title: U_PHH_4_15

data_processing:
Sequencing reads were aligned to the Homo sapiens reference genome (hg38) with TopHat (v2.1.0).
HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene.
Gene expression levels were evaluated as transcripts per million (TPM).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: SmartSeq2.ReadCount.txt: Tab-delimited text file includes read count values for each sample.
Supplementary_files_format_and_content: SmartSeq2.TPM.txt: Tab-delimited text file includes TPM values for each sample.

extract_protocol:
Single-cell RNA-seq was performed according to the Smart-seq2 protocol as reported previously (Picelli et al., 2014). After the cells were digested into a single-cell suspension, each single-cell sample was manually selected under a microscope with a mouth pipette and transferred into lysis buffer containing 1.9 µl of 0.2% Triton X-100 (Sigma), 1 µl of 10 µM oligo (dT) primer, 1 µl of 10 mM dNTP mix (New England Biolabs), 0.1 µl of 40 U/µl RNase inhibitor (New England Biolabs) and 0.05 µl of ERCC spike-in RNA (a dilution of 1:300,000, Life Technologies). After single-cell lysis, the sample was mixed with 0.29 µl H2O, 2 µl of 5× Superscript II first-strand buffer, 2 µl of 5 M Betaine (Sigma), 0.5 µl of 100 mM DTT, 0.06 µl of 1 M MgCl2, 0.1 µl of 100 µM TSO primer, 0.25 µl of 40 U/µl RNase inhibitor and 0.5 µl of 200 U/µl SuperScript II reverse transcriptase (Invitrogen). After reverse transcription was performed, 2.25 µl H2O, 12.5 µl KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 0.25 µl of 10 µM IS PCR primer were added to the sample. Then, PCR preamplification was conducted for 18 cycles. Next, cDNA samples were purified with VAHTS DNA Clean Beads XP beads (Vazyme).
Purified cDNA (2 ng) was prepared for library construction using a TruePrep DNA Library Prep Kit (Vazyme) with a 0.4× standard reaction system, and PCR amplification was conducted for 8 cycles. Finally, the library was purified and size-selected, and fragments with a peak size of ~350 bp were analyzed with an Advanced Analytical Fragment Analyzer.

tag: cell type

value: Uncultured adult human primary hepatocyte


title: RNA-seq_Gut rep1

status: Public on Apr 20 2021

type: SRA

city: Anderlecht

first: Alizee

last: Vercauteren Drubbel

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

library_source: transcriptomic

data_processing:
Paired-end reads were mapped against the mouse reference genome GRCm38 using STAR software (version 2.5.3a)
Annotations Mus_musculus.GRCm38.90.gtf were obtained from ftp.Ensembl.org
Gene level counts were obtained using HTSeq
Total raw counts were uploaded on degust 4.1.1 and analyzed using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample and genome annotations

molecule: total RNA

organism: Mus musculus

source_name: Gut

extract_protocol:
Tissues were digested, sorted in TRK lysis buffer and extracted using E.Z.N.A Total RNA Kit. RNA quality was checked before library preparation using a Bioanalyzer 2100.
Libraries were obtained using the Ovation Solo RNA-seq System (NuGen) following manufacturer's recommendations and loaded on a Novaseq 6000 (Illumina)

tag: tissue

value: Gut

tag: processed sample name

tag: raw name

tag: strain

value: mixed genetic background

tag: genotype

tag: cell sorting

value: Cells have been sorted on YFP expression


title: NN_30

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet

data_processing:
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale with the edgeR package in Bioconductor.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated files with raw gene counts and TMM-CPM-log2 normalized values respectively for each gene in each sample
Supplementary_files_format_and_content: Comma seperated file with metadata,

molecule: polyA RNA

organism: Homo sapiens

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads

tag: group

value: NN

tag: subjectid

tag: Sex

value: female

value: Ectocervix


title: NN_28


title: RNA sequencing sheep2-Skeletal-muscle biological replicate 2

city: Chengdu

first: jin

last: long

address: Hui ming

country: China

institute: Sichuan Agricultural University

description:
sheep2-Skeletal-muscle
sheep_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

organism: Ovis aries

source_name: Skeletal muscle

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Small-tail Han sheep

value: Skeletal muscle

tag: age

value: Adult


title: NN_27


title: NN_29


title: U_PHH_4_12

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

source_name: Liver

growth_protocol: Human endoderm stem cells were generated from hPSCs and maintained in serum-free conditions as described previously (Cheng et al., 2012). For the hepatocyte differentiation, the EnSCs were dissociated into a single-cell suspension with 0.25% trypsin-EDTA, and then the cells were suspended in a 500 mL spinner flask at a density of 1×10e6 cells per milliliter in 300 mL hepatic specification medium, mixed with Matrigel at the final concentration of 4%, that contained ascorbic acid (Wako), MTG (Sigma), bFGF (10 ng/ml), TGF-α (20 ng/ml), EGF (10 ng/ml), VEGF (10 ng/ml), BMP4 (50 ng/ml), HGF (25 ng/ml), dexamethasone (Dex) (40 ng/ml, Sigma), and 1% DMSO (Sigma) (from day 0 to day 6, Stage I). From day 6 to day 12 (Stage II), the medium was replaced with hepatoblast formation medium containing ascorbic acid, MTG, bFGF (10 ng/ml), HGF (25 ng/ml), EGF (20 ng/ml), VEGF (10 ng/ml), oncostatin M (OSM) (20 ng/ml), Dex (40 ng/ml), 1% DMSO, Compound E (0.1 μM, Millipore), A83-01 (0.5 μM, Selleck), and Vitamin K1 (6 g/ml, Sangon). Then, the medium was changed to maturation medium, which contained ascorbic acid, MTG, HGF (25 ng/ml), OSM (20 ng/ml, PeproTech), Dex (40 ng/ml), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and erlotinib HCl (EGFi) (2 μM, Stemgent) (from day 12 to day 24, Stage 3H). The above differentiation medium was SFD-based (Cheng et al., 2012). From day 24, the hepatic spheres were cultured in hepatocyte culture medium (HCM, Lonza) that consisted of ascorbic acid, MTG, 8 bromo-cAMP (1 mM, Biolog), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and EGFi (2 μM) (from day 24 to day 30, Stage 4H). The medium was changed every 2 days. The cells were maintained in a 5% CO2, 5% O2, 90% N2 environment (from day 0 to day 18), and then in a 5% CO2/ambient air environment (from day 18 to day 30). The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise. For the cholangiocyte differentiation, the hepatoblasts were generated from EnSCs using the method as aforementioned. After hepatoblast formation, the hepatic spheres were cultured in SFD-based cholangiocyte specification medium containing ascorbic acid, MTG, FGF10 (50 ng/ml), Activin A (50 ng/ml), and retinoic acid (3 μM, Sigma) (from day 12 to day 15, Stage 3C). Then, the medium was changed to maturation medium, which contained HGF (25 ng/ml), EGF (50 ng/ml), TGF-β (5 ng/ml, PeproTech), Dex (40 ng/ml), and TPPB (0.5 μM, Calbiochem) (from day 16 to day 21, Stage 4C). The basic medium used for this final stage was biliary differentiation medium (BDM) (Sampaziotis et al., 2015). The cells were cultured in a 5% CO2, 5% O2, 90% N2 environment. The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise.


title: RNA sequencing sheep2-Spleen biological replicate 2

description:
sheep2-Spleen
sheep_exp.txt

source_name: Spleen

value: Spleen


title: U_PHH_4_13


title: RNA sequencing sheep3-Adipose biological replicate 3

description:
sheep3-Adipose
sheep_exp.txt

source_name: Adipose

value: Adipose


title: RNA sequencing sheep2-Liver biological replicate 2

description:
sheep2-Liver
sheep_exp.txt

value: Liver


title: NN_26


title: RNA-seq_Junction rep4

source_name: Columnar part of the junction

value: Columnar part of the junction

value: Cells have been sorted on high EpCam and YFP expression


title: U_PHH_4_14


title: RNA-seq_Stomach rep2

source_name: Stomach

value: Stomach


title: U_PHH_4_17


title: U_PHH_4_11


title: RNA-seq_Stomach rep1


title: RNA sequencing sheep3-Liver biological replicate 3

description:
sheep3-Liver
sheep_exp.txt


title: RNA-seq_Junction rep3


title: U_PHH_4_16


title: U_PHH_4_10


title: RNA sequencing sheep2-Kidney biological replicate 2

description:
sheep2-Kidney
sheep_exp.txt

source_name: Kidney

value: Kidney


title: RNA-seq_Junction rep2


title: U_PHH_4_09

value: Uncultured adult human primary hepatocyte


title: RNA sequencing sheep2-Heart biological replicate 2

description:
sheep2-Heart
sheep_exp.txt

source_name: Heart

value: Heart


title: RNA-seq_Junction rep1

value: mixed genetic background


title: NN_23


title: RNA sequencing sheep2-Adipose biological replicate 2

description:
sheep2-Adipose
sheep_exp.txt


title: U_PHH_4_08


title: NN_22


title: U_PHH_4_07


title: RNA sequencing sheep1-Spleen biological replicate 1

description:
sheep1-Spleen
sheep_exp.txt


title: RNA sequencing sheep1-Skeletal-muscle biological replicate 1

description:
sheep1-Skeletal-muscle
sheep_exp.txt


title: U_PHH_4_05


title: RNA sequencing sheep1-Lung biological replicate 1

description:
sheep1-Lung
sheep_exp.txt

source_name: Lung

value: Lung


title: RNA-seq_K5SmoM2K8YFP YFP- rep3

source_name: Esophagus

value: Esophagus

value: Cells have been sorted on high expression of EpCam and without YFP expression


