title: ZCCgCN3 miRNA-seq

data_processing:
miRNA-Seq: Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
miRNA-Seq: Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
miRNA-Seq: The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
miRNA-Seq: The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
miRNA-Seq: The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: http://tpia.teaplant.org/web/Download/Genomic_data/Teaplant_CSS_Genome.fas.gz
Supplementary_files_format_and_content: excel,expression profiles

value: Colletotrichum gloeosporioides and exogenous caffeine-inoculated


title: LJCK1 Degradome-seq

status: Public on Dec 29 2021

type: SRA

city: Nanjing

first: Anburaj

last: Jeyaraj

state: Jiangsu

address: No. 1 Weigang

country: China

institute: Nanjing Agricultural University

library_source: transcriptomic

data_processing:
Library strategy: Degradome-Seq
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2，3，or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: http://tpia.teaplant.org/web/Download/Genomic_data/Teaplant_CSS_Genome.fas.gz
Supplementary_files_format_and_content: excel,expression profiles

molecule: total RNA

organism: Camellia sinensis

source_name: Tea leaves

growth_protocol: Two-year-old tea plants [Camellia sinensis (L.) O. Kuntze, susceptible cultivar Longjing43 (LJ43) and the resistant cultivar Zhongcha108 (ZC108)] with different levels of resistance to anthracnose were pre-incubated in an artificial climate chamber at 25 ± 1 °C with 85 ± 5 % relative humidity, 14/10 h (day/night) photoperiod and photosynthetic photo flux density (300 μmol m-2 s-1) for 2 weeks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500/Hiseq 4000 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: After 2 weeks of acclimation, tea plants were subjected to inoculation with C. gloeosporioides and exogenous treatment of caffeine for the identification of miRNA regulatory networks in response to C. gloeosporioides stress. Tea plants were also mock-inoculated with sterile distilled water. All experimental plants were watered duly and fertilized with Hoagland’s solution once a week.

tag: tissue

value: Leaves collected at 7dpi

tag: genotype

value: Longjing

tag: fungal pathogen

value: Mock-inoculated


title: app002-ctrl

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

library_source: genomic

data_processing:
Library strategy: targeted amplicon sequencing
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
Genome_build: mm10
Supplementary_files_format_and_content: For CHANGE-seq_ text files containing identified off-target sites

molecule: genomic DNA

organism: Homo sapiens

source_name: cell lysate_HEK293T

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells

extract_protocol: Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus.In vivo treatment was delivery by AAV or Ad5 mediated delivery via systemic injection.

value: cell lysate_HEK293T

value: Prime-editor with pegRNA

value: targeted amplicon sequencing

value: prime-edited genomic locus


title: Shield_dnmt1_mKD_H2AK119ub_rep1

city: Beijing

first: Wei

last: Xie

address: Zhongguancun street, Haidian

department: THU-PKU Center for Life Sciences

institute: Tsinghua University

data_processing:
Library strategy: CUT&RUN
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

organism: Danio rerio

source_name: embryo

growth_protocol: The wild-type AB strain was used in the experiments. The females after OMIS were fed with live adult brine shrimp thrice a day. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).

extract_protocol:
CUT&RUN was conducted based on previously published protocol (Xia et al., 2019) with modifications in cell permeation to adapt it for zebrafish embryos. Embryos were deyolked by tweezers manually and transferred into 1.5 mL conventional, non-low-binding tube (Axygen). Then tubes were flicked several times to disperse cells in embryos, and resuspended by 60 ul washing buffer (20 mM HEPES-KOH, pH = 7.5; 150 mM NaCl; 0.5 mM Spermidine and Roche complete protease inhibitor). 10 µl Concanavalin-coated magnetic beads (Polyscience, Cat 86057) for each sample were gently washed twice, resuspended by binding buffer (20 mM HEPES-KOH, pH = 7.5; 10 mM KCl; 1 mM CaCl2; 1 mM MnCl2), and added carefully to the cells.
The cells with beads were incubated at 23℃ for 30 min on Thermomixer (Eppendorf) at 400 rpm, then held at magnetic stand to exclude buffer, and resuspended by 75 µl antibody buffer (washing buffer supplied with 0.02% digitonin and 2 mM EDTA, freshly made) with H3K4me3 (validated homemade) (Zhang et al., 2016) antibody, or H3K27me3 antibody (Active Motif, Cat 61017), or H2AK119ub antibody (CST, Cat 8240s) diluted at ratio of 1:100. Then the samples were incubated at 4℃ on Thermomixer overnight at 400 rpm. On the second day, the samples were washed by digitonin-washing buffer several times on magnetic stand, and resuspended with 50 µl digitonin-washing buffer supplied with 700 ng/ml pA-MNase, which is kindly provided by Dr. Steven Henikoff, and incubated at 4℃ on Thermomixer for 3hrs at 400 rpm. After that, the cells were washed by digitonin-washing buffer on magnetic stand, and resuspended by 100 µl digitonin-washing buffer on ice for at least 2 min. Targeted region digestion was activated by adding 2 µl 100 mM CaCl2 for 30 min in ice, then stopped by 100 µl 2 X stop buffer (340 mM NaCl; 20 mM EDTA, pH = 8.0; 4 mM EGTA, pH = 8.0; 50 µg/ml RNase; 100 µg/ml glycogen; 0.02% digitonin suppled with spike-in DNA) and fully vortexed. To release fragments, the samples were incubated at 37℃ on Thermomixer at 400 rpm for 20 min. Then the supernatants were purified by phenol chloroform and ethanol purification, and subjected to Tru-seq library construction using NEBNext Ultra II DNA Library Prep kit (NEB, Cat E7645S) as standard protocols. The amplified DNA was size-selected using AMPure Beads for 200-800 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of dnmt1 MO were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 11 min before microinjection.

tag: strain

value: AB

value: WT

tag: developmental stage

value: Shield

value: embryo

tag: treatment

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: LJCK3 Degradome-seq

value: exogenous caffeine-inoculated


title: eIF2B4-4Pe-r1


title: Shield_ctrl_H2AK119ub_rep2

treatment_protocol: Briefly, on the first day of OMIS (Wu et al., 2018b), adult females at 5-12 month old were anesthetized in 550 µg/ml tricaine (Sigma, Cat A5040) in a petri dish. Then the fish was placed on a damp sponge with specific buffer (5.4 mM KCl, 136.8 mM NaCl, 4.2 mM NaHCO3, 0.44 mM KH2PO4, 0.25 mM Na2HPO4, and 0.5% (wt/vol) BSA). A cut was made on one side of belly to expose the ovary. The diluted MOs were microinjected into each oocyte. Rhodamine B (Sigma, Cat R8881) was co-injected with MOs as a dye. After injection, the wound on the belly was sewed with a surgical sewing needle carefully and quickly. Once the operation was done, the female was transferred into fish water supplemented with 32 µg/ml tricaine, 10 unit/ml penicillin and 10 µg/ml streptomycin (HyClone, Cat SV30010). Then the fish was transferred to fish water containing gradually reduced concentrations of tricaine. In the evening of the second day, the female was paired with a wild type male. In the morning of the third day, the pair started to chase and lay fertilized eggs naturally. The injected oocyte-derived embryos were identified by co-injected dye (rhodamine B) at very early developmental stages. The injection doses of standard control MO (cMO) were 5 ng per oocyte in the same assay. MOs were dissolved in RNase-free water, and heated to 65°C for 10 min before microinjection.

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: M328P_miRNeg_A

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen - miRNeasy

tag: cell type

value: BRAFV600E mutant human melanoma

tag: genotype/variation

value: miR-Neg overexpression

tag: amount in (µg)

tag: rin number


title: Dome_ctrl_H3K4me3_rep1

value: Dome


title: adrb2-ctrl


title: ZCCgCN2 miRNA-seq

value: Leaves collected at 7dpi

value: Zhongcha

value: Colletotrichum gloeosporioides and exogenous caffeine-inoculated


title: Shield_ctrl_H2AK119ub_rep1


title: app1-3Pe-r2

value: cell lysate_HEK293T


title: eIF2B4-4Pe-r2

value: Prime-editor with pegRNA


title: eIF2B4P244L006

value: targeted amplicon sequencing


title: eIF2B4-4PedRnase-r1

value: prime-edited genomic locus


title: app1-3PedRnase-r1


title: app1-3Pe-r1


title: ZCCgCN1 miRNA-seq


title: Dome_ctrl_H2AK119ub_rep1

value: AB


title: app001-ctrl


title: ZCCN2 miRNA-seq


title: ZCCN3 miRNA-seq


title: Shield_dnmt1_mKD_H3K27me3_rep2

value: WT


title: ZCCN1 miRNA-seq


title: adrb1-1Pe-r2


title: adrb1-ctrl


title: adrb1-1-PedRnase-r2


title: app1-3PedRnase-r2


title: adrb1-1Pe-r1


title: ZCCg3 miRNA-seq


title: Shield_ctrl_H3K27me3_rep2

value: Shield


title: Shield_dnmt1_mKD_H3K27me3_rep1

value: embryo


title: adrb1-1-PedRnase-r1


title: ARV Drug Treatment 2

city: Orlando

first: Manish

last: Gupta

state: Florida

address: 6900 Lake Nona Blvd

department: Burnet School of Biomedical Sciences

country: USA

institute: University of Central Florida

data_processing:
Filtered and sequenced reads were mapped using HISAT2 algorithms with reference genome Rattus norvegicus release 97
Transcripts were assembled using StringTie v1.3.3b
CuffCompare v2.1.1 was used to compare transcripts
Fragments per kilobase of transcript sequence per Millions base pairs sequenced (FPKM), the most common method were used in estimating gene expression levels
Read count was adjusted by Trimmed Mean of M-values (TMM), then differential expression analysis was performed by using the EdgeR R package
Genome_build: Rattus norvegicus release 97
Supplementary_files_format_and_content: Differentially regulated genes for NRVC treated with ARVs were identified using DESeq2 R package

organism: Rattus norvegicus

source_name: Primary Cardiomyocytes_ARV Drug

growth_protocol: Neonatal rat ventricular cardiomyocytes (NRVCs) were isolated from the 2-3 days old Harlan Sprague–Dawley rats and plated in 6 well plates at 100000 cells per well.

