1% GlutaMAX, 1% NEAAs, 0.055 mM 2-mercaptoethanol, 1% penicillin-streptomycin (Invitrogen), and 50 ng/ml basic fibroblast growth factor (bFGF) the next day (day 0); with induction by the small molecule cocktail C6FAE (20 µM CHIR99021, 10 µM 616452, 50 µM Forskolin, 0.05 µM AM580, and 5 µM EPZ004777)


title: C6FAE-C6F(L) 1

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: MEF 3

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx

treatment_protocol: strandard fibroblast culture medium: DMEM+10% FBS


title: C6FAE 1

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: MEF 1

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: C6FAE 3

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: MEF 2

description:
gene_FPKM 2.xlsx
gene_Count 2.xlsx


title: Trophoblast stem cells, WT input, biol rep 1

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

data_processing:
Sequence reads were mapped to GrCM38/mm10 using  STAR aligner (sorted by coordinate) and bowtie2 aligner with samtools (MAPQ >1) for the RNA-seq and meDIP-seq fastq files, respectively.
Read count extraction and normalization were performed on the RNA-seq BAM files using hitseq count (order=pos, mode=inteRsection-nonempty, stranded=reveRse)
Assembly: mm10
Supplementary files format and content: tab-delimited text files with raw counts per gene

growth_protocol: Trophoblast stem cells were maintained in 20% FBS in RPMI1640, supplemented with antibiotics/antimycotics, sodium pyruvate, BME, bFGF, and heparin in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using Trizol reagant and DNA was harvested using standard SDS lysis buffer
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep kit. meDIP libraries were prepared using NEB ultra II DNA Library Prep kit.

value: Trophoblast stem cells

tag: cell state

value: stem


title: Trophoblast stem cells, Padi2/3 DKO input, biol rep 2

value: Padi2/3 DKO


title: Trophoblast stem cells, Padi2/3 DKO input, biol rep 1


title: Trophoblast stem cells, WT input, biol rep 2


title: Trophoblast stem cells, Padi2/3 DKO meDIP-seq, biol rep 3


title: Trophoblast stem cells, Padi2/3 DKO meDIP-seq, biol rep 4


title: Trophoblast stem cells, WT meDIP-seq, biol rep 3


title: Trophoblast stem cells, WT meDIP-seq, biol rep 5


title: Trophoblast stem cells, Padi2/3 DKO RNA-seq, biol rep 5


title: Trophoblast stem cells, Padi2/3 DKO meDIP-seq, biol rep 1


title: Trophoblast stem cells, WT meDIP-seq, biol rep 1


title: Trophoblast stem cells, WT meDIP-seq, biol rep 4


title: Trophoblast stem cells, WT meDIP-seq, biol rep 2


title: Trophoblast stem cells, Padi2/3 DKO RNA-seq, biol rep 2


title: Trophoblast stem cells, Padi4 DKO RNA-seq, biol rep 3

value: Padi4 KO


title: Trophoblast stem cells, Padi3 DKO RNA-seq, biol rep 1

value: Padi3 KO


title: Trophoblast stem cells, Padi3 DKO RNA-seq, biol rep 3


title: Trophoblast stem cells, Padi3 DKO RNA-seq, biol rep 4


title: Trophoblast stem cells, Padi4 DKO RNA-seq, biol rep 1


title: Trophoblast stem cells, Padi3 DKO RNA-seq, biol rep 2


title: Trophoblast stem cells, Padi2 DKO RNA-seq, biol rep 4

value: Padi2 KO


title: Trophoblast stem cells, Padi2 DKO RNA-seq, biol rep 3


title: Trophoblast stem cells, Padi2/3 DKO meDIP-seq, biol rep 2


title: Trophoblast stem cells, WT RNA-seq, biol rep 6


title: Trophoblast stem cells, Padi2/3 DKO RNA-seq, biol rep 4


title: Trophoblast stem cells, WT RNA-seq, biol rep 7


title: Trophoblast stem cells, Padi2/3 DKO RNA-seq, biol rep 1


title: Trophoblast stem cells, Padi2/3 DKO RNA-seq, biol rep 3


title: Trophoblast stem cells, WT RNA-seq, biol rep 8


title: Trophoblast stem cells, Padi2 DKO RNA-seq, biol rep 2


title: Trophoblast stem cells, WT RNA-seq, biol rep 5


title: Trophoblast stem cells, WT RNA-seq, biol rep 3


title: Trophoblast stem cells, WT RNA-seq, biol rep 4


title: Trophoblast stem cells, Padi4 DKO RNA-seq, biol rep 2


title: Trophoblast stem cells, WT RNA-seq, biol rep 2


title: Double_rep3

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

data_processing:
RNA seq datafiles were trimmed using the Trimmomatic tool
Reads were aligned against Mus musculus reference genome (mm39) using HISAT2 and gene-, cds-, and transcripts-level expression were computed through Cufflinks
The reads were assembled using StringTie to get transcript-leve expression counts
The counts file was imported to edgeR to analyze differential gene expression between samples
Assembly: Mus musculus reference genome (mm39)
Supplementary files format and content: matrix table with counts-per-million from all samples in a tab-delimited text file

source_name: Lens

extract_protocol:
For RNA-sequencing (RNA-Seq) experiments, mouse embryonic lenses at stage E16.5 (n = 8 lenses per biological replicate) were collected from  collected from control (Mafg+/-:Mafk+/-), compound (Mafg-/-:Mafk+/-) and double KO (Mafg-/-:Mafk-/-).  RNA isolation was performed using the mirVanaTM RNA isolation kit (Life Technologies, Grand Island, NY).  Total RNA isolation, followed by removal of small molecular weight RNA was performed according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: double KO (Mafg-/-:Mafk-/-)

value: Embryonic day E16.5

value: lens


title: Compound_rep3

value: compound (Mafg-/-:Mafk+/-)


title: Compound_rep2


title: Double_rep2


title: Double_rep1


title: Control_ (Mafg+/-:Mafk+/-) rep3

value: control (Mafg+/-:Mafk+/-)


title: Control_ (Mafg+/-:Mafk+/-) rep1


title: Control_ (Mafg+/-:Mafk+/-) rep2


title: P14_iOHC-45

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control. Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for smartseq.

source_name: induced OHCs (iOHCs) from the cochlear inner hair cells after Tbx2 deletion

extract_protocol: Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).

treatment_protocol: Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).

value: Cochlea

tag: age

value: postnatal day 14

value: vGlut3-P2A-iCreER/+; Tbx2 flox/-; Ai9/+


title: P14_iOHC-42


title: P14_iOHC-44


title: P14_iOHC-43


title: P14_iOHC-41


title: Trophoblast stem cells, WT RNA-seq, biol rep 1

value: WT


title: P14_iOHC-38


title: P14_iOHC-39


title: P14_iOHC-36


title: P14_iOHC-37


title: P14_iOHC-40


title: P14_iOHC-33


title: Compound_rep1


title: P14_iOHC-34


title: P14_iOHC-35


title: P14_iOHC-31


title: P14_iOHC-30


title: P14_iOHC-46


title: P14_iOHC-32


title: P14_iOHC-29


title: P14_iOHC-26


title: P14_iOHC-27


title: P14_iOHC-25


title: P14_iOHC-28


title: P14_iOHC-22


title: P14_iOHC-23


title: P14_iOHC-24


title: P14_iOHC-19


title: P14_iOHC-18


title: P14_iOHC-20


title: P14_iOHC-17


title: Huh7_oeVec

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deepTools.

source_name: Huh 7

growth_protocol: Huh 7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:24ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).   CUT&Tag was performed according to the recommended protocol of NovoNGS® CUT&Tag High‐Sensitivity Kit (Novoprotein, Jiangsu, China).  RNA samples were extracted using TRIzol reagent (Invitrogen, CA, USA).   0-8).
For the ChIPseq, input amounts of DNA was converted into high quality libraries for next-generation sequencing on the Illumina platform using the NEBNext Ultra II DNA Library Prep Kit. Bead based size selection was performed for final library size selection to obtain ChIP-seq libraries containing fragments of 250 bp to 500 bp.   For the RNA-seq, the sequencing library was prepared using an Illumina mRNA-seq sample preparation kit and was then subjected to paired-end sequencing on the Illumina HiSeq platform.   CUT&Tag was performed according to the manufacturer's protocol (Novoprotein, Shanghai, China). The DNA was mixed with a universal i5 and a uniquely barcoded i7 primer. The sample was placed in a Thermocycler for PCR, and post-PCR clean-up was performed by bead based size selection and cleanup.
CUT&Tag, ChIP-Seq and RNA-seq

treatment_protocol: To set up stable cell lines overexpressed or knockdown ARID3A, Huh7 cells were seeded in 6well plates at the cell density of 50%-70%. Lentiviruses were constructed and collected to infect them. Infected cells were sorted with puromycin 24 hours later. The transfection assay was done using RNAiMAX (Invitrogen) with 5μM siKDM3A or siNC according to the manufacturer's protocol. The infection or transfection efficiency were confirmed by qPCR or WB assays. Extraction steps were started at least 48 hours after infection or transfection.