title: RNA-seq_K5SmoM2K8YFP YFP- rep2


title: U_PHH_4_04


title: RNA-seq_Embryo rep1

source_name: Embryonic esophagus E13.5

value: Embryonic esophagus E13.5

value: Cells have been sorted on EpCam and YFP expression


title: RNA-seq_Embryo rep2


title: U_PHH_4_06


title: RNA-seq_K5SmoM2K8YFP YFP- rep1


title: RNA sequencing sheep1-Liver biological replicate 1

description:
sheep1-Liver
sheep_exp.txt

value: Small-tail Han sheep

value: female


title: RNA sequencing sheep1-Kidney biological replicate 1

description:
sheep1-Kidney
sheep_exp.txt

value: Adult


title: U_PHH_4_03


title: NN_24

value: NN

value: Ectocervix


title: U_PHH_4_02


title: RNA sequencing sheep1-Heart biological replicate 1

description:
sheep1-Heart
sheep_exp.txt


title: NN_18


title: NN_19


title: NN_20


title: NN_21


title: NN_15


title: RNA sequencing sheep1-Adipose biological replicate 1

description:
sheep1-Adipose
sheep_exp.txt

value: Adipose


title: NN_14


title: RNA-seq_K5SmoM2K8YFP YFP+ rep1

value: Cells have been sorted on high expression of EpCam and YFP


title: NN_13


title: Input for post-stage II gametocytes_rep2

city: Pretoria

first: Jessica

middle: I

last: Connacher

address: Lynnwood road, Hatfield

country: South Africa

institute: University of Pretoria

description: Post-stage II input_2

library_source: genomic

data_processing:
Sequencing reads were trimmed using Trimmomatic (v 0.32.3)
Trimmed reads were mapped to the P. falciparum 3D7 genome (v39, obtained from PlasmoDB) using BWA-MEM (v0.4.1)
Samtools (v1.1.2) was used to remove duplicate reads
bamCoverage, bamCompare and bigwigCompare (deepTools, v3.1.2.0.0) tools were used to obtain log2-transformed ChIP/input tracks, averaged for two biological replicates for further analysis
deepTools (v3.1.2.0.0) bamCoverage and htseq-count were used to obtain read counts, with the P. falciparum 3D7 genome annotation (v39) obtained from PlasmoDB. These counts were used to calculate average log2ChIP/input values and averaged for two independent biological replicates for each population except H3K36me3 in pre-stage II gametocytes (only 1 replicate). These values were used for subsequent analysis; average log2ChIP/input values for 750 bp upstream of start sites are provided for each gene within each sample as a processed data file.
Genome_build: P. falciparum 3D7 v39
Supplementary_files_format_and_content: Processes data files: bigwig files obtained using bamCoverage, bamCompare and bigwigCompare from deepTools (v3.1.2.0.0) representing log2 -transformed ChIP/input averaged for two biological replicates for each sample (Except for H3K36me3 in pre-stage II with only 1 replicate).
Supplementary_files_format_and_content: Upstream_read_count_matrix contains average log2ChIP/input scores for 750 bp upstream of start sites for all P. falciparum genes for which sequencing data was obtained for pre-stage II, stage II and post-stage II gametocyte samples.

molecule: genomic DNA

organism: Plasmodium falciparum NF54

source_name: Post-stage II gametocytes

growth_protocol: Gametocyte cultures were generated as described previously (Reader et al., 2015, DOI: 10.1186/s12936-1015-0718-z) P. falciparum (NF54) asexual parasites [maintained in human erythrocytes (5% haematocrit) in complete culture medium (RPMI 1640 (Sigma-Aldrich) supplemented with 25 mM HEPES, 20 mM glucose, 200 μM hypoxanthine, 0.2% (w/v) sodium bicarbonate, 24 μg/ml gentamycin and 0.5% (w/v) AlbuMAX II) at 37°C and under hypoxic conditions (90% N2, 5% O2, and 5% CO2)] were synchronised (>95% ring stage parasites) using 5% D-sorbitol for two consecutive replication cycles and were then subjected to glucose starvation and a reduced haematocrit (4%) to induce gametocyte commitment. N-acetylglucosamine (50 mM) supplemented media was changed daily from day 1 of development to remove residual asexual parasites.

extract_protocol:
ChIP was performed as previously described (Josling et al., 2020, DOI: 10.1038/s41467-020-15026-0) Nuclei were isolated on day 2 (Pre-stage II gametocytes), day 7 (stage II gametocytes), or day 7 (Post-stage II gametocytes) of gametocyte development. Crosslinked nuclei were resuspended in Covaris shearing buffer (containing 0.1% SDS, 10 mM Tris pH 8.1, 1 mM EDTA) followed by sonication using a Covaris M220 ultrasonicator (sonication conditions: 5% duty cycle, 75 W peak incident power, 200 cycles per burst, time 300 s). Sonicated chromatin was  pre-cleared using Protein A/G magnetic beads (Pierce) for two hr, followed by incubation of the pre-cleared chromatin with antibodies and magnetic beads overnight. A small volume of the chromatin was treated as a mock immunoprecipitation (no antibody) to serve as input material. Anti-rabbit H3K36me2 (Abcam, ab9049) and H3K36me3 (abcam, ab9050) antibodies were used for immunoprecipitations with beads washed and bound to DNA the following day using elution buffer. Reversal of crosslinking was preformed overnight at 45°C followed by the treatment of DNA with RNase A (37°, 30 min) and Proteinase K (45°, 2hr). The DNA was purified using the Qiagen MinElute kit and quantified by Qubit HS DNA assay.
Barcoded libraries were constructed as previously described (Josling et al., 2020, DOI: 10.1038/s41467-020-15026-0) using NEBNext DNA library Prep reagents (New England Biolabs) following a standard preparation protocol for Illumina TruSeq single-end sequencing.  DNA was end-repaired (30 min, 20°C), purified (Agencourt AMPure XP beads, Beckman Coulter), dA-tailed (30 min, 37°C) and purified once more using Ampure XP beads.  Illumina DNA barcodes (NEXTflex, 1/10 dilution) were ligated to DNA fragments with T4 DNA ligase (15 min, 20°C) with DNA subsequently size selected for 250 bp inserts (Ampure XP beads) and PCR-amplified (12-15 cycles) with Kapa HiFi (Kapa biosystems).

treatment_protocol: Chromatin was cross-linked using 1% formaldehyde (10 min, 37°C) followed by 0.125 mM glycine quenching prior to extraction. Gametocytes were then isolated from host erythrocytes using 0.1% (w/v) saponin (10 min, 4°C)

tag: day of development

value: Day 7

tag: parasite/gametocyte stage

value: Stage III, Stage IV gametocytes

tag: chip antibody


title: U_PHH_4_01

value: Uncultured adult human primary hepatocyte


title: NN_11


title: U_PHH_3_24


title: U_PHH_3_25


title: RNA-seq_K5SmoM2 rep4

value: Cells have been sorted on high expression of EpCam


title: RNA-seq_K5SmoM2 rep5


title: RNA-seq_K5SmoM2 rep6


title: U_PHH_3_23


title: NN_16


title: RNA-seq_K5SmoM2K8YFP YFP+ rep3

value: mixed genetic background


title: NN_09


title: Input for post-stage II gametocytes_rep1

description: Post-stage II input_1


title: H3K36me2 in post-stage II gametoytes_rep2

description: Post-stage II_H3K36me2_2

value: anti-H3K36me2 (Abcam, ab9049)


title: NN_08


title: H3K36me3 in post-stage II gametoytes_rep2

description: Post-stage II_H3K36me3_2

value: anti-H3K36me3 (Abcam, ab9050)