extract_protocol:
Total RNA was isolated using mini spil column from Qiagen
Libraries were prepared according to Illumina's instructions In brief, first and second strand synthesis was performed using standard protocol of TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). cDNA fragments ~400 bp were obtained on gel electrophoresis and followed by PCR amplification. cDNA library was sequenced using Illumina’s HiSeq 2000 with four RNA-seq libraries per lane.

treatment_protocol: NRVCs were treated with 5µM ARVs (Ritonavir, Abacavir, Atazanavir and Lamivudine, (Selleck Chemicals Llc, Pittsburgh, PA)) for 24 hours

tag: srtain

value: Sprague Dawley

tag: cells isolated

value: Heart Ventricles

value: ARV drugs Treatment

tag: duration of treatment

value: 24 hours


title: Control 3

source_name: Primary Cardiomyocytes_control

value: DMSO Treatment


title: Control 1


title: ZCCg1 miRNA-seq


title: ARV Drug Treatment 3


title: Dome_ctrl_H3K27me3_rep1

value: Dome

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: ARV Drug Treatment 1


title: ZCCK3 miRNA-seq

value: Leaves collected at 7dpi

value: Zhongcha

value: Mock-inoculated


title: ZCCK2 miRNA-seq


title: Shield_dnmt1_mKD_scRNA_seq_rep1

description:
single cell RNA
scRNA-seq

data_processing:
All STEM-seq datasets were mapped to the danRer7 reference genome by Bismark (Krueger and Andrews, 2011). Reads were trimmed with cutadaptor (Martin, 2011) using parameters: --minimum-length 20 --pair-filter=any. Alignments were performed with the following parameters: -N 1 -X 600 --score_min L,0,-0.6. Multi-mapped reads and PCR duplicates were removed. bismark_methylation_extractor was used to calculate the DNA methylation level.
Total RNA-seq data were firstly processed using Trim Galore! with default parameters to trim the adapter-containing and low quality reads. The filtered data were then mapped to the zebrafish reference genome (danRer7) by STAR (version: STAR_2.5.3a_modified) (Dobin et al., 2013) with the following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outSAMunmapped Within --outSAMattrIHstart 0 --outWigStrand Stranded --outFilterMultimapNmax 20 --twopassMode Basic. The gene expression level was normalized to fragments per kilobase of transcript per million mapped (FPKM) values using Cufflinks (version 2.2.1) (Trapnell et al., 2012).
The scRNA-seq data were processed with Cell Ranger 3.1 for genome alignment (danRer10), transcript counting, and gene-cell-barcode matrix generation. Before the downstream analysis, cells with unique detected genes lower than <2,000 and higher than 6,000 genes were discarded, and cells with high percentage of mitochondrial genes (>5%) were removed too. Subtypes of cells were identified with Seurat 3.0 through the integrating of control and mKD embryos at dome and shield stages with setting control embryos as reference. To make the data comparable samples, we performed SCTransform normalization separately for each dataset. To further reduce the bais caused by sequencing depth of scRNA-seq and percentage of mitochondrial genes, UMI variance and percent.mt were regressed out from SCTransform normalized data matrix by linear model with negative binomial distribution.
All ChIP-seq reads were aligned to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To visualize the STAR ChIP-seq signal in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted. Replicates of STAR ChIP-seq were pooled for the downstream analysis.
The ATAC-seq data were mapped to the zebrafish reference genome (danRer7) using Bowtie2 (version 2.2.2) (Langmead and Salzberg, 2012) with the parameters –t –q –N 1 –L 25. All unmapped reads, non-uniquely mapped reads and PCR duplicates were removed. For downstream analysis, the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM). To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized. To visualize the CUT&RUN signals in the UCSC genome browser, each read was extended by 250 bp and the coverage for each base was counted.
Genome_build: danRer7
Supplementary_files_format_and_content: Matrix for scRNA-seq data, gene expression table for total RNA-seq data, Bigwig and narrowPeak for ChIP-seq and ATAC-seq data

extract_protocol:
Cell dissociation protocol was based on a previously described method (Farrell et al., 2018) with modifications to adapt it for 10x Genomics platform. Briefly, dnmt1 mKD and control embryos were collected 20 min after fertilization and cultured as mentioned before. Then 15 embryos at dome or shield stages for each sample were transferred into plastic Petri dishes that had previously been coated with 2% agarose and soaked with DMEM/F12 media (Gibco/Life Technologies, Cat 11330032) at least 2hrs. Next, embryos at desired stages were dechorionated and deyolked manually by forceps and transferred to a 1.5 ml Eppendorf tube with 50 µl DMEM/F12 media. Dissections were performed for up 15 min. The volume of DMEM/F12 meida containing embryos was adjusted to 200 µl, then cells were mechanically dissociated by flicking the tube 30 times and pipetting mixture 10 times through a 200 µl tip. The volume was adjusted to 1 ml with PBS containing 1.0% BSA, and spun to pellet cells at 300 g for 30s. The supernatant was removed and cells were resuspended in 80 µl of PBS containing 0.1% BSA and 20% Optiprep (StemCell, Cat 07820), aiming for a concentration above 100 cells/µl. Cells were then passed through a cell sieve (100 µm for dome stage and 70 µm for shield stage).
Single cell RNA-seq library was performed with Chromium Next GEM Single Cell kit (10x Genomics, Cat PN-1000121) based on standard protocol. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: ZCCK1 miRNA-seq


title: Dome_ctrl_H3K27me3_rep2


title: Shield_ctrl_scRNA_seq_rep2

description:
single cell RNA
scRNA-seq


title: LJCgCN3 miRNA-seq

value: Longjing

value: Colletotrichum gloeosporioides and exogenous caffeine-inoculated


title: Shield_ctrl_scRNA_seq_rep1

description:
single cell RNA
scRNA-seq

value: AB


title: LJCgCN2 miRNA-seq


title: ZCCg2 miRNA-seq


title: Control 2


title: HFD 653, islet miRNA

city: Wallace Wurth Building, Sydney

first: Margaret

middle: J

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: miRNA gene expression of islets from female offspring of fathers fed high-fat chow.

hyb_protocol: Cy3-labelled miRNA was added to a hybridization cocktail containing 10X GE Blocking agent, 2X Hi-RPM Hybridisation buffer and Hyb spikes according to the manufacturer’s instructions (Agilent). This whole hybridization mixture was denatured at 100°C for 5 minutes, cooled on ice for 5 minutes and hybridized to Agilent Whole Rat miRNA Microarrays (AMADID: 019159 for 613, 639, 615, 603, 607, 653 and AMADID: 031189 for 640, 652, 635) for 20 hours at 55°C in a rotating (20 rpm) Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one colour scan setting for 8x15K array slides (Scan area Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%). The scanned images were analyzed with Feature Extraction Software v10.7.3.1 (Agilent) using protocol ffmiRNA107_sep09 to obtain background subtracted and spatially detrended.

data_processing: Raw data on each array were normalized independently using RMA (Lopez-Romero P, Gonzalez MA, Callejas S, Dopazo A, and Irizarry RA. Processing of Agilent microRNA array data. BMC Res Notes 3: 18, 2010.), implemented in the Partek (Partek Genome Suite v6.4) miRNA expression workflow. Control probes (n=22) and miRNAs detected on none of the arrays using the IsGeneDetected flag were filtered out. Processed signal intensities are presented in the GeneView.txt file. Differential gene expression between HFD vs. Control were detected using ANOVA.

source_name: islet from female offspring of fathers fed on high-fat diet

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng total RNA using the miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: At 15 weeks of age, fathers were mated with normal females consuming chow to generate the F1 offspring.

extract_protocol: Total RNA was extracted using the miRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fathers fed on HFD vs. control were mated with females on normal chow. The female offspring's islet transcriptomics were analyzed through microarray analysis.

tag: gender

value: female

value: islets

value: father fed high-fat diet


title: Dome_dnmt1_mKD_scRNA_seq_rep2

description:
single cell RNA
scRNA-seq

value: WT

value: embryo


title: HFD 607, islet miRNA

value: Sprague Dawley


title: HFD 644, islet miRNA


title: Shield_dnmt1_mKD_scRNA_seq_rep2

description:
single cell RNA
scRNA-seq

value: Shield


title: LJCgCN1 miRNA-seq


title: HFD 603, islet miRNA


title: Control 639, islet miRNA

description: miRNA gene expression of islets from female offspring of fathers fed standard chow.

source_name: islet from female offspring of fathers fed on control chow

value: father fed standard diet


title: Control 615, islet miRNA


title: Control 602, islet miRNA


title: 5dpf_tail_dnmt1_zKO_total_RNA_seq_rep2

description: Total RNA-seq

source_name: larva

growth_protocol: The dnmt1 mutant TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).