value: HCC

value: Huh7 cells were infected with oeVec lentivirus, renew the medium after 8 hours later, for another 24 hours,sorting the positive cells with puromycin.


title: P14_iOHC-16


title: P14_iOHC-14


title: P14_iOHC-15


title: P14_iOHC-13


title: P14_iOHC-12


title: P14_iOHC-11


title: P14_iOHC-7


title: P14_iOHC-9


title: P14_iOHC-8


title: P14_iOHC-6


title: P14_iOHC-3


title: P14_iOHC-2


title: P14_iOHC-4


title: P14_WT IHC-55

source_name: Wild type cochlear inner hair cells

value: vGlut3-P2A-iCreER/+; Ai9/+


title: P14_iOHC-1


title: P14_WT IHC-54


title: P14_iOHC-5


title: P14_iOHC-21


title: P14_WT IHC-49


title: P14_WT IHC-51


title: P14_WT IHC-48


title: P14_WT IHC-47


title: P14_WT IHC-50


title: P14_WT IHC-46


title: P14_iOHC-10


title: P14_WT IHC-45


title: P14_WT IHC-42


title: P14_WT IHC-41


title: P14_WT IHC-40


title: P14_WT IHC-37


title: P14_WT IHC-38


title: P14_WT IHC-39


title: P14_WT IHC-53


title: P14_WT IHC-34


title: P14_WT IHC-35


title: P14_WT IHC-36


title: P14_WT IHC-33


title: P14_WT IHC-30


title: P14_WT IHC-28


title: P14_WT IHC-32


title: P14_WT IHC-31


title: P14_WT IHC-29


title: P14_WT IHC-52


title: P14_WT IHC-27


title: P14_WT IHC-26


title: P14_WT IHC-25


title: P14_WT IHC-24


title: P14_WT IHC-44


title: P14_WT IHC-22


title: P14_WT IHC-23


title: P14_WT IHC-43


title: P14_WT IHC-20


title: P14_WT IHC-19


title: P14_WT IHC-18


title: P14_WT IHC-17


title: P14_WT IHC-14


title: P14_WT IHC-16


title: P14_WT IHC-12


title: P14_WT IHC-13


title: P14_WT IHC-10


title: P14_WT IHC-15


title: P14_WT IHC-9


title: P14_WT IHC-6


title: P14_WT IHC-7


title: P14_WT IHC-8


title: P14_WT IHC-4


title: P14_WT IHC-5


title: P14_WT IHC-21


title: P14_WT IHC-1


title: P30_WT IHC-49

value: postnatal day 30


title: P14_WT IHC-2


title: P14_WT IHC-3


title: P30_WT IHC-48


title: P14_WT IHC-11


title: P30_WT IHC-47


title: P30_WT IHC-46


title: P30_WT IHC-50


title: sRNA_ndx1-4_rep3

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.

data_processing:
The results were analysed using the sRNAnalyzer pipeline as follows: Illumina adapters were trimmed by Cutadapt and reads were then size selected in the 19-25 nt range.
Using sRNAnalyzer, size selected reads were aligned to the miRbase database and a recently published comprehensive small RNA locus database.
Differential sRNA expression between Col-0 and ndx1-4 samples was determined by DESeq2 and results were plotted in R.
Assembly: A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0).
Supplementary files format and content: tsv files contain the expression data (read counts) from col0 and ndx1-4 samples (3-3 replicas), log2 fold change.

organism: Arabidopsis thaliana

source_name: 10-day-old seedling

growth_protocol: 2 g of 10-day-old seedlings of Col-0, and ndx1-4 plants were harvested.

extract_protocol:
Total RNA was purified from Col-0 and ndx1-4 seedlings (3-3 biological replicates) using phenol-chloroform extraction. The quality of total RNA samples was checked by an Agilent bioanalyzer (RIN > 9).
Small DNA libraries were prepared according to Illumina’s NEBNext® Multiplex Small RNA Library Prep protocol. sRNA-seq libraries were sequenced using an Illumina NextSeq500 instrument with 1x50 bp reads.

value: Seedling

value: 10 days


title: sRNA_ndx1-4_rep2


title: P30_WT IHC-45


title: sRNA_ndx1-4_rep1


title: P30_WT IHC-43


title: P30_WT IHC-42


title: sRNA_col0_rep2

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.

value: Wild type (Col0)


title: P30_WT IHC-41


title: sRNA_col0_rep1


title: P30_WT IHC-40


title: Hi-C_col0

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.
Paired-end Hi-C; reads1 and reads2 in different raw files; col0 (wild).

data_processing:
Raw Hi-C libraries (.fastq files) were processed by the Juicer toolbox using default parameters, except that appropriate restriction enzyme cutting sites - provided by the Arima-HiC kit (GATC and GANTC) - were introduced into the script files. Hi-C reads were mapped to the A. thaliana TAIR10 reference genome and MAPQ>=30 reads were retained for further analysis.
Quantitative differences in Hi-C interactions (Col-0 (wild type) vs. ndx1-4 mutant) were identified at 25 kb resolution by the Slitherine pipeline (https://gitlab.pasteur.fr/gmillot/slitherine). Slitherine runs the Serpentine tool to smooth local noise in Hi-C interaction maps and identifies statistically significant differences between Hi-C contact matrices.
Assembly: A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0).
Supplementary files format and content: Hi-C data (hic files) are from col0 and ndx1-4 (two replicas) samples.
Supplementary files format and content: Quantitative differences (tsv file) in Hi-C interactions (Col-0 (wild type) vs. ndx1-4 mutant) were identified at 25 kb resolution by the Slitherine pipeline.

extract_protocol:
Hi-C experiments were performed by the Arima HiC Kit (Arima Genomics). 10-day-old Columbia wild type (Col-0) and ndx1-4 seedlings were crosslinked with 1% formaldehyde. According to the Arima User Guide for Plant tissue (https://arimagenomics.com/), 1 g of crosslinked plant tissue was used as a starting material for isolation of nuclei. Plant samples were ground in liquid nitrogen using a mortar. 20 ml of PTNI buffer was then added (250 mM Sucrose, 20 mM HEPES pH 8.0, 5 mM KCl, 1mM MgCl2, 40% glycerol, 0.1 mM PMSF, 1% protease inhibitor cocktail (Sigma), 0.25% Triton X-100, 0.1% mercaptoethanol) and samples were purified two times by using a double-layer Mirachlot (Merk). Nuclei were washed several times in PTNI buffer as described in the Arima-HiC User Guide.
Proximity ligated in situ Hi-C libraries were then constructed according to the Arima User Guide. Hi-C samples were fragmented to an average size of 400 bp (Bioruptor UCD-300, Diagenode; low intensity mode, 3 x 5 min; 30 sec ON, 30 sec OFF). NGS libraries for Illumina sequencing were prepared using the Accel-NGS 2S Plus DNA Library Kit and Accel-NGS 2S Indexing Kit (Swift Biosciences). To estimate the proper number of PCR cycles for library amplification, Arima-QC2 values were determined using the KAPA Library Quantification Kit (Roche). NGS library amplifications were performed until the estimated PCR cycle numbers (usually between 5-9) using the Kapa Library Amplification Kit (Roche). NGS libraries were then sequenced on an Illumina NextSeq 500 platform (2x150 nt, paired end reads) using a NextSeq 500 High Output v2 kit (Illumina).


title: Hi-C_ndx1-4_rep2

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end Hi-C; reads1 and reads2 in different raw files; replica 2.


title: Hi-C_ndx1-4_rep1

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end Hi-C; reads1 and reads2 in different raw files; replica 1.


title: P30_WT IHC-39


title: MDA-MB-231RR, biological rep2

city: Cuajimalpa de Moreles

first: Isidro

middle: Xavier

last: Perez-Añorve

state: CIUDAD DE MÉXICO

address: Vasco de Quiroga 4871, Contadero.

department: Departamento de Ciencias Naturales

country: Mexico

institute: Universidad Autónoma Metropolitana

description: MDA-MB-231RR 2

hyb_protocol: Following fragmentation, 6 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the protocol suggest by fabrican.

data_processing: The data were analyzed with Expression Console of Affymetrix default analysis was Gene expression.

source_name: Breast cancer tumor cell line with radioresistant phenotype

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: MCF-7, MCF-7RR, MDA-MB-231 and MDA-MB-231RR cell lines were cultured in Dulbecco’s modified Eagle’s medium (Gibco, Gaithersburg, MD, USA) supplemented with 10% fetal bovine serum at 37 °C in a 5% CO2 atmosphere.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells received 15 sequential fractions of 2 Gy week, allowing irradiated cell populations a period of recovery between exposures. Non-irradiated controls were handled identically to the irradiate cells without radiation exposure. All of the experiments were performed within 4–10 passages after the final irradiation.

