title: Untreated/control_6 h MIA PaCa2 cell line Rep1

description:
MIA PaCa2 cell line Rep1
0


title: AK83_luteolin_rep_1

status: Public on Jun 04 2020

type: SRA

city: Sesto Fiorentino

first: Giovanni

last: Bacci

state: FI

address: via Madonna del Piano, 6

department: Department of Biology

country: Italy

institute: University of Florence

description:
overall_collapsed.tsv
AK83_raw_counts.tsv

library_source: transcriptomic

data_processing:
Basecalls and demultiplexing performed using bcl2fastq2 version 2.20
Trimming performed using StreamingTrim algorithm version 1.0 (with a quality threshold of 20)
Reads quantification with SALMON version 1.1
Normalization and analyses conducted using DESeq2 version 1.18
Genome_build: ASM696v1 (Sinorhizobium meliloti 1021); ASM34606v1 (Sinorhizobium meliloti 2011); ASM14779v3 (Sinorhizobium meliloti AK83)
Supplementary_files_format_and_content: Stats file generated by bcl2fastq2; raw count files are tab separated matrices reporting SALMON quantification

molecule: total RNA

organism: Sinorhizobium meliloti

source_name: Bacterial culture

growth_protocol: Overnight cultures of S. meliloti, grown in M9-succinate medium at 30°C at 130 rpm were diluted to an OD600 of 0.05 in 5 ml of M9-succinate and incubated untill an OD of 0.4 was reached.

extract_protocol:
After incubation, cells were blocked with RNAprotect Bacteria (Qiagen) and total RNA was extracted using RNeasy Mini kits (Qiagen) from 0.5 ml of culture following the manufacturer’s instructions, including on column DNase I treatment
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 uM of luteolin or one of the three alfalfa root exudates normalised to the total organic carbon present was added to each of the cultures and incubated for additiona 4 hours at 30°C with shaling at 130 rpm.

tag: strain

tag: treatment

value: luteolin


title: HiC_St15_females_mofRNAi_rep1

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
processed data file: st15_TADs.bed
processed data file: st15_mof_f_2500bp.A.norm_cor.h5
processed data file: st15_mof_f_2500bp.X.norm_cor.h5
processed data file: st15_mof_f_40000bp_compartments.bedgraph
processed data file: st15_mof_f_TADs_insulation.bw

library_source: genomic

data_processing:
Hi-C: Hi-C data processing was performed using the Hi-C pipeline of SnakePipes v1.0 and HiCExplorer v2.3. Hi-C matrices were built at a resolution of 2.5kb with a fixed bin size. Autosomes and X chromosomes were separated to take into account the males single X compared to the females XX at stage 15. Fastq files from females were thus downsampled by 2 to produce the stage 15 females X chromosome matrices. The different biological and sequencing replicates were merged in one Hi-C matrix per condition (depending on the stage, control RNAi or mof RNAi, chromosome type and sex in the case of stage 15 samples) using `hicSumMarices`. Iterative correction (ICE) was applied on these merged matrices using `hicCorrectMatrix` following the SnakePipes Hi-C pipeline. TADs were called using `hicCallTADs --minDepth 7500 --maxDepth 100000 --step 2500 --correctForMultipleTesting fdr --thresholdComparisons 0.09 --delta 0.01 -p 100`. A/B compartments were called using sliding windows of defined size in order to be able to call compartments correctly in the stage 5 samples since the compartmentalization is quite low in early embryonic stages in D. melanogaster.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Hi-C: corrected matrices at 2500bp resolution are provided as h5 format from HiCExplorer. This format can be converted to other formats through hicConvertFormat from HiCExplorer. Consensus TAD boundaries position are provided as BED files. TAD insulation scores are provided genome-wide as bigwig files, the lower the values, the stronger the TAD boundaries. A/B compartments are provided as bedGraph files, with positive values corresponding to the active (A) compartment, and negative values corresponding to the inactive (B) compartment.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: female embryos st15

growth_protocol: D. melanogaster flies were maintained in standard Drosophila medium at 25oC.

extract_protocol:
Hi-C: D. melanogaster dechorionated embryos were fixed using 1.8 % formaldehyde for 15 min at RT. 50-100 embryos were hand staged based on morphology for the late embryonic stage 15 (14-16h AEL) or the mid-nuclear cycle 14 stage. The latter stage contains nuclei purely to S phase. The next mitosis takes place during gastrulation (Yuan et al., 2016). We employed a modified version of the in situ Hi-C protocol (Rao et al., 2014) described in Ramírez et al. 2018. Briefly, nuclei were extracted with a pestle in 50 µl ice-cold lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2 % IGEPAL CA-630) and additional 150 µl ice-cold lysis buffer was added. From here, we followed the protocol as described in Ramírez et al. 2018 except for the following modifications: nuclei were digested for 3 hr in total using 2 µl DpnII (NEB, R0543M, 150 U/ sample), half of enzyme amount added after 1.5 hr. During ligation, the ligase (T4 DNA ligase, NEB 0202S) was also added in two steps. DNA purification was performed using the Zymo ChIP DNA Clean & Concentrator kit (D5205). To increase the fraction of valid Hi-C reads, dangling ends were removed using 3 U of T4 DNA polymerase for 30 min at 20 °C with addition of 100 µM dGTP and dATP. After biotin pull-down, all DNA bound to beads was used for library preparation and libraries were sequenced paired-end, with a read length of 75 bp.
NEB Next Ultra II

treatment_protocol: Maternal RNAi using mat-a-Gal4 (Bloomington Stock number 7062).

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP positive

tag: tissue

value: embryos st15

tag: Sex

value: female

tag: technique

value: Hi-C


title: AK83_lodi_rep_2

value: lodi root exudate


title: 40 nM SOP1812_6 h MIA PaCa2 cell line Rep3

city: London

first: Stephen

last: Neidle

address: Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

description:
MIA PaCa2 cell line Rep3
0

data_processing:
Illumina run data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software (v2.19).
Fastq files were pre-processed to remove adapter contamination and poor quality sequences using the program Trimmomatic (v0.36)
Duplication levels were estimated using JE-Suite50
Reads per transcript were counted using the program FeatureCounts51 (v1.4.6p5)
Genome_build: Mapped to a recent human genome build (UCSC hg38: https://genome.ucsc.edu/) using the RNA-seq alignment tool STAR (v2.5b: https://github.com/alexdobin/STAR)
Supplementary_files_format_and_content: Excel format, contains differential expression data for 6 h and 24 h SOP1812 exposure

organism: Homo sapiens

source_name: pancreatic cancer

growth_protocol: MIA PaCa-2 cells were seeded in 100 mm plates (6 h = 2.5 × 10^6 cells/plate and 24 h = 1.0 × 10^6 cells/plate) and incubated overnight.

extract_protocol:
Total RNA was extracted from 2 - 4 x 10^6 cells using the RNeasy mini kit (Qiagen, cat no. 74104) and on-column DNase1 digestion (Qiagen, cat no. 79254)
RNA-seq libraries were generated using the KAPA mRNA Library HyperPrep Kit for Illumina Platforms.

treatment_protocol: Cells were treated with40 nM SOP1812 or vehicle (DMSO) for 6 h and 24 h

tag: source

value: ATCC cell line

tag: cell type

value: pancreas ductal adenocarcinoma cell line


title: BI005_marm027_Spencer_Caud_rxn1

city: Boston

first: Fenna

middle: Marie

last: Krienen

state: MA

address: 77 Ave Louis Pasteur, NRB 260

department: Genetics

country: USA

institute: Harvard Medical School

description:
single-nucleus gene expression data based on 3' transcript counts
marm.str.int.10X.raw.dge.txt.gz

data_processing:
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts

organism: Callithrix jacchus

source_name: Adult Marmoset Brain

extract_protocol:
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)

tag: platform

value: Striatum; Caudate


title: iPCR, Doxy conc 0, bio rep 2, tech rep 2

city: Stanford

first: Mark

middle: A

last: Kay

address: 269 Campus Drive

institute: Stanford University

data_processing:
For ligation-mediated PCR, BBMap v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence. BBMap BBDuk was used to filter out reads for which there was amplification into the provirus from the 5' LTR and trim overlapping reads of primer read-through. BBMap demuxbyname was used to complete demultiplexing of technical replicates using the Read 1 linker-unique sequences, allowing for a hamming distance of 3. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 2500, filtering for uniquely mapped and properly matched read pairs. UMI-tools dedup was used to deduplicate aligned reads using the --ignore-umi flag. For each read pair, we required that they maintain the correct predicted orientation: the LTR junction read is ?upstream? of the breakpoint read if aligned to the + strand, or "downstream" if aligned to the - strand. Read 2 LTR junction positions were clustered within 20bp to generate a set of consensus junctions. Clonal abundance was computed as the depth-normalized number of unique breakpoints for each junction after clustering breakpoint positions within 5bp, scaled to the maximum number of breakpoints in any sample. We required that consensus sites be recovered in both technical replicates associated with a biological replicate and have at least two unique breakpoints to be accepted. A set of population-wide consensus sites was generated by repeating junction clustering across all technical replicates.
For inverse PCR, BBTools v.38.60 BBDuk was used to quality trim read 3? ends and filter out low quality reads while error-correcting overlapping regions. UMI-tools v1.0.0 extract was used to trim reads of primer sequence and extract barcodes. In Read 1, barcodes were extracted while discarding all remaining sequence up to the reconstituted AseI/NdeI restriction site (excluding the last two, non-consensus bases). BBTools BBDuk was then used to filter out reads for which there was amplification into the provirus from the 3' LTR and trim primer read-through. Paired reads were aligned to the GRCh38.p12 genome assembly using the STAR aligner v.2.7.1a with --alignIntronMax 1 --alignMatesGapMax 3850, filtering for uniquely mapped and properly matched read pairs. Consensus sites were generated by clustering Read 2 LTR junction positions within 20bp and technical replicates were subsequently merged. Inverse PCR consensus sites were mapped back to provirus consensus sites, requiring that iPCR and LM-PCR LTR junctions be mapped to opposite strands and overlap at their LTR junction positions by not more than 10bp using bedtools v2.28.0 intersect.
Processing of normalization (DNA barcodes) and expression (RNA barcodes) reads were carried out in an identical manner. Forward and reverse reads were merged using BBTools v38.60 BBMerge while filtering low quality reads and error-correcting overlapping regions. UMI-toolsv1.0.0 extract was used to extract barcodes. Unique barcodes were collapsed and counted.
The set of accepted barcodes were those that had at least five normalization reads in both of a pair of technical replicates, and two mapping reads at a single site by inverse PCR. A barcode was definitively assigned to a site if at least 90% of the total reads for that barcode mapped to the site, with fewer than 2.5% mapping to a secondary locus.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: provirus_sites_w_abundance.txt: Provirus sites and number of unique breakpoints for each from LM-PCR sequencing
Supplementary_files_format_and_content: barcodes_norm_expr_raw_counts.txt: Raw normalization and expression counts for each mapped barcode
Supplementary_files_format_and_content: mapped_barcodes.txt: Genomic locations of mapped barcodes
Supplementary_files_format_and_content: README.txt: Python regex and sequences for genomic DNA extraction, barcode extraction, and demultiplexing of LM-PCR data

source_name: HAP1 cells

growth_protocol: HAP1 cells infected with a lentivirus-encoded dual Tet-ON expression system and targeted with barcoded AAV library were grown in complete IMDM supplemented with 7ug/mL blasticidin S-hydrochloride.