extract_protocol:
The embryos were dechorionated manually by tweezers and transferred into 750 µl Trizol (Invitrogen, Cat 15596018). About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform (Amresco, Cat 0757) was added and mixed thoroughly. The mixture was then transferred into phasemaker tube (Invitrogen, Cat A33248) and spun at 14,000 rpm for 15 min. Next, the top phase was taken out from the tube, added 1 µl LPA (Sigma, Cat 56575) and mixed well using pipettes. Then, RNA was precipitated by adding 750 µl isopropanol (Sigma, Cat 59304) at -20℃ overnight. At next day, the tube was spun at 14,000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol, re-suspend in 20 µl RNase-free water and stored at -80℃ for later usage.
NEBNext rRNA Depletion Kit (NEB, Cat E6310S) was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly, rRNA were hybridized with probes and digested with RNase H, then excess probes were digested with DNase I. After that, NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double-stranded cDNA was synthesized with NEB Next first-strand (NEB, Cat E7771S) and second-strand synthesis modules (NEB, Cat E7550S), then purified with Ampure XP beads (Beckman, Cat A63882). Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit (NEB, Cat E7645S). DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix (KAPABiosystem, Cat RR2602). The amplified DNA was size-selected using Ampure XP beads for 200-500 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

treatment_protocol: Embryos at 5 days post fertilization were euthanized with tricaine, and tail was dissected carefully by tweezers. After brief grinding, tissues froze at -80℃ for later usage.

value: TL

value: larva tail

value: untreated


title: Control 613, islet miRNA


title: 5dpf_tail_dnmt1_zKO_total_RNA_seq_rep1

description: Total RNA-seq


title: PC-3-BM.2

city: Barcelona

first: Marta

last: Garcia Lopez

address: Pg. de la Vall d'Hebron, 119-129

department: Oncology

country: Spain

institute: Vall d'Hebron Research Institute

description: gene expression data from  PC-3-BM cells

hyb_protocol: 5 ug of fragmented and labeled ssDNA was hybridized per array using standard Affymetrix protocols (WT Plus Reagent kit)

scan_protocol: Arrays were scanned in the Genetitan Platformf for 17 hours at 45º

data_processing: Data were processed using the limma (v3.24) package in the R (v3.2) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Data were summarized and limited to core probe set only.

label: biotin

source_name: highly metastatic PC-3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA using WT Plus Reagent kit

growth_protocol: Prostate cancer cells were grown in immunocompromised mice

extract_protocol: mRNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: Metastatic cells were isolated from bones.

tag: cell line

value: prostate cancer cell line PC-3

tag: metastatic potential

value: high


title: LJCN3 miRNA-seq

value: Leaves collected at 7dpi

value: exogenous caffeine-inoculated


title: LJCN1 miRNA-seq

value: Longjing


title: LJCN2 miRNA-seq


title: COM+Met-5

city: Wuhan

first: Haoran

last: Liu

state: Hubei

address: Jiefang avenue 1095

department: Urology

institute: Tongji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm

organism: Mus musculus

source_name: BMDMs

growth_protocol: BMDMs were isolated from C57BL/6J mice.Tibias and femurs were removed from the dead mice, and the bone marrow was rinsed with cold sterile phosphate-buffered saline (PBS) and cultured in RPMI 1640 medium with 10% FBS and 50 ng/mL M-CSF for 7 days in an environment of 37°C and 5% CO2. After 5 days of culturing, the medium was changed to remove unattached cells, and the adherent cells were further cultured for subsequent experiments. TECs were isolated and cultured from kidney tissue samples obtained from WT mice.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs were plated in the upper chamber of 6-well Transwell plates with a pore size of 0.4 μm (Corning, USA), while TECs were plated in the lower chamber. In the COM and COM + Met groups, TECs were treated with COM (100 μg/mL) for 24 h and BMDMs were treated with Met (5.0mM) for 24 h.

value: treated with Met and co-cultured with COM-TECs

value: BMDMs


title: COM+Met-2


title: COM+Met-3


title: COM+Met-4


title: COM+Met-6


title: 5dpf_tail_WT_total_RNA_seq_rep2

description: Total RNA-seq

growth_protocol: The wild-type TL strain was used in the experiments. The adult fish were fed with live adult brine shrimp in the morning and evening. All embryos were raised in Holtfreter’s solution at 28.5C and staged as described previously (Kimmel et al., 1995).


title: PC-3.2

description: gene expression data from  PC-3 cells

source_name: parental PC-3 cells

value: poor


title: PC-3.1

description: gene expression data from  PC-3 cells


title: PC-3-BM.1


title: COM+Met-1


title: LJCg3 miRNA-seq


title: Dome_ctrl_scRNA_seq_rep2

description:
single cell RNA
scRNA-seq

value: AB

value: Dome

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: 5dpf_tail_WT_total_RNA_seq_rep1

description: Total RNA-seq

value: WT


title: COM-6

value: treated with PBS and co-cultured with COM-TECs


title: LJCg2 miRNA-seq


title: 5dpf_head_dnmt1_zKO_total_RNA_seq_rep2

description: Total RNA-seq

treatment_protocol: Embryos at 5 days post fertilization were euthanized with tricaine, and head was dissected carefully by tweezers. After brief grinding, tissues froze at -80℃ for later usage.

value: larva head


title: COM-3


title: COM-4


title: COM-2


title: LJCg1 miRNA-seq


title: COM-1


title: 5dpf_head_dnmt1_zKO_total_RNA_seq_rep1

description: Total RNA-seq

value: TL


title: NC-6

value: treated with PBS and co-cultured with TECs


title: LJCK3 miRNA-seq

value: Mock-inoculated


title: 5dpf_head_WT_total_RNA_seq_rep2

description: Total RNA-seq

value: untreated


title: LJCK2 miRNA-seq


title: NC-4


title: NC-2


title: COM-5


title: Shield_dnmt1_mKD_total_RNA_seq_rep2

description: Total RNA-seq

value: Shield

value: embryo

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: NC-1


title: Shield_ctrl_total_RNA_seq_rep2

description: Total RNA-seq


title: LJCK1 miRNA-seq

value: Leaves collected at 7dpi

value: Longjing


title: SWNTs+ssRNA (RT5)

city: Berkeley

first: Markita

middle: Patricia

last: Landry

state: California

address: Stanley Hall

department: Chemical and Biomolecular Engineering

institute: University of California Berkeley

data_processing:
Base calling performed using NovaSeq Control Software v1.4.0
HI-SAT2 was used to map the reads to the Arabidopsis genome (TAIR10) using the default values.
FeatureCounts (version 2.0.1) was used to assign reads to Arabidopsis transcripts (TAIR10).
edgeR (version 3.30.3) was used to identify differentially expressed genes.
Supplementary_files_format_and_content: Feature counts of every gene in Arabidopsis TAIR10 genome
Supplementary_files_format_and_content: Relative feature counts (compard to non-treated samples)

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Wild-type Columbia-0 Arabidopsis thaliana plants were grown in the greenhouse under the following conditions: 24˚C high and 21˚C low, 16 h light and 8 h dark, and 70% average humidity.

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen cat. 74904) using RNase-Free DNase (Qiagen cat. 79254) following manufacturer instructions
Libraries were prepared using Kapa Biosystems library preparation kit with mRNA selection with poly-A magnetic beads.

treatment_protocol: Leaves were infiltrated (approx. vol 40 µL) with a 1 mL needleless syringe (BD, cat. no. 14-823-434) loaded with water, SWNTs+ssRNA (50 ng/µL) or pDNA+PEI-SWNTs (50 ng/µL)

value: Columbia-0 wild type

value: SWNTs+ssRNA

value: Leaves


title: Shield_ctrl_total_RNA_seq_rep1

description: Total RNA-seq

value: AB


title: Shield_dnmt1_mKD_total_RNA_seq_rep1

description: Total RNA-seq


title: TB11381

city: London

first: Yaohe

last: Wang

address: John Vane Science Centre,  Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Barts Cancer Institute

data_processing:
RNA-Seq reads were aligned to mm10 using Hisat2
Reads were processed with Samtools.
Count files were generated by mapping reads to the mouse genome (GRCm38) version9 (Ensembl 84) using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] files are tab formatted text files containing counts on the mouse genome (GRCm38) version9 (Ensembl 84)

source_name: KPC cell line

growth_protocol: Cells were cultured in DMEM supplemented with 5%FBS in 37º CO2 incubator.

extract_protocol:
Samples' total RNA was extracted by Trizol and 200ng total RNA sample was purified by oligo-dT beads.
mRNA isolation and fragmentation: 200ng total RNA sample was purified by oligo-dT beads, then poly (A)-containing mRNA were fragmented into small pieces with Elute, Prime, Fragment Mix . cDNA synthesis: First-strand cDNA was generated by First Strand Master Mix and Super Script II(Invitrogen) reverse transcription(Reaction condition：25℃ for 10 min；42℃ for 50 min；70℃for 15 min). Then adding Second Strand Master Mix to synthes the second-strand cDNA (16℃1h). End repair, add A and adaptor ligation: the purified Fragmented cDNA combine with End Repair Mix, incubate at30℃ 30min. Purify the end-repaired DNA with Ampure XP Beads (AGENCOURT). Then add A-Tailing Mix , mix well by pipetting, incubate at 37℃ 30 min. Adapter Ligation : Combine the Adenylate 3'Ends DNA, RNA Index Adapter and Ligation Mix, mix well by pipetting. Incubate the ligate reaction at 30℃ 10 min. Purify the end-repaired DNA with Ampure XP Beads (AGENCOURT). RCR: Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix were performed to enrich the cDNA fragments. Then the PCR products are purified with Ampure XP Beads (AGENCOURT).