title: RNA-seq_K5SmoM2 rep3

value: Esophagus


title: RNA-seq_K5SmoM2K8YFP YFP+ rep2


title: H3K36me3 in post-stage II gametoytes_rep1

description: Post-stage II_H3K36me3_1


title: NN_07


title: NN_06


title: U_PHH_3_20


title: U_PHH_3_21


title: RNA-seq_K5SmoM2 rep2


title: RNA-seq_K5SmoM2 rep1


title: U_PHH_3_22


title: RNA-seq_WT rep6

value: wild type

value: Cells have been sorted on low expression of EpCam


title: U_PHH_3_19


title: Input for stage II gametocytes_rep2

description: Stage II_input_2

source_name: Stage II gametocytes

value: Day 4

value: Stage I, Stage II gametocytes


title: H3K36me3 in stage II gametocytes_rep2

description: Stage II_H3K36me3_2


title: NN_02

value: female


title: U_PHH_3_18


title: H3K36me2 in stage II gametocytes_rep2

description: Stage II_H3K36me2_2


title: NN_03

value: NN


title: U_PHH_3_17


title: RNA-seq_WT rep4


title: H3K36me2 in post-stage II gametoytes_rep1

description: Post-stage II_H3K36me2_1


title: U_PHH_3_16


title: RNA-seq_WT rep3


title: HESN_29

value: HESN

value: Ectocervix


title: U_PHH_3_15


title: NN_01


title: HESN_28


title: RNA-seq_WT rep2


title: H3K36me3 in stage II gametocytes_rep1

description: Stage II_H3K36me3_1


title: U_PHH_3_14


title: Input for stage II gametocytes_rep1

description: Stage II_input_1


title: H3K36me2 in stage II gametocytes_rep1

description: Stage II_H3K36me2_1


title: HESN_27


title: Input for pre-stage II gametocytes_rep2

description: Pre-stage II_input_2

source_name: Pre-stage II gametocytes

value: Day 2

value: Asexual parasites, stage I gametocytes


title: NN_04


title: ATAC-seq_K5SmoM2 rep3

description: The cells have been sorted based on high EpCam expression

data_processing:
ATACseq paired-end reads of 50 bp were trimmed for adaptor sequences (using Trimmomatic).
ATAC-seq paired-end reads were then aligned to the mouse GRCm38 genome (using Bowtie2)
Mitochondrial reads and reads aligned to scaffolds and undefined chromosomes were excluded from downstream analysis.
Duplicated reads were removed by Picard tools.
Read start sites were adjusted to represent the center of the transposon binding event as described in Li et al., 2009.
Peak calling was performed on each individual sample using Macs2.
TDF files were generated using igv.
bigWig files were generated using bamCoverage from deepTools in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: TDF binary files generated using igv. BigWig indexed binary file format generated using deepTools (bin size=50pb, scaling factor=1.0), files normalized for sequencing depth.

extract_protocol:
Tissues were digested, sorted in 1ml PBS 3% FBS. Nuclei were isolated to proceed to transposase reaction (Illumina). DNA was purified using the MinElute purification kit.
DNA libraries were PCR amplified (NEBNext High-Fidelity 2x PCR Master Mix, New England Biolabs), indexed using primers described by Buenrostro et al. (2013), and double size selected (from 150 to 1200 bp) using AmpureXP magnetic beads (Beckman) following the manufacturer's recommendations. The multiplexed libraries were loaded on a NovaSeq 6000 (Illumina) using a S2 flow cell and paired-end sequences were produced using a 200 Cycle Kit.

tag: sample identification


title: RNA-seq_WT rep5


title: U_PHH_3_12


title: U_PHH_3_10


title: HESN_25


title: H3K36me2 in pre-stage II gametoytes_rep2

description: Pre-stage II_H3K36me2_2


title: U_PHH_3_11


title: ATAC-seq_K5SmoM2 rep2


title: ATAC-seq_K5SmoM2 rep1


title: HESN_26


title: HESN_24


title: Input for pre-stage II gametocytes_rep1

description: Pre-stage II_input_1


title: HESN_23


title: RNA-seq_WT rep1


title: ATAC-seq_WT rep2

description: The cells have been sorted based on low EpCam expression


title: H3K36me3 in pre-stage II gametocytes_rep1

description: Pre-stage II_H3K36me3_1


title: U_PHH_3_09


title: H3K36me2 in pre-stage II gametocytes_rep1

description: Pre-stage II_H3K36me2_1


title: G6PD overexpression(OE) in H929 cells

city: 中国江苏

first: rui

last: li

address: 138 Xianlin Road, Nanjing 210023, China

institute: Nanjing University of Chinese Medicine

description:
HGLR
AllSample.fpkm

data_processing:
The original image file obtained by Illumina novaseq is transformed into original sequenced reads by Casava base calling analysis, which we call raw data or raw reads. The results are stored in fastq file format
Remove the low quality sequence: remove more than 40% of the total reads whose base number is less than or equal to 15
Clean reads were compared to reference genome by Hisat2. Then only sequencing read to reference genome was analyzed by comparison
The mapped reads were spliced by Stringtie software, and the splicing results were compared with the original genome annotation information
Asprofile software was used to classify and count the alternative splicing events predicted by stringtie
We used sentieon to identify potential SNPs based on the comparison results of sequencing reads and reference genomes
Genome_build: We use bowtie2 to align clean reads to reference transcripts, and then use rsem to call bowtie2's alignment results for statistics, to get the number of reads on each transcripts from each sample, and carry out FPKM transformation,
Supplementary_files_format_and_content: The input data of gene differential expression analysis is expected_ Count data.

source_name: Multiple Myeloma cells

extract_protocol:
RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: overexpression


title: U_PHH_3_08

value: Uncultured adult human primary hepatocyte


title: ATAC-seq_WT rep3


title: U_PHH_3_07


title: H929 wildtype(WT) cells

description:
HWLR
AllSample.fpkm

value: wildtype


title: HESN_22


title: U_PHH_3_13


title: ATAC-seq_WT rep1


title: U_PHH_3_06


title: HESN_21


title: G6PD overexpression(OE) in ARP1 cells

description:
AGLR
AllSample.fpkm


title: HESN_20


title: Experiment 2: Ancestral E. faecalis with S. aureus, rep 5

city: Oxford

first: Kayla

middle: C

last: King

address: 11a Mansfield Road

department: Department of Zoology

country: United Kingdom

institute: University of Oxford

description:
WTCHG_687548_73845168
WTCHG_687958_73845168

data_processing:
Raw reads were checked for quality using FastQC (0.11.5).
Current (release 96) GTF and cDNA FASTA files were downloaded from the ensemble database for C. elegans (WBcel235 version of the C. elegans reference genome). A transcript index was created using kallisto and the C. elegans WBcel235 cDNA FASTA file.
Pseudoalignment was then performed using Kallisto with 100 bootstraps.
The outputs from kallisto were then analysed in sleuth, testing for treatment.
Genome_build: WBcel235
Supplementary_files_format_and_content: Kallisto output: Tab separated text file containing Kallisto abundance estimates including TPM.

organism: Caenorhabditis elegans

source_name: Ancestral E. faecalis with S. aureus

growth_protocol: Sterile and age-synchronised nematode eggs were collected using the bleach-sodium hydroxide solution. These eggs were kept in M9 buffer without food, shaking overnight at 88rpm and 20°C to further synchronise the age of each worm. These worms were then transferred to NGM plates with E. coli as food and kept at 20°C. Approximately 5000 worms were raised on each plate for two days. E. faecalis and S. aureus were then grown overnight in 6ml THB in a shaking incubator (200rpm) at 30°C. After standardising the bacterial cultures to OD600 of 1.00, either 120µl of E. faecalis, E. coli or S. aureus culture was spread onto Trypic Soy Broth (TSB) agar exposure plates for single infection treatments, whilst a mixture of 120µl S. aureus and 120µl E. faecalis was spread onto TSB plates for co-infection treatments. These plates were cultured overnight at 30°C. At this point, worms were washed 3 times in 50ml M9 buffer using gravity. Approximately 2000 young adult worms were then exposed to the bacterial lawns and were incubated at 25°C for 12h. After 12h exposure, worms were washed off each plate with M9 buffer. All samples were washed off within 10 minutes and were processed in a random order, using a random number generator. The collected worms were washed 5 times by diluting the worms in 10ml M9 buffer using gravity to settle the worms. For each replicate, approximately 1000 worms were collected in 50ul of M9 and added to 1ml Trizol in an Eppendorf tube.