extract_protocol:
Genomic DNA was extracted from frozen cell pellets of 12e6 cells using the GeneJET Genomic DNA Purification Kit in two technical replicates for every biological replicate.   Total RNA was extracted using the Monarch Total RNA MiniPrep kit from samples frozen in 1X Protection Buffer, including in-column DNase I treatment, in two technical replicates for every biological replicate. 2ug of RNA was reverse transcribed with RNase H treatment in a 21ul reaction using the Superscript III First Strand cDNA Synthesis Kit with oligo(dT) primers.
Ligation-mediated PCR (LM-PCR) to map provirus sites was performed as previously described (Sherman et al., Mol Ther Methods Clin Dev, 2016; PMID: 28344990) except that 5 cycles of linear amplification plus 7 cycles of exponential amplification were used in the second round of PCR and primers were adapted to standard Illumina sequencing primers. Samples with different indexes were pooled together and sequenced on an Illumina MiSeq using 2x300bp paired-end reads.
For inverse PCR to map integrated barcodes, 4ug genomic DNA was digested in a 200ul reaction with 1X NEB Buffer 3.1, 134U AseI (NEB), and 134U NdeI (NEB). Digests were purified through a Monarch PCR & DNA Cleanup Kit column. 3 x 600ng purified digested DNA was self-ligated with 2800U high concentration T4 DNA Ligase (NEB) and incubated at 4ºC overnight in a volume of 400ul. Final PCR template was obtained by phenol:chloroform:isoamyl alcohol extraction and ethanol precipitation. DNA pellets were dissolved in 30ul water and 5ul of each sample was used as template to amplify fragments containing both an integrated barcode and genomic DNA adjacent to the 5? LTR of the corresponding provirus site. iPCR was performed over two rounds in 12 independent reactions, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of second round PCR products were pooled and cleaned up using 0.8X Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina NextSeq 500 using 2x150bp paired-end reads.
PCR to measure normalized barcode expression was performed over two rounds in 10 independent reactions using 100ng genomic DNA or 1.68ul cDNA, using ExoI/rSAP (NEB) to remove primers between rounds. Equal volumes of the second round PCR products were pooled and cleaned up using 1.2X (normalization) or 1X (expression) Agencourt AMPure XP beads, then pooled with other samples having different indexes, and sequenced on an Illumina HiSeq4000 using 2x100bp paired-end reads.

treatment_protocol: Expression samples were treated with either 100ng/mL or 0ng/mL doxycycline prior to extraction.

tag: doxy concentration

tag: target site

value: Doxycycline-inducible provirus


title: AK83_lodi_rep_1


title: HiC_St15_females_controlRNAi_rep2

description:
processed data file: st15_TADs.bed
processed data file: st15_wt_f_2500bp.A.norm_cor.h5
processed data file: st15_wt_f_2500bp.X.norm_cor.h5
processed data file: st15_wt_f_40000bp_compartments.bedgraph
processed data file: st15_wt_f_TADs_insulation.bw

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304) expressed in Sxl-GFP genetic background; Sorted to be GFP positive


title: Marm025_V1_08012018

description:
single-nucleus gene expression data based on 3' transcript counts
marm.ctx.int.DS.raw.dge.txt.gz

value: Dropseq

value: Neocortex; V1


title: iPCR, Doxy conc 0, bio rep 2, tech rep 1


title: st15_H3_controlRNAi_Rep3

description: processed data file: st15_H3_controlRNAi_log2Input_min140_ext_rep3.bw

data_processing:
ChIP-seq: Data processing was done using the snakePipes pipeline (https://doi.org/10.1093/bioinformatics/btz436). The DNA-mapping followed by the ChIP-seq pipeline were used. The default parameters were used.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: ChIP-seq: bigwigs log2 to Input, 1x coverage using bamCompare from deepTools, chrX was excluded for scalefactor calculation. Fragments below 140 bp were removed.

source_name: mixed stage 15 embryos

extract_protocol:
ChIPseq: Dechorionated embryos were fixed using 1% Formaldehyde for 15min at RT. After fixation, they were hand picked for the desired developmental stage and frozen at -80oc until further use. Nuclei were isolated using short covaris sonication followed by chromatin digestion using Micrococcal nuclease and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)

value: mixed stage 15 embryos

value: ChIP-seq

tag: chip antibody

value: anti-H3 (Cell Signaling 2650S)


title: AK83_camporegio_rep_3

value: camporegio root exudate


title: HiC_St15_females_controlRNAi_rep1


title: iPCR, Doxy conc 0, bio rep 1, tech rep 2


title: AK83_camporegio_rep_2


title: marm023_Pu_merged_corrected

description:
single-nucleus gene expression data based on 3' transcript counts
marm.str.int.DS.raw.dge.txt.gz

value: Striatum; Putamen


title: HiC_St15_females_mofRNAi_rep2

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP positive

value: embryos st15


title: iPCR, Doxy conc 0, bio rep 1, tech rep 1


title: marm023_PFCo_merged

value: Neocortex; PFC


title: AK83_blank_rep_3

value: no treatment


title: HiC_St15_males_mofRNAi_rep1

description:
processed data file: st15_TADs.bed
processed data file: st15_mof_m_2500bp.A.norm_cor.h5
processed data file: st15_mof_m_2500bp.X.norm_cor.h5
processed data file: st15_mof_m_40000bp_compartments.bedgraph
processed data file: st15_mof_m_TADs_insulation.bw

source_name: male embryos st15

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP negative

value: male

value: Hi-C


title: marm023_PFCm_merged_corrected


title: iPCR, Doxy conc 100, bio rep 2, tech rep 2

value: Doxycycline-inducible provirus


title: iPCR, Doxy conc 100, bio rep 2, tech rep 1


title: HiC_St15_males_controlRNAi_rep2

description:
processed data file: st15_wt_m_2500bp.A.norm_cor.h5
processed data file: st15_wt_m_2500bp.X.norm_cor.h5
processed data file: st15_wt_m_40000bp_compartments.bedgraph
processed data file: st15_wt_m_TADs_insulation.bw
processed data file: st15_TADs.bed

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304) expressed in Sxl-GFP genetic background; Sorted to be GFP negative


title: AK83_blank_rep_2


title: HiC_St15_males_controlRNAi_rep1


title: AK83_blank_rep_1


title: iPCR, Doxy conc 100, bio rep 1, tech rep 2


title: HiC_St5_mofRNAi_rep2

description:
processed data file: st5_mof_2500bp.A.norm_cor.h5
processed data file: st5_mof_2500bp.X.norm_cor.h5
processed data file: st5_mof_40000bp_compartments.bedgraph
processed data file: st5_mof_TADs_insulation.bw
processed data file: st5_TADs.bed

source_name: blastoderm embryos nc14

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 58281)

value: blastoderm embryos nc14


title: marm023_Hipp_sl07.merged_updated

description:
single-nucleus gene expression data based on 3' transcript counts
marm.hippo.int.raw.dge.txt.gz

value: Dropseq

value: Hippocampus


title: 1021_verbena_rep_3

description:
overall_collapsed.tsv
1021_raw_counts.tsv

value: verbena root exudate


title: iPCR, Doxy conc 100, bio rep 1, tech rep 1


title: HiC_St5_mofRNAi_rep1


title: marm023_Caud_merged

value: Striatum; Caudate


title: HiC_St5_controlRNAi_rep3

description:
processed data file: st5_TADs.bed
processed data file: st5_wt_2500bp.A.norm_cor.h5
processed data file: st5_wt_2500bp.X.norm_cor.h5
processed data file: st5_wt_40000bp_compartments.bedgraph
processed data file: st5_wt_TADs_insulation.bw

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)


title: 1021_verbena_rep_2


title: marm023_V1_merged_corrected

value: Neocortex; V1


title: A8 Mock

city: Chapel Hill

first: Lishan

last: Su

state: NC

address: 125 Mason Farm Rd

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina

data_processing:
Illumina bcl2fastq combines all per-cycle BCL files from a Nextseq500/550 run and translates  them into FASTQ files.
10xGenomics chromium single cell software Cell Ranger version 2.1.0 analysis pipelines performed sample demultiplexing, barcode processing, and single cell 3' gene counting.
Output files of the 10X Cell Ranger pipeline were stored in a folder named "outs".
Single cell gene expression raw data were processed using the single cell R software Seurat 3.
Genome_build: hg19
Supplementary_files_format_and_content: Output of the 10X Cell Ranger pipeline consisting of the filtered gene-barcode matrix of UMI counts in Market Exchange (MEX) format (matrix.mtx file) and two tab separated metadata files: the genes.tsv file containing the list of genes in the matrix.mtx file and the barcodes.tsv file containing the barcodes represented in the matrix.mtx file.

molecule: polyA RNA

source_name: hCD45+ splenocytes

extract_protocol:
Single cells were loaded to 10x Genomics Chromium chip (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel bead in Emulsion (GEM). GEM-reverse transcription was performed with the following condition: 55 ℃ for 2 h, 85 ℃ for 5min; held at 4 ℃.
Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell’ Gel Bead and Library Kit. After RT, GEMs were broken, and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific) and SPRIselect Reagent Kit (0.6x SPRI; Beckman Coulter). cDNA was amplified using with the following condition: 98 ℃ for 3min; cycled 14x: 98 ℃ for 15 s, 67 ℃ for 20 s, and 72 ℃ for 1min; 72 ℃ for 1min; held at 4 ℃. cDNA product was cleaned up using the SPRIselect Reagent Kit. Indexed sequencing libraries were constructed with the reagents in the GemCode Single-Cell 3’ Library Kit.

treatment_protocol: Mice were anesthetized and infected with HIV-1 (JR-CSF) through retro-orbital injection. hCD45+hCD3-hCD19- human leukocytes were obtained from spleens of 2 mock and 2 HIV-1 infected humanized mice 3 weeks post HIV-1 infection.

tag: sample id

tag: condition

value: Mock

tag: humanization procedure

value: Humanized NRG-hu HSC mice were generated by intrahepatic injection of 2x105 CD34+ hematopoietic progenitor cells derived human fetal liver into newborn (2 to 5 days old) NRG (NOD-Rag2-/- γc-/-) mice.

value: hCD45+hCD3-hCD19-  splenocyte from humanized mice


title: Marm022_V1_08012018


title: AK83_camporegio_rep_1

value: camporegio root exudate


title: HiC_St15_males_mofRNAi_rep2

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP negative

value: embryos st15


title: 1021_verbena_rep_1


title: HiC_St5_controlRNAi_rep2

value: Hi-C


title: A7 Mock


title: marm022_Pu_collected_room_temp

value: Striatum; Putamen


title: A6 HIV-1

value: HIV-1 infected


title: marm023_NACC_merged

value: Striatum; Nucleus accumbens


title: 1021_luteolin_rep_2

value: luteolin


title: marm022_Pu_collected_on_ice

value: Dropseq


title: Marm022_PFCvl_07312018

value: Neocortex; PFC


title: RNAseq_St15_mofRNAi_female_embryos_04

description:
st15_mofRNAi_females_rep4
processed data file: st15_RNAseq_counts.txt

data_processing:
Quality control, mapping and count retrieval were done as described in Bhardwaj, V. et al. "snakePipes: facilitating flexible, scalable and integrative epigenomic analysis" https://doi.org/10.1093/bioinformatics/btz436
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files include gene counts.