value: breast cancer

tag: breast cancer subtype

value: TNBC

tag: phenotype

value: radioresistant


title: P30_WT IHC-38

tag: tissue


title: MCF-7 parental, biological rep2

description: MCF-7 PARENTAL 2

source_name: Breast cancer tumor cell line

value: Luminal

value: parental


title: MCF-7RR, biological rep1

description: MCF-7RR 1


title: MDA-MB-231RR, biological rep1

description: MDA-MB-231RR 1


title: MDA-MB-231 parental, biological rep2

description: MDA-MB-231 PARENTAL 2


title: MDA-MB-231 parental, biological rep1

description: MDA-MB-231 PARENTAL 1


title: P30_WT IHC-37

tag: strain


title: P30_WT IHC-44


title: MCF-7RR, biological rep2

description: MCF-7RR 2


title: sRNA_col0_rep3


title: DRIP_ndx1-4_ip_rep2

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files (replica 2); ip (fastq), IP/input (bigWig).

data_processing:
Sequenced reads were aligned to the A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0) using the bowtie2 algorithm with the default parameters.
Samtools (REF) was used for making .bam files and indexing. Low mapping quality and PCR-duplicated reads were omitted from downstream analysis (http://broadinstitute.github.io/picard/). Deeptools2 bamCoverage was used to create RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage files (.bedgraph and .bigwig). Read densities were calculated for 20 bp bins (--binSize 20 --operation ratio --smoothLength 60 –normalizeUsing RPKM) and IP/input bigwig ratios were made by bigwigCompare.
MACS2 was used with default settings to identify DRIP peaks in Col-0 and ndx1-4 samples, respectively. The DRIP signal detected in both ndx1-4 and Col-0 samples was reduced to background by RNaseH1 treatment.
Assembly: A. thaliana reference genome (TAIR10; NCBI; Ecotype: Columbia-0).
Supplementary files format and content: bigwig files are from the IP/input ratio and RNaseH1 treated experiments (col0 and ndx1-4).
Supplementary files format and content: bed files contain the processed peaks (col0 and ndx1-4).
Library strategy: DRIP-seq

extract_protocol:
Plants were cross-linked under a vacuum chamber by phosphate buffered saline (PBS) containing 1% formaldehyde for 2x5 minutes. Excess formaldehyde was quenched by adding glycine to a final concentration of 0.125 M. Chromatin was purified and resuspended in Nuclei lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 20mM Hepes KOH pH 7.4, 10mM MgCl2, 0.5% Triton X-100, 5mM DTT and Protease Inhibitors) followed by Proteinase K treatment (Thermo Fisher Scientific) and crosslink-reversal in the same step, at 65°C, overnight. Total nucleic acid was prepared by phenol-chloroform extraction and precipitated with 2-volumes of ice cold isopropanol and 1/10 volume 4M ammonium-acetate. Samples were then divided into two equal parts: half of the samples were treated with 8 µl of RNaseH (5000 U/ml, New England Biolabs) at 37°C, overnight. Nucleic acid preps were diluted 4-fold in a ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 1.2 mM EDTA, 1.1% Triton X-100, 167 mM NaCl) and DNA was fragmented by sonication to an average fragment size of 250-500 bp (low intensity, 3 x 5 min; 30 sec ON, 30 sec OFF, Bioruptor UCD-300, Diagenode). Dynabeads Protein A magnetic beads (ThermoFisher Scientific) were pre-blocked with PBS/EDTA containing 0.5% BSA. To immobilize the S9.6 antibody, 50 µl pre-blocked Dynabeads Protein A slurry was incubated with 10 μg of S9.6 antibody in IP buffer (50 mM Hepes/KOH at pH 7,5; 0,14 M NaCl; 5 mM EDTA; 1% Triton X-100; 0,1% Na-Deoxycholate, ddH2O) at 4°C for 4 hours, with rotation. Six micrograms of fragmented genomic DNA were added to the mixture and gently rotated at 4°C, overnight. Beads were washed two times with 1 ml of ChIP lysis buffer (low salt,50 mM Hepes/KOH pH 7.5, 0.14 M NaCl, 5 mM EDTA pH 8, 1% Triton X-100, 0.1% Na-Deoxycholate), 1 ml of high-salt ChIP lysis buffer (50 mM Hepes/KOH pH 7.5, 0.5 M NaCl, 5 mM EDTA pH 8, 1% Triton X-100, 0.1% Na-Deoxycholate), 1 ml of wash buffer (10 mM Tris-HCl at pH 8, 0.25 M LiCl, 0.5% NP-40, 0.5% w/v sodium deoxycholate, 1 mM EDTA at pH 8) and 1 ml of TE buffer (100 mM Tris-Cl at pH 8, 10 mM EDTA at pH 8) at 4°C. Elution was performed in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 15 min at 65°C. After purification by a NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel), DRIP samples were analysed by quantitative real-time PCR (qPCR) performed with a LightCycler 480 SYBR Green I Master mix (Roche) and a QuantStudio 12K Flex Real-Time PCR System (Thermo Fisher Scientific).
DRIP-seq libraries were prepared according to Illumina’s TruSeq ChIP Sample Preparation protocol except that the uracil tolerant KAPA HiFi HotStart DNA Polymerase (Kapa Bio) was used. Briefly, the enriched DRIP DNA samples were end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Libraries were sequenced using 150 nt paired end read with Illumina NextSeq500 (Genomic Medicine and Bioinformatics Core Facility of the University of Debrecen).

tag: primer antibody

value: S9.6 antibody


title: DRIP_ndx1-4_rnaseh

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files; ip; RNaseH1 treated.


title: P30_WT IHC-36

value: Cochlea


title: DRIP_ndx1-4_ip_rep1

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files (replica 1); ip (fastq), IP/input (bigWig).


title: P30_WT IHC-35


title: DRIP_ndx1-4_input

description:
A. thaliana reference genome (TAIR10)
ndx1-4 mutant 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files; input.


title: P30_WT IHC-32


title: MCF-7 parental, biological rep1

description: MCF-7 PARENTAL 1


title: DRIP_col0_ip_rep2

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files (replica 2); ip (fastq), IP/input (bigWig).


title: P30_WT IHC-31


title: DRIP_col0_ip_rep1

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files (replica 1); ip (fastq), IP/input (bigWig).


title: P30_WT IHC-30


title: dhx38-- rep3

city: WuHan

first: Jiayi

last: Tu

address: LUOYU ROAD

institute: Huazhong university of science and technology

description: Please see the file sibling_and_dhx38--rep3_idname.list.txt on the series record for a key to the gene IDs.

data_processing:
RNA-Seq quality control and filtering using fastp software
input files after quality control were aligned to Zebrafish genome (Ensembl GRCz11) by STAR software using 2-pass strategy
gene expression data were extracted using featureCounts software and differential analysis were performed using edgeR
alternative splicing analysis were implemented by software rMATS and visualized using rmats2sashimiplot for significant differential splicing events
Genome_build: GRCz11
Supplementary_files_format_and_content: diff_genes.txt: NCPM of all genes in three groups in dhx38 siblings and mutants. mt, mutant; sib, sibling.
Supplementary_files_format_and_content: sig_diff_genes.txt: NCPM of significantly differentially expressed genes in dhx38 siblings and mutants. mt, mutant; sib, sibling.

organism: Danio rerio

source_name: Tail tissue

extract_protocol:
Total RNA from the trunk region of siblings and dhx38--embryos at 36 hpf was extracted using Trizol (Invitrogen). RNA sample quality and quantity were evaluated with both Bioanalyzer 2100 (Agilent) and Nanodrop. RNA-Seq was performed on an Illumina HiSeq2000 platform by Beijing Novogene and Biomarker.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: tail tissue

value: AB

value: 36 hpf


title: P30_WT IHC-29


title: dhx38-- rep1


title: dhx38-- rep2


title: DRIP_col0_input

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files; input.


title: sibling rep1

value: WT sibling


title: DRIP_col0_rnaseh

description:
A. thaliana reference genome (TAIR10)
Wild type 10-day-old seedling.
Paired-end DRIP-seq; reads1 and reads2 in different raw files; ip; RNaseH1 treated.