treatment_protocol: No special treatment

value: KPC cell line

value: With Kras 12D and p53R172H mutation


title: KP-AC

source_name: WT somatic cells reprogrammed cell line, modified K and P


title: TB32043


title: NC-3

value: BMDMs


title: KPC

source_name: KPC mouse fibroblast reprogrammed cell line


title: TB32047


title: SWNTs+ssRNA (RT3)


title: Dome_dnmt1_mKD_total_RNA_seq_rep2

description: Total RNA-seq

value: WT

value: Dome


title: SWNTs+ssRNA (RT2)


title: Rat blood vessel-case

city: China

first: aiqun

last: chen

address: Changlelu, 68#

institute: Nanjing First Hospital

data_processing:
We identified the top variable genes across single cells by using the method described in Macosko et al.1 Briefly, the average expression and dispersion were calculated for each gene, genes were subsequently placed into several bins based on expression. Principal component analysis (PCA) was performed to reduce the dimensionality on the log transformed gene-barcode matrices of top variable genes. Cells were clustered based on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in the percentage of expressed cells was used to identify significantly differentially expressed genes between clusters. Here, we use the R package SingleR, a novel computational method for unbiased cell type recognition of scRNA-seq, with the reference transcriptomic datasets (https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/) to infer the cell of origin of each of the single cells independently and identify cell types. Moreover, we screen for differentially expressed genes (DEGs) between case and control groups based on the FindMarkers function of Seurat.2 In need of statistically significant data, inclusion criteria were meet as fold change ( >1.5 ) and p value ( >0.05 ).
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: blood vessel

extract_protocol:
1.1 GEM Generation & Barcoding 1.1.1 Prepare Master Mix a. Prepare Master Mix on ice. Pipette mix 15x and centrifuge briefly. b. Add 33.4 μl Master Mix into each tube of a PCR 8-tube strip on ice. c. Assemble Chromium Chip B in a 10x Chip Holder. d. Dispense 50% Glycerol Solution into Unused Chip Wells i. 75 μl to unused wells in row labeled 1. ii. 40 μl to unused wells in row labeled 2. iii. 280 μl to unused wells in row labeled 3. e. Prepare Master Mix + Cell Suspension f. dispense 75 μl Master Mix + Cell Suspension into the bottom center of each well in row labeled 1 without introducing bubbles. g. Prepare Gel Beads Snap the Gel Bead strip into a 10x Vortex Adapter. Vortex 30 sec. h. Slowly aspirate 40 μl Gel Beads. Dispense into the wells in row labeled 2 without introducing bubbles. i. Dispense 280 μl Partitioning Oil into the wells in row labeled 3j. Attach 10x Gasket Run the Chromium Controller 1.1.2 Transfer GEMs a. Place a tube strip on ice. b. Slowly aspirate 100 μl GEMs from the lowest points of the Recovery Wells in the top row without creating a seal between the tips and the bottom of the wells. c. If multiple chips are run back-to-back, cap/ cover the GEM-containing tube strip and place on ice for no more than 1 h. d. GEM-RT Incubation e. Store at 4°C for up to 72 h or at −20°C for up to a week, or proceed to the next step. 2.2 Post GEM–RT Cleanup & cDNA Amplification 1.2.1 Post GEM-RT Cleanup – Dynabeads a. Add 125 μl Recovery Agent to each sample at room temperature. DO NOT pipette mix or vortex the biphasic mixture. Wait 60 sec. b. Slowly remove 125 μl Recovery Agent/Partitioning Oil (pink) from the bottom of the tube. DO NOT aspirate any aqueous sample. c. Prepare Dynabeads Cleanup Mix. d. Vortex and add 200 μl to each sample. Pipette mix 10x (pipette set to 200 μl). e. Incubate 10 min at room temperature. Pipette mix again at ~5 min after start of incubation to resuspend settled beads. f. Prepare Elution Solution I. Vortex and centrifuge briefly. g. At the end of 10 min incubation, place on a 10x Magnetic Separator-High position (magnet-High) until the solution clears. A white interface between the aqueous phase and Recovery Agent is normal. h. Remove the supernatant. i. Add 300 μl 80% ethanol to the pellet while on the magnet. Wait 30 sec. j. Remove the ethanol. k. Add 200 μl 80% ethanol to pellet. Wait 30 sec. l. Remove the ethanol. m. Centrifuge briefly. Place on the magnet-Low. n. Remove remaining ethanol. Air dry for 1 min. o. Remove from the magnet. Immediately add 35.5 μl Elution Solution I. p. Pipette mix (pipette set to 30 μl) without introducing bubbles. q. Incubate 2 min at room temperature. r. Place on the magnet-Low until the solution clears. s. Transfer 35 μl sample to a new tube strip. 1.2.2 cDNAAmplification a. Prepare cDNA Amplification Mix on ice. Vortex and centrifuge briefly b. Add 65 μl cDNAAmplification Reaction Mix to 35 μl sample. c. Pipette mix 15x (pipette set to 90 μl). Centrifuge briefly. d. Incubate in a thermal cycler with the following protocol. e. Store at 4°C for up to 72 h or proceed to the next step. 2.2.3 cDNA Cleanup – SPRIselect a. Vortex to resuspend the SPRIselect reagent. Add 60 μl SPRIselect reagent (0.6X) to each sample and pipette mix 15x (pipette set to 150 μl). b. Incubate 5 min at room temperature. c. Place on the magnet-High until the solution clears. d. Remove the supernatant. e. Add 200 μl 80% ethanol to the pellet. Wait 30 sec. f. Remove the ethanol. g. Repeat steps e and f for a total of 2 washes. h. Centrifuge briefly and place on the magnet-Low. i. Remove any remaining ethanol. Air dry for 2 min. DO NOT exceed 2 min as this will decrease elution efficiency. j. Remove from the magnet. Add 40.5 μl Buffer EB. Pipette mix 15x. k. Incubate 2 min at room temperature. l. Place the tube strip on the magnet-High until the solution clears. m. Transfer 40 μl sample to a new tube strip. n. Store at 4°C for up to 72 h or at −20°C for up to 4 weeks, or proceed to the next step.
2.3.1 Fragmentation, End Repair & A-tailing
a. Prepare a thermal cycler with the following incubation protocol. .
b. Vortex Fragmentation Buffer. Verify there is no precipitate. c. Prepare Fragmentation Mix on ice. Pipette mix and centrifuge briefly.
d. Transfer ONLY 10 μl purified cDNA sample from cDNA Cleanup (step 2.3n) to a tube strip. e. Add 25 μl Buffer EB to each sample.
f. Add 15 μl Fragmentation Mix to each sample. g. Pipette mix 15x (pipette set to 35 μl) on ice. Centrifuge briefly. h. Transfer into the pre-cooled thermal cycler (4°C) and press “SKIP” to initiate the protocol. 2.3.2 Post Fragmentation, End Repair & A-tailing Double Sided Size Selection – SPRIselect
a. Vortex to resuspend SPRIselect reagent. Add 30 μl SPRIselect (0.6X) reagent to each sample. Pipette mix 15x (pipette set to 75 μl). b. Incubate 5 min at room temperature. c. Place on the magnet-High until the solution clears. DO NOT discard supernatant. d. Transfer 75 μl supernatant to a new tube strip. e. Vortex to resuspend SPRIselect reagent. Add 10 μl SPRIselect reagent (0.8X) to each sample. Pipette mix 15x (pipette set to 80 l). f. Incubate 5 min at room temperature. g. Place on the magnet-High until the solution clears. h. Remove 80 μl supernatant. DO NOT discard any beads. i. Add 125 μl 80% ethanol to the pellet. Wait 30 sec. j. Remove the ethanol. k. Repeat steps i and j for a total of 2 washes. l. Centrifuge briefly. Place on the magnet-Low until the solution clears. Remove remaining ethanol. DO NOT over dry to ensure maximum elution efficiency. m. Remove from the magnet. Add 50.5 μl Buffer EB to each sample. Pipette mix 15x. n. Incubate 2 min at room temperature. o. Place on the magnet-High until the solution clears. p. Transfer 50 μl sample to a new tube strip. 2.3.3 Adaptor Ligation
a. Prepare Adaptor Ligation Mix. Pipette mix and centrifuge briefly.
b. Add 50 μl Adaptor Ligation Mix to 50 μl sample. Pipette mix 15x (pipette set to 90 μl). Centrifuge briefly. c. Incubate in a thermal cycler with the following protocol.
2.3.4 Post Ligation Cleanup – SPRIselect
a. Vortex to resuspend SPRIselect Reagent. Add 80 μl SPRIselect Reagent (0.8X) to each sample. Pipette mix 15x (pipette set to 150 μl). b. Incubate 5 min at room temperature. c. Place on the magnet-High until the solution clears. d. Remove the supernatant. e. Add 200 μl 80% ethanol to the pellet. Wait 30 sec. f. Remove the ethanol. g. Repeat steps e and f for a total of 2 washes. h. Centrifuge briefly. Place on the magnet-Low. i. Remove any remaining ethanol. Air dry for 2 min. DO NOT exceed 2 min as this will decrease elution efficiency. j. Remove from the magnet. Add 30.5 μl Buffer EB. Pipette mix 15x. k. Incubate 2 min at room temperature. l. Place on the magnet-Low until the solution clears. m. Transfer 30 μl sample to a new tube strip. 2.3.5 Sample Index PCR
a. Choose the appropriate sample index sets to ensure that no sample indices overlap in a multiplexed sequencing run. Record the 10x Sample Index name (PN-220103 Chromium i7 Sample Index Plate well ID) used. b. Prepare Sample Index PCR Mix.
c. Add 60 μl Sample Index PCR Mix to 30 μl sample.
d. Add 10 μl of an individual Chromium i7 Sample Index to each well and record the well ID used. Pipette mix 5x (pipette set to 90 μl). Centrifuge briefly. e. Incubate in a thermal cycler with the following protocol. 2.3.6 Post Sample Index PCR Double Sided Size Selection – SPRIselect
a. Vortex to resuspend the SPRIselect reagent. Add 60 μl SPRIselect Reagent (0.6X) to each sample. Pipette mix 15x (pipette set to 150 μl). b. Incubate 5 min at room temperature. c. Place the magnet-High until the solution clears. DO NOT discard supernatant. d. Transfer 150 μl supernatant to a new tube strip. e. Vortex to resuspend the SPRIselect reagent. Add 20 μl SPRIselect Reagent (0.8X) to each sample. Pipette mix 15x (pipette set to 150 μl). f. Incubate 5 min at room