source_name: st15 embryos

extract_protocol:
st15 embryos: 14-16h embryos were inspected under the stereoscope and were selected for the desired stages and for Sxl-GFP presence or absence to distinguish their gender. 25 embryos were homogenized in Trizol and total mRNA was isolated using the microRNA Zymo Kit. RNA Quality was assessed by Fragment Analyzer.
TruSeq Stranded mRNA.

tag: genotype

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP positive

value: st15 embryos

value: female


title: 1021_luteolin_rep_3


title: 1021_luteolin_rep_1


title: RNAseq_St15_mofRNAi_female_embryos_03

description:
st15_mofRNAi_females_rep3
processed data file: st15_RNAseq_counts.txt


title: marm022_PFCdl_sl02_merged


title: 1021_lodi_rep_3

value: lodi root exudate


title: Endy-F2_S17

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
raw sequence intensities obtained in nextseq500 instrument, converted to basecalls using bcl2fastq sofware,
trim reads, truSeq adaptors trimed using cutadapt and partk flow, minimum length set to 25
aligned reads to refseq index (V82) of human genome (hg38) using bowt
quntification performed to refseq index (V82) of human genome (hg38) in partek flow, using IM algorithm
normalization performed using RPKM
Genome_build: hg38 RefSeq Transcript 82 2017-08-02
Supplementary_files_format_and_content: two data matrix files of raw and normalized count abundance is provided as a CSV file for all six samples

source_name: HUVEC

growth_protocol: HUVECs were grown to confluence in media containing endothelial cell growth factors, in gelatin coated cell culture plates

extract_protocol:
Qiagen Rneasy
Illumina TruSeq Stranded mRNA Library Prep Kit
Libraries were diluted to 4nM, pooled, and run at 0.8pM final concentration with a 1% PhiX spike-in on the NextSeq 500 instrument (Illumina) with a single 75bp read, using the NextSeq 500/550 High Output Kit v2 (75 cycles).

treatment_protocol: NS1 or mock was added directly to spent media in wells and incubated for 4 hrs

value: human umbilical vein endothelial cells (HUVECS)

tag: passage

value: pass 2-5

value: NS1 50 ug/ml


title: RNAseq_St15_mofRNAi_female_embryos_02

description:
st15_mofRNAi_females_rep2
processed data file: st15_RNAseq_counts.txt


title: A5 HIV-1

value: Humanized NRG-hu HSC mice were generated by intrahepatic injection of 2x105 CD34+ hematopoietic progenitor cells derived human fetal liver into newborn (2 to 5 days old) NRG (NOD-Rag2-/- γc-/-) mice.

value: hCD45+hCD3-hCD19-  splenocyte from humanized mice


title: marm022_NACC


title: 1021_lodi_rep_2


title: Endy-F1_S16


title: Endy-A3_S3

value: mock


title: RNAseq_St15_mofRNAi_female_embryos_01

description:
st15_mofRNAi_females_rep1
processed data file: st15_RNAseq_counts.txt


title: marm022_HF_sl08_merged

value: Hippocampus


title: 1021_lodi_rep_1


title: RNAseq_St15_controlRNAi_female_embryos_04

description:
st15_controlRNAi_females_rep4
processed data file: st15_RNAseq_counts.txt

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304) expressed in Sxl-GFP genetic background; Sorted to be GFP positive


title: Marm022_Hippo_07202018


title: Endy-A2_S2


title: RNAseq_St15_controlRNAi_female_embryos_03

description:
st15_controlRNAi_females_rep3
processed data file: st15_RNAseq_counts.txt


title: Endy-A1_S1


title: HiC_St5_controlRNAi_rep1

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)

value: blastoderm embryos nc14

value: Hi-C


title: Marm022_Cd

value: Dropseq

value: Striatum; Caudate


title: 1021_camporegio_rep_2

value: camporegio root exudate


title: RNAseq_St15_controlRNAi_female_embryos_02

description:
st15_controlRNAi_females_rep2
processed data file: st15_RNAseq_counts.txt

value: st15 embryos


title: 1021_camporegio_rep_3


title: RNAseq_St15_mofRNAi_male_embryos_04

description:
st15_mofRNAi_males_rep4
processed data file: st15_RNAseq_counts.txt

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281) expressed in Sxl-GFP genetic background; Sorted to be GFP negative

value: male


title: Macaque_A13180_PFC

description:
single-nucleus gene expression data based on 3' transcript counts
mq.ctx.int.raw.dge.txt.gz

organism: Macaca mulatta

source_name: Adult Macaque Brain

value: Neocortex; PFC


title: HCT116_PolyA_seq_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

data_processing:
NextSeq Control Software 1.4 was used for basecalls.
Reads were trimmed for polyG sequence, and polyA sequence shorter than 11nt were discarded. PolyA lengths were counted from basecalls.
Sequenced reads were trimmed for polyA and adaptor sequence, and reads longer than 20nt were mapped to GRCH38 whole genome using tophat2 with parameters -a 8 -m 0 -g 2 --microexon-search --report-secondary-alignments --read-edit-dist 4 N 2 --b2-N 1
the median of polyA sequence length was calculated of each gene.
Genome_build: GRCH38
Supplementary_files_format_and_content: txt file, the median of polyA length of each gene in each sample

source_name: HCT116 cells

extract_protocol:
Total RNA was extracted with Trizol and treated with RQ1 DNase (Promega) to remove DNA
Total RNA was partially fragmented with RNase T1. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads. 3’ adaptor was added to purified mRNAs, followed by reverse transcription performed with RT primer harboring 5' adaptor sequence and randomized hexamer. The cDNAs were purified and PCR amplified for library construction for Illumina NextSeq 500 system.

value: human colon cancer cells

tag: cell line


title: 1021_blank_rep_3

tag: strain

value: no treatment


title: Endy-F3_S18

value: human umbilical vein endothelial cells (HUVECS)

value: pass 2-5

tag: treatment

value: NS1 50 ug/ml


title: 1021_camporegio_rep_1


title: Macaque_A13179_PFC

tag: tissue


title: HCT116_PolyA_seq_2

source_name: HCT117 cells


title: HEK293T_PolyA_seq_2

source_name: HEK294T cells

value: human embryonic kidney cells


title: Macaque_A13180_V1

value: Neocortex; V1


title: HEK293T_PolyA_seq_1

source_name: HEK293T cells


title: RNAseq_St15_mofRNAi_male_embryos_02

description:
st15_mofRNAi_males_rep2
processed data file: st15_RNAseq_counts.txt

tag: Sex


title: 1021_blank_rep_1


title: RNAseq_St15_controlRNAi_male_embryos_04

description:
st15_controlRNAi_males_rep4
processed data file: st15_RNAseq_counts.txt

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304) expressed in Sxl-GFP genetic background; Sorted to be GFP negative


title: RNAseq_St15_mofRNAi_male_embryos_01

description:
st15_mofRNAi_males_rep1
processed data file: st15_RNAseq_counts.txt


title: ferret_V1_rxn2

description:
single-nucleus gene expression data based on 3' transcript counts
ferret.ctx.int.raw.dge.txt.gz

organism: Mustela putorius furo

source_name: Adult Ferret Brain


title: 1021_blank_rep_2

source_name: Bacterial culture


title: Macaque_A13179_V1


title: si-PTB_PolyA_seq_2

source_name: HeLa cells

value: human cervical cancer cells

value: HeLa


title: RNAseq_St15_controlRNAi_male_embryos_02

description:
st15_controlRNAi_males_rep2
processed data file: st15_RNAseq_counts.txt


title: Macaque_A13180_PFC_Kollidon-VA64

value: Dropseq


title: Macaque_A13180_Kollidon-12


title: si-PTB_PolyA_seq_1


title: ferret_V1_rxn1


title: HeLa_PolyA_seq_2


title: ferretP42_str_nova_rxn2

description:
single-nucleus gene expression data based on 3' transcript counts
ferret.str.int.raw.dge.txt.gz

value: Striatum


title: RNAseq_St15_controlRNAi_male_embryos_01

description:
st15_controlRNAi_males_rep1
processed data file: st15_RNAseq_counts.txt


title: Macaque_A13180_PFC_DB-only


title: HeLa_PolyA_seq_1


title: RNAseq_S2_Mof_RNAi_02

description:
S2_Rep2_Mofkd
processed data file: S2_mofvscontrolRNAi_counts.tsv

source_name: S2 cells

growth_protocol: Dmel2 S2 cells (gift from Boutros lab) were cultured in Express 5 Serum Free Medium supplemented with 10% Glutamax. We used 10ug of dsRNA per 1 million cells and incubated them at 25o for 3 days.

extract_protocol:
S2 cells: dsRNAs against mof or gfp were prepared according to the DRSC protocol via standard T7 in vitro transcription of DNA template using the HiScribe™ T7 High Yield RNA Synthesis Kit (NEB E2040S) (http://www.flyrnai.org/DRSC-PRS.html).
TruSeq Stranded mRNA.

value: S2 (Dmel-2)


title: ferretP42_str_nova_rxn1


title: U87OE_TMZ_day14 rep3

city: tianjin

first: Kai

last: Huang

address: anshan roud

institute: tianjin medical university

data_processing:
SOAPnuke(v1.5.2) software used for basecalling.
RNA-seq reads were mapped to hg19 whole genome by Hisat2 software.
DEseq2 method was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format files include FPKM values

source_name: U87 cell

growth_protocol: The cells were routinely maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS, HyClone, Logan, UT, USA) in a humidified 5% CO2 atmosphere at 37℃.