title: sibling rep2


title: P30_WT IHC-28


title: P30_WT IHC-34


title: sibling rep3


title: P30_WT IHC-23


title: P30_WT IHC-27


title: P30_WT IHC-33


title: Day 8 KO CXCR5+ rep1

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Reads were aligned with hiSAT2
Aligned reads were assigned to genes with FeatureCounts
Assembly: mm10
Supplementary files format and content: Text file with counts

source_name: Spleen

extract_protocol: Qiagen RNAeasy Micro Kit

value: Spleen

value: P14 cells

value: CD8 T cells

value: LCMV clone 13 infection

tag: days post-infection

tag: subset


title: P30_WT IHC-24

value: postnatal day 30

value: vGlut3-P2A-iCreER/+; Ai9/+


title: P30_WT IHC-26


title: P30_WT IHC-25


title: P30_WT IHC-22


title: Day 8 WT Tim3+ rep2

value: WT


title: Day 8 WT Tim3+ rep1


title: P30_WT IHC-20


title: Day 8 KO Tim3+ rep2


title: Day 8 KO Tim3+ rep1


title: P30_WT IHC-21


title: P30_WT IHC-19


title: Naive WT rep2

value: Naïve


title: Naive KO rep2


title: Naive WT rep1


title: P30_WT IHC-17


title: Day 15 WT CXCR5+ rep2


title: Day 15 WT CXCR5+ rep3


title: P30_WT IHC-14


title: P30_WT IHC-15


title: Day 15 KO CXCR5+ rep3


title: P30_WT IHC-9


title: P30_WT IHC-8


title: Naive KO rep1


title: Day 15 WT CXCR5+ rep1


title: Day 15 KO CXCR5+ rep2


title: P30_WT IHC-11


title: P30_WT IHC-12


title: Day 15 WT Tim3+ rep3


title: Day 15 WT Tim3+ rep2


title: P30_WT IHC-16


title: P30_WT IHC-7


title: Day 15 WT Tim3+ rep1


title: P30_WT IHC-10


title: P30_WT IHC-13


title: P30_WT IHC-18


title: Day 15 KO Tim3+ rep2


title: Day 15 KO Tim3+ rep1


title: P30_WT IHC-5


title: P30_WT IHC-4


title: Day 8 WT CXCR5+ rep2


title: Day 15 KO CXCR5+ rep1


title: P30_WT IHC-3


title: Day 8 WT CXCR5+ rep1


title: P30_WT IHC-2


title: Day 8 KO CXCR5+ rep2


title: P30_WT IHC-1


title: epidermal layer of K14 conditional IL-9R KO

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

country: Japan

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

data_processing:
Illumina NovaSeq Sysyem software v1.6 used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 using TopHat v2.0.13.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were culculated using Cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab de includes FPKM values for each Sample.

source_name: epidermal cell layer of ear

extract_protocol:
Total RNA was extracted from the epidermal cell layers by using Trizol reagent. Illumina TruSeq Standerd mRNA Library Prep Kit(Cat#20020594) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for swqurncing using standard Illumina protocols.

treatment_protocol: 5 % Imiquimod cream was applied on ears of WT mice and K14 conditional Il9ra KO mice for 6 consecutive days. Ears were removed and soaked in 1 mg/ml dispase II (Wako, Tokyo, Japan) at 37˚C for 1 hr and then epidermal cell layers were obtained under a stereo microscope.

value: epidermal cell layer of ear

value: IMQ day 6

value: K14 conditional Il9ra KO


title: epidermal layer of Cntl

value: wild type


title: Day 30 KO CXCR5+ rep2

value: Tgfbr2 KO


title: Day 30 KO CXCR5+ rep3


title: Day 30 KO CXCR5+ rep1


title: Day 30 WT Tim3+ rep2


title: Day 30 WT Tim3+ rep3


title: Day 30 KO Tim3+ rep3


title: Day 30 WT Tim3+ rep1


title: DT003

first: Tania

last: Wong

state: New Jersey

address: 205 South Orange Avenue

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers NJ Medical School

description: Single cells from the lungs of a BL/6 mouse infected intranasally with K. pneumoniae MKP103 (48 h post infection)

data_processing:
The data was processed using cellranger (v5.0.1) from 10x Genomics using the Mus musculus reference genome mm10-2020-A
Genome_build: mm10
Supplementary_files_format_and_content: info.tar: tar files containing Cell Ranger’s log files
Supplementary_files_format_and_content: outs.tar: tar files containing Cell Ranger’s output files including count matrices and other analyses performed by Cell Ranger

source_name: MKP103-infected BL/6 mouse

growth_protocol: K. pneumoniae was grown in Luria broth prior to preparing the inocula for intranasal mouse infection

extract_protocol:
Mouse lungs were excised and each was minced to small pieces in 1 ml of an enzyme mixture containing 20 mg/ml dispase, 2 mg/ml collagenase type I, 1 mg/ml elastase, and 1 unit/ml DNase. The minced lungs were digested at 37ºC for 30 min and strained over a 70 𝜇m strainer, which was rinsed with 1 ml PBS containing 10% FBS four times. The strained contents were centrifuged at 1,400 rpm for 7 min at 4ºC and the supernatants were discarded. The cell pellets were resuspended in RBC lysis buffer and incubated on ice for 3 min prior to the addition of PBS containing 10% FBS and centrifugation to remove red blood cells. The resulting cell pellets were resuspended in PBS containing 0.04% (w/v) bovine serum albumin to a concentration of 1 x 106 cells/ml for 10x Genomics Chromium 3' sc-RNA-seq microfluidic cell processing, library preparation, and sequencing.
scRNA-Seq Libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to manufacturer's instructions.

treatment_protocol: Mice were administered intranasally with PBS, viable MKP103 or purified MKP103 LPS and the murine lungs were excised 48 h post infection.

value: lung


title: DT001

description: Single cells from the lungs of an uninfected BL/6 mouse

source_name: Uninfected (PBS) BL/6 mouse

value: uninfected


title: Day 30 KO Tim3+ rep2

description:
1_Tim3_KO1
2_Tim3_KO2


title: DT006

description: Single cells from the lungs of an Irg1-/- mouse infected intranasally with K. pneumoniae MKP103 (48 h post infection)

source_name: MKP103-infected Irg1-/- mice


title: M2

description: Total RNA from uninfected Irg1-/- mouse lungs

data_processing:
basecalling using bcl2fastq  '2.20.0'
alignment using star aligner  '2.7.3a'
filtering using samtools (1.9), duplicates were marked using picard '2.22.3'; gatk = '4.2.0.0'
read quantification for mouse samples using featurecounts (M1,M2,M3,M5,M7,M8,M9,M10,M11,M14 and M16); read quantification for host samples using kallisto (K1, K2 and K3); subread = '1.6.3'
differential gene expression analysis using DEseq2 in Rstudio; R = '3.5.3',
Genome_build: mouse: GRCm38 fasta and gtf from Gencode vM21
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Uninfected (PBS) Irg1-/- mouse

growth_protocol: MKP103 was grown in Luria broth prior to bacterial RNA extraction

extract_protocol:
As per manuscript
According to the manufacturer’s instructions, Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete kit (NuGEN #0363-32)

treatment_protocol: Total RNA (host and bacteria) were extracted from murine lungs at 48 h post infection

tag: infection status

tag: mouse genotype

tag: bacterial genotype


title: M3


title: Day 30 KO Tim3+ rep1

tag: cell line

tag: cell type

tag: treatment


title: M1


title: M11

description: Total RNA from uninfected BL/6 mouse lungs


title: Naïve rep2

tag: genotype


title: Naïve rep1


title: M10


title: Day 30 WT CXCR5+ rep3


title: Day 30 WT CXCR5+ rep1


title: DT004

description: Single cells from the lungs of a BL/6 mouse administered purified LPS from K. pneumoniae MKP103 intranasally (48 h)

source_name: MKP103 LPS-treated mouse

value: MKP103 LPS-treated


title: Day 30 WT CXCR5+ rep2


title: Con3_plasmic exosome_delivery_T4

city: chengdu

first: wang

last: xiaodong

state: China

address: Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University.

description: Gene expression in delivery plasma exosomes

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarray Kit (Release 21.0,8x60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on  the Agilent DNA Microarray Scanner (G2505C) using  one color scan setting for 4x180k array slides (Scan  Area 61x21.6 mm, Scan resolution 3um, Dye channel  is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature  Extraction Software 10.7.1.1 (Agilent) using default  parameters to obtain background subtracted and  spatially detrended Processed Signal intensities as  the raw data. Raw data were normalized in quantile  algorithm with Genespring 13.0(Agilent). Probe that  at least 1 out of 2 samples flagged as Detected were  maintained.

source_name: Con3, plasmic exosome, delivery, T4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2  μg RNA using the One-Color Low RNA Input Linear  Amplification PLUS kit (Agilent) according to the  manufacturer's instructions, followed by RNAeasy  column purification (QIAGEN, Valencia, CA). Dye  incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit  (Applied Biosystem p/n AM1556 ) following the  manufacturer's instructions.