value: rat cartoid artery

value: cartoid balloon injury

tag: age

value: 12 weeks

value: SD


title: SWNTs+ssRNA (RT4)

tag: tissue


title: SWNTs+ssRNA (RT1)

tag: genotype


title: Rat blood vessel-control


title: Dome_dnmt1_mKD_total_RNA_seq_rep1

description: Total RNA-seq

value: embryo


title: NC-5

value: treated with PBS and co-cultured with TECs


title: 5dpf_head_WT_total_RNA_seq_rep1

description: Total RNA-seq

value: TL

value: larva head

value: untreated


title: Control

city: Princeton

first: Prakriti

last: Paul

state: NJ

address: South Drive

institute: Lewis-Sigler Institute, Princeton University

data_processing:
Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only pass-filtered reads were used for further analysis.
Reads that aligned to phix (using Bowtie version 1.1.1) were removed.
The FASTQ files from each lane were combined and demultiplexed into files for each sample using the barcode sequences allowing one mismatch (using barcode_splitter version 0.18.2).
Single-cell analysis was run with Cellranger count (version 2.0.1) using genome ci_kh_ghostdb_mchsv40_cfpsv40 (Ciona intestinalis (KH2012, Ghost Database) plus mchsv40 and cfpsv40 inserts).
Genome_build: ci_kh_ghostdb_mchsv40_cfpsv40 (Ciona intestinalis (KH2012, Ghost Database) plus mchsv40 and cfpsv40 inserts
Supplementary_files_format_and_content: gene–barcode matrices

organism: Ciona intestinalis

source_name: embryos

growth_protocol: Wild-type Ciona intestinalis type A (also called Ciona robusta) adults were obtained from M-Rep (San Diego, CA) and the National Bio-Resource Project for Ciona in Japan. Sperm and eggs were collected by dissecting the sperm and gonadal ducts.

extract_protocol:
For each sample, 120 morphologically normal late tailbud embryos were used for single-cell RNA-seq assays. Dissociation of the embryos and single-cell RNA-seq assays by 10x Genomics chromium system were done as described previously (Horie et al. 2018).
Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina). All of the libraries were sequenced using Illumina HiSeq 2500 Rapid flowcells (Illumina) with paired-end 26 + 125 nucleotide reads following standard Illumina protocols

treatment_protocol: Microinjections of misexpression constructs were performed as described previously (Horie et al. 2018). CesA>POU IV (2.5ng/l) + CesA>GFP (5.0ng/l) injected eggs and control eggs were fertilized side by side, and allowed to develop to the late tailbud stage (13.5h after fertilization at 18°C).

value: late tailbud II

value: None/uinjected

value: whole embryos


title: Pou4_misexpressed

value: Injected with CesA>PouIV and CesA>CFP


title: 256_cell_dnmt1_mKD_total_RNA_seq_rep2

description: Total RNA-seq

value: AB

value: 256 cell

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: PEI-SWNTs+pDNA (DT4)

value: Columbia-0 wild type

value: PEI-SWNTs+pDNA

value: Leaves


title: PEI-SWNTs+pDNA (DT3)


title: 256_cell_dnmt1_mKD_total_RNA_seq_rep1

description: Total RNA-seq

value: WT


title: DT6606

source_name: KP cell line

value: KP cell line

value: With Kras 12D


title: PEI-SWNTs+pDNA (DT2)


title: PEI-SWNTs+pDNA (DT1)


title: Oocyte_dnmt1_mKD_total_RNA_seq_rep2

description: Total RNA-seq

source_name: oocyte

extract_protocol:
The oocytes were dechorionated manually by tweezers and transferred into 750 µl Trizol (Invitrogen, Cat 15596018). About 10 fresh embryos were transferred into Trizol and vortexed until no visible particles. 150 µl chloroform (Amresco, Cat 0757) was added and mixed thoroughly. The mixture was then transferred into phasemaker tube (Invitrogen, Cat A33248) and spun at 14,000 rpm for 15 min. Next, the top phase was taken out from the tube, added 1 µl LPA (Sigma, Cat 56575) and mixed well using pipettes. Then, RNA was precipitated by adding 750 µl isopropanol (Sigma, Cat 59304) at -20℃ overnight. At next day, the tube was spun at 14,000 rpm for 30 min and supernatant was removed. The pellet was washed with freshly 70% ethanol, re-suspend in 20 µl RNase-free water and stored at -80℃ for later usage.
NEBNext rRNA Depletion Kit (NEB, Cat E6310S) was used to deplete ribosomal RNA according to the manufacture’s instruction. Briefly, rRNA were hybridized with probes and digested with RNase H, then excess probes were digested with DNase I. After that, NEBNext RNA sample purification beads were used to purify rRNA depleted RNA. Purified RNA was fragmented before cDNA synthesis at 95℃ for 8 min. Double-stranded cDNA was synthesized with NEB Next first-strand (NEB, Cat E7771S) and second-strand synthesis modules (NEB, Cat E7550S), then purified with Ampure XP beads (Beckman, Cat A63882). Synthesized cDNA was subjected to library preparation with NEBNext Ultr II DNA Library Prep Kit (NEB, Cat E7645S). DNA was end-repaired, adenylated, and ligated to TruSeq sequencing adaptors. DNA were amplified using KAPA HF HotStart ReadyMix (KAPABiosystem, Cat RR2602). The amplified DNA was size-selected using Ampure XP beads for 200-500 bp DNA fragments. All libraries were sequenced by Illumina Hi-Seq 1500 or 2500 or XTen platform according to manufacturer’s instruction.

value: Oocyte

value: oocyte


title: 256_cell_ctrl_total_RNA_seq_rep1

description: Total RNA-seq

source_name: embryo

value: embryo

value: Oocyte microinjection with Rhodamine B and control MO at oogenesis III stage (GV)


title: Oocyte_dnmt1_mKD_total_RNA_seq_rep1

description: Total RNA-seq


title: Water (WT5)

value: Water


title: Water (WT4)


title: Oocyte_ctrl_total_RNA_seq_rep2

description: Total RNA-seq


title: PEI-SWNTs+pDNA (DT5)


title: Water (WT3)


title: tumor_hmb_pd1_4

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

hyb_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.

data_processing: data were normalized and batch corrected using TAC4 software

source_name: tumor

label_protocol: GeneChip® WT PLUS Reagent Kit (Affymetrix) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the kit. Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays

extract_protocol: Total RNA was extracted by trizsol and RNeasy Kit (Qiagen) from homogenized tumor samples

treatment_protocol: HMB supplementation began one week prior to tumor cell injection, with mice randomized to receive either Ctrl (AIN-93G) or Ctrl+HMB, once tumors were established following injection of 200K PANC02 cells s.c. mice were treated with 200µg anti-PD1 every 3 days.

value: tumor


title: tumor_hmb_pd1_7

scan_protocol: Hybridization, washing, staining and scanning of the Affymtrix peg plate was carried out using the Affymetrin GeneTitan MC Instrument.


title: tumor_hmb_pd1_5


title: 256_cell_ctrl_total_RNA_seq_rep2

description: Total RNA-seq


title: tumor_hmb_pd1_6


title: Water (WT2)


title: Shield_dnmt1_mKD_BS_seq

description: STEM-seq

extract_protocol:
The deyolked oocytes were lysed with 20 µl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, pH 8.0, 0.5% NP-40) and 2 µl protease K (Roche, Cat 10910000) for at least 3hrs at 55℃.
After heat-inactivation, spike-in λ-DNA (Promega, Cat D150A) was added at a mass ratio of 1/200. Bisulfite conversion was performed with the EpiTect Fast Bisulfite Conversion Kit (Qiagen, Cat 59824). The converted DNA was subjected to column purification and desulfonation on MinElute DNA spin columns (Qiagen, Cat 59824) with carrier RNA (Qiagen, Cat 59824) according to the manufacturer’s instructions. The purified DNA was eluted in 30 µl of elution buffer and ready for TELP library preparation (Peng et al., 2015).

