title: scRNA_NK_Toxo_d0_Spl

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

library_source: transcriptomic

data_processing:
FastATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
FastATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used  in peak calling. Regions of open chromatin were identified by MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Only regions called in both replicates were used in downstream analysis.
RNA-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0. Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
RNA-Seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
scRNA-seq: Sequence reads from all samples were processed and aggregated using Cell Ranger. Aggregated data was further analyzed by Seurat(Macosko et al., 2015).Downstream analyses and heatmap generation were performed with R using Rstudio. To
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq; bedgraph for histone modification ChIP-seq

molecule: total RNA

organism: Mus musculus

growth_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.

extract_protocol:
FastATAC-Seq: FastATAC-Seq was performed according to a published protocol(Corces et al., 2016)
RNA-Seq: RNA-seq was performed as described previously with slight modification (Hirahara et al., 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
RNA-Seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
scRNA-seq: Freshly sorted NK cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
scRNA-seq: The generated scRNA-Seq libraries were sequenced using a 50 cycle (paired-end) with a HiSeq 3000 (Illumina).

treatment_protocol: Toxoplasma gondii infection protocol: Mice of at least 8 weeks of age were inoculated with an average of 15 cysts of type II avirulent T.gondii strain ME-49 by intraperitoneal injection

tag: strain

tag: tissue

value: spleen

tag: cell type

value: Natural killer cells

tag: surface marker

tag: culture condition

value: ex vivo

tag: description for exp id


title: 1_E2_ESRRA_DBD_cycle4_rep1

status: Public on Oct 28 2020

type: SRA

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

library_source: genomic

data_processing:
Sequencing data of each HT-SELEX cycle was aligned to the oligo library using BWA. More specific details to identify pbSNPs can be found in methods of associated manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Text file summarizing measurements of allelic TF binding to all SNPs tested was included.

molecule: other

organism: synthetic construct

source_name: Synthesized DNA

extract_protocol: SELEX: Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5Âµg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).