extract_protocol:
For each replicate, approximately 1000 worms were collected in 50ul of M9 and added to 1ml Trizol in an Eppendorf tube. These samples were vortexed for 20 seconds and then freeze-thawed 3 times using dry ice and a heat block (40C) to break the nematode cuticle. They were subsequently stored at -80C. RNA was then extracted using Zymo spin columns, following the manufacturer’s instructions with on-column DNA digestion using DNase I. The resulting RNA was quantified by Qubit (Invitrogen) and all samples were diluted to the same final concentration.
Library preparation and sequencing were then performed by the Oxford Genomics Centre. The mRNA fraction was selected from the RNA using the polyA signal and converted to cDNA. Second strand cDNA synthesis incorporated dUTP. The cDNA was then end-repaired, A-tailed and adapter-ligated. Prior to amplification, samples underwent uridine digestion. The prepared libraries were size selected, multiplexed and quality controlled before paired end sequencing over five units of a flow cell. Sequencing was carried out using NovaSeq6000 with 150bp paired end reads.

treatment_protocol: For different treatments, different exposure plates were created: either 120µl of E. faecalis, E. coli or S. aureus culture was spread onto Trypic Soy Broth (TSB) agar exposure plates for single infection treatments, whilst a mixture of 120µl S. aureus and 120µl E. faecalis was spread onto TSB plates for co-infection treatments.

value: Adult stage

value: ~1000 C. elegans whole bodies

tag: treatment

value: Ancestral E. faecalis with S. aureus


title: U_PHH_3_05

tag: cell type


title: Experiment 2: Ancestral E. faecalis with S. aureus, rep 4

description:
WTCHG_687548_73835167
WTCHG_687958_73835167

tag: tissue


title: HESN_19

source_name: Ectocervix


title: U_PHH_3_04


title: U_PHH_3_03


title: HESN_18


title: Chondrocyte SR3335 Treated rep3

city: Hong Kong

first: Tongzhou

last: Liang

state: Hong Kong

address: 30 Ngan Ching Street

department: Department of Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

data_processing:
Illumina Casava1.8 software used for basecalling
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.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Chondrocyte SR3335 Treated

extract_protocol:
Chondrocytes were washed with PBS, and RNA was harvested using Trizol reagent. 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 the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Chondrocytes were treated with vehicle and 1μM SR3335 for 24 hours.

value: treated with SR3335 for 24 hours

value: human cartilage


title: Experiment 2: Ancestral E. faecalis with S. aureus, rep 2

description:
WTCHG_687548_73815165
WTCHG_687958_73815165


title: Experiment 2: Ancestral E. faecalis with S. aureus, rep 3

description:
WTCHG_687548_73825166
WTCHG_687958_73825166


title: Chondrocyte SR3335 Treated rep2


title: Experiment 2: Ancestral E. faecalis with S. aureus, rep 1

description:
WTCHG_687548_73805164
WTCHG_687958_73805164


title: HESN_15


title: Chondrocyte SR3335 Treated rep1


title: Chondrocyte Vehicle Treated rep3

source_name: Chondrocyte Vehicle Treated

value: treated with DMSO for 24 hours


title: U_PHH_3_01

source_name: Liver


title: HESN_14


title: U_PHH_3_02


title: U_PHH_2_29


title: HESN_13


title: U_PHH_2_28


title: HESN_12


title: Chondrocyte Vehicle Treated rep2


title: U_PHH_2_27


title: Experiment 2: Covolved E. faecalis with S. aureus, rep 5

description:
WTCHG_687548_73795163
WTCHG_687958_73795163

source_name: Covolved E. faecalis with S. aureus

value: Covolved E. faecalis with S. aureus


title: Chondrocyte Vehicle Treated rep1


title: Experiment 2: Covolved E. faecalis with S. aureus, rep 4

description:
WTCHG_687548_73125192
WTCHG_687958_73125192


title: ARP1 wildtype(WT) cells

description:
AWLR
AllSample.fpkm


title: Sort-2 av+b5neg

city: Parkville

first: Jacqueline

last: Schiesser

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

data_processing:
Sequenced reads were mapped to the whole human genome (GrCh38 assembly) with the Spliced Transcript Alignment to a Reference (STAR) software (version 2.7.3) using default parameters. Nonuniquely mapping reads and read pairs with unpaired alignments were excluded.
Read counts for each gene were determined using featureCounts as part of the Rsubread VERSION library
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human pancreatic islet

extract_protocol:
Isolated human pancreatic islets were stained with antibodies against ITGAV and ITGB5 and sorted by FACS using a BD Influx (BD Biosciences) or BD FACSAria Fusion (BD Biosciences). RNA extraction of FACS purified populations was performed using an Isolate II RNA microkit as directed by the manufacturer (Bioline, BIO-65042).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Pancreatic islet

tag: isolated population

value: ITGAV+ ITGB5neg

tag: itgav antibody

value: Mouse Biotin anti-human CD51 (ITGAV) (Biolegend, 327906)

tag: itgb5 antibody

value: Sheep anti-hIntegrin b5 -biotin (R&D systems, BAF3824)


title: Experiment 2: Covolved E. faecalis with S. aureus, rep 2

description:
WTCHG_687548_73105190
WTCHG_687958_73105190

tag: genotype


title: U_PHH_2_26


title: Experiment 2: Covolved E. faecalis with S. aureus, rep 3

description:
WTCHG_687548_73115191
WTCHG_687958_73115191


title: Experiment 2: Covolved E. faecalis with S. aureus, rep 1

description:
WTCHG_687548_73095189
WTCHG_687958_73095189


title: Sort-2 avhib5hi

value: ITGAVhi ITGB5hi


title: HESN_11

value: HESN

value: female

value: Ectocervix


title: HESN_17


title: HESN_09


title: HESN_10


title: Sort-2 avlob5lo

value: ITGAVlo ITGB5lo


title: U_PHH_2_25

value: Uncultured adult human primary hepatocyte


title: U_PHH_2_24


title: HESN_08


title: Experiment 1: Control E. coli OP50, rep 4

description:
WTCHG_687548_73075187
WTCHG_687958_73075187

source_name: Control E. coli OP50

value: Adult stage

value: Control E. coli OP50


title: Experiment 1: Control E. coli OP50, rep 3

description:
WTCHG_687548_73065186
WTCHG_687958_73065186

value: ~1000 C. elegans whole bodies


title: Sort-1 av+b5neg


title: U_PHH_2_23


title: HESN_07


title: Sort-1 avlob5lo


title: HESN_06


title: Experiment 1: Control E. coli OP50, rep 2

description:
WTCHG_687548_73055185
WTCHG_687958_73055185


title: Experiment 1: Control E. coli OP50, rep 1

description:
WTCHG_687548_73045184
WTCHG_687958_73045184


title: HESN_05


title: Experiment 1: Evolved E. faecalis, rep 5

description:
WTCHG_687548_73035183
WTCHG_687958_73035183

source_name: Evolved E. faecalis

value: Evolved E. faecalis


title: U_PHH_2_21


title: BrUseqRep3_ELOFKO30mDRB_SSPE_TagDir

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description:
genome used to map data to Hg38
processed data file: BrUseq_Averages_25to50_50to100kb-TOP3000_AND_Above100-TOP400_Combined.xlsx

data_processing:
Library strategy: BrU-seq
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).   For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.   For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.   ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5’-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC’s genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

source_name: RPE1-iCas9 ELOF1-KO

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50 µl Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5 µl Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2 µg/µl Digitonin (Promega, #G9441), and incubated at 37 °C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100 µM DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37°C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37°C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4°C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3 µg antibody (Antibodies are listed in Table S3) overnight at 4°C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65°C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer’s protocol. Up to 5 × 106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl™ RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions, and sequenced in a single lane on an Illumina HiSeq4000.