value: plasma

tag: disease state

value: control

tag: donor number

tag: time

value: delivery

tag: gender

value: female


title: Con3_plasmic exosome_third trimester_T3

institute: West China Second University Hospital, Sichuan University

description: Gene expression in third trimester plasma exosomes

source_name: Con3, plasmic exosome, third trimester, T3

value: third trimester


title: KO rep3

value: Spleen

value: P14 cells

value: CD8 T cells

value: LCMV clone 13 infection


title: WT rep4

value: WT


title: KO rep4


title: Con3_plasmic exosome_second trimester_T2

description: Gene expression in second trimester plasma exosomes

source_name: Con3, plasmic exosome, second trimester, T2

value: second trimester


title: Con2_plasmic exosome_delivery_T4

source_name: Con2, plasmic exosome, delivery, T4


title: KO rep2


title: Con3_plasmic exosome_first trimester_T1

description: Gene expression in first trimester plasma exosomes

source_name: Con3, plasmic exosome, first trimester_T1

value: first trimester


title: WT rep1


title: WT rep2


title: Con2_plasmic exosome_third trimester_T3

source_name: Con2, plasmic exosome, third trimester_T3


title: KO rep1


title: Con2_plasmic exosome_first trimester_T1

source_name: Con2, plasmic exosome, first trimester, T1


title: Con1_plasmic exosome_third trimester_T3

source_name: Con1, plasmic exosome, third trimester, T3


title: M9

description: Total RNA (murine and bacterial RNA) from the lungs of MKP103-infected Irg1-/- mouse

organism:
Mus musculus
Klebsiella pneumoniae subsp. pneumoniae

source_name: MKP103-infected Irg1-/- mouse


title: Con1_plasmic exosome_first trimester_T1

source_name: Con1, plasmic exosome, first trimester, T1


title: Con1_plasmic exosome_second trimester_T2

source_name: Con1, plasmic exosome, second trimester, T2


title: M8


title: WT rep3

source_name: Spleen


title: M5


title: ICP3_plasmic exosome_delivery_T4

source_name: ICP3, plasmic exosome, delivery, T4

value: ICP


title: M16

description: Total RNA (murine and bacterial RNA) from the lungs of MKP103-infected BL/6 mouse

source_name: MKP103-infected BL/6 mouse


title: ICP2_plasmic exosome_delivery_T4

source_name: ICP2, plasmic exosome, delivery, T4


title: ICP3_plasmic exosome_second trimester_T2

source_name: ICP3, plasmic exosome, second trimester_T2


title: M15


title: ICP2_plasmic exosome_third trimester_T3

source_name: ICP2, plasmic exosome, third trimester, T3


title: wt_rep3

city: Stockholm

first: Stefan

last: Åström

address: Svante Arrhenius väg 20B

country: Sweden

institute: Stockholm University

data_processing:
Reads were trimmed off low quality bases and adapters using trimmomatic/0.32
Trimmed reads were mapped using bowtie/1.1.2 to the referencegenome sacCer3 / R64-1-1.
Multi randompos: all reads including multimapping reads, for which 1 randomly selected alignment is reported. Uniq best map: only reads for which one best alignment existed are reported.
Coverage tracks normalised to 1x coverage were computed using deepTools/2.3.1. Effective genome size 12 400 000 bp was used. Bin size was 1 bp.
DANPOS was used genome-wide for nucleosome positioning and occupancy analysis, using triplicates of the conditions in the same run.
Genome_build: sacCer3, W303
Supplementary_files_format_and_content: NN.mapping protocol.danpos2 (results for pooled replicates of condition NN)
Supplementary_files_format_and_content: NN-MM.mapping protocol.danpos2 (results of pooled replicates of ratio of conditions NN to MM)
Supplementary_files_format_and_content: W303: WT nucleosome positioning, sir2 nucleosome positioning and sir2/WT difference.

organism: Saccharomyces cerevisiae W303

source_name: yeast culture

growth_protocol: YEPD cultures, log phase

extract_protocol:
Rizzo, J. M., Bard, J. E., & Buck, M. J. (2012). Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. BMC Mol Biol, 13, 15. doi:10.1186/1471-2199-13-15
ThruPLEX DNA-seq library preparation kit (Rubicon Genomics)

treatment_protocol: untreated

tag: strain background

tag: growth media

value: YEPD

value: untreated


title: wt_rep2


title: M7

tag: tissue

value: lung


title: ICP2_plasmic exosome_second trimester_T2

source_name: ICP2, plasmic exosome, second trimester, T2


title: ICP2_plasmic exosome_first trimester_T1

source_name: ICP2, plasmic exosome, first trimester, T1


title: Rhiarthinge FLAG-ChIP replicate 2

city: Vienna

first: Lisa

last: Baumgartner

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

description:
Rhiarthinge_in2
Rhino construct with artificial hinge domain

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.3.0) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.3.0) with 3 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files

organism: Drosophila melanogaster

source_name: ovary

growth_protocol: 25˚C, 12h dark/light

extract_protocol:
Chromatin immunoprecipitation (ChIP) was carried out according to Lee et al. (2006)
ChIP-seq libraries were prepared using the NEB Next Ultra II DNA Library for Illumina (NEB).

value: ovary

tag: chip antibody

value: anti-FLAG antibody (Sigma F1804-1MG)


title: RhiGCN4 input  2

description: Rhino construct with GCN4 dimerization domain in place of CSD


title: ICP1_plasmic exosome_first trimester_T1

source_name: ICP1, plasmic exosome, first trimester, T1

value: plasma


title: Rhiarthinge input  2

description: Rhino construct with artificial hinge domain


title: ICP1_plasmic exosome_second trimester_T2

source_name: ICP1, plasmic exosome, second trimester, T2


title: sir2_rep3

value: sir2 mutant


title: ICP3_plasmic exosome_third trimester_T3

source_name: ICP3, plasmic exosome, third trimester, T3

value: female


title: Rhiarthinge CG2678-ChIP  replicate 2


title: ICP1_plasmic exosome_third trimester_T3

source_name: ICP1, plasmic exosome, third trimester, T3

value: third trimester


title: sir2_rep2


title: AML1166T AML1167T2 ROI_23

city: Boston

first: Yan

last: Tang

address: 20 Shattuck street

institute: Brigham and Women's Hospital

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

source_name: kidney tumor

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
OTHER: GeoMx Seq

tag: slide id

tag: roi number

tag: segment type

value: SMA+

tag: disease

value: angiomyolipoma

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: characteristic


title: AML1166T AML1167T2 ROI_24


title: M14

tag: infection status

tag: mouse genotype

tag: bacterial genotype


title: sir2_rep1

tag: genotype

tag: treatment


title: RhiGCN4 CG2678-ChIP  replicate 2

description:
RhiGCN4_in2
Rhino construct with GCN4 dimerization domain in place of CSD

tag: cell line


title: AML1166T AML1167T2 ROI_22


title: RhiGCN4 FLAG-ChIP  replicate 2


title: AML1166T AML1167T2 ROI_21


title: AML1166T AML1167T2 ROI_20


title: AML1166T AML1167T2 ROI_19


title: ICP1_plasmic exosome_delivery_T4

source_name: ICP1, plasmic exosome, delivery, T4

tag: disease state

tag: donor number

tag: time

value: delivery

tag: gender


title: wt_rep1

tag: strain background

tag: growth media


title: AML1166T AML1167T2 ROI_18

tag: slide id

tag: roi number

tag: segment type

tag: disease


title: AML1166T AML1167T2 ROI_16

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: characteristic


title: AML1166T AML1167T2 ROI_17


title: AML1166T AML1167T2 ROI_15


title: AML1166T AML1167T2 ROI_14


title: AML1166T AML1167T2 ROI_12


title: AML1166T AML1167T2 ROI_13


title: AML1166T AML1167T2 ROI_8


title: AML1166T AML1167T2 ROI_7


title: AML1166T AML1167T2 ROI_11


title: AML1166T AML1167T2 ROI_6


title: AML1166T AML1167T2 ROI_5


title: AML1166T AML1167T2 ROI_4


title: AML1166T AML1167T2 ROI_3


title: AML1166T AML1167T2 ROI_2


title: AML1166T AML1167T2 ROI_1


title: patient #7-derived adult stem cell, D14

city: Pohang

first: Hyeonji

last: Kim

address: 77 Cheongam-ro

country: South Korea

institute: Pohang University of Science and Technology

data_processing:
Filtering. The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8.
Sequence alignment. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options (refer to “Alignment” of “Help” section in the html report) with “-quantMode TranscriptomeSAM” option for estimation of transcriptome expression level.
Gene expression estimation. Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness. To improve the accuracy of the measurement, “--estimate-rspd” option was applied. All other options were set to default values. To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Gene expression estimation. Based on the estimated read counts in the previous step, DEGs were identified using the R package called TCC v.1.26.0. TCC package applies robust normalization strategies to compare tag count data. Normalization factors were calculated using the iterative DESeq2/edgeR method. Q-value was calculated based on the p-value using the p.adjust function of R package with default parameter settings. The DEGs were identified based on the qvalue threshold less than 0.05 for correcting errors caused by multiple-testing.
Gene Ontology (GO) analysis. GO database provides a set of hierarchical controlled vocabulary classified in 3 categories:  Biological Proccess(BP), Cellular Component(CC) and Molecular Function(MF). For functional characterization of the DEGs, GO based trend test was carried out using the R package called GOseq through the Wallenius non-central hypergeometric distribution. Selected genes of P-values < 0.05 following the test were regarded it as statistically significant.
Assembly: GRCh38 (Ensembl 99)
Supplementary files format and content: tab-delimited text files include read count, FPKM, TPM values for each Sample

molecule: polyA RNA

source_name: nasal turbinate

growth_protocol: Adult stem cells were cultured in normal Dulbecco's modified Eagle's medium (Gibco, USA) containing 10% (v/v) fetal bovine serum (Gibco, USA) and 1% (v/v) penicillin/streptomycin (Sigma-Aldrich, USA) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen).
The libraries were prepared for 151 bp paired-end sequencing using the TruSeq stranded mRNA Sample Preparation Kit (Illumina, USA).