tag: library strategy

value: SELEX

tag: tf

value: ESRRA

tag: tf type

value: DBD

tag: cycle

tag: plate

tag: replicate


title: 1_E2_ESRRA_DBD_cycle2_rep1


title: 1_E2_ESRRA_DBD_cycle3_rep1


title: scRNA_NK_Toxo_d7_Pec

value: Peritoneal exudate


title: scRNA_NK_Toxo_d3_Spl


title: FastATAC_NK_S4KO_exvivo_rep2

molecule: genomic DNA

value: Spleen


title: 1_E2_ESRRA_DBD_cycle1_rep1


title: FastATAC_NK_S4KO_untreated_rep2


title: 1_E6_ARNTL2_DBD_cycle2_rep1


title: 1_E5_SOHLH2_DBD_cycle4_rep1


title: 1_E5_SOHLH2_DBD_cycle3_rep1


title: 1_E1_THRB_DBD_cycle4_rep1

value: THRB


title: 1_E1_THRB_DBD_cycle1_rep1


title: FastATAC_NK_S4KO_IL12_rep2


title: 1_E5_SOHLH2_DBD_cycle1_rep1


title: FastATAC_NK_S4KO_IL2_12_rep2


title: 1_E12_NANOG_DBD_cycle4_rep1

value: NANOG


title: FastATAC_NK_S4KO_IL2_rep2


title: scRNA_NK_Toxo_d3_Pec


title: 1_E4_NEUROG2_DBD_cycle1_rep1


title: 1_E1_THRB_DBD_cycle3_rep1


title: 1_E1_THRB_DBD_cycle2_rep1


title: 1_E12_NANOG_DBD_cycle2_rep1


title: FastATAC_NK_S4KO_untreated_rep1


title: 1_E12_NANOG_DBD_cycle3_rep1


title: FastATAC_NK_S4KO_IL2_rep1


title: FastATAC_NK_S4KO_exvivo_rep1


title: FastATAC_NK_S4KO_IL12_rep1


title: FastATAC_NK_WT_exvivo_rep2


title: FastATAC_NK_WT_exvivo_rep1


title: FastATAC_NK_WT_IL2_12_rep2


title: FastATAC_NK_WT_IL12_rep2


title: FastATAC_NK_S4KO_IL2_12_rep1


title: FastATAC_NK_WT_untreated_rep2


title: FastATAC_NK_WT_IL2_rep1


title: 1_E11_MESP2_DBD_cycle4_rep1


title: FastATAC_NK_WT_IL12_rep1


title: FastATAC_NK_WT_IL2_rep2


title: 1_E11_MESP2_DBD_cycle2_rep1


title: FastATAC_NK_Toxo_d7_Spl_rep4


title: 1_E11_MESP2_DBD_cycle3_rep1


title: FastATAC_NK_WT_untreated_rep1


title: 1_E12_NANOG_DBD_cycle1_rep1


title: FastATAC_NK_Toxo_d3_Pec_rep1


title: FastATAC_NK_WT_IL2_12_rep1


title: FastATAC_NK_Toxo_d7_Pec_rep1


title: FastATAC_NK_Toxo_d3_Spl_rep4


title: 1_E11_MESP2_DBD_cycle1_rep1


title: FastATAC_NK_Toxo_d3_Spl_rep5


title: Group3-Asc-TMDKOAsc-1

city: Los Angeles

first: David

last: Casero

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

institute: UCLA

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.7) was used to generate the genome index and perform single-ended alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M20 genome annotation). Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Data in supplementary file ProDisExpression.genesfpkm.txt was generated from gene-level count summaries after per-sample normalization in units of FPKMs: counts for kilobase of gene mappable length and million of total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: Ascending colon

growth_protocol: To produce mice with induced deficiency of O-glycans specifically in colon, C1galt1-floxed (C1galt1f/f);C3GnT-/- females were crossed with previously generated C1galt1f/f;VillinCre-ERT2 (TM-IEC C1galt1f/f) mice on a C3GnT+/- background to generate C1galt1f/f;VillinCre-ERT2;C3GnT-/- (TM-DKO) and WT littermates. All mutant mice and WT littermates were on a C57BL/6J (BL/6) and 129/SvImJ (129/Sv) mixed background. Inbred WT mice (BL/6, Balb/c, and 129SvJ mice) were obtained from the Jackson Laboratory. Outbred WT CD1 mice and Swiss Webster (SW) mice and Sprague Dawley rat were bred in house. Animals were fed standard chow (PicoLab Rodent Diet 20; LabDiet 5053). Animals were housed in a specific pathogen free facility (SPF). All animal experiments were approved by the Institutional Animal Care and Use Committee of Oklahoma Medical Research Foundation.

extract_protocol:
RNA was extracted using the Zymo Direct-Zol RNA MiniPrep Plus (cat# R2070, Irvine, CA) as per the manufacturer’s instructions. Total RNA was quantified and 260/280 ratios determined using Nanodrop (all samples with a 260/280>1.97). 1μg of total RNA was used as starting material for each sample.
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics with Kapa hyper Prep Kits with RiboErase. The workflow consists of rRNA depletion, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina Hiseq3000 for a single read 50 run.

treatment_protocol: To generate mice with induced O-glycan deficiency in either the ascending or descending colon, mutant or WT littermates were injected intraperitoneally with 0.5 mg tamoxifen (TM, or ~20 mg/kg, MP Bio-medicals) in an ethanol/sunflower seed oil mixture (1:9 (v/v)) daily for 5 consecutive days, and mice were analyzed for deletion 5 or 10 days post final TM treatment. The dosage of TM was determined after serial titrations and characterization of different TM dosages in different mutant models.