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: Cells were treated with 350 µM TMZ for 7 and 14 days.

value: glioblastoma cells

value: U87 cells transduced with lentivirus encoding EGFRvIII


title: MaleMouse_PC

description:
single-nucleus gene expression data based on 3' transcript counts
mouse.nuc.cortical_interneurons.raw.dge.txt.gz

organism: Mus musculus

source_name: P60-70 Male Mice


title: RNAseq_S2_Mof_RNAi_01

description:
S2_Rep1_Mofkd
processed data file: S2_mofvscontrolRNAi_counts.tsv


title: ferret_PFC_rxn2


title: FemaleMouse_PC

source_name: P60-70 Female Mice


title: ferret_PFC_rxn1


title: RNAseq_S2_GFP_RNAi_03

description:
S2_Rep3_GFPkd
processed data file: S2_mofvscontrolRNAi_counts.tsv


title: MaleMouse_FC


title: FemaleMouse_FC


title: U87OE_TMZ_day7 rep3


title: U87OE_TMZ_day7 rep2


title: RNAseq_S2_GFP_RNAi_01

description:
S2_Rep1_GFPkd
processed data file: S2_mofvscontrolRNAi_counts.tsv


title: 01.13.17.FrozenP2


title: RNAseq_S2_Mof_RNAi_03

description:
S2_Rep3_Mofkd
processed data file: S2_mofvscontrolRNAi_counts.tsv


title: U87OE_TMZ_day7 rep1


title: 01.13.17.FreshP1


title: PolII_ChIPseq mofRNAi_rep2

description: St5_PolII_mofRNAi_InputSubstracted.bigwig

data_processing:
ChIP-seq: Data processing was done using the bioRxiv. 2018, DOI: 10.1101/407312 pipeline. The DNA-mapping followed by the ChIp-seq pipeline were used. The default parameters were used.
Genome_build: dm6
Supplementary_files_format_and_content: ChIP-seq: bigwig normalized to Input, 1x coverage using bamCompare from deepTools, chrX was excluded for scalefactor calculation

source_name: blastoderm embryos c14

growth_protocol: D. melanogaster flies were maintained  in standard Drosophila medium at 25oC.

extract_protocol:
ChIPseq: Dechorionated embryos were fixed using 0.1% Formaldehyde for 15min at RT. After fixation, they were hand picked for the desired developmental stage and frozen at -80oc until further use. Nuclei were isolated using short covaris sonication followed by chromatin digestion using Micrococcal nuclease and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 16h. After RNaseA and proteinaseK treatment, the DNA from input and immunoprecipitation was purified using phenol-chloroform extraction and ethanol precipitation.
NEB Next Ultra II

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)

value: blastoderm embryos c14

tag: technique

value: Mnase-ChIP-seq

tag: antibody

value: anti-RPB3 (Akhtar home made antibody)


title: U87OE_day14 rep3

tag: cell type


title: P60STRRep3P2

description:
single-nucleus gene expression data based on 3' transcript counts
F_GRCm38.81.P60Striatum.raw.dge.txt.gz

tag: platform


title: PolII_ChIPseq mofRNAi_rep1


title: Input_PolII_ChIPseq mofRNAi_rep2


title: U87OE_TMZ_day14 rep2


title: U87OE_day14 rep2


title: Input_PolII_ChIPseq mofRNAi_rep1


title: U87OE_TMZ_day14 rep1


title: U87OE_day14 rep1


title: P60STRRep2P2


title: 25min rep 2

city: Leuven

first: Cedric

last: Lood

address: Kasteelpark Arenberg 20 - box 2460

department: Division of Animal and Human Health Engineering

country: Belgium

institute: KU Leuven

data_processing:
Raw reads quality control performed with trimmomatic, seqtk, and fastqc
Alignment to reference genome using TopHat2 with stranded (filename includes .str) and non-stranded depending on sample
Read counts using HTSeq-count
Normalization of counts within the triplicates of a given condition using TPM
Host DGE comparing late infection with no infection was performed as described in Blasdel et al. 2018 (Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer)
Genome_build: Pseudomonas aeruginosa PAO1 with accession number NC_002516.2, and PA5oct denovo assembled genome (see related publication)
Supplementary_files_format_and_content: Phage PA5oct count tables and normalization in xlsx format, host DGE count tables and normalization in xlsx format

organism:
Pseudomonas aeruginosa PAO1
Pseudomonas virus PA5oct

source_name: Pseudomonas aeruginosa PAO1 growing exponentially in LB synchronoulsy infected with phage PA5oct

growth_protocol: LB exponential growth

extract_protocol:
Organic extraction
truseq stranded mRNA

treatment_protocol: Viral infection as described in Blasdel et al. 2018, Preparing cDNA libraries from lytic phage-infected cells for whole transcriptome analysis by RNA-Seq, Springer

tag: infection time

value: 25 minutes


title: RNAseq_S2_GFP_RNAi_02

description:
S2_Rep2_GFPkd
processed data file: S2_mofvscontrolRNAi_counts.tsv


title: P60STRRep2P1


title: PolII_ChIPseq controlRNAi_rep1

description: St5_PolII_controlRNAi_InputSubtracted.bigwig

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)


title: U87OE_day7 rep2


title: 25min rep 1


title: P60STRRep3P1


title: P60STRRep1P3


title: P60STRRep1P4


title: U87OE_day7 rep1


title: St15_H3_msl3RNAi_rep1

source_name: stage 15 embryos, 14-16h

value: progeny of mat-a-tubGal4/msl-3RNAi mothers crossed to their siblings (Bloomington stocks:7062 & 57261)

value: stage 15 embryos, 14-16h

value: anti-H3(Cell Signaling, 2650S)


title: st15_Input_males

value: Bloomington 24105 -sorted male embryos


title: U87OE_day7 rep3


title: U87OE_day_0 rep1


title: AGS_exosome_rep1

type: RNA

city: Zhengzhou

first: peiming

last: zheng

address: 7 Weiwu Road

institute: People’s Hospital of Zhengzhou University

description: Exosome derived from AGS culture media

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: AGS derived exosome

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Four human GCC lines (MGC803, BGC823, SGC7901, and AGS) and one normal human gastric (GES-1) cell line were  cultured at 37 °C with 5% CO2 in 1640/DMEM containing 10% exosome-depleted FBS. Exosomes from the culture media (CM) of four GC cells (GCCs) and human gastric epithelial cells were isolated using ExoQuick solution kit.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified byRNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

value: AGS

value: AGS derived exosome

value: gastric cancer


title: st15_H4K16ac_males

value: Bloomington 24105 - sorted male embryos

value: anti-H4K16ac(Merck Milipore, 07-329)


title: MGC_exosome_rep1

description: Exosome derived from MGC culture media

source_name: MGC derived exosome

value: MGC derived exosome


title: BGC_exosome_rep1

description: Exosome derived from BGC culture media

source_name: BGC derived exosome

value: BGC derived exosome


title: 15min rep 3

value: 15 minutes


title: 5min rep 3

value: 5 minutes


title: U87OE_day_0 rep3

value: glioblastoma cells

value: U87 cells transduced with lentivirus encoding EGFRvIII


title: 15min rep 2


title: 5min rep 2


title: P60HippoRep6P3

description:
single-nucleus gene expression data based on 3' transcript counts
F_GRCm38.81.P60Hippocampus.raw.dge.txt.gz

value: Dropseq

value: Hippocampus


title: Input_PolII_ChIPseq controlRNAi_rep1

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)

value: blastoderm embryos c14

value: Mnase-ChIP-seq


title: 25min rep 3

value: 25 minutes


title: U87OE_day_0 rep2


title: P60STRRep1P2

value: Striatum


title: U87NC_TMZ_day14 rep3

value: U87 cells transduced with lentivirus encoding vector


title: P60STRRep1P1


title: GES_exosome_rep1

description: Exosome derived from GES culture media

source_name: GES derived exosome

value: GES derived exosome

value: gastric normal


title: St15_H3_mofRNAi_rep2

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)

value: stage 15 embryos, 14-16h

value: anti-H3(Cell Signaling, 2650S)


title: SGC_exosome_rep1

description: Exosome derived from SGC culture media

source_name: SGC derived exosome

value: SGC derived exosome

value: gastric cancer


title: St15_H3_mofRNAi_rep1


title: 5min rep 1

value: 5 minutes


title: U87NC_TMZ_day14 rep2

value: glioblastoma cells


title: St15_H3_controlRNAi_rep2


title: P60HippoRep6P1

value: Dropseq


title: St15_H3_controlRNAi_rep1


title: DuvrY-pUvrY

city: Tainan

first: Yi-Wei

address: No.1 University Road

country: Taiwan

institute: NCKU

data_processing:
Ion Proton system used for basecalling
Mapping and whole transcriptome analysis (TopHat and Bowtie2 software package)
RNA-Seq analysis (Partek software package)
Genes were derived from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=1156800
Genome_build: ASM31519v1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Aeromonas dhakensis

source_name: bacteria

growth_protocol: 18 hours (overnight) cultured at 37oC with shaking under 200rpm

extract_protocol:
RNA was harvested using RNeasy Protect Bacteria Mini Kit (Qiagen, Cat. No. 74524).
RNA libraries were prepared for sequencing using Ion Total RNA-seq Kit V2 and IonOneTouch 2 system

tag: genotype/variation

value: DuvrY-pUvrY mutant

tag: age

value: 18hr (overnight culture)

tag: medium

value: LB


title: P60HippoRep6P2

value: Hippocampus


title: St15_H4K16ac_msl3RNAi_rep1

value: progeny of mat-a-tubGal4/msl-3RNAi mothers crossed to their siblings (Bloomington stocks:7062 & 57261)

value: Mnase-ChIP-seq

value: anti-H4K16ac(Merck Milipore, 07-329)


title: P60HippoRep5P2


title: P60HippoRep5P3


title: AAK1

value: wild type


title: U87NC_TMZ_day14 rep1

value: U87 cells transduced with lentivirus encoding vector


title: St15_H4K16ac_mofRNAi_rep2

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)


title: DuvrY

value: DuvrY mutant


title: P60HippoRep4P3


title: U87NC_TMZ_day7 rep3


title: St15_H4K16ac_mofRNAi_rep1

value: stage 15 embryos, 14-16h


title: U87NC_TMZ_day7 rep2


title: U87NC_day14 rep3


title: SWI3C-RNAi_D_ATACseq_2

first: Yu

last: Chang

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

data_processing:
For RNA-seq analysis, the raw reads were filtered by fastp with the parameter “-q 30” (Chen et al., 2018) and checked by FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) to ensure the exclusion of adaptor and low quality sequences. The resulting reads were mapped to rice reference genome RGAP 7 (Kawahara et al., 2013) using STAR v1.5.2 (Dobin et al., 2013) with default parameters. The alignments were further filtered (-b -f 2 -F 524 -q 5), sorted and indexed by SAMtools v1.9 (Li et al., 2009) before the transcripts were assembled and count by StringTie v1.3.6 (Pertea et al., 2015) according to the reference genome. Differential gene expression was determined by DESeq2 with the gene count matrix generated by StringTie at the threshold of |log2(Fold Change)|≥1 and adjust P value <0.05.
For ATAC-seq analysis, the filtered reads were mapped to the reference genome using Bowtie2 v 2.2.6 (Langmead and Salzberg, 2012) with parameters “--no-unal --threads 8 --sensitive -k 1 -q”. Redundant reads were removed using Picard v2.60 (http://broadinstitute.github.io/picard/). Peak-calling was using MACS2 (version 2.1.0) (Zhang et al., 2008) with parameters “--nomodel --shift -100 --extsize 200”. If multiple peaks resided within 50 bp to each other, they were considered as a single peak. For differential peak analysis we used DiffBind (Stark & Brown, 2011) based on DESeq2 method. The differential peaks were filtered out by the threshold of log2(Fold Change) ≥0.5, FDR<0.05, and P value <0.05.
Genome_build: RGAP 7
Supplementary_files_format_and_content: For RNA-Seq, each .tab file contains coverage, FPKM, and TPM for the sample. For ATAC-Seq, pooled reads dencity of the three replicates is presented by the bigWig file.