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample.

tag: cell line

tag: uv-c dose

value: mock

tag: time after uv-c

value: not applicable

tag: pre-treatment

value: 1h pretreatment with 10 uM DRB, followed by 30 min labeling with 2mM BrU

tag: molecule subtype

value: nascent RNA (BrU-seq)


title: BrUseqRep3_WT30mDRB_SSPE_TagDir

source_name: RPE1-iCas9 WT

value: WT

value: 1h pretreatment with 100 uM DRB, followed by 30 min labeling with 2mM BrU


title: Experiment 1: Control E. coli OP50, rep 5

description:
WTCHG_687548_73085188
WTCHG_687958_73085188

tag: age


title: U_PHH_2_20


title: HESN_03

tag: group

tag: subjectid

tag: Sex


title: Experiment 1: Evolved E. faecalis, rep 3

description:
WTCHG_687548_73015181
WTCHG_687958_73015181


title: BrUseqRep3_ELOFKO8h_SSPE_TagDir

value: 8 hours

value: directly prior to harvest, treatment with 2mM BrU for 30 min


title: U_PHH_2_19


title: Sort-1 avhib5hi

value: Pancreatic islet

value: ITGAVhi ITGB5hi

value: Mouse Biotin anti-human CD51 (ITGAV) (Biolegend, 327906)

value: Sheep anti-hIntegrin b5 -biotin (R&D systems, BAF3824)


title: HESN_01

value: HESN

value: female

value: Ectocervix


title: U_PHH_2_22

value: Uncultured adult human primary hepatocyte


title: Experiment 1: Evolved E. faecalis, rep 1

description:
WTCHG_687548_72995179
WTCHG_687958_72995179

value: Adult stage

value: ~1000 C. elegans whole bodies

value: Evolved E. faecalis


title: U_PHH_2_17


title: BrUseqRep3_ELOFKO3h_SSPE_TagDir

value: 3 hours


title: BrUseqRep3_ELOFKO0h_SSPE_TagDir

value: mock

value: not applicable

value: nascent RNA (BrU-seq)


title: U_PHH_2_16


title: U_PHH_2_15


title: Peripheral neutrophils healthy donor3

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

country: Italy

institute: Humanitas research

description:
Sorted neutrophil from healthy peripheral blood
Lib_CGA-33_S3

data_processing:
Demultiplexing with “bcl2fastq2”  Software (version 2.19.0)
Alignment with STAR (version 2.6.1)
Gene summarized counts were processed in R (version 3.5.2).Genes whose expression was major than 2 reads were filtered and vst normalized with the R package DESeq2 (version 1.22.2).
Genome_build: GRCh38 genome guided by GENCODE annotation (version 33)

source_name: Peripheral blood

extract_protocol:
Neutrophils were isolated from whole blood by negative selection using MACSxpress whole blood neutrophils isolation kit (Miltenyi Biotec). Purity of neutrophils was > 97.9
RNA was purified with the Direct-zol RNA Microprep or Miniprep Kit (Zymosan), according to manufacturer’s instructions. RNA quality control was performed with the 4200 Tape Station system (Agilent). Total-RNA-sequencing library preparation was performed starting from 1 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara). Libraries obtained were qualitatively assessed by using TapeStation 4200 (Agilent) and quantified by Qubit Fluorimeter (Thermofisher). Afterwards, they were multiplexed in equimolar pools and sequenced on a NextSeq-550 Illumina Platform generating at least 80 million 75bp-PE reads per sample

treatment_protocol: Untreated neutrophils from healthy peripheral blood

tag: gender

value: M


title: Experiment 1: Ancestral E. faecalis, rep 5

description:
WTCHG_687548_72985178
WTCHG_687958_72985178

source_name: Ancestral E. faecalis

tag: treatment

value: Ancestral E. faecalis


title: BrUseqRep3_WT24h_SSPE_TagDir

value: WT

value: 24 hours

value: directly prior to harvest, treatment with 2mM BrU for 30 min


title: Experiment 1: Ancestral E. faecalis, rep 4

description:
WTCHG_687548_72975177
WTCHG_687958_72975177


title: HESN_04


title: Experiment 1: Evolved E. faecalis, rep 4

description:
WTCHG_687548_73025182
WTCHG_687958_73025182


title: BrUseqRep3_ELOFKO24h_SSPE_TagDir


title: HESN_02


title: U_PHH_2_18

tag: cell type


title: Experiment 1: Ancestral E. faecalis, rep 3

description:
WTCHG_687548_72965176
WTCHG_687958_72965176

tag: tissue


title: BrUseqRep3_WT8h_SSPE_TagDir

value: 8 hours


title: BrUseqRep3_WT3h_SSPE_TagDir


title: U_PHH_2_13


title: U_PHH_2_14


title: Experiment 1: Evolved E. faecalis, rep 2

description:
WTCHG_687548_73005180
WTCHG_687958_73005180


title: RNA sequencing Dog3-Spleen biological replicate 3

description:
Dog3-Spleen
dog_exp.txt

organism: Canis lupus familiaris

source_name: Spleen

tag: breed

value: Beagle dog

value: Spleen

value: Adult


title: RNA sequencing Dog3-Skeletal-muscle biological replicate 3

description:
Dog3-Skeletal-muscle
dog_exp.txt

source_name: Skeletal muscle

value: Skeletal muscle

value: female


title: BrUseqRep3_WT0h_SSPE_TagDir


title: Experiment 1: Ancestral E. faecalis, rep 2

description:
WTCHG_687548_72955175
WTCHG_687958_72955175

value: Adult stage

value: ~1000 C. elegans whole bodies


title: Experiment 1: Ancestral E. faecalis, rep 1

description:
WTCHG_687548_72945174
WTCHG_687958_72945174


title: RNA sequencing Dog3-Lung biological replicate 3

description:
Dog3-Lung
dog_exp.txt

source_name: Lung

value: Lung


title: U_PHH_2_12

value: Uncultured adult human primary hepatocyte


title: U_PHH_2_11


title: Experiment 1: Coevolved E. faecalis, rep 5

description:
WTCHG_687548_72935173
WTCHG_687958_72935173

source_name: Coevolved E. faecalis

value: Coevolved E. faecalis


title: Peripheral neutrophils healthy donor2

description:
Sorted neutrophil from healthy peripheral blood
Lib_CGA-32_S2


title: RNA sequencing Dog3-Liver biological replicate 3

description:
Dog3-Liver
dog_exp.txt

value: Liver


title: Experiment 1: Coevolved E. faecalis, rep 4

description:
WTCHG_687548_72925172
WTCHG_687958_72925172


title: BrUseqRep4_ELOFKO30mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-4_CTGAAGCT-TAAGATTA_S210
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx

data_processing:
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).
For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.
For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.
ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5'-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC's genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50  l Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5  l Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2  g/ l Digitonin (Promega, #G9441), and incubated at 37  C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100  M DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37 C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37 C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4 C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3  g antibody (Antibodies are listed in Table S3) overnight at 4 C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. Up to 5   106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl(tm) RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's instructions, and sequenced in a single lane on an Illumina HiSeq4000.

value: mock

value: not applicable

value: 3h pretreatment with DRB, followed by 30 min labeling with 2mM BrU

value: nascent RNA (BrU-seq)


title: U_PHH_2_09


title: BrUseqRep5_ELOFKO60mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-6_CGGCTATG-GTCAGTAC_S212
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx


title: Peripheral neutrophils healthy donor1

description:
Sorted neutrophil from healthy peripheral blood
Lib_CGA-31_S1

value: F


title: RNA sequencing Dog3-Kidney biological replicate 3

description:
Dog3-Kidney
dog_exp.txt

source_name: Kidney

value: Kidney


title: Experiment 1: Coevolved E. faecalis, rep 3

description:
WTCHG_687548_72915171
WTCHG_687958_72915171


title: BrUseqRep5_WT60mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-5_TAATGCGC-ACGTCCTG_S211
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx

value: WT

value: 3h pretreatment with DRB, followed by 30 min DRB release, followed by 30 min labeling with 2mM BrU


title: RNA sequencing Dog3-Adipose biological replicate 3

description:
Dog3-Adipose
dog_exp.txt

source_name: Adipose

value: Beagle dog

value: Adipose

value: Adult


title: BrUseqRep4_WT30mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-2_ATTCAGAA-TCAGAGCC_S208
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx


title: BrUseqRep4_ELOFKO60mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-3_GAATTCGT-CTTCGCCT_S209
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx


title: RNA sequencing Dog3-Heart biological replicate 3

description:
Dog3-Heart
dog_exp.txt

source_name: Heart

value: Heart

value: female


title: U_PHH_2_08


title: Experiment 1: Coevolved E. faecalis, rep 2

description:
WTCHG_687548_72905170
WTCHG_687958_72905170

value: Adult stage

value: ~1000 C. elegans whole bodies


title: U_PHH_2_07

value: Uncultured adult human primary hepatocyte


title: Experiment 1: Coevolved E. faecalis, rep 1

description:
WTCHG_687548_72895169
WTCHG_687958_72895169

value: Coevolved E. faecalis


title: U_PHH_2_05


title: U_PHH_2_10


title: BrUseqRep4_WT60mDRB_SSPE_TagDir

description:
genome used to map data to Hg38
2048-MP-1_GAGATTCC-AGGATAGG_S206
processed data file: Metageneprofile_BrUseq_Mock_WT-ELOFKO_Combined_20210106.xlsx

value: mock


title: U_PHH_2_06


title: RNA sequencing Dog2-Spleen biological replicate 2

description:
Dog2-Spleen
dog_exp.txt

value: Spleen


title: U_PHH_2_04


title: SE_5

city: Jinan, Shandong

first: Wenyan

last: Kang

address: No. 44-1 Wenhua Road West

institute: Shandong university

data_processing:
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Genome_build: hg38