value: Shield


title: tumor_hmb_6


title: tumor_hmb_5


title: tumor_pd1_5


title: Dome_mKD_ctrl_BS_seq

description: STEM-seq

value: Dome


title: tumor_ctrl_4


title: tumor_hmb_7


title: tumor_ctrl_6


title: tumor_ctrl_5


title: tumor_ctrl_3


title: tumor_pd1_6


title: Oocyte_dnmt1_mKD_BS_seq_rep2

description: STEM-seq

value: AB


title: Water (WT1)


title: Oocyte_ctrl_total_RNA_seq_rep1

description: Total RNA-seq


title: tumor_hmb_4


title: Non-treated (NT5)

value: Non-treated


title: Non-treated (NT4)


title: Oocyte_dnmt1_mKD_BS_seq_rep1

description: STEM-seq

value: Oocyte microinjection with Rhodamine B and dnmt1 MO at oogenesis III stage (GV)


title: tumor_hmb_3


title: Non-treated (NT2)

value: Columbia-0 wild type


title: tumor_hmb_pd1_3


title: Non-treated (NT1)


title: TBP_11

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the mouse genome (mm10) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

source_name: mouse melanoma

growth_protocol: Mouse strains 1) Tyr::CreERT2;Braf(CA/wt);Pten(fl/fl) and 2) Tyr:CreER;Braf(CA/wt);Pten(fl/fl);Ezh2(fl/fl) were genotyped

extract_protocol:
Melanomas were harvested and RNA was extracted after tissue disaggregation.
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp single-end reads.

treatment_protocol: Melanomas were induced by topical application of 10-15 microliters of 4-hydroxytamoxifen applied to shaved dorsal skin

value: Melanoma

value: braf;pten melanomas (TBP)


title: TBP_13


title: TBP_12


title: tumor_pd1_4


title: tumor_pd1_3


title: tumor_hmb_pd1_1


title: tumor_pd1_1


title: TKO_LUNG

city: Philadelphia

first: Mayassa

last: Bou-Dargham

state: Pennsylvania

address: 421 Curie Blvd

department: pathology and laboratory medicine

institute: University of Pennsylvania

description: single cell RNA seq of lung

data_processing:
sequencing was done at the sequencing core of the Children Hospital of Philadelpia (CHOP)
Data were processed in R using Seurat 3.2.2
raw counts data were read in R and normalized by log-transformation
Cells with a mitochondrial ratio above 0.2 were removed
Using Seurat’s “FindIntegrationAnchors” and “IntegrateData” functions, cells from WT and KO mice were integrated into a single analysis
Supplementary_files_format_and_content: Files are formated as 3 tsv files: barcodes, genes, and matrix.mtx.gz (tsv filtered and aligned files or unprocessed)
Supplementary_files_format_and_content: Gut_normalized.metadata.csv (processed metadata in R)

source_name: Lung

extract_protocol:
Eight to 10-week-old female naïve mice of WT, TKO, and DKO genotypes (three mice per group) were perfused with PBS, and lungs were collected. After digestion of lung tissue, percoll was used to enrich immune cells. Briefly, lung samples were suspended in 44% percoll (GE17-0891-01, Sigma Millipore), and then 67% percoll was added slowly and carefully to the bottom of 50 ml tubes. Cells were then spun at 1000 g, 10 mins at 4 °C, and cells at the interface of the percoll gradient were collected and stained with anti-CD45-FITC. Live CD45+ cells were sorted and subjected to single-cell RNAseq. The cell viability was maintained at more than 90% and no less than 10000 cells per group were loaded to generate libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: naïve mice

value: Tnfaip8-/- (TKO)

tag: Sex

value: female

value: 8-10  weeks

value: Lung


title: tumor_pd1_2


title: tumor_hmb_2


title: tumor_hmb_pd1_2


title: tumor_hmb_1


title: tumor_ctrl_1


title: tumor_ctrl_2


title: gastroc_HMB_4

source_name: gastroc muscle

value: gastrocnemius muscle


title: gills samples 3 under  transport 16h

city: WuXi

first: Tao

last: Zheng

address: No.69, Xuejiali, Nanquan Town, Binhu District, Wuxi City, Jiangsu Province, China

institute: Wuxi Fisheries College, Nanjing Agricultural University

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Str_G_3

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: second gill on the left of each fish

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gill

tag: developmental stage

value: juvenile

value: transport 16h


title: WT_LUNG

description: single cell RNA seq of lung

tag: strain

value: Wildtype


title: gills samples 2 under  transport 16h

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Str_G_2

tag: treatment


title: gastroc_HMB_7


title: gastroc_HMB_6


title: gastroc_HMB_3


title: TBPE_4

tag: cell type

tag: genotype/variation

value: braf;pten melanomas with ezh2 genetic inactivation (TBPE)


title: gastroc_HMB_5


title: TBPE_3


title: DKO_LUNG

description: single cell RNA seq of lung

value: double knockout for Tnfaip8-/- (TKO) and Tipe2-/- (T2KO)


title: TBP_10


title: gills control sample 2

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Con_G_2

value: untreated


title: Keratinocytes 3 weeks (replicate4)

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: .txt

source_name: Keratinocytes

growth_protocol: The skin of mice was incubated overnight in dispase solution (4 mg/ml, in KC medium) at 4°C. The epidermis was prepared, divided into small pieces and incubated in TrypLE for 15 min at 37°C. After suspension in S-MEM medium (Sigma-Aldrich), strong shaking and passage through a 70 mM cell strainer, the cells were plated on pre-coated plates for 5 h, followed by a PBS wash step and incubation in serum-free SFM KC medium (Gibco) containing 0.06 mM Ca++. Cells were splitted at 90% confluence.

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer.
Barcoded mRNA seq libraries were prepared from 140 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual (with a final amplification of 12 cycles) . Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

treatment_protocol: untreated

value: in vitro cultivated keratinocytes prepared from the tail of adult mouse

tag: weeks of cultivation


title: Keratinocytes 3 weeks (replicate2)


title: gills control sample 1

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Con_G_1


title: Keratinocytes 3 weeks (replicate3)


title: MCK-TD_B

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
The sequencing data were processed through standard analytical pipelines at BGI.
Each sample produced more than 20M clean reads that were mapped to the mm9 reference genome using STAR.
Then, Cufflinks was used to generate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) table.

source_name: GTN muscle

growth_protocol: Conventional mouse culture

extract_protocol:
Trizol and DNAase I treatment
Routine library prep by BGI

value: GTN muscle

value: MCK-TD


title: gills control sample 3

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Con_G_3


title: TBPE_2

value: Melanoma


title: Keratinocytes 3 weeks (replicate1)


title: Con_G

value: Con-TD


title: MCK-TD_A


title: Keratinocytes 1 week (replicate4)


title: Con_F


title: gastroc_ctrl_7


title: Keratinocytes 1 week (replicate3)


title: Keratinocytes 1 week (replicate2)


title: gastroc_ctrl_5


title: Brain Atx2 RNA 3

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: BDGP6.93
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Drosophila 3rd instar larvae brain

growth_protocol: Cornmeal food (Drosophila) or Xpress medium (S2 cells)

extract_protocol:
TruSeq mRNA-seq library prep according to manufacturer's instructions
libraries were constructed according to illumina instructions

treatment_protocol: S2 cells with dsRNA against Atx2

value: whole larval brain lysate

value: 3rd instar larvae

value: elav gal4>Atx2 shRNA


title: gastroc_ctrl_4


title: gastroc_HMB_2


title: gastroc_ctrl_2


title: gastroc_ctrl_3


title: gastroc_ctrl_6


title: Tm 93-1

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

description: Gene expression after 93 days from uninfected ileocecal region

hyb_protocol: For each sample, a total of 600 ng of cRNA was fragmented and hybridized overnight at 65°C.

scan_protocol: After hybridization, slides were washed before being scanned on a SureScan Microarray Scanner (Agilent Technologies) and

data_processing: data was processed using Feature Extraction v10.7.3.1 software

source_name: Ileocecal region, 93 days post-infection, uninfected, mouse 1

label_protocol: Total RNA (100 ng) from each sample was labelled as described in One colour microarray based gene expression analysis protocol (Agilent technologies, Santa Clara, CA, USA) using the Agilent Quick-Amp Labeling kit according to the manufacturer’s instructions. After purification using an RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany), cRNA yield and incorporation efficiency (specific activity) into the cRNA were determined using a NanoDrop 2000 (Thermo Scientific, CA, USA) spectrophotometer

growth_protocol: Mice were administered with 4 mg/L of dexamethasone (Merck, Lyon, France) through drinking water. Dexamethasone treatment started 2 weeks prior to inoculation with the parasite and maintained during the entire experimentation. Dexamethasone-containing water was replaced three times a week. Infective doses of C. parvum (105 oocysts / mouse) were prepared and inoculated by oral-gastric gavage. Uninfected animals were inoculated with PBS

extract_protocol: At specific time points, the individual mice were euthanized and the caecum tissue was harvested then placed in 4 times volumes of RNAlater (Qiagen, Valencia, CA, USA) before storage at -80 ºC. Total RNA was isolated from tissue using TRIzol™ Reagent (Invitrogen, CA, USA) and treated with DNAse I (Sigma Life Sciences, Saint-Louis, MO, USA) according to manufacturer’s protocol. RNA quality and quantity were determined using Agilent RNA6000 Nano kit by capillary electrophoresis

value: ileocecal region

value: Female

value: 20 weeks

tag: infection status

value: uninfected


title: Tm 93-2

source_name: Ileocecal region, 93 days post-infection, uninfected, mouse 2


title: Brain Control 3


title: Cp 93-2

description: Gene expression after 93 days from infected ileocecal region

source_name: Ileocecal region, 93 days post-infection, infected, mouse 2

value: infected


title: Cp 93-3

source_name: Ileocecal region, 93 days post-infection, infected, mouse 3


title: Cp 93-1

source_name: Ileocecal region, 93 days post-infection, infected, mouse 1


title: Cp 93-4

source_name: Ileocecal region, 93 days post-infection, infected, mouse 4


title: gills samples 1 under  transport 16h

description:
(Tachysurus fulvidraco♀ × P. vachellii♂)
Str_G_1

value: gill

value: juvenile

value: transport 16h


title: Tm 93-3

source_name: Ileocecal region, 93 days post-infection, uninfected, mouse 3


title: Keratinocytes Nfat5-Knockout (replicate2)