organism: Oryza sativa Japonica Group

source_name: seedling root from OsSWI3C-RNAi plants, under drought condition, replicate2

growth_protocol: Seedling (25-day-old) roots from hydroponic culture were harvested for genomic DNA or total RNA extraction.

extract_protocol:
Seedling roots were splintered into pieces and nuclei were isolated using ice-cold buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 3 mM DTT, 0.2% TritonX-100) then filtered with a 100 μm filter. Nuclei were stained with DAPI and loaded into a flow cytometer (Becton Dickinson FACSCalibur). Nuclei were sorted and collected 200,000 in a 1.5-ml centrifuge tube containing lysis buffer. Nuclei were resuspended in 1× TD buffer (Illumina) and 4 μL Tn5 transposes (Illumina) were added. The transposition reaction was performed in a thermocycler by centrifugation at 300 rpm for 30 min at 37 °C, and directly purified the DNA with a TaKaRa MiniBEST DNA Fragment Purification Kit (Potter et al., 2018). DNA libraries were amplified for a total of eleven cycles as described (Buenrostro et al., 2013) and purified the product with AMPure® XP Beads Kit.
Library construction was performed by Novogene Inc (Tianjin, China) accroding to the standard protocol of Illumina.

treatment_protocol: Seedlings were grown in normal condition (28°C during day light, 22°C at night).  For drought stress treatment, the seedlings were deprived from water supply for three hours before sampling.

value: OsSWI3C-RNAi root

tag: developmental stage

value: 4-leaf stage

value: drought


title: P60HippoRep5P1


title: SWI3C-RNAi_D_ATACseq_3

source_name: seedling root from OsSWI3C-RNAi plants, under drought condition, replicate3


title: St15_H4K16ac_controlRNAi_rep2

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)


title: U87NC_TMZ_day7 rep1

value: glioblastoma cells


title: P60HippoRep4P2

value: Dropseq


title: St15_H4K16ac_controlRNAi_rep1


title: U87NC_day14 rep2


title: P60HippoRep4P1


title: SWI3C-RNAi_D_ATACseq_1

source_name: seedling root from OsSWI3C-RNAi plants, under drought condition, replicate1


title: Input_St15_msl3RNAi_rep1


title: ZH11-WT_D_ATACseq_3

source_name: seedling root from ZH11-WT, under drought condition, replicate3

value: ZH11-WT root


title: U87NC_day14 rep1


title: HippoRep3P3


title: ZH11-WT_D_ATACseq_2

source_name: seedling root from ZH11-WT, under drought condition, replicate2


title: HippoRep3P2


title: ZH11-WT_D_ATACseq_1

source_name: seedling root from ZH11-WT, under drought condition, replicate1


title: U87NC_day7 rep3

source_name: U87 cell


title: U87NC_day7 rep2


title: HippoRep3P1

source_name: P60-70 Male Mice


title: NMCP1OE_D_ATACseq_3

source_name: seedling root from OsNMCP1-OE plants, under drought condition, replicate3

value: OsNMCP1-OE root


title: Input_st15_controlRNAi_rep1


title: Input_st15_controlRNAi_rep2


title: P60HippoRep1P2

value: Hippocampus


title: HippoRep2P1


title: st7_H4K16ac_rep1

source_name: gastrulating embryos

value: w- OR

value: gastrulating embryos


title: Input_St15_mofRNAi_rep2

source_name: stage 15 embryos, 14-16h

value: Mnase-ChIP-seq


title: U87NC_day0 rep1


title: P60HippoRep1P1


title: st7_H4K16ac_rep2

value: anti-H4K16ac(Merck Milipore, 07-329)


title: HippoRep2P2


title: 15min rep 1

source_name: Pseudomonas aeruginosa PAO1 growing exponentially in LB synchronoulsy infected with phage PA5oct

value: 15 minutes


title: U87NC_day0 rep3

value: U87 cells transduced with lentivirus encoding vector


title: U87NC_day7 rep1


title: NMCP1OE_D_ATACseq_2

source_name: seedling root from OsNMCP1-OE plants, under drought condition, replicate2


title: ZH11-WT_D_RNAseq_3

extract_protocol:
Total RNA was extracted by TRIzol® reagent (AmbionTM, Lot No. 15596018) /chloroform extraction according to the manufacturer’s instructions.
Library construction was performed by Novogene Inc (Tianjin, China) accroding to the standard protocol of Illumina.


title: B6J_nTr20_del_4_batch2_forebrain_RNA

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: rRNA depleted total RNA

data_processing:
Forebrain RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM20 transcript reference.
Hippocampus RNA-seq was mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Hippocampus RNA-seq and ribosome profiling reads were counted at the gene-level using featureCounts. The RNA-seq data was quantifified by counting reads overlapping exons and the ribosome profiling data was quantified by counting reads overlapping CDS regions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts for hippocampus RNA-seq and ribosome profiling samples.

source_name: Forebrain

extract_protocol:
For forebrain samples, forebrains were isolated, and stored in RNAlater and frozen at -20C. Following ribosomal RNA depletion, the remaining RNA was purified, fragmented, and libraries were prepared using TruSeq Stranded Total RNA with RiboZero-Mouse (Illumina). mRNA libraries for the assessment of translational efficiency in the B6JN and B6JN-nTr20-/- hippocampus were prepared using the TruSeq v2 mRNA kit (Illumina). mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. Ribosome profiling libraries were generated from B6N and B6N-nTr20-/- hippocampi. Libraries were constructed as previously described (Ingolia et al., 2012)
RNA libraries were prepared for sequencing using standard Illumina protocols and ribosome profiling libraries were prepared following the protocol described in Ingolia et al., 2012

value: Forebrain

value: 8 weeks old

tag: batch

value: Batch 2


title: st7_Input_rep2


title: ZH11-WT_D_RNAseq_1

value: 4-leaf stage


title: ZH11-WT_D_RNAseq_2

value: drought


title: st7_Input_rep1


title: Input_St15_mofRNAi_rep1

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)

value: stage 15 embryos, 14-16h


title: B6J_nTr20_del_3_batch2_forebrain_RNA

description: rRNA depleted total RNA

tag: genotype


title: ATACseq_st5_msl3RNAi_rep2

data_processing:
ATAC-seq: Quality control, mapping and trimming of the reads using trimgalore was done through the "DNA-mapping" pipeline from the SnakePipes software (https://github.com/maxplanck-ie/snakepipes/)  v1.1.2 (bioRxiv. 2018, DOI: 10.1101/407312)  including filtering of multimappers and keeping only properly paired reads. For calling open chromatin peaks the "ATAC-seq" pipeline from snakePipes was used.
Genome_build: dm6
Supplementary_files_format_and_content: ATAC-seq: open chromatin peaks called using MACS2 the snakePipes pipeline

source_name: blastoderm embryos nc14

extract_protocol:
ATAC-seq: D. melanogaster dechorionated embryos were fixed using 1% formaldehyde for 15min at RT. 25 or 100 embryos were hand staged based on morphology for cycle 9-13 or Mid nuclear cycle 14 corresponding to st3-4 and st5 respectively. Nuclei isolation was achieved using Covaris sonication and nuclei filtering. Nuclei pellet was dissolved in 50ul of cold buffer containing 10mM Tris- HCl pH=7.4, 10 mM NaCl, 3 mM MgCl2, 15 mM HEPES (pH 7.6) and 0.1% NP-40. A 10min centrifugation at 500g followed. Further processing for ATAC-seq was adapted from (31) Briefly, the nuclei pellet was resuspended in Tn5 Reaction mix containing 2.5 Tn5 from the Nextera DNA Library Prep Kit from Illumina (cat. No 15027987), 25ul Buffer 2x and 22.5ul H20. The tagmentation reaction took place at 37o shaking at 800rpm. After precisely 30min, the samples were placed on ice and 250ul of PB buffer from the MinElute PCR Purification Kit (cat. No 28004) was added to stop the reaction. DNA purification was followed according to manufacture’s instructions. Pure DNA was amplified using 12 PCR cycles using the NebNext Polymerase (M0541S) for the library amplification.
Nextera

value: progeny of mat-a-tubGal4/msl-3RNAi mothers crossed to their siblings (Bloomington stocks:7063 & 57261)

value: blastoderm embryos nc14

value: ATAC-seq


title: NMCP1OE_D_RNAseq_3

value: OsNMCP1-OE root


title: NMCP1OE_D_ATACseq_1

source_name: seedling root from OsNMCP1-OE plants, under drought condition, replicate1


title: B6J_nTr20_del_2_batch2_forebrain_RNA

description: rRNA depleted total RNA


title: U87NC_day0 rep2

value: glioblastoma cells


title: B6J_nTr20_del_1_batch2_forebrain_RNA

description: rRNA depleted total RNA


title: NMCP1OE_D_RNAseq_2


title: ATACseq_st5_msl3RNAi_rep1


title: ATACseq_st5_controlRNAi_rep2

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)


title: NMCP1OE_D_RNAseq_1


title: ATACseq_st5_controlRNAi_rep1


title: SWI3C-RNAi_ATACseq_3

source_name: seedling root from OsSWI3C-RNAi plants, under normal condition, replicate3

value: OsSWI3C-RNAi root

value: normal


title: SWI3C-RNAi_ATACseq_2

source_name: seedling root from OsSWI3C-RNAi plants, under normal condition, replicate2


title: B6J_nTr20_Tg_4_batch2_forebrain_RNA

description: rRNA depleted total RNA


title: ATACseq_st3-4_mofRNAi_rep2

source_name: preblastoderm embryos nc9-13

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 58281)

value: preblastoderm embryos nc9-13


title: B6J_nTr20_Tg_3_batch1_forebrain_RNA

description: rRNA depleted total RNA

value: Forebrain

value: Batch 1


title: SWI3C-RNAi_ATACseq_1

source_name: seedling root from OsSWI3C-RNAi plants, under normal condition, replicate1


title: B6J_nTr20_Tg_1_batch1_forebrain_RNA

description: rRNA depleted total RNA

value: 8 weeks old


title: ATACseq_st3-4_mofRNAi_rep1


title: ZH11-WT_ATACseq_3

source_name: seedling root from ZH11-WT, under normal condition, replicate3

treatment_protocol: Seedlings were grown in normal condition (28°C during day light, 22°C at night). For drought stress treatment, the seedlings were deprived from water supply for three hours before sampling.

value: ZH11-WT root

value: 4-leaf stage


title: ATACseq_st3-4controlRNAi_rep2

source_name: preblastoderm embryos nc9-12

value: preblastoderm embryos nc9-12


title: B6J_4_batch1_forebrain_RNA

description: rRNA depleted total RNA

value: hypomorphic mutant for n-Tr20


title: ZH11-WT_ATACseq_2

source_name: seedling root from ZH11-WT, under normal condition, replicate2


title: B6J_nTr20_Tg_2_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: ZH11-WT_ATACseq_1

source_name: seedling root from ZH11-WT, under normal condition, replicate1


title: B6J_3_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: RNAseq_St7_mofRNAi_female_embryos_04

description:
St7_RNAseq_counts.txt
St7_mofRNAi_female_04
single embryo

data_processing:
quality control,mapping and count retrieval was done as described in Bhardwaj, V. et al. "snakePipes enable flexible, scalable and integrative epigenomic analysis." Biorxiv 407312 (2018). doi:10.1101/407312
Genome_build: dm6
Supplementary_files_format_and_content: gene counts

source_name: gastrulating embryos, st7

extract_protocol:
Embryos of the desired staged were identified under the stereoscope. Single embryos were homogenized in Trizol and total mRNA was isolated using the microRNA Zymo Kit. RNA Quality was assesed by Fragment Analyzer.
Truseq Stranded mRNA