value: Mixed BL/6-129SvJ

value: Ascending colon

tag: genotype

value: TM-DKOAsc

tag: cage

value: C

tag: Sex

value: F

tag: age

value: 3.2 months


title: Group3-Asc-TMDKOAsc-2


title: Group3-Asc-TMDKOAsc-3


title: Group2-Asc-Control-3

value: Control

value: B

value: 2.6 months


title: Group3-Asc-Control-1


title: Group3-Asc-Control-2


title: Group2-Asc-TMDKOAsc-2


title: Group2-Asc-TMDKOAsc-1


title: 1_D9_TGIF2LX_DBD_cycle4_rep1


title: 1_E10_GSC2_DBD_cycle2_rep1


title: 1_E10_GSC2_DBD_cycle3_rep1


title: 1_E10_GSC2_DBD_cycle1_rep1


title: Group1-Asc-TMDKOAsc-2

value: C57BL/6 Background

value: A

value: 3.4 months


title: Group2-Asc-Control-1


title: Group2-Asc-Control-2


title: Group3-Desc-TMDKOAsc-3

source_name: Descending colon

value: Descending colon


title: 1_E10_GSC2_DBD_cycle4_rep1

value: SELEX

value: DBD


title: Group1-Asc-TMDKOAsc-3


title: 1_D9_TGIF2LX_DBD_cycle2_rep1


title: Group1-Asc-Control-1


title: 1_D8_SIX6_DBD_cycle3_rep1


title: 1_D9_TGIF2LX_DBD_cycle3_rep1


title: 1_D9_TGIF2LX_DBD_cycle1_rep1


title: 1_D8_SIX6_DBD_cycle4_rep1


title: Group3-Desc-TMDKOAsc-2


title: Group3-Desc-TMDKOAsc-1


title: Group2-Desc-TMDKOAsc-2


title: 1_D8_SIX6_DBD_cycle2_rep1


title: Group2-Desc-TMDKOAsc-1


title: 1_D7_MIXL1_DBD_cycle4_rep1


title: Group3-Desc-Control-2


title: Group2-Desc-Control-1


title: 1_D7_MIXL1_DBD_cycle3_rep1


title: Group3-Desc-Control-1


title: Group2-Desc-Control-2


title: Group1-Desc-TMDKOAsc-3


title: Group2-Desc-Control-3


title: Group1-Desc-TMDKOAsc-2


title: Group1-Asc-TMDKOAsc-1


title: Group1-Asc-Control-2


title: 1_D7_MIXL1_DBD_cycle2_rep1


title: Group1-Desc-Control-1


title: Group1-Desc-Control-2


title: 1_D7_MIXL1_DBD_cycle1_rep1


title: 1_D6_KIAA2018_DBD_cycle3_rep1


title: 1_D6_KIAA2018_DBD_cycle2_rep1


title: 1_D8_SIX6_DBD_cycle1_rep1


title: X123_E_3_F

city: Aurora

first: Richard

middle: A

last: Radcliffe

state: CO

address: 12850 E Montview Blvd., Room V20-3124

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

data_processing:
Alignment to the reference genome (TopHat2; v2.06).
Whole gene quantification (HTSeq).
HTSeq output filtered for genes expressed above a certain threshold using RPLG method (Reads Per Length of Gene): RPLG = (reads * 100) / gene length. Genes with a median RPLG greater than 1 in either of the two treatment groups were retained for further analysis.
Raw reads were normalized and quantified (DESeq2).
Transformation to an approxiamtely normal distribution (VST; variance stabilization transfromation method in DESeq2).
Genome_build: mm10
Supplementary_files_format_and_content: Single csv file that includes a matrix of the expression abundance of 14,184 genes X 232 samples. Values are the DESeq2/VST normalized output for each full transcript.

molecule: polyA RNA

source_name: brain

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini kits. Quantity and quality were determined using a NanoDrop™ spectrophotometer and an Agilent 2100 BioAnalyzer. Samples were enriched for poly-A RNA using the Invitrogen Dynabeads mRNA Purification kit.
Paired-end (2x100, expected size of 300 bp), strand-specific, cluster-ready libraries were prepared from the poly-A enriched RNA using the Illumina ScriptSeq RNA-Seq Library Preparation Kit v2.

treatment_protocol: Saline (0.01 ml/g, ip) or ethanol in saline (5 g/kg, ip; 20% v/v); mice were euthanized for tissue collection at 8 hours post treatment.

tag: strain name

tag: strain number

value: postnatal day 56-106

value: whole brain

tag: treatment

value: ethanol (5 g/kg, ip)


title: 1_D6_KIAA2018_DBD_cycle1_rep1


title: 1_D5_DRGX_DBD_cycle3_rep1

value: DRGX


title: 1_D5_DRGX_DBD_cycle2_rep1


title: 1_D5_DRGX_DBD_cycle4_rep1


title: 1_D5_DRGX_DBD_cycle1_rep1


title: 1_D4_ATOH1_DBD_cycle4_rep1


title: X112_E_3_E

tag: tissue


title: X114_E_2_E


title: X122_E_3_F


title: X122_E_2_D


title: X114_E_3_F


title: X115_E_2_E


title: X122_E_1_C


title: X115_E_3_F


title: X114_E_1_E


title: X123_E_2_E


title: X123_E_1_C


title: X112_E_2_D


title: X112_E_1_A


title: X107_E_2_D


title: 1_D4_ATOH1_DBD_cycle3_rep1


title: X107_E_3_E


title: Group1-Desc-TMDKOAsc-1

tag: strain

value: TM-DKOAsc


title: X107_E_1_A


title: X115_E_1_C


title: X103_E_3_F


title: 1_D4_ATOH1_DBD_cycle1_rep1


title: X103_E_2_C


title: 1_D3_SOX15_DBD_cycle3_rep1


title: 1_D6_KIAA2018_DBD_cycle4_rep1


title: X103_E_1_A


title: X100_E_3_F


title: 1_D3_SOX15_DBD_cycle4_rep1


title: X101_E_1_A


title: X100_E_2_D


title: 1_D3_SOX15_DBD_cycle2_rep1


title: X101_E_3_E


title: X101_E_2_C


title: FITC.DTR3

type: RNA

city: Saint Louis

first: Hannah

middle: Leigh

last: Miller

state: MO

address: 4519 Gibson Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: ear skin from CLEC4C-DTR mouse treated with DT q 48h during FITC contact hypersensitivity protocol