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen). Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Nano chip on Agilent's bioanalyzer.
Barcoded mRNA seq libraries were prepared from 500 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual (with a final amplification of 11 cycles) . Concentration was determined using Invitrogen’s Qubit HS assay and fragment size was analyzed on Agilent’s 2100 Bioanalyzer on a HS DNA chip.

value: in vitro cultivated keratinocytes prepared from the tail of adult Nfat5-deficient mouse


title: Brain Atx2 RNA 2


title: gastroc_ctrl_1

value: gastrocnemius muscle


title: Brain Control 2


title: BMDM_HMB+LPS_6

source_name: BMDM

growth_protocol: bone marrow cells were isolated from C57/bl6 mice, cells were differentiated using L929 cell conditioned media as published http://abc.org.br/IMG/pdf/doc-4272.pdf

extract_protocol: RNA was extracted using qiagen RNeasy Micro Kit, RNA quality was checked using an Agilent bioanalyzer.

treatment_protocol: To induce M1-like polarization, BMDM were treated with 10ng/ml LPS for 48 h in the presence or absence of HMB (1mM)

value: macrophage

value: HMB+LPS


title: Keratinocytes 1 week (replicate1)

value: Wildtype

value: in vitro cultivated keratinocytes prepared from the tail of adult mouse


title: Brain Atx2 RNA 1

value: whole larval brain lysate


title: Cp 45-3

description: Gene expression after 45 days from infected ileocecal region

source_name: Ileocecal region, 45 days post-infection, infected, mouse 3

value: 13 weeks


title: Keratinocytes Wildtype (replicate2)

value: in vitro cultivated keratinocytes prepared from the tail of adult wildtype mouse


title: Brain Control 1

value: 3rd instar larvae


title: S2 Atx2 RNA 3

source_name: S2 cells

value: S2 cell lysate

value: Atx2 dsRNA


title: Keratinocytes Wildtype (replicate1)


title: Cp 45-2

source_name: Ileocecal region, 45 days post-infection, infected, mouse 2

value: ileocecal region

value: Female


title: gastroc_HMB_1


title: BMDM_HMB+LPS_5


title: treatment group 2

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of transcript sequence per  Millions (FPKM) were calculated based on the length of the gene and reads count mapped  to this gene.FPKM considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes count and  FPKM values for each Sample and genes.

source_name: proliferated neural progenitor cells

growth_protocol: For the isolation of embryonic NPCs, the forebrain of embryonic 14 mice were dissected and cultured, cells were cultured and expanded with DMEM/F-12 medium containing 2% B27 (minus vitamin A), 20 ng/ml EGF, 20 ng/ml FGF-2, 2 mM L-glutamine and 1% antibiotic-antimycotic (proliferation medium) in a 5% CO2 incubator at 37°C. The medium was half replaced every 2 days.

extract_protocol:
collect cell samples and add 1mL TRIZO,Lfully cleavage,add 200 μl chloroform and shake tube vigorously for 35s,After incubation on ice for 2min, the supernatant was centrifuged, transferred to a new EP tube, 600 μl isopropyl alcohol and 2  μl  glycogen were added. After full incubation, the supernatant was centrifuged, and the precipitation was cleaned with 70% alcohol. The supernatant was discarded after centrifugation, and the precipitation was dried and dissolved with RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: we performed lentivirus infection expressing shRNA against Rybp to deplete Rybp in NPCs.

value: embryonic

value: neural progenitor cells

tag: shRNA

value: shRybp


title: S2 Control 3


title: treatment group 1


title: AVE-3

city: Nanjing

first: Siyu

address: No.68, Changle Road

data_processing:
Sequencing data is called raw reads. First, we filter out rRNA, low-quality, adaptor contamination, and reads with too many N bases. Clean reads were then aligned to the reference genome and transcriptome, respectively. The RNA is then carried out quantification, differentially analysis, clustering, time-series analysis (if any), and enrichment.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. . Compared with other software, HISAT has the advantages of high speed, high sensitivity and accuracy, and low memory consumption. HISAT's index based on Burrows-Wheeler transform and Ferragina-Manzini (FM) uses two types of indexes: whole genome indexes and partial genome indexes. See the HISAT alignment diagram for the details and statistics of genome mapping results.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:    1) Remove the reads containing the adaptor(adaptor pollution);    2) Remove reads whose N content is greater than 5%;    3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).    The filtered "Clean Reads" are saved in FASTQ format.
Sequence alignment software is used to align the clean reads after quality control to the reference genome, so that the gene or transcript expression in the sample can be quantified. At the same time, the overall analysis of the transcriptome sequencing is performed, including the randomness of the transcript.
Sequence alignment software is used to align the clean reads after quality control to the reference gene set, so as to quantify the gene or transcript expression in the sample. At the same time, the overall analysis of the transcriptome sequencing is performed, including the coverage and distribution of the transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene counts for every gene and every sample

source_name: astrocytes

extract_protocol:
RNA was extracted from adult astrocytes using Trizol. After removing the ribosomal RNA, the RNA library was prepared.
1)rRNA removal: rRNA were removed from the total RNA; 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB

value: brain

value: Injected intraperitoneally with 10 mg/kg AVE0991 once a day for 30 consecutive days


title: BMDM_HMB+LPS_4

value: macrophage


title: Cp 45-1

source_name: Ileocecal region, 45 days post-infection, infected, mouse 1

value: infected


title: Kerationcytes Nfat5-Knockout (replicate1)

source_name: Keratinocytes

value: in vitro cultivated keratinocytes prepared from the tail of adult Nfat5-deficient mouse


title: BMDM_HMB+LPS_3

value: HMB+LPS


title: AVE-2


title: ctrl group 2

value: ctrl


title: S2 Atx2 RNA 2


title: Tm 45-4

description: Gene expression after 45 days from uninfected ileocecal region

source_name: Ileocecal region, 45 days post-infection, uninfected, mouse 4

value: 13 weeks

value: uninfected


title: AVE-1


title: BMDM_HMB+LPS_2


title: Tm 45-3

source_name: Ileocecal region, 45 days post-infection, uninfected, mouse 3


title: BMDM_LPS_5

value: LPS


title: BMDM_LPS_6


title: Tm 45-2

source_name: Ileocecal region, 45 days post-infection, uninfected, mouse 2


title: Tm 45-1

source_name: Ileocecal region, 45 days post-infection, uninfected, mouse 1


title: ctrl group 1


title: S2 Control 2

value: S2 cell lysate


title: APP-3

value: Injected intraperitoneally with vehicle (0.9percent sterile saline) once a day for 30 consecutive days


title: S2 Atx2 RNAi 1

value: Atx2 dsRNA


title: BMDM_LPS_4


title: S2 Control 1


title: APP-2


title: APP-1


title: NC_2

first: Lufeng

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: breast cancer cells

growth_protocol: Cells were cultured in L-15 medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were treated with HET0016 (5 μM) for 48 h, and subjected to  deep sequencing, in triplicate, using Illumina GAIIx.

value: Breast cancer cell line


title: NC_1


title: Rpb3 ChIP-seq (no SM) Repl. 3 [AGH64_9]

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 Center Drive, 6/230

institute: NIH, NICHD

description:
Biological replicate 3
AGH64_9

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Gcn4, TBP, myc-tagged chromatin remoderlers and Rpb3 were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig (Lengths used in .bw files; Range: 50 - 300 bp)

organism: Saccharomyces cerevisiae

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ino80∆::kanMX4

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

tag: genetic information

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 ino80{delta}::kanMX4

value: Formaldehyde-fixed and sonicated


title: BMDM_LPS_3


title: HET_1


title: BMDM_LPS_2


title: BMDM_HMB_6

value: HMB


title: Rpb3 ChIP-seq (no SM) Repl. 2 [AGH64_8]

description:
Biological replicate 2
AGH64_8


title: Rpb3 ChIP-seq (no SM) Repl. 2 [AGH101_14]

description:
Biological replicate 2
AGH101_14

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2∆::kanMX4 HIS3MX6::PTETSTH1

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2{delta}::kanMX4 HIS3MX6::PTETSTH1


title: Non-treated (NT3)

source_name: Leaves

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen cat. 74904) using RNase-Free DNase (Qiagen cat. 79254) following manufacturer instructions
Libraries were prepared using Kapa Biosystems library preparation kit with mRNA selection with poly-A magnetic beads.

value: Columbia-0 wild type

value: Non-treated

value: Leaves


title: Mouse_BM_ATF4_CHIP

city: Guangzhou

first: Yan

last: Sun

state: Guangdong

address: Zhong shan 2nd Road, Building 74

institute: Sun Yat-sen University

description: Mouse_BM_ATF4_CHIP-2_vs_input_2_peaks.bed

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq data were mapped to the human genome (GRCh38) or mouse genome (GRCm38 ) by using Bowtie2
Data were filtered using the following specifications…
ChIP peaks were called using model-based analysis of ChIP-seq 14 (MACS2), with the input sample as the control.
Enrichment heatmaps that surrounds ChIP peaks were produced by using deeptools, and signal plotting of individual genes was generated using the Integrated Genome Viewer
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: peak were called using macs2

growth_protocol: KG1a cells culture:  To make the complete growth medium, add the following components to the base medium: fetal bovine serum to a final concentration of 20%.