treatment_protocol: Adult stem cells at passage 6 were encapsulated in cornea-derived decellularized extracellular matrix hydrogel at a concentration of 5 × 106 cells ml−1 and cultured in differentiation medium containing 10 ng ml−1 KGF/EGF for 14 days.

tag: tissue

value: nasal turbinate

tag: cell type

value: stem cell

tag: genotype

value: Normal

value: Differentiation into keratocyte


title: patient #9-derived adult stem cell, D14

tag: treatment


title: patient #5-derived adult stem cell, D14


title: patient #9-derived adult stem cell, D0


title: patient #1-derived adult stem cell, D14


title: patient #8-derived adult stem cell, D14


title: patient #7-derived adult stem cell, D0


title: patient #8-derived adult stem cell, D0


title: AML1166T AML1167T2 ROI_9


title: AML1166T AML1167T2 ROI_10


title: patient #1-derived adult stem cell, D0


title: patient #5-derived adult stem cell, D0


title: RNA-seq-03-PAF1AID-Aux-0h

city: Chicago

first: Yuki

last: Aoi

state: IL

address: 303 E Superior St. SQBRC 7-300

department: Biochemistry & Molecular Genetics

institute: Northwestern University

description: poly(A)+ RNA-seq

data_processing:
For RNA-seq, low-quality bases were removed from 3’ end of reads using cutadapt 1.14 (Martin, 2011). Reads were aligned to human GRCh38 genome assembly with Ensembl transcript annotation GRCh38 release 103 using STAR 2.7.5 (Dobin et al., 2013). For spike-ins, reads were also aligned to fly BDGP6 genome assembly with Ensembl transcript annotation BDGP6 release 102. Reads with non-primary alignment were discarded. Counting reads were performed using featureCounts 2.0.0 (Liao et al., 2014) with transcript annotations described above.
Assembly: GRCh38
Supplementary files format and content: csv file contains raw read counts at human and spike-in fly genes for each sample..

growth_protocol: Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (Gibco #15140-122) in CO2 incubators.

extract_protocol:
For RNA-seq, total RNA from 1 million DLD-1 cells was extracted using RNeasy Mini kit, followed by enrichment of polyadenylated RNA using NEBNext Poly(A) mRNA Magnetic isolation module.
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture.

tag: cell line

value: Colorectal adenocarcinoma

value: PAF1-AID OsTIR1

value: Auxin 0h


title: RNA-seq-03-PAF1AID-Aux-6h

description: poly(A)+ RNA-seq

value: Auxin 6h


title: RNA-seq-04-PAF1AID-Aux-6h

description: poly(A)+ RNA-seq


title: RNA-seq-04-PAF1AID-Aux-0h

description: poly(A)+ RNA-seq


title: RNA-seq-04-PAF1AID-Aux-2h

description: poly(A)+ RNA-seq

value: Auxin 2h


title: RNA-seq-03-PAF1AID-Aux-2h

description: poly(A)+ RNA-seq


title: RNA-seq-02-SPT6AID-Aux-0h

description: poly(A)+ RNA-seq

value: SPT6-AID OsTIR1


title: RNA-seq-01-SPT6AID-Aux-6h

description: poly(A)+ RNA-seq


title: RNA-seq-02-SPT6AID-Aux-6h

description: poly(A)+ RNA-seq


title: RNA-seq-02-SPT6AID-Aux-2h

description: poly(A)+ RNA-seq


title: RNA-seq-01-SPT6AID-Aux-2h

description: poly(A)+ RNA-seq


title: RPB12_ChIP_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

data_processing:
Adapters were trimmed with cutadapt (v2.10) in paired-end mode with the following parameters: -q 15,15 –minimum-length 18. Trimmed reads were first aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1) with the ‘--very-sensitive-local’ options (for TELP libraries).
Aligned reads were then filtered by sambamba (v0.7.0) combined with SAMtools (v 0.1.19) to remove PCR duplicates and low mapping quality scores (MAPQ < 20). For each experimental replicate, uniquely mapped reads were downsampled to match the lowest coverage level (32 million reads) among all the samples before calling peaks, which was carried out using MACS2 (v2.2.5) with a stringent setting “–nomodel –shiftsize 100 –extsize 200 –p 0.01” over input control
High-confidence peaks shared across two biological replicates with irreproducible discovery rate (IDR) < 0.05 were selected for each RPB group.
The ChIP reads at each genomic position were normalized and converted to bigwig format using bamCoverage from deeptools toolkit (v3.4.3).
For subsequent meta-gene analysis and browser visualization, replicates for each biological condition were merged into one bigwig track file.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files of ChIP-seq data were generated using deepTools with library size normalized to equal.

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: Wild-type and Pol II subunit degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2.

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40U MNase (NEB, M0247), followed by sonication as previously described (Yongpeng et al., 2020). 1μl GFP antibodies (Abcam, Ab290) and 30μl Protein G beads (Thermo Fisher, 10004D) were used to enrich Pol II subunit-DNA complexes.
ChIP DNA were subjected to TELP library construction (Peng et al., 2015). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: Cells were passaged in 15 cm dish and directly cross-linked when cell confluency reached about 70%.

value: mouse embryonic stem cells (V6.5)

value: GFP tagged mESCs

tag: antibody

value: GFP(Abcam, Cat#ab290, lot#GR3222604-1)


title: RPB11_ChIP_rep2


title: RPB10_ChIP_rep2


title: RPB12_ChIP_rep1


title: PRO-seq-03-PAF1AID-Veh2h-HS1h

description: PRO-seq

data_processing:
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome, then the strand-specific bigwig files were generated.
Assembly: hg38
Supplementary files format and content: bigWig files contain strand-specific, spike-in normalized PRO-seq signal.
Library strategy: PRO-seq

molecule: nuclear RNA

extract_protocol:
PRO-seq sample preparation was performed according to the previously described qPRO-seq protocol (Judd et al., 2020). ~1 million DLD-1 nuclei  mixed with spike-in Drosophila S2 nuclei were used for nuclear run-on assay.
For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. PRO-seq libraries were prepared according to the previously described qPRO-seq protocol (Judd et al., 2020).

value: Vehcle 2h HS 1h


title: PRO-seq-03-PAF1AID-Veh2h-NHS1h

description: PRO-seq

value: Vehcle 2h NHS 1h


title: RPB10_ChIP_rep1


title: PRO-seq-03-PAF1AID-Aux2h-NHS1h

description: PRO-seq

value: Auxin 2h NHS 1h


title: PRO-seq-01-SPT6AID-Aux2h-HS1h

description: PRO-seq

value: Auxin 2h HS 1h


title: RPB11_ChIP_rep1


title: PRO-seq-01-SPT6AID-Veh2h-HS1h

description: PRO-seq


title: PRO-seq-01-SPT6AID-Aux2h-NHS1h

description: PRO-seq


title: RPB9_ChIP_rep2


title: RPB9_ChIP_rep1


title: PRO-seq-01-SPT6AID-Veh2h-NHS1h

description: PRO-seq


title: PRO-seq-03-PAF1AID-Aux2h-HS1h

description: PRO-seq


title: ChIP-seq-23-RPB1N-SPT6NELFcAID-Aux-2h

description: ChIP-seq Pol II (total)

data_processing:
For ChIP-seq, single-end raw reads trimmed by cutadapt 1.14 (Martin, 2011) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. The bigwig files with normalized counts were generated using deepTools 3.1.1 bamCoverage (Ramírez et al., 2016).
Assembly: hg38
Supplementary files format and content: bigWig files contain spike-in normalized ChIP-seq signal.
Supplementary files format and content: bed files contain coordinates of genes or pause sites that were used in this study.

extract_protocol:
For ChIP-seq in human DLD1 cells, ~30 million cells were crosslinked with 1% paraformaldehyde in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples. Chromatin was sonicated with the Covaris E220. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA).