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)

value: gastrulating embryos, st7

value: female


title: RNAseq_St7_mofRNAi_female_embryos_03

description:
St7_RNAseq_counts.txt
St7_mofRNAi_female_03
single embryo


title: NMCP1OE_ATACseq_3

source_name: seedling root from OsNMCP1-OE plants, under normal condition, replicate3

value: OsNMCP1-OE root


title: B6J_2_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: RNAseq_St7_mofRNAi_female_embryos_02

description:
St7_RNAseq_counts.txt
St7_mofRNAi_female_02
single embryo


title: B6J_1_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: B6N_nTr20_del_4_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: RNAseq_St7_mofRNAi_female_embryos_01

description:
St7_RNAseq_counts.txt
St7_mofRNAi_female_01
single embryo


title: NMCP1OE_ATACseq_2

source_name: seedling root from OsNMCP1-OE plants, under normal condition, replicate2


title: ZH11-WT_RNAseq_3


title: B6J_nTr20_Tg_4_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: NMCP1OE_ATACseq_1

source_name: seedling root from OsNMCP1-OE plants, under normal condition, replicate1


title: RNAseq_St7_controlRNAi_female_embryos_06

description:
St7_RNAseq_counts.txt
St7_control_female_06
single embryo

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)


title: B6N_nTr20_del_3_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: ZH11-WT_RNAseq_2


title: RNAseq_St7_controlRNAi_female_embryos_05

description:
St7_RNAseq_counts.txt
St7_control_female_05
single embryo


title: ZH11-WT_RNAseq_1


title: RNAseq_St7_controlRNAi_female_embryos_04

description:
St7_RNAseq_counts.txt
St7_control_female_04
single embryo


title: B6N_nTr20_del_2_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: ATACseq_st3-4controlRNAi_rep1

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7063 & 36304)

value: ATAC-seq


title: B6N_nTr20_del_1_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: RNAseq_St7_controlRNAi_female_embryos_03

description:
St7_RNAseq_counts.txt
St7_control_female_03
single embryo


title: NMCP1OE_RNAseq_1

value: normal


title: WT3D

city: Beijing

first: naixuan

last: cheng

address: Capital Medical University, No.10 Xitoutiao, You An Men, Fengtai District

institute: School of Basic Medical Sciences, Capital Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to GCF_000001635.26_GRCm38.p6 using HISAT
Raw counts and Fragments Per Kilobase Million(FPKM) were calculated by Bowtie2: -q -L 16 --phred64 -p 6
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each Sample

source_name: tibialis anterior muscle

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Four samples were pooled into one sample for miRNA sequencing at each time-point. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique barcodes, followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using realtime quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China)

treatment_protocol: Mice were anesthetized and the tibialis anterior muscles were injected with 10 mM cardiotoxin (30 mL; Sigma, St. Louis, MO, USA) or saline as a control.

value: tibialis anterior muscle

tag: time point

value: day 3 post-cardiotoxin injury

value: wildtype

value: wild type


title: WT0D

value: day 0 post-cardiotoxin injury


title: RNAseq_St7_controlRNAi_female_embryos_02

description:
St7_RNAseq_counts.txt
St7_control_female_02
single embryo


title: B6N_4_batch1_forebrain_RNA

description: rRNA depleted total RNA

value: Forebrain

value: 8 weeks old

value: wild-type n-Tr20

value: Batch 1


title: NMCP1OE_RNAseq_2

value: 4-leaf stage


title: WT1D

value: day 1 post-cardiotoxin injury


title: SS5

city: Lanzhou

first: Pengfei

last: Wang

state: Gansu

address: No. 1 Yingmen village, Anning District

institute: Gansu Agricultural University

data_processing:
Firstly, clean reads were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A /T / G / C and low-quality reads from raw data. Simultaneously, Q20, Q30, and GC-content of the raw data were calculated. Then, we chose a certain range of length from clean reads to do all the downstream analyses. Lastly, the miRNA tags were mapped to pig reference genome (Sus scrofa 10.2) by Bowtie [18] without mismatch to analyze their expression and distribution on the reference genome.
Mapped small RNA tags were used to looking for known miRNA. miRBase 20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo and mirdeep2  were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria : Normalization formula: Normalized expression = mapped readcount/total reads*1000000. Differential expression analysis was performed using the DESeq R package. The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Predicting the target gene of miRNA was performed by miRanda , RNAhybrid  and PITA.
GOseq software was used to analyze the GO function of differentially expressed miRNA target genes, and KOBAS software was used to analyze the KEGG signal pathway of miRNA target genes to understand the function of differentially expressed miRNA.
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: Readcount and TPM

organism: Sus scrofa

source_name: Y x L

extract_protocol:
Spleen were removed, flash frozen and  total RNA was extracted from each sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: 7-day old

tag: group

value: sensitive group


title: SS4


title: RNAseq_St7_controlRNAi_female_embryos_01

description:
St7_RNAseq_counts.txt
St7_control_female_01
single embryo

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)

value: gastrulating embryos, st7

value: female


title: 12_20_2017_HDC_AN18172

description:
single-nucleus gene expression data based on 3' transcript counts
hum.str.int.DS.raw.dge.txt.gz

data_processing:
Sequencing Reads were aligned against the relevant genome build using STAR
Aligned Reads within a gene were collapsed to UMI(XM)-Gene Pairs and associated with single-cells through a cell barcode (XC) shared on Read 1
A count matrix - called the digital gene expression (DGE) matrix - was output for GAD1+/GAD2+ interneurons. Columns belong to STAMPs (cells) and transcript counts (rows)
Genome_build: GRCm38.81 (mouse); MusPutFur1.0 (ferret); calJac3 (marmoset); rheMac8 (macaque); hg19 (human)
Supplementary_files_format_and_content: digital gene expression matrix; comma-delimited file with columns = cells and rows = transcript counts

source_name: Human Postmortem Brain

extract_protocol:
dx.doi.org/10.17504/protocols.io.2srged6
Drop-seq (Macosko et al. 2014 Cell)

value: Dropseq

value: Striatum; Caudate


title: SS3


title: B6N_1_batch1_forebrain_RNA

description: rRNA depleted total RNA

source_name: Forebrain

tag: strain


title: B6N_2_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: B6N_3_batch1_forebrain_RNA

description: rRNA depleted total RNA


title: RNAseq_St7_mofRNAi_male_embryos_06

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_06
single embryo

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)

value: male


title: HD_AN01202_P1


title: RNAseq_St7_mofRNAi_male_embryos_04

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_04
single embryo


title: RNAseq_St7_mofRNAi_male_embryos_05

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_05
single embryo


title: SS1


title: SS2


title: RNAseq_St7_mofRNAi_male_embryos_03

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_03
single embryo


title: Cn_AN08191_10X_rxn2

description:
single-nucleus gene expression data based on 3' transcript counts
hum.str.int.10X.raw.dge.txt.gz


title: SR5

value: resistant group


title: Cn_AN08191_10X_rxn1_cDNAleftoutOverNight


title: SR4


title: RNAseq_St7_mofRNAi_male_embryos_02

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_02
single embryo


title: D1PL.112817

description:
single-nucleus gene expression data based on 3' transcript counts
adHumInt.raw.dge.txt.gz

value: Neocortex; Parietal Cortex


title: RNAseq_St7_mofRNAi_male_embryos_01

description:
St7_RNAseq_counts.txt
St7_mofRNAi_male_01
single embryo


title: GFP_4h_rep1

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

description:
ILC2 cells transduced with MIGR1 vector
GFP_4h_idr.conservative_peak.narrowPeak
GFP-3_4h_S6_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig

data_processing:
Raw fastq files were processed using the ENCODE-DCC ATAC-Seq Pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapters were trimmed with CutAdapt and aligned to mm10 using Bowtie2.
Aligned data were filtered for PCR duplicates, blacklisted regions, and shifted +4bp for the + strand and -5bp for the – strand.
Peaks were called using MACS2 (Zhang et al., 2008) and filtered by Irreproducible Discovery Rate (IDR < 0.1) (https://github.com/nboley/idr). Differential peak calling was performed using DiffBind (Stark R, Brown G (2011))
Signal enrichment tracks were generated with MACS2 "bdgcmp -m ppois" and represent the stastical significance of the fold enrichment of signal over expected background.
Genome_build: mm10
Supplementary_files_format_and_content: IDR peaksets in narrowPeak format; p-value signal tracks in bigWig format

source_name: ILC2 cells

extract_protocol:
ATAC transposase reactions were carried out using the NX#-TDE1, TAGMENT DNA enzyme and buffer from Illumina. The reaction was purified using Qiagen miniElute columns, which is followed by PCR amplification with matching primers. The PCR products were purified using magnetic beads and eluted in EB buffer (Qiagen).
ATAC libraries were prepared for sequencing using standard Illumina protocols

value: plck-Id1 mice

value: thymus

tag: transduction

value: GFP


title: 12_20_2017_HDC_AN18805

tag: tissue


title: SR3


title: E47_4h_rep2

description:
ILC2 cells transduced with MIGR1 vector expressing E47-ER
E47_4h_idr.conservative_peak.narrowPeak
E47-3_4h_S5_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: RNAseq_St7_controlRNAi_male_embryos_07

description:
St7_RNAseq_counts.txt
St7_control_male_07
single embryo

tag: Sex


title: SR2


title: D2MC.112917

value: Neocortex; Motor Cortex


title: RNAseq_St7_controlRNAi_male_embryos_06

description:
St7_RNAseq_counts.txt
St7_control_male_06
single embryo


title: SR1


title: RNAseq_St7_controlRNAi_male_embryos_05

description:
St7_RNAseq_counts.txt
St7_control_male_05
single embryo


title: E47_16h_rep2

description:
ILC2 cells transduced with MIGR1 vector expressing E47-ER
E47_16h_idr.conservative_peak.narrowPeak
E47-3_16h_S1_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: E47_4h_rep1

description:
ILC2 cells transduced with MIGR1 vector
E47_4h_idr.conservative_peak.narrowPeak
E47-3_4h_S5_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: GFP_4h_rep2

description:
ILC2 cells transduced with MIGR1 vector expressing E47-ER
GFP_4h_idr.conservative_peak.narrowPeak
GFP-3_4h_S6_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: Cn_AN08191_10X_rxn3


title: D1MC.112717


title: GFP_16h_rep2

description:
ILC2 cells transduced with MIGR1 vector expressing E47-ER
GFP_16h_idr.conservative_peak.narrowPeak
GFP-3_16h_S2_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: Cn_AN08536_PosteriorCaudate.072618