source_name: human periodontal ligament tissue

growth_protocol: Cells were cultured with 6-well plates at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated, evaluated the quality, reverse-transcribed to cDNA,
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

treatment_protocol: Cells were treated  with Ex-4, SDF-1 and Ex-4+SDF-1 and culured at 21d in the presence of osteogenic medium

value: human periodontal ligament stem cells

tag: donor

value: donor 5

tag: culture time


title: S_5


title: Experiment 2:  S. aureus, rep 5

description:
WTCHG_687548_70195283
WTCHG_687958_70195283

source_name: S. aureus

tag: genotype

value: S. aureus


title: RNA sequencing Dog2-Skeletal-muscle biological replicate 2

description:
Dog2-Skeletal-muscle
dog_exp.txt

value: Skeletal muscle


title: Experiment 2:  S. aureus, rep 4

description:
WTCHG_687548_70185282
WTCHG_687958_70185282


title: U_PHH_2_03

source_name: Liver


title: E_5


title: Experiment 2:  S. aureus, rep 3

description:
WTCHG_687548_70175281
WTCHG_687958_70175281


title: RNA sequencing Dog2-Liver biological replicate 2

description:
Dog2-Liver
dog_exp.txt

value: Liver


title: U_PHH_2_02


title: Experiment 2:  S. aureus, rep 2

description:
WTCHG_687548_70165280
WTCHG_687958_70165280


title: RNA sequencing Dog2-Kidney biological replicate 2

description:
Dog2-Kidney
dog_exp.txt

value: Kidney


title: U_PHH_2_01


title: NC_5


title: Experiment 2:  S. aureus, rep 1

description:
WTCHG_687548_70155279
WTCHG_687958_70155279


title: SE_4

value: donor 4


title: RNA sequencing Dog2-Heart biological replicate 2

description:
Dog2-Heart
dog_exp.txt

value: Beagle dog


title: U_PHH_1_06


title: S_4


title: RNA sequencing Dog2-Adipose biological replicate 2

description:
Dog2-Adipose
dog_exp.txt

value: Adipose

value: Adult


title: Experiment 2: Control E. coli OP50, rep 5

description:
WTCHG_687548_70145278
WTCHG_687958_70145278

value: Control E. coli OP50


title: RNA sequencing Dog1-Spleen biological replicate 1

description:
Dog1-Spleen
dog_exp.txt

value: female


title: U_PHH_1_05


title: E_4


title: NC_4


title: Experiment 2: Control E. coli OP50, rep 2

description:
WTCHG_687548_70115275
WTCHG_687958_70115275

value: Adult stage

value: ~1000 C. elegans whole bodies


title: SE_3

value: donor 3


title: RNA sequencing Dog1-Skeletal-muscle biological replicate 1

description:
Dog1-Skeletal-muscle
dog_exp.txt


title: U_PHH_1_04

value: Uncultured adult human primary hepatocyte


title: RNA sequencing Dog1-Lung biological replicate 1

description:
Dog1-Lung
dog_exp.txt

value: Lung


title: RNA sequencing Dog2-Lung biological replicate 2

description:
Dog2-Lung
dog_exp.txt


title: Experiment 2: Control E. coli OP50, rep 3

description:
WTCHG_687548_70125276
WTCHG_687958_70125276


title: Experiment 2: Control E. coli OP50, rep 1

description:
WTCHG_687548_70105274
WTCHG_687958_70105274


title: S_3

value: human periodontal ligament stem cells


title: U_PHH_1_03


title: Experiment 2: Evolved E. faecalis with S. aureus, rep 5

description:
WTCHG_687548_70095273
WTCHG_687958_70095273

source_name: Evolved E. faecalis with S. aureus

value: Evolved E. faecalis with S. aureus


title: U_PHH_1_02


title: RNA sequencing Dog1-Liver biological replicate 1

description:
Dog1-Liver
dog_exp.txt


title: E_3


title: RNA sequencing Dog1-Kidney biological replicate 1

description:
Dog1-Kidney
dog_exp.txt


title: Experiment 2: Evolved E. faecalis with S. aureus, rep 4

description:
WTCHG_687548_70085272
WTCHG_687958_70085272


title: NC_3


title: Experiment 2: Control E. coli OP50, rep 4

description:
WTCHG_687548_70135277
WTCHG_687958_70135277

source_name: Control E. coli OP50


title: RNA sequencing Dog1-Heart biological replicate 1

description:
Dog1-Heart
dog_exp.txt

value: Heart


title: Hi-C data of Pig replicate 6 sequenced by NovaSeq-6000

data_processing:
Basecalls performed using CASAVA version 1.4
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Juicer
TADs were identified using DomainCaller
Genome_build: Rnor_6.0, OryCun2.0, Sscrofa11.1, Oar_v3.1, Felis_catus_6.2 and CanFam3.1
Supplementary_files_format_and_content: valid read pairs text files
Supplementary_files_format_and_content: binned raw and normalized 2D contact matrices text files
Supplementary_files_format_and_content: TAD text files

organism: Sus scrofa

source_name: Adipose tissue

extract_protocol:
1 g adipose tissue were pulverized, and 37% formaldehyde was added to obtain a final concentration of 4% for chromatin cross-linking. Mixture were incubated at room temperature (20–25℃) for 30 minutes, then glycine was added to obtain a final concentration of 0.25 mol/L to quench the formaldehyde. The mixture was then centrifuge at 1,500×g for 10 min at room temperature, and sediment was added the lysis buffer and homogenized. Homogenate was centrifuge at 5,000×g for adipocytes sediment. Nuclei of formaldehyde-fixed adipose tissue were permeabilized and DNA was digested with 200 units of MboI (a 4-cutter restriction enzyme) for one hour at 37 ℃. The restriction fragment overhangs were filled and labbled by biotinylated nucleotides, then ligated in a small volume.
After crosslink reversal, ligated DNA was purified and sheared to a length of 300–500 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina NovaSeq 6000 sequencing.

value: Bama

value: Back fat/Upper layer of backfat

tag: developmental stage


title: Experiment 2: Evolved E. faecalis with S. aureus, rep 3

description:
WTCHG_687548_70075271
WTCHG_687958_70075271


title: Hi-C data of Pig replicate 5 sequenced by NovaSeq-6000


title: SE_2

value: donor 2


title: RNA sequencing Dog1-Adipose biological replicate 1

description:
Dog1-Adipose
dog_exp.txt


title: Experiment 2: Evolved E. faecalis with S. aureus, rep 2

description:
WTCHG_687548_70065270
WTCHG_687958_70065270


title: S_2


title: Hi-C data of Pig replicate 4 sequenced by NovaSeq-6000


title: Experiment 2: Evolved E. faecalis with S. aureus, rep 1

description:
WTCHG_687548_70055269
WTCHG_687958_70055269


title: Hi-C data of Rabbit replicate 2 sequenced by NovaSeq-6000

organism: Oryctolagus cuniculus

value: Japanese big-ear white rabbit

value: Back fat


title: E_2


title: Hi-C data of Pig replicate 2 sequenced by NovaSeq-6000


title: NC_2


title: Hi-C data of Pig replicate 3 sequenced by NovaSeq-6000


title: Hi-C data of Pig replicate 1 sequenced by NovaSeq-6000


title: Hi-C data of Rabbit replicate 1 sequenced by NovaSeq-6000


title: U_PHH_1_01


title: S_1

value: donor 1


title: SE_1


title: CB1-YDJ-1

first: Bo

last: Zeng

state: Sichuan

address: 211 Huimin road, Wenjiang district

description: Spatial transcriptome data of Psoas muscle sample from Landrace pig

data_processing:
Library strategy: Spatial transcriptomic sequencing
Sample demultiplexing, image alignment, barcode processing, and gene counting were performed by using Space Ranger (version 1.1) according to the 10× GENOMICS Spatial Gene Expression analysis pipelines (https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome).
Annotation information of MYH2 and MYH4 genes (from old Sscrofa11.1 release-90, representative gene of muscle fiber type IIA and IIB) were added in the GTF file, because of annotation information of MYH2 and MYH4 genes are lacking in ensembl release-100.
We used the "spaceranger counts" command for reads mapping and gene counting. The H&E stained photos of tissue sections, slide serials and capture area information of each sequencing sample were provided in this counting step for automatic fiducial alignment and tissue detection.
The Loupe Browser software (10X) was used to quickly visualize the spatial results. We evaluated the biological reliability of all spots in each sample and unreliable spots were filter out by using the Manual Alignment function
Genome_build: ensembl-Sscrofa11.1-release100
Supplementary_files_format_and_content: H5 Matrix table with clean gene counts for every gene and every spots

source_name: Psoas Major

extract_protocol:
RNA capture: The tissue sections on Visium Spatial slide were permeabilized according to the protocol provided by 10x Genomics
Fragmented and barcoded porcine RNA were used as the carrier material. The spike-in constituted around 25% of the libraries. ST cDNA libraries were diluted to 4nM and sequenced on the Illumina NovaSeq 6000 platform using paired-end sequencing. Sequenced at a mean depth of 50 million paired-end reads depth which resulted in an average library saturation at above 90%.