value: SPT6-AID/NELF-C-AID OsTIR1

tag: chip antibody

value: RPB1 NTD (Cell signaling # 14958S)


title: ChIP-seq-01-INPUT-SPT6AID-Veh-2h

description: ChIP-seq input

value: Vehcle 2h


title: ChIP-seq-23-RPB1N-SPT6NELFcAID-Veh-2h

description: ChIP-seq Pol II (total)


title: RPB8_ChIP_rep2


title: RPB7_ChIP_rep1


title: RNA-seq-01-SPT6AID-Aux-0h

description: poly(A)+ RNA-seq


title: ChIP-seq-22-RPB1N-SPT6NELFcAID-Aux-2h

description: ChIP-seq Pol II (total)


title: P30_WT IHC-6

data_processing:
FastQC (v0.11.9) and Trimmomatic (v0.39) were used for quality control. Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.1.0) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v1.3.5) with default parameters.
Raw counts were calculated by HTSeq (v0.10.0) software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for smartseq.

source_name: Wild type cochlear inner hair cells

extract_protocol: Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).

tag: strain

value: Cochlea

tag: age

value: postnatal day 30

value: vGlut3-P2A-iCreER/+; Ai9/+


title: ChIP-seq-21-NELF-C-SPT6AID-Aux-2h

description: ChIP-seq NELF-C

value: Colorectal adenocarcinoma

value: NELF-C (Cell Signaling # 12265)


title: ChIP-seq-22-RPB1N-SPT6NELFcAID-Veh-2h

description: ChIP-seq Pol II (total)


title: RPB6_ChIP_rep2


title: ChIP-seq-21-NELF-C-SPT6AID-Veh-2h

description: ChIP-seq NELF-C


title: RPB5_ChIP_rep2


title: ChIP-seq-20-NELF-C-SPT6AID-Aux-2h

description: ChIP-seq NELF-C

value: Auxin 2h


title: RPB5_ChIP_rep1


title: RPB6_ChIP_rep1


title: ChIP-seq-19-RPB1N-SPT6PAF1AID-Aux-2h

description: ChIP-seq Pol II (total)

value: SPT6-AID/PAF1-AID OsTIR1


title: ChIP-seq-20-NELF-C-SPT6AID-Veh-2h

description: ChIP-seq NELF-C

value: SPT6-AID OsTIR1


title: RPB8_ChIP_rep1

value: mouse embryonic stem cells (V6.5)

value: GFP tagged mESCs


title: RPB7_ChIP_rep2

value: GFP(Abcam, Cat#ab290, lot#GR3222604-1)


title: ChIP-seq-19-RPB1N-SPT6PAF1AID-Veh-2h

description: ChIP-seq Pol II (total)


title: RPB4_ChIP_rep1


title: ChIP-seq-18-RPB1N-SPT6PAF1AID-Aux-2h

description: ChIP-seq Pol II (total)


title: RPB3_ChIP_rep2


title: RPB3_ChIP_rep1


title: RPB2_ChIP_rep2


title: ChIP-seq-18-RPB1N-SPT6PAF1AID-Veh-2h

description: ChIP-seq Pol II (total)


title: RPB1_ChIP_rep2


title: ChIP-seq-17-RTF1-SPT6AID-Veh-2h

description: ChIP-seq RTF1

value: RTF1 (Bethyl # A301-329A)


title: ChIP-seq-16-RTF1-SPT6AID-Aux-2h

description: ChIP-seq RTF1


title: RPB4_ChIP_rep2


title: RPB1_ChIP_rep1


title: ChIP-seq-17-RTF1-SPT6AID-Aux-2h

description: ChIP-seq RTF1


title: GFP_ChIP_rep2


title: ChIP-seq-16-RTF1-SPT6AID-Veh-2h

description: ChIP-seq RTF1


title: GFP_ChIP_rep1


title: Input_rep2

value: Input mESCs


title: ChIP-seq-15-CDC73-SPT6AID-Aux-2h

description: ChIP-seq CDC73


title: ChIP-seq-15-CDC73-SPT6AID-Veh-2h

description: ChIP-seq CDC73


title: Input_rep1


title: ChIP-seq-13-LEO1-SPT6AID-Aux-2h

description: ChIP-seq LEO1

value: LEO1 (Bethyl # A300-175A)


title: ChAR-Seq_RPB9_IAA_3h_rep2

description:
ChAR-Seq_RPB9_IAA_3h_plus.bw
ChAR-Seq_RPB9_IAA_3h_minus.bw

data_processing:
Library strategy: ChAR-Seq
ChAR-seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, ribosomal reads were first removed by mapping to one copy of the mouse rDNA sequence. After adapter trimming and quality control with cutadapt and RseQC separately, clean reads were then aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only reads that were properly paired and uniquely aligned were retained for subsequent processing. Reads that mapped to the mouse (or human) genome were normalized to total reads originating from Drosophila spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
Plus- and minus-strand were assigned to uniquely mapped reads using SAMtools, and the final BAM files were converted to bigwig, separated by strand, and normalized to spike-in controls using bamCoverage from deeptools. Finally, bigWig score tracks for visualization prepared for different biological replicates but for the same treatment were merged to an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Then raw read counts were calculated per gene, in a strand-specific manner, based on annotations described in the Gene list definition section below, using featureCounts (Liao et al., 2014).
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: bigwig files

growth_protocol: For ChAR-seq, RPB1, RPB3, RPB6, RPB9 and piRPB3 degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 uM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The Schneider 2(S2) cells were cultured in complete Schneider’s Drosophila Medium (Invitrogen, Cat#21720024) supplemented with 10% FBS (CellMax, Cat#SA311.02) at room temperature.

extract_protocol:
Cells were collected and added to 10% S2 cells. The chromatin-associated RNA were extracted as reported (Dev M. Bhatt et al., 2012).
Chromatin-associated RNA were delivered to Novogene Company. The concentration, purity, and integrity of RNA were examined and followed by ribosomal RNA depletion and strand-specific library construction.
TELP libraries

treatment_protocol: Cells were treated with 2 μg/ml Doxycycline for 12 h to induce OsTir1 expression, then treated with or without 500 uM IAA for 1 h or 3h to induce target protein degradation.

value: RPB9 degron 3h mESCs

tag: fraction

value: Chromatin-associated RNA


title: ChIP-seq-14-WDR61-SPT6AID-Veh-2h

description: ChIP-seq WDR61

value: Vehcle 2h

value: WDR61 (Proteintech # 22536-1-AP)


title: ChIP-seq-14-WDR61-SPT6AID-Aux-2h

description: ChIP-seq WDR61


title: ChIP-seq-13-LEO1-SPT6AID-Veh-2h

description: ChIP-seq LEO1


title: ChIP-seq-12-LEO1-SPT6AID-Aux-2h

description: ChIP-seq LEO1


title: ChAR-Seq_RPB9_IAA_3h_rep1


title: ChAR-Seq_RPB9_IAA_0h_rep2

description:
ChAR-Seq_RPB9_IAA_0h_plus.bw
ChAR-Seq_RPB9_IAA_0h_minus.bw

value: RPB9 degron 0h mESCs


title: ChAR-Seq_RPB6_IAA_3h_rep2

description:
ChAR-Seq_RPB6_IAA_3h_plus.bw
ChAR-Seq_RPB6_IAA_3h_minus.bw

value: RPB6 degron 3h mESCs


title: RPB2_ChIP_rep1


title: ChIP-seq-12-LEO1-SPT6AID-Veh-2h

description: ChIP-seq LEO1

value: Colorectal adenocarcinoma


title: ChAR-Seq_RPB6_IAA_3h_rep1


title: ChIP-seq-11-PAF1-SPT6AID-Aux-2h

description: ChIP-seq PAF1

value: PAF1 (Cell signaling # 12883)


title: ChIP-seq-11-PAF1-SPT6AID-Veh-2h

description: ChIP-seq PAF1


title: ChAR-Seq_RPB6_IAA_1h_rep2

description:
ChAR-Seq_RPB6_IAA_1h_plus.bw
ChAR-Seq_RPB6_IAA_1h_minus.bw

value: RPB6 degron 1h mESCs


title: ChIP-seq-09-RPB1N-Parental-Aux-6h

description: ChIP-seq Pol II (total)

value: Auxin 6h

value: RPB1 NTD (Cell signaling # 14958S)


title: ChIP-seq-10-PAF1-SPT6AID-Aux-2h

description: ChIP-seq PAF1

value: SPT6-AID OsTIR1

value: Auxin 2h


title: ChIP-seq-10-PAF1-SPT6AID-Veh-2h

description: ChIP-seq PAF1


title: ChAR-Seq_RPB6_IAA_0h_rep2

description:
ChAR-Seq_RPB6_IAA_0h_plus.bw
ChAR-Seq_RPB6_IAA_0h_minus.bw

value: mouse embryonic stem cells (V6.5)