title: SC4

value: control group


title: RNAseq_St7_controlRNAi_male_embryos_04

description:
St7_RNAseq_counts.txt
St7_control_male_04
single embryo


title: E47_16h_rep1

description:
ILC2 cells transduced with MIGR1 vector
E47_16h_idr.conservative_peak.narrowPeak
E47-3_16h_S1_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: GFP_16h_rep1

description:
ILC2 cells transduced with MIGR1 vector
GFP_16h_idr.conservative_peak.narrowPeak
GFP-3_16h_S2_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pooled.pval.signal.bigwig


title: SC5

value: Spleen


title: Maternal immune cells – neg_rep4 input DNA

city: Hamburg

first: Jiabin

address: Martinistr. 52

data_processing:
Bases less than Q30 and adapter sequences of the MeDIP-seq reads were trimmed, and any reads shorter than 36 nt removed using Trimmomatic v0.36
After the quality control of the trimmed data, which was performed using FASTQC, they were aligned to the MM10 genome using BWA, resulting in BAM files.
The alignment files were then filtered to include only uniquely mapped reads. For the detection of differentially methylated regions (DMRs), the tool diffReps was utilized.
Default parameters were used except for the adaption of window size to 800 nt.
The genes with significantly DMRs (p-value < 0.0001) were filtered and analyzed in IGV.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using bedGraphToBigWig

source_name: Maternal immune cells

growth_protocol: C57BL/6J, C57BL/6 Rag2-/-Il2rg-/-, and Balb/c Rag2-/-Il2rg-/- mice were obtained from the animal breeding facility of University Medical Center Hamburg-Eppendorf. The Il2rg locus is referred to as c (gamma chain) throughout the manuscript. Balb/c CD45.1 (CByJ.SJL(B6)-Ptprca/J) were purchased from the Jackson Laboratory. Mice were maintained in the animal facility of University Medical Center Hamburg-Eppendorf with food and water provided ad libitum in a 12-hour light/12-hour dark cycle.

extract_protocol:
Cord blood was obtained from participating women who gave birth at the University Medical Center Hamburg. Samples were generally processed within 2 h after delivery, cord blood mononuclear cells (CBMC) were extracted from whole blood using Biocoll (Biochrome/Merck) gradient centrifugation and stored until analysis in liquid nitrogen in RPMI1640/20% heat-inactivated FBS supplemented with 10% DMSO. Maternal whole blood and fetal cord blood was frozen for subsequent DNA extraction.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Mating of 8-10-week-old females was initiated at 1 to 3 p.m. for five consecutive days. Presence of a vaginal plug 7 to 9 a.m. the following morning and designated as gestational day (E) 0.5. Fetal loss rate was calculated as the percentage of abortions among implantation sites. Pregnancy was confirmed on E10.5 by a 10-15% body weight increase relative to E0.5.   In order to restore circulating adaptive immune cells in mothers, adaptive-immune-cell-deficient Rag2-/-γc-/- pregnant females (mated to Balb/c) on E12.5 were anesthetized using CO2 and retroorbitally adoptively transferred with 10x106 cells isolated from peripheral blood, uterus-draining inguinal and paraaortic lymph nodes, and spleen of gestational-age matched C57BL/6 females (mated to Balb/c).

value: maternal microchimeric cells from Mmc- offspring mice

value: MMC-

tag: chip antibody

value: 5-methylcytidine antibody

tag: treatment


title: Maternal immune cells – neg_rep5 input DNA

institute: University Medical Center Hamburg-Eppendorf

tag: cell type


title: SC2

value: 7-day old


title: SC3


title: RNAseq_St7_controlRNAi_male_embryos_01

first: Asifa

address: Stuebeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
St7_RNAseq_counts.txt
St7_control_male_01
single embryo

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)

value: gastrulating embryos, st7


title: RNAseq_St7_controlRNAi_male_embryos_03

description:
St7_RNAseq_counts.txt
St7_control_male_03
single embryo


title: SC1


title: RNAseq_St5_mofRNAi_female_embryos_02

description:
St5_RNAseq_counts.txt
St5_mofRNAi_female_02
single embryo

source_name: blastoderm embryos, nc14

value: blastoderm embryos, nc14

value: female


title: Maternal immune cells – pos_rep4 input DNA

value: maternal microchimeric cells from Mmc+ offspring mice

value: MMC+


title: Maternal immune cells – neg_rep2 input DNA


title: Maternal immune cells – pos_rep5 input DNA


title: CV3_IEC

city: Durham

first: Lihua

last: Ye

address: 213 Research Drive, 327 CARL building

department: MGM Department

institute: Duke University

data_processing:
Adapters were trimmed using Trim Galore!(Galaxy Version 0.4.2) by automatic detection
Trimmed reads were mapped to the danRer10 genome using HISAT2(Galaxy Version 2.0.5.1) using default settings
Gene counts were generated using ht-seq count (Galaxy Version 0.6.1galaxy3) and Ensembl gene annotations (GRCz10.82) using default settings and a minimum quality of 10.
Gene count tables were used as input for Deseq2 (Galaxy Version 2.11.39) using default settings
Genome_build: danRer10
Supplementary_files_format_and_content: Matrix table with gene counts for everygene and every sample

organism: Danio rerio

source_name: intestine

growth_protocol: Gnotobiotic zebrafish

extract_protocol:
Total RNA was extracted from cell pellets using the Argencourt RNAdvance Cell V2 kit (Beckman) following the manufacturer’s instructions.  RNA amplification prior to library preparation had to be performed. The Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara) was used to generate full-length cDNA.  mRNA transcripts were converted into cDNA through Clontech’s oligo(dT)-priming method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: Conventionalized

value: Other intestinal epithelium cells


title: Maternal immune cells – pos_rep2 input DNA


title: Maternal immune cells – neg_rep5

value: Mmclow


title: GF3_IEC

value: Germ-free


title: CV3_EEC

value: Enteroendocrine cells


title: GF3_EEC


title: RNAseq_St5_controlRNAi_female_embryos_01

city: Freiburg

description:
St5_RNAseq_counts.txt
St5_control_female_01
single embryo

value: progeny of mat-a-tubGal4/mofRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 58281)


title: RNAseq_St7_controlRNAi_male_embryos_02

description:
St7_RNAseq_counts.txt
St7_control_male_02
single embryo

value: male


title: RNAseq_St5_mofRNAi_male_embryos_04

description:
St5_RNAseq_counts.txt
St5_mofRNAi_male_04
single embryo


title: CV2_IED


title: Maternal immune cells – neg_rep4

value: maternal microchimeric cells from Mmc- offspring mice


title: CV2_EEC


title: Maternal immune cells – neg_rep2

value: MMC-


title: RNAseq_St5_mofRNAi_male_embryos_03

description:
St5_RNAseq_counts.txt
St5_mofRNAi_male_03
single embryo


title: Maternal immune cells – pos_rep5

value: 5-methylcytidine antibody

value: Mmc+


title: RNAseq_St5_mofRNAi_female_embryos_01

description:
St5_RNAseq_counts.txt
St5_mofRNAi_female_01
single embryo


title: GF2_IEC


title: RNAseq_St5_controlRNAi_female_embryos_02

description:
St5_RNAseq_counts.txt
St5_control_female_02
single embryo


title: Maternal immune cells – pos_rep4


title: RNAseq_St5_mofRNAi_male_embryos_02

description:
St5_RNAseq_counts.txt
St5_mofRNAi_male_02
single embryo


title: RNAseq_St5_mofRNAi_male_embryos_01

description:
St5_RNAseq_counts.txt
St5_mofRNAi_male_01
single embryo


title: GF2_EEC


title: Maternal immune cells – pos_rep2


title: RNAseq_St5_controlRNAi_male_embryos_04

description:
St5_RNAseq_counts.txt
St5_control_male_04
single embryo

value: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks:7062 & 36304)


title: CV1_IEC


title: RNAseq_St5_controlRNAi_male_embryos_03

description:
St5_RNAseq_counts.txt
St5_control_male_03
single embryo


title: Col5a1CKO_plus_Cilengitide scRNA-seq

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NextSeq 500 Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to human reference genome (refdata-cellranger-mm10-3.0.0) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Col5a1 knock out mouse with cilengitide treatment

extract_protocol:
1wk post MI hearts were harvested and digested by liberase as described later. After digestion, cells were incubated with 10µM Calcein AM (Abcam, ab141420) and flow sorted to identify live cells followed by library preparation.
Library was generated by Chromium™ Single Cell 3’ Library Construction (10x Genomics).

value: heart cells

value: Col5a1 knock out


title: CV1_EEC


title: Col5a1CKO scRNA-seq

source_name: Col5a1 knock out mouse without cilengitide treatment


title: FX1

first: Jason

middle: Robert

last: Mock

state: North Carolina

address: 125 Mason Farm Rd, Marsico Hall 7229G

department: Internal Medicine

description:
Resolving AT2 Tregs present rep1
mRNA expression data from mouse lung regulatory T cells

hyb_protocol: Fragmented and labeled cDNA was used to prepare a hybridization cocktail with the Affymetrix GeneTitan Hybridization Wash and Stain Kit for WT Arrays. Hybridization, washing, staining and scanning of the Affymtrix peg plate arrays was carried out using the Affymetrin GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

scan_protocol: Scanning of the Affymetrix peg plate arrays was carried out using the Affymetrix GeneTitan MC Instrument. GeneChip Command Console Software (AGCC) was used for GeneTitan Instrument control.

data_processing: Affymetrix Expression Console Software was used for basic data analysis and quality control. Microarray data were preprocessed by RMA (Robust Multiarray Average) background correction, GC content and sequence correction, quantile normalization, and median polish summarization, and expression levels compared using ANOVA on log2 intensities to identify transcripts that were differentially expressed between genotype and treatment groups.  Differentially expressed (DE) mRNAs were filtered at Benjamini-Hochberg FDR < 0.1, and fold change > 1.5, and expression patterns of DE transcripts were visualized using hierarchical clustering.  Expression analyses were performed using Partek Genomics Suite (Partek Inc., St. Louis. MO, USA).  Gene Set Enrichment Analysis (GSEA) was performed to identify significant Gene Ontology (GO) biological processes.

label: biotin

source_name: Resolving Lung Type II alveolar epithelial cells Tregs present

label_protocol: Total RNA (225 ng) was used to synthesize fragmented and labeled sense-strand cDNA and hybridize onto Affymetrx arrays. The Affymetrix HT WT User Manual was followed to prepare the samples. Briefly, the WT Expression HT Kit for Robotics (Ambion) was used to generate sense-strand cDNA from total RNA.  Following synthesis of sense-strand cDNA, the cDNA was fragmented and labeled with the Affymetrix GeneChip HT Terminal Labeling Kit.  The Beckman Coulter Biomek FXP Laboratory Automation Workstation with the Target Express set up was used to prepare the samples with these two kits.

extract_protocol: Total RNA was isolated using Zymo Direct-zol RNA MiniPrep with TRI Reagent miRNeasy kits from Zymo Research (Irvine, CA, USA) according to the manufacturer's instruction with the following modifications: 1) snap-frozen cells were lysed in at least 125 mL of TRI reagent without thawing cells; 2) cells were not centrifuged to collect debris or DNaseI-treated before applying to column. ALl samples were eluted in 25 mL of DNase/RNase-Free water.