treatment_protocol: The representative oxidative slow psoas major muscle (PM) were collected from two pigs for ST experiments. Fresh porcine PM tissue were cut into about 6.5mm*6.5mm*1cm size and snap-frozen in liquid nitrogen to avoid crystal formation. Then tissue samples were embedded in Optimal Cutting Temperature (OCT) and stored at -80℃. For ST analysis, the samples were sectioned on a cryostat at a thickness of 15μm and place the section within a capture area on the Visium Spatial slide.

value: Landrace

value: muscle

value: Chengdu, China

tag: reference assembly


title: CB1-YDJ-2

value: female


title: E_1


title: C4

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

country: USA

institute: OSU

data_processing:
Basecalling is performed using CASAVA 1.X version
Sequencing reads were aligned to the canine reference genome CamFam3.1 using Bowtie2 v2.2.4 (PMID: 22388286) with “-t -k 1 -p 8 --very-sensitive --no-discordant --no-mixed --reorder -X 2000”
Broad peak calls were generated using Macs2 with “--format BAMPE -g hs -B --broad --nomodel --shift -100 --extsize 200” parameters and p-value cutoff of 10-5 (PMID: 18798982).
Spearman correlation of read counts per 10 kilobase was generated using deepTools multiBamSummary and plotCorrelation functions, and outlier samples were eliminated
An absolute fold change of 2 and FDR cutoff of 10% were used to identify chromatic regions of differential accessibility
Genome_build: canFam3.1
Supplementary_files_format_and_content: peak txt files
Supplementary_files_format_and_content: Bigwig files were generated using deepTools bamCoverage function with “--binSize 20 --smoothLength 60 --normalizeUsing CPM --ignoreForNormalization chrX chrM” parameters

source_name: lymph node

growth_protocol: Cell lines were cultured in complete RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine (Invitrogen, Carlsbad, CA), 100 units/ml of penicillin and streptomycin (Gibco), and cultured at 37°C in 5% CO2.

extract_protocol:
Genomic DNA was isolated from cellular nuclei.
Genomic DNA was immediately resuspended in transposase reaction mix using the Nextera DNA Library Prep Kit (Illumina, San Diego, CA) followed by purification with the Qiagen Minlute Kit. Tagmented DNA was amplified  and index using the Nextera Index Kit (Illumina) followed by an additional purification step with the Qiagen MinElute Kit as described elsewhere.

treatment_protocol: Cell lines CLBL-1 and 17-71 were treated with 100 nM of PR220, a selective protein arginine methyltransferase (PRMT5) inhibitor. Cell line CLBL-1 was collected at day 2 and cell line 17-71 was collected at day 4, according to cell line sensitivity and biomarker analysis of global protein symmetric di-methylation and H4R3me2s.

tag: cell line

tag: agent

value: 100 nM of PR220

value: B-cell Lymphoma


title: Hi-C data of Dog replicate 2 sequenced by NovaSeq-6000

value: Beagle dog

value: Adult


title: Hi-C data of Sheep replicate 2 sequenced by NovaSeq-6000

value: Small-tail Han sheep

value: Abdominal subcutaneous adipose


title: C3

value: Control


title: Hi-C data of Human replicate 3 sequenced by NovaSeq-6000

data_processing:
Basecalls performed using CASAVA version 1.4
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Juicer
TADs were identified using DomainCaller
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: valid read pairs text files
Supplementary_files_format_and_content: binned raw and normalized 2D contact matrices text files
Supplementary_files_format_and_content: TAD text files

value: Asian

value: male


title: Hi-C data of Dog replicate 1 sequenced by NovaSeq-6000


title: NC_1

value: human periodontal ligament stem cells


title: C6


title: Cx43_icKO_acute

type: RNA

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

country: Japan

institute: Kyushu University

description: Cx43 icKO sample from peak phase

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: Cx43 icKO, peak phase

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: brain

value: Cx43 icKO

tag: Stage

value: peak phase


title: Cx43_icKO_onset

description: Cx43 icKO sample from onset phase

source_name: Cx43 icKO, onset phase

value: onset phase


title: C2


title: Hi-C data of Sheep replicate 1 sequenced by NovaSeq-6000

tag: age


title: at-leaf.h3.wt.replicate3

city: Uppsala

first: Juan

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

description: Arabidopsis thaliana leaf of wt (Columbia-0)

data_processing:
Bisulfite-seq: The 150 bp long pair-end reads were first quality trimmed by removing the first 5 bases from the 5' end and the last 20 bases from the 3' end. Reads were mapped to the TAIR10 reference genome using Bismark (Version: v0.16.3) in PE mode (--score_min L,0,-0.6). Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor.
ChIP-seq: Reads passing a quality control were mapped to the Arabidopsis (TAIR10) genome using Bowtie (Langmead, 2010) in single-end mode allowing for up to two mismatches. Mapped reads were deduplicated and extended to the estimated average length of the genomic fragments (270 bp). Coverage was estimated and normalized to 10 million of reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: ChIP-seq: BedGraph files representing average values of Read per Ten Million Mapped reads for each 50 bp across the genome. Format:  <chromosme><bin_start><bin_end><read_per_ten_million>

organism: Arabidopsis thaliana

source_name: AT leaf wt

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 days and grown under long day conditions.

extract_protocol:
ChIP was performed as previously described (Moreno-Romero, Jiang et al. 2016)
Libraries were generated using the Ovation Ultralow Library System (NuGEN, San Carlos, USA)

treatment_protocol: no treatment

value: leaf

value: wt (Col-0)


title: B6


title: Hi-C data of Human replicate 2 sequenced by NovaSeq-6000


title: Hi-C data of Human replicate 1 sequenced by NovaSeq-6000


title: Cx43_icKO_pre

description: Cx43 icKO sample from pre-immunized stage

source_name: Cx43 icKO, pre-immunized stage

value: pre-immunized stage


title: C5

value: 100 nM of PR220


title: at-leaf.h3.wt.replicate2


title: B4

value: B-cell Lymphoma


title: BrUseqRep2_ELOFKO24h_SSPE_TagDir

description:
nascent RNA (BrU-seq)
genome used for mapping:
Hg38

source_name: RPE1-iCas9 ELOF1-KO

tag: uv-c dose

tag: time after uv-c

value: 24 hours

tag: pre-treatment

value: directly prior to harvest, treatment with 2mM BrU for 30 min

tag: chip-antibody

value: not applicable

tag: molecule subtype

value: nascent RNA (BrU-seq)


title: Hi-C data of Sheep replicate 3 sequenced by NovaSeq-6000

value: Small-tail Han sheep

tag: tissue

value: Abdominal subcutaneous adipose

value: Adult

tag: Sex

value: female


title: at-leaf.h3.wt.replicate1


title: RS_HS_MDAMB231_CTL

city: Xiamen

first: Zhicheng

last: Gong

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: breast cancer

growth_protocol: cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Cells were lyzed by trizol.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd  Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of NEBNext rRNA Depletion Kit (NEB E6310). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (NEB, E7760), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-Ten at Amogene (Xiamen, China) Biotech Co., Ltd following the vendor's recommended protocol.