value: RPB6 degron 0h mESCs


title: ChAR-Seq_RPB3_IAA_3h_rep2

description:
ChAR-Seq_RPB3_IAA_3h_plus.bw
ChAR-Seq_RPB3_IAA_3h_minus.bw

value: RPB3 degron 3h mESCs


title: ChAR-Seq_RPB6_IAA_0h_rep1


title: ChIP-seq-09-RPB1N-Parental-Aux-0h

description: ChIP-seq Pol II (total)

value: Auxin 0h


title: ChAR-Seq_RPB3_IAA_3h_rep1


title: ChAR-Seq_RPB3_IAA_1h_rep2

description:
ChAR-Seq_RPB3_IAA_1h_plus.bw
ChAR-Seq_RPB3_IAA_1h_minus.bw

value: RPB3 degron 1h mESCs


title: ChIP-seq-08-PAF1-PAF1AID-Aux-2h

description: ChIP-seq PAF1

value: PAF1-AID OsTIR1


title: ChIP-seq-08-PAF1-PAF1AID-Veh-2h

description: ChIP-seq PAF1

value: Vehcle 2h


title: ChAR-Seq_RPB3_IAA_0h_rep2

description:
ChAR-Seq_RPB3_IAA_0h_plus.bw
ChAR-Seq_RPB3_IAA_0h_minus.bw

value: RPB3 degron 0h mESCs

value: Chromatin-associated RNA


title: ChAR-Seq_RPB9_IAA_0h_rep1

value: RPB9 degron 0h mESCs


title: ChIP-seq-07-PAF1-PAF1AID-Aux-2h

description: ChIP-seq PAF1

value: Colorectal adenocarcinoma


title: ChAR-Seq_RPB3_IAA_0h_rep1


title: ChAR-Seq_RPB3_IAA_1h_rep1


title: Karpas

city: TOULOUSE

first: FABIENNE

last: MEGGETTO

address: 2 AVENUE HUBERT CURIEN

institute: CRCT

data_processing:
Fastq raw data cleaning with cutadapt-3.4 (cutadapt -e 0.2 -m 1 -g AAGCAGTGGTATCAACGCAGAGTAC -o FileName_5pTrimmed.fastq.gz FileName.fastq.gz then cutadapt -e 0.2 -m 1 -a GTACTCTGCGTTGATACCACTGCTT -o TrimmedFileName.fastq.gz FileName_5pTrimmed.fastq.gz)
circRNA identification with CIRI-long-v1.0.3 (CIRI-long call -i TrimmedFileName.fastq.gz -o step1 -r genome.fa -p SampleName -a genome.gtf -t 10 then CIRI-long collapse -i SampleFile.lst -o step2 -p SampleName -r genome.fa -a genome.gtf -t 10)
Genome_build: Homo_sapiens.GRCh38.dna.MAIN.fa and Homo_sapiens.GRCh38.87.chr.gtf
Supplementary_files_format_and_content: tab-delimited text files reporting  circRNA candidates (two columns : Id and counting)  Id under the form chr:begin-end

source_name: anaplastic large-cell lymphoma cell line

growth_protocol: Standard cell culture of wild-type cell lines.

extract_protocol:
Cells were harvested and RNA was isolated with Trizol.
Depletion of ribosomal RNA. Exonuclease digest and negative selection of poly(A) transcripts to enrich for circular RNAs. cDNA library preparation (SMARTer) and PCR amplification.
Oxford Nanopore long-read RNA sequencing (SQK-LSK109 kit with native barcoding kit EXP-NBD104, BC01-04)

treatment_protocol: No special treatment of the cells was applied.

tag: cancer type

value: anaplastic large-cell lymphoma


title: COST


title: ChIP-seq-07-PAF1-PAF1AID-Veh-2h

description: ChIP-seq PAF1

value: PAF1 (Cell signaling # 12883)


title: SUP-M2


title: ChAR-Seq_RPB6_IAA_1h_rep1

value: RPB6 degron 1h mESCs


title: ChAR-Seq_RPB1_IAA_3h_rep2

description:
ChAR-Seq_RPB1_IAA_3h_plus.bw
ChAR-Seq_RPB1_IAA_3h_minus.bw

value: RPB1 degron 3h mESCs


title: ChAR-Seq_RPB1_IAA_3h_rep1


title: ChIP-seq-06-RPB1N-PAF1AID-Aux-2h

description: ChIP-seq Pol II (total)

value: RPB1 NTD (Cell signaling # 14958S)


title: ChIP-seq-09-RPB1N-Parental-Aux-2h

description: ChIP-seq Pol II (total)

value: Auxin 2h


title: SU-DHL-1


title: ChIP-seq-05-RPB1N-PAF1AID-Aux-6h

description: ChIP-seq Pol II (total)

value: Auxin 6h


title: ChIP-seq-06-RPB1N-PAF1AID-Veh-2h

description: ChIP-seq Pol II (total)


title: ChAR-Seq_RPB1_IAA_1h_rep1

description:
ChAR-Seq_RPB1_IAA_1h_plus.bw
ChAR-Seq_RPB1_IAA_1h_minus.bw

value: mouse embryonic stem cells (V6.5)

value: RPB1 degron 1h mESCs


title: ChIP-seq-05-RPB1N-PAF1AID-Aux-2h

description: ChIP-seq Pol II (total)


title: ChIP-seq-05-RPB1N-PAF1AID-Aux-0h

description: ChIP-seq Pol II (total)

value: Auxin 0h


title: ChIP-seq-04-SPT6-SPT6AID-Aux-2h

description: ChIP-seq SPT6

value: SPT6-AID OsTIR1

value: SPT6 (Cell signaling # 15616)


title: After gilteritinib

city: Iwaki

first: Jinichi

last: Mori

state: Fukushima

address: 57, Jyoban kamiyunagayamachi kaminodai

institute: Jyoban Hospital Tokiwa Foundation

description: Whole genome lysate

data_processing:
Paired-end sequencing were performed on the Illumina NextSeq 500 sequencer . Reads were mapped to the  hg19 reference sequence using Burrows-Wheeler Aligner (BWA-MEM: ver. 0.7.17-r1188), and duplicate  reads were removed with Picard (ver. 2.18.16).
Mapping by Bowtie2
Peak calling was performed using MACS2 (ver. 2.1.2) and PePr  (ver. 1.1.24) with default parameters respectively. Peak annotation were conducted by HOMER (ver.4.9.1) with default settings.
Assembly: GRch38
Supplementary files format and content: tab-delimited text files include  peak values for each sample

source_name: AML cells

extract_protocol:
Cells were lysed and the rearrangement reaction was performed using Tn5 Transposase (Illumina Catalog #FC121-1030) for 30 min at 37°C.
The reaction solution was purified with Qiagen MinElute PCR Purification Kit. Next, five cycles of PCR with custom Nextera PCR primers were performed using NEBNext Q5 Hot Start HiFi PCR Master Mix. The number of additional PCR cycles was determined by qPCR of the partially amplified product. PCR products were prepared using Agencourt AMPure XP beads using the manufacturer's The PCR products were purified using Agencourt AMPure XP beads by double size selection (left ratio: 1.4X, right ratio: 0.5X) according to the manufacturer's protocol.

treatment_protocol: Blood samples were collected immediately before first dose of gilteritinib and 4 days after initiation of the treatment. The CD34+ cells were isolated from the blood samples using CD34 MicroBead Kit UltraPure according to the manufacture’s instruction

tag: disease state

value: acute myeloid leukemia (AML)

value: AML cells

value: gilteritinib


title: ChIP-seq-04-SPT6-SPT6AID-Veh-2h

description: ChIP-seq SPT6

value: Vehcle 2h


title: ChAR-Seq_RPB1_IAA_1h_rep2

value: Chromatin-associated RNA


title: snRNAseq

city: Qingdao

first: Hai

middle: Xia

last: Qu

address: No. 5, Donghai Zhong Road

institute: Qingdao Municipal Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-1.2.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hepatocellular carcinoma

extract_protocol: For scRNA-seq, freshly excised tissue was rinsed with RPMI 1640 medium (Thermo Fisher Scientific, Inc.) and cut into 1-2-mm pieces. The samples were incubated at 37°C for 40 min with digestive solution, containing 0.25% trypsin (Thermo Fisher Scientific, Inc.) and 10 μg/ml DNase I (Sigma-Aldrich; Merck KGaA) dissolved in 5% FBS (Thermo Fisher Scientific, Inc.). Samples were manually oscillated every 5 min, and filtered twice using a 40-μm nylon mesh (Thermo Fisher Scientific, Inc.). Erythrocytes were removed using 1X Red Blood Cell Lysis Solution (Thermo Fisher Scientific, Inc.).

value: hepatocellular carcinoma

tag: Sex

value: male

value: 65 years old


title: Before gilteritinib

description: Whole genome lysate

value: untreated