treatment_protocol: Anesthetized mouse strains C57BL/6, Foxp3EGFP (C57BL/6 background), or Foxp3DTR (C57BL/6 background) received Escherichia coli LPS O55:B5 (3mg/kg) instilled intratracheally into the lungs. Type II alveolar epithelial cells from single cell suspension from the lungs were enriched by depleting CD31+ and CD45+ cells before sorted using a FACSAria (Becton Dickinson, San Jose, CA). Briefly, we utilized two transgenic strains, (Foxp3EGFP; Foxp3DTR Jackson Laboratory) to study differential transcript expression of type II alveolar epithelial cells in the presence (Foxp3EGFP) or absence (Foxp3DTR) of Foxp3+ Tregs. Foxp3EGFP mice express green fluorescent protein (GFP) downstream of the endogenous Foxp3 stop codon, resulting in fluorescence of all Foxp3+ Tregs. The Foxp3DTR mice express the human diphtheria toxin receptor (DTR) along with GFP, whose genes have been inserted into the 3’ untranslated region of the Foxp3 locus. These mice allow specific elimination of Foxp3+ Tregs in vivo through intraperitoneal (i.p.) administration of diphtheria toxin (DT). This results in apoptosis of Treg without significant systemic toxicity. By examining the effects of Treg depletion in the presence of other lymphocytes, we can better understand the cellular interactions that govern resolution of lung injury.  At 7 days post LPS-induced injury, single cell suspensions were prepared from enzymatically digested and dissected mouse lungs from these three strains. The cells were washed with PBS containing 2 mM EDTA and 1.5% bovine serum albumin (FACS buffer). The cells were filtered through a 100 mM filter, and then the filter samples were subjected to negative selection by depleting CD31+ and CD45+ cells using MojoSort biotin nanobeads per manufacturer's protocols  (Biolegend, San Diego, CA). The CD31-CD45- cell populations were resuspended in FACS buffer at a concentration of 2 x 107 cells/mL, and then subjected to cell sorting for CD326+ MHCII+CD104-CD24-T1a- cells, which are type II alveolar epithelial cells. Sorted cells were collected for mRNA analysis. Cells were kept at 4-8°C during staining and sorting.

value: Type II alveolar epithelial cells

value: Foxp3EGFP C57BL/6 background

value: 8-12 weeks


title: DT1

description:
Resolving AT2 depleted Tregs rep1
mRNA expression data from mouse lung regulatory T cells

source_name: Resolving Lung Type II alveolar epithelial cells in absence of Tregs

value: Foxp3DTR C57BL/6 background


title: DT3

description:
Resolving AT2 depleted Tregs rep3
mRNA expression data from mouse splenic regulatory T cells


title: FX2

description:
Resolving AT2 Tregs present rep2
mRNA expression data from mouse lung regulatory T cells


title: DT2

description:
Resolving AT2 depleted Tregs rep2
mRNA expression data from mouse splenic regulatory T cells


title: GF1_IEC

value: Other intestinal epithelium cells


title: DT4

description:
Resolving AT2 depleted Tregs rep4
mRNA expression data from mouse splenic regulatory T cells


title: FX3

description:
Resolving AT2 Tregs present rep3
mRNA expression data from mouse lung regulatory T cells


title: FX4

description:
Resolving AT2 Tregs present rep4
mRNA expression data from mouse lung regulatory T cells


title: RNAseq_St5_controlRNAi_male_embryos_02

last: Akhtar

description:
St5_RNAseq_counts.txt
St5_control_male_02
single embryo

value: blastoderm embryos, nc14


title: CKO scRNA-seq

source_name: Col5a1 knock out mouse


title: WT5

description:
Control AT2 rep5
mRNA expression data from mouse lung regulatory T cells

source_name: Control Lung Type II alveolar epithelial cells

value: C57BL/6 background


title: DT5

description:
Resolving AT2 depleted Tregs rep5
mRNA expression data from mouse lung regulatory T cells


title: FX5

description:
Resolving AT2 Tregs present rep5
mRNA expression data from mouse lung regulatory T cells


title: Ctrl scRNA-seq

source_name: wild type control animal

value: WT


title: GF1_EEC

value: Germ-free

value: Enteroendocrine cells


title: WT3

description:
Control AT2 rep3
mRNA expression data from mouse lung regulatory T cells


title: RNAseq_St5_controlRNAi_male_embryos_01

description:
St5_RNAseq_counts.txt
St5_control_male_01
single embryo

value: male


title: WT2

description:
Control AT2 rep2
mRNA expression data from mouse lung regulatory T cells


title: WT4

description:
Control AT2 rep4
mRNA expression data from mouse lung regulatory T cells


title: Swab validation 47

status: Public on Jun 03 2020

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

data_processing:
Fastq files were subjected to adaptor trimming by TrimGalore
FastQC were subsequently applied for quality checking of Fastq files.
To estimate DNAm levels for each CpG based on BBA-seq data we used the Bismark tool
Genome_build: hg19
Supplementary_files_format_and_content: Text files list the beta values for all the targeted CpGs

source_name: Buccal swab

extract_protocol:
Genomic DNA was isolated from peripheral blood with the QIAamp DNA Mini Kit (Qiagen),or from buccal swab with NucleoSpin Tissue Kit (Macherey-Nagel). Then was bisulfite converted by the EZ DNA Methylation Kit (Zymo)
10 pM DNA library was diluted with 15% PhiX spike-in control and eventually subjected to 250 bp pair-end sequencing on a MiSeq lane (Illunima, CA, USA) using Miseq reagent V2 Nano kit (Illumina).
Library_Strategy: BBA-seq

tag: gender

value: F

tag: disease state

value: Healthy

value: Buccal swab


title: Swab validation 46

value: M


title: Swab validation 49


title: WT1

institute: University of North Carolina

description:
Control AT2 rep1
mRNA expression data from mouse lung regulatory T cells


title: Swab validation 45


title: Round Spermatids-negative

city: Lucknow

first: Singh

last: Rajender

state: Uttar Pradesh

address: Lucknow

country: India

institute: Central Drug Research Institute

data_processing:
The ChIP-seq reads obtained from the sequencer were demultiplexed using bcl2fastq tool. Quality and adapter trimming was done using FastQC software.
The processed data/reads were then aligned with rat genomic assembly rn6 by using Bowtie 1.2 (parameters -m 1 -best).
Peak calling was done using MACS1.4 with p-value threshold of 0.001 and 10% of FDR cut-off.
Genome_build: Rn6
Supplementary_files_format_and_content: bed files

organism: Rattus norvegicus

source_name: testis

extract_protocol:
Round spermatid cell lysates were prepared from nuclei by sonication and specific Histone modification antibodies were used for histone-DNA chromatin immunoprecipitation (ChIP) assays using the SimpleChIP Enzymatic Chromatin IP kit (9003, CST, USA) according to the protocol provided by the manufacturer.
Immunoprecipitated DNA fragments were subjected to library preparation using TrueSeq DNA Kit (FC-121-2001, Illumina, USA). NEB Next index set 3 was used for barcoding and adapter ligation (E7710S, NEB, USA).  Briefly, 5 – 10 ng of ChIP DNA was subjected to end repair which converts the overhangs resulted from fragmentation into blunt ends using an end repair mix. This end repair mix has 3' to 5' exonuclease activity which removes the 3' overhangs and the polymerase activity fills in the 5' overhangs. After this step, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments which prevent the end repaired fragments from ligating to each other which is called as A tailing. Following this step, adapter ligation was performed where adapters having indexes were ligated to the ends of the DNA fragments, enabling them for hybridization onto a flow cell. Purification of adapter ligated fragments followed by enrichment of library was done to amplify DNA fragments having adapter sequences. DNA sequencing was performed in Illumina NextSeq 500 platform (Illumina Inc, USA) with a read length of 75 bp and paired end chemistry.

value: round spermatids

value: Sprague-Dawley

value: no treatment


title: Swab validation 48


title: Swab validation 44


title: Swab validation 39


title: Swab validation 43


title: Swab validation 36


title: Swab validation 34


title: Round Spermatids-H3K4me3

value: mouse anti-histone H3 (tri methyl K4) antibody (2 μg/IP) (ab12209, Abcam, UK)


title: Swab validation 38


title: Swab validation 40


title: Swab validation 35


title: Swab validation 42


title: Swab validation 32


title: Swab validation 31


title: Swab validation 28


title: Swab validation 41


title: Swab validation 33


title: Swab validation 29


title: Swab validation 27


title: Swab validation 26


title: Swab validation 25


title: Swab validation 24


title: Swab validation 21


title: Swab validation 22


title: Swab validation 23


title: Swab validation 16


title: Swab validation 18


title: Swab validation 30


title: Swab validation 20


title: Swab validation 13


title: Swab validation 8


title: Swab validation 14


title: Swab validation 11


title: Swab validation 15


title: Swab validation 5


title: Swab validation 4


title: Swab validation 12


title: Swab validation 1


title: Swab validation 2


title: Swab validation 17


title: Swab validation 9


title: Swab validation 37


title: Swab validation 19


title: Swab training 46


title: Swab validation 7


title: Swab training 43


title: Swab training 45


title: Swab training 41


title: Swab validation 6


title: Swab validation 10


title: Swab validation 3


title: Swab training 38


title: Swab training 33


title: Swab training 35


title: Swab training 34


title: Swab training 39


title: Swab training 24


title: Swab training 44


title: Swab training 37


title: Swab training 30


title: Swab training 23


title: Swab training 36


title: Swab training 20


title: Swab training 42


title: Swab training 32


title: Swab training 29


title: Swab training 26


title: Swab training 40


title: Swab training 18


title: Swab training 27


title: Swab training 22


title: Swab training 17


title: Swab training 19


title: Swab training 16


title: Swab training 15


title: Swab training 14


title: Swab training 31


title: Swab training 25


title: Swab training 28


title: Swab training 21


title: Swab training 13


title: Swab training 11


title: Swab training 8


title: Swab training 9


title: Swab training 3


title: Swab training 6


title: Blood validation 35

source_name: Peripheral blood

value: Peripheral blood


title: Swab training 10


title: Swab training 5


title: Swab training 7


title: Swab training 1


title: Blood validation 33


title: Blood validation 39


title: Blood validation 36


title: Swab training 4


title: Blood validation 37


title: Blood validation 34


title: Swab training 2


title: Blood validation 38


title: Blood validation 32


title: Blood validation 30


title: Blood validation 28


title: Blood validation 25


title: Swab training 12


title: Blood validation 29


title: Blood validation 26


title: Blood validation 27


title: Blood validation 24


title: Blood validation 22


title: Blood validation 21


title: Blood validation 23


title: Blood validation 20


title: Blood validation 16


title: Blood validation 17


title: Blood validation 18


title: Blood validation 31


title: Blood validation 14


title: Blood validation 10


title: Blood validation 12


title: Blood validation 9


title: Blood validation 11


title: Blood validation 13


title: Blood validation 15


title: Blood validation 6


title: Blood validation 8


title: Blood validation 4


title: Blood validation 3


title: Blood validation 2


title: Blood validation 1


title: Blood training 37


title: Blood training 36


title: Blood training 35