treatment_protocol: Cells were infected with indicated lentivirus

tag: treatment

value: shCtrl


title: RS_HS_MDAMB231_LSD1_KD


title: Cx43_f_f_acute

description: Control sample from peak phase

source_name: Control, peak phase

value: brain

value: Control


title: RS_HS_MDAMB231_OTUD7B_KD


title: Cx43_f_f_pre

description: Control sample from pre-immunized stage

source_name: Control, pre-immunized stage


title: B3


title: Cx43_f_f_onset

description: Control sample from onset phase

source_name: Control, onset phase

value: onset phase


title: ChIP-seq_H3K4me2_OTUD7B KD

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1 with the default options.
The bigwig files were generated by using HOMER, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Briefly, cells were fixed with 1% formaldehyde (Sigma) for 10 min at room temperature (RT) (for H3Kme2 and H3K9me2 ChIP), or fixed with DSG (2 × 10−3 m) (Proteochem) for 45 min at RT (for LSD1 ChIP), and washed twice with PBS. Fixation was stopped by adding glycine (0.125 m) and incubated for 5 min at RT, followed by washing with PBS twice. Cells were then lysed using cell lysis buffer (50 × 10−3 m Tris‐HCl pH = 8.0, 0.5% NP40 and 50 × 10−3 m NaCl) to remove the cytosol proteins. The pellet was resuspended in 1% SDS lysis buffer (for H3K4me2 or H3K9me2 ChIP) or nuclear lysis buffer (1% Triton X‐100, 2 × 10−3 m EDTA pH = 8.0, 400 × 10−3 m NaCl, 20 × 10−3 m Tris‐HCl pH = 7.8, and 0.1% SDS) (for LSD1 ChIP). Chromatin DNA was sheared to 300–500 bp average in size through sonication. The lysates were immunoprecipitated with control IgG or the indicated specific antibodies overnight at 4 °C, followed by incubation with protein G magnetic beads (Invitrogen) for 4 h. After washing and elution, the protein–DNA complex was reversed by heating overnight at 65 °C. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to high‐throughput sequencing.
The libraries were constructed following Illumina/NEB’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

tag: chip antibody

value: anti-H3K4me2 (Millipore, Cat# 07-030)


title: ChIP-seq_LSD1_OTUD7B KD

value: anti-LSD1 (Bethyl, Cat# A300-215A)


title: ChIP-seq_H3K4me2_Ctrl

value: sgCtrl


title: RIP-input

city: jinan

first: Shourong

last: Wang

address: 44 Wenhua Xi Road

institute: Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36)
the clean reads underwent rRNA deleting through RNAcentralto get effective reads
Genomic alignment (version from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads
RIPseekre(version 1.18.0) was employed to perform peak calling,then Hommer(version:4.8) to annotate the peaks
Genome_build: hg19
Supplementary_files_format_and_content: peak text file

extract_protocol:
Cells were lysed and protein-RNA complexes were isolated with antibody.
Antibody immunoprecipitation RNA was quality control with QubitTM (Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, 100ng RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA).

tag: cell type

value: serous ovarian cancer cell line

tag: genotype/variation


title: B2

value: B-cell Lymphoma


title: RIP-Flag-USP39

tag: antibody


title: at-leaf.h3k9me2.wt.replicate3

value: leaf

tag: genotype

value: wt (Col-0)


title: BrUseqRep2_ELOFKO8h_SSPE_TagDir

tag: cell line

value: 8 hours

value: directly prior to harvest, treatment with 2mM BrU for 30 min

value: not applicable


title: BrUseqRep2_ELOFKO3h_SSPE_TagDir

value: 3 hours

value: nascent RNA (BrU-seq)


title: at-leaf.h3k9me2.wt.replicate1


title: B1

tag: agent


title: BrUseqRep2_ELOFKO0h_SSPE_TagDir

value: mock


title: ChIP-seq_LSD1_Ctrl


title: A2780-shUSP39#3

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were filtered to obtain clean reads after removal of reads containing adapter and at low quality
High-quality reads were mapped to the human reference genome hg19 using HISAT2 software
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

tag: transfection method

value: lenti-virus


title: BrUseqRep2_WT24h_SSPE_TagDir

source_name: RPE1-iCas9 WT

value: WT

tag: uv-c dose

value: 24 hours


title: BrUseqRep2_WT8h_SSPE_TagDir

tag: time after uv-c


title: BrUseqRep2_WT3h_SSPE_TagDir

tag: pre-treatment


title: A2780-shUSP39#2


title: lzJ

first: Haiming

last: Huang

address: No. 8, Xishiku St., Xicheng Dist.

institute: Peking University First Hospital

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
The result of alignment with the reference genome was stored in a binary file, called a bam file. Using the Stringtie software to assemble the reads, the new transcript was spliced. Then the candidate lncRNA transcripts were selected by comparing the gene annotation information of the reference sequence produced by Cuffcompare software. Finally, transcripts with coding potential were screened out by CPC , CNCI, Pfam and PLEK to obtain lncRNA predicted sequences. Aligning the sequencing reads of each sample with the sequence of mRNA transcript sequences, known lncRNA sequences and lncRNA prediction sequences by bowtie2,  and using eXpress to make gene quantitative analysis, the FPKM value and counts value(the number of reads for each gene in each sample) were obtained.
Using the estimateSizeFactors function of the DESeq (2012) R package to normalize the counts, and using nbinomTest function to calculate pvalue and flodchange values for the difference comparison. Selecting differential transcripts with p-values <= 0.05 and flodchange >= 2，and analysising differential mRNA GO and KEGG enrichment by Hypergeometric Distribution Test.
Genome_build: GRCH38
Supplementary_files_format_and_content: FPKM for every gene and every sample

source_name: bladder cancer

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp/125bp paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: deep infiltrating tumor region

tag: tumor stage


title: yjxB

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt

value: superficial tumor region


title: yjxJ

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt


title: BrUseqRep2_WT0h_SSPE_TagDir

tag: chip-antibody

tag: molecule subtype


title: lzB

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt

tag: tissue


title: BrUseqRep2_ELOFKO30m_SSPE_TagDir

value: 1h pretreatment with DRB, followed by 30 min labeling with 2mM BrU


title: at-leaf.h3k9me2.wt.replicate2


title: 03_Kidney-33

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

description: in vitro kidney differentiation derived from human IPSC

hyb_protocol: WT plus Affymetrix chemistry

scan_protocol: scan of Clariom S human slide on affymetrix microarray station

data_processing: RMA normalization TAC 4.0 software

label: biotin

source_name: kidney derived IPSC

label_protocol: WT plus Affymetrix chemistry

growth_protocol: in vitro kidney differentiation starting from human IPSC

extract_protocol: total RNA was extract from the cell culture and a quantity of 100 ng was investigated to start microarray probe synthesis

treatment_protocol: with or without kidney differentiation

value: kidney derived IPSC


title: A2780-pGIPZ-nc#2

value: serous ovarian cancer cell line

value: pGIPZ-NC


title: RNA-seq data of Human replicate 3 sequenced by HiSeq X-ten

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: genes expression level (TPM) text file

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform.

tag: ethinicity

value: Asian

value: Abdominal subcutaneous adipose

tag: age

tag: developmental stage

value: Adult

tag: Sex

value: male


title: BrUseqRep2_ELOFKO15m_SSPE_TagDir

value: not applicable

value: 1h pretreatment with DRB, followed by 15 min labeling with 2mM BrU


title: Athaliana_ATAF2ox-3-1 (replicate 1)

city: Pullman

first: Hao

last: Peng

state: WA

department: Crop and Soil Sciences

institute: Washington State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2/2.1.0 was used to build reference from Arabdopsis genome Athaliana_447_TAIR10.fa and map the RNASeq reads with parameters --dta -x -q
The sam files generated were conveted to bam files by Samtools/1.9.
Athaliana_447_Araport11.gene.gtf was used for transcript assembly and quantification with StringTie/2.1.4.
Differential expression analysis was performed using Ballgown.
Genome_build: Athaliana_447_TAIR10.fa
Supplementary_files_format_and_content: gtf files with transcript assembly and quantification information.
Athaliana_stringtie_merged.gtf (Merged)

source_name: Four-day old seedlings

growth_protocol: Arabidopsis seeds were plated on half-strength MS media, put in the dark cold room for four days (stratification), and grew on 10uE white light for four days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Kit (Qiagen). The DNase I Digestion Set (Sigma) was used for on-column elimination of genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: Stage

value: Seedling

value: Four days

value: Whole plant

value: ATAF2 overexpression line


title: Athaliana_ATAF2ox-3-3 (replicate 3)

tag: genotype


title: 01-PB33-1

description: human IPSC

source_name: IPSC

tag: cell type

value: IPSC


title: RNA-seq data of Human replicate 2 sequenced by HiSeq X-ten

city: Chengdu

source_name: Adipose tissue


title: A2780-pGIPZ-nc#3

tag: cell line

value: lenti-virus


title: 02-PB33-2

description: human IPSC


title: lxdB

city: Beijing

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt

value: superficial tumor region


title: Athaliana_ATAF2ox-3-2 (replicate 2)


title: A2780-shUSP39#1

tag: transfection


title: lxdJ

description:
lncRNA_FPKM.txt
mRNA_FPKM.txt

value: deep infiltrating tumor region


title: BrUseqRep2_WT30m_SSPE_TagDir

value: WT

value: mock

value: 1h pretreatment with DRB, followed by 30 min labeling with 2mM BrU

value: nascent RNA (BrU-seq)


title: RNA sequencing Mouse-Spleen biological replicate 1

description:
Mouse-Spleen
mouse_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

source_name: Spleen

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Spleen

value: female


title: Athaliana_ataf2-2-1 (replicate 1)

value: ATAF2 knockout line


title: 04_Kidney-33

value: kidney derived IPSC