extract_protocol:
The ChIP procedure was performed according to a previously described protocol (Lee et al., 2006; Ying et al., 2017), using 10mg anti-ATF4 antibody (Abcam)
Enriched DNA fragments were subjected to the preparation of standard libraries for ChIP-seq, according to the manufacturer’s instructions, and the resulting ChIP-seq libraries were sequenced on an Illumina Hi-seq X-Ten (Annoroad Gene Technology Co., Ltd).

value: Bone marrow cells

tag: chip antibody

value: anti-ATF4 antibody (Abcam, ab184909)


title: Rpb3 ChIP-seq (no SM) Repl. 2 [AGH101_12]

description:
Biological replicate 2
AGH101_12

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1


title: Mouse_BM_ATF4_input


title: Rpb3 ChIP-seq (no SM) Repl. 1 [AGH101_11]

description:
Biological replicate 1
AGH101_11

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1


title: Rpb3 ChIP-seq (no SM) Repl. 2 [AGH101_10]

description:
Biological replicate 2
AGH101_10

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 snf2∆::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4


title: HET_2


title: HH8_Chicken_scRNA-Seq#2

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Genome_build: GRCg6a

organism: Gallus gallus

source_name: Hypothalamus

extract_protocol: scRNA-Seq following 10x V3.0 guideline

value: Hypothalamus

value: Hamburger Hamilton Stage 8

value: Mixed


title: BMDM_HMB_4

source_name: BMDM

value: macrophage


title: BMDM_HMB_2


title: myc ChIP-seq (+SM) Repl. 3 [AGH144_20]

description:
Biological replicate 3
AGH144_20

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 gcn4∆::kanMX4 INO80::myc13::HIS3MX6

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 gcn4{delta}::kanMX4 INO80::myc13::HIS3MX6


title: ßGal

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then   F  PKM   of each gene was calculated based on the length of the gene and reads count mapped   to this   gene.  F  PKM,   expected  number  of  Fragment  s  Per  Kilobase  of  transcript  sequence  per   Millions  base  pairs  sequenced  ,  considers  the  effect  of  sequencing  depth  and  gene  length   for the reads count at the same time, and is currently the most commonly used method for   estimating gene expression  levels (  Tr  apnell, Cole, et al., 2010  )
Genome_build: Ensemble_GRCm38.90
Supplementary_files_format_and_content: Excel file with FPKM values

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 mice (8-9 weeks old) were injected with purified different adenovirus (βGal, GBP5, GBP51-306, GBP5307-586) via tail vein, respectively, for ten days.

value: Liver

value: 8-9 weeks

tag: adenovirus

value: Beta-Gal


title: HH8_Chicken_scRNA-Seq#1


title: Rpb3 ChIP-seq (no SM) Repl. 1 [AGH64_7]

description:
Biological replicate 1
AGH64_7

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 ino80{delta}::kanMX4

value: Formaldehyde-fixed and sonicated


title: myc ChIP-seq (+SM) Repl. 1 [AGH144_18]

description:
Biological replicate 1
AGH144_18


title: BMDM_CTRL_6

value: Ctrl


title: myc ChIP-seq (+SM) Repl. 2 [AGH144_19]

description:
Biological replicate 2
AGH144_19


title: BMDM_CTRL_3


title: BMDM_CTRL_4


title: BMDM_HMB_5

value: HMB


title: BMDM_HMB_1


title: BMDM_CTRL_2


title: BMDM_HMB_3


title: BMDM_CTRL_5


title: BMDM_CTRL_1


title: HH20/21_Chicken_scRNA-Seq

value: Hamburger Hamilton 20/21


title: GBP5


title: L12 3: Leaves at 12 weeks after planting

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Manihot esculenta

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: Cassava cultivar KU50 stem cuttings were planted in the field at Rayong Field Crop Research Center, Rayong, Thailand. Three independent biological replicates were harvested at 4, 8, and 12 weeks after planting. The roots were classified as fibrous and pre-tuberous (diameter < 2 mm), intermediate storage (diameter = 2–5 mm), and mature storage (diameter > 5 mm) (Sojikul et al. 2015; Teerawanichpan et al. 2008) (Fig. 1a). The cortex and parenchyma region of the intermediate storage and mature storage roots were collected separately. All samples were kept on dry ice during the transport from Thailand to Japan. The samples were frozen with liquid nitrogen and then crushed roughly with a multi-beads shocker (Yasui Kikai Corporation, Osaka, Japan). The in vitro KU50 plantlets obtained from the CIAT germplasm collection were maintained as previously described by Utsumi et al. (2017).

extract_protocol: Total RNA was purified according to manual protocol using RNeasy Plant Mini kit protocol (QIAGEN) followed by Plant RNA reagent protocol (Invitrogen). The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80ºC until further use.

tag: tag

value: Leaf


title: L12 1: Leaves at 12 weeks after planting


title: L12 2: Leaves at 12 weeks after planting


title: myc ChIP-seq (no SM) Repl. 3 [AGH144_17]

description:
Biological replicate 3
AGH144_17


title: Rpb3 ChIP-seq (no SM) Repl. 1 [AGH101_09]

description:
Biological replicate 1
AGH101_09


title: HH18/19_Chicken_scRNA-Seq#2

tag: age

value: Hamburger Hamilton 18/19


title: myc ChIP-seq (no SM) Repl. 2 [AGH144_16]

description:
Biological replicate 2
AGH144_16


title: HH10_Chicken_scRNA-Seq

tag: tissue

value: Hamburger Hamilton 10


title: myc ChIP-seq (no SM) Repl. 1 [AGH144_15]

description:
Biological replicate 1
AGH144_15


title: HH13/14_Chicken_scRNA-Seq

value: Hamburger Hamilton 13/14


title: myc ChIP-seq (+SM) Repl. 2 [AGH144_14]

description:
Biological replicate 2
AGH144_14

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 gcn4∆::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 gcn4{delta}::kanMX4


title: myc ChIP-seq (+SM) Repl. 1 [AGH144_13]

description:
Biological replicate 1
AGH144_13


title: myc ChIP-seq (+SM) Repl. 3 [AGH144_10]

description:
Biological replicate 3
AGH144_10

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 INO80-myc13::HIS3MX6


title: myc ChIP-seq (no SM) Repl. 2 [AGH144_12]

description:
Biological replicate 2
AGH144_12


title: myc ChIP-seq (no SM) Repl. 1 [AGH144_11]

description:
Biological replicate 1
AGH144_11


title: HH18/19_Chicken_scRNA-Seq#1

value: Hypothalamus


title: M0 macrophages rep3

city: Xi’an

first: Yangguang

last: Ma

address: Changle West Road No. 127

institute: Department of Orthopedics, The First Affiliated Hospital of Air Force Military Medical University

description: Sample A3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Text file includes FPKM values for each Sample

source_name: M0 macrophages

growth_protocol: The femur and tibia of 6- to 8-week-old C57BL/6 mice were extracted, and their bone marrow cavities were flushed with PBS. The cell-containing pellet was resuspended in pretreated Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS, 1% penicillin/streptomycin solution, and 10 ng/mL macrophage colony-stimulating factor (M-CSF; R&D Systems).  Bone marrow cells were induced to M0 macrophages with M-CSF conditioned medium (10% FBS, 1% penicillin-streptomycin double-antibody, DMEM high-glucose medium, 10 ng/mL M-CSF). Cells were differentiated in fresh conditioned medium for 7 days until the cells matured in culture.

extract_protocol:
Total RNA was isolated from macrophage sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).  Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mature M0 macrophages were polarized to M1 macrophages after the addition of lipopolysaccharide (LPS; Sigma-Aldrich) and interferon-γ (IFN-γ; Sigma-Aldrich) to the medium.

value: femur and tibia

value: M0 mouse bone marrow-derived macrophages

value: 6-8 weeks postpartum

tag: genotype

value: wild type

value: non-PBM-treated


title: M0 macrophages rep2

description: Sample A2


title: HH15/16_Chicken_scRNA-Seq

value: Hamburger Hamilton 15/16

value: Mixed


title: LT_HSC_ATF4-KO2

data_processing:
cDNA library construction and sequencing were performed by GENEWIZ using Illumina NovaSeq 6000 platform.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.2.1) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files include normalized reads each Sample

source_name: bone marrow

growth_protocol: Cells were isolated from mice tibia and femur,long-term HSCs were sorted using FACS

extract_protocol:
Total RNA was extracted from long-term HSCs using TRIzol reagent (Takara) according to manufacturer’s instructions.
The RNA-seq library was prepared  using customized protocol based on Smart-seq2

value: bone marrow

value: LT-HSC

value: ATF4 KO


title: NrCAM KO - Hypothalamus

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat was used to perform downstream analysis following the standard pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: h5ad fild

extract_protocol: scRNA-Seq - following the manufacturer's (10x Genomics, v3.0)

value: 8 weeks

value: NrCAM KO


title: Wildtype - Hypothalamus

value: Wildtype


title: myc ChIP-seq (no SM) Repl. 3 [AGH144_7]

description:
Biological replicate 3
AGH144_7

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 INO80-myc13::HIS3MX6

value: Formaldehyde-fixed and sonicated