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Pathway analysis was performed with GSEA software from the Broad Institute using MSigDB Hallmark and Canonical Pathways gene sets (http://software.broadinstitute.org/gsea/index.jsp). Volcano plots and differential expression analysis was performed using Multiplot studio and Morpheus with a threshold of 2 fold change and a minimum P value significance threshold of 0.05 (after False Discovery Rate [FDR] correction for the number of tests).
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm8.mps

label: biotin

source_name: FITC treated ear, CLEC4C-DTR+ 3, DT treated

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice were raised in SPF facility and used for experiments at ages 10-12 weeks.

extract_protocol: RNA was prepared from whole skin using RNeasy Mini (Qiagen).

treatment_protocol: Mice were injected with 200ng diptheria toxin on day -1, 1, 3, and 5.  Mice were anesthetized with ketamine/xylazine mixture and a 3 cm x 3 cm patch was shaved on the abdomen. 100μL of 0.5% FITC solution dissolved in 1:1 mixture of acetone and dibutyl phthalate was applied epicutaneously to the shaved skin on day 0 and day 2. On day 6, 20μL of 0.5% FITC solution was applied to the right ear and 20μL of acetone/dibutyl phthalate solventwas applied to the left ear.

value: ear pinna


title: 1_D2_NR4A3_DBD_cycle4_rep1


title: FITC.WT3

description: ear skin from littermate control mouse treated with DT q 48h during FITC contact hypersensitivity protocol

source_name: FITC treated ear, CLEC4C-DTR- 3, DT treated

value: littermate control


title: X100_E_1_I


title: FITC.DTR2

source_name: FITC treated ear, CLEC4C-DTR+ 2, DT treated


title: FITC.WT2

source_name: FITC treated ear, CLEC4C-DTR- 2, DT treated


title: FITC.DTR1

source_name: FITC treated ear, CLEC4C-DTR+ 1, DT treated


title: 1_D3_SOX15_DBD_cycle1_rep1


title: X99_E_3_E


title: FITC.WT1

source_name: FITC treated ear, CLEC4C-DTR- 1,DT treated


title: X99_E_1_C


title: X98_E_3_H


title: X98_E_2_J


title: 1_D4_ATOH1_DBD_cycle2_rep1


title: 1_D2_NR4A3_DBD_cycle2_rep1


title: X94_E_3_E


title: X94_E_2_D


title: 1_D2_NR4A3_DBD_cycle1_rep1


title: X93_E_2_D


title: 1_D1_LHX1_DBD_cycle4_rep1


title: X94_E_1_A


title: X93_E_1_A


title: X92_E_1_A


title: X99_E_2_D


title: X92_E_2_C


title: 1_D1_LHX1_DBD_cycle2_rep1


title: X89_E_3_I


title: X89_E_2_D


title: 1_D12_NKX6-2_DBD_cycle4_rep1


title: X98_E_1_D


title: X89_E_1_A


title: X87_E_1_D


title: 1_D1_LHX1_DBD_cycle1_rep1


title: X84_E_3_E


title: X87_E_3_G


title: X87_E_2_G


title: X84_E_2_D


title: 1_D12_NKX6-2_DBD_cycle3_rep1


title: X84_E_1_A


title: X86_E_2_F


title: X86_E_3_G


title: 1_D12_NKX6-2_DBD_cycle2_rep1


title: X92_E_3_I


title: 1_D1_LHX1_DBD_cycle3_rep1


title: X80_E_3_E


title: X80_E_1_A


title: 1_D2_NR4A3_DBD_cycle3_rep1


title: 1_D11_LHX5_DBD_cycle4_rep1


title: X86_E_1_B


title: X80_E_2_D


title: 1_D11_LHX5_DBD_cycle1_rep1


title: 1_D11_LHX5_DBD_cycle3_rep1


title: X52_E_3_G


title: 1_D11_LHX5_DBD_cycle2_rep1


title: X70_E_3_E


title: X70_E_1_B


title: 1_D10_BHLHA15_DBD_cycle3_rep1


title: X76_E_2_B


title: X76_E_1_A


title: X52_E_1_D


title: X52_E_2_F


title: 1_D10_BHLHA15_DBD_cycle4_rep1


title: X70_E_2_D


title: X48_E_3_H


title: 1_D12_NKX6-2_DBD_cycle1_rep1


title: 1_D10_BHLHA15_DBD_cycle1_rep1


title: 1_D10_BHLHA15_DBD_cycle2_rep1


title: X76_E_3_E


title: X48_E_2_F


title: X43_E_1_A


title: X43_E_3_E


title: X43_E_2_I


title: X48_E_1_D


title: X41_E_3_H


title: 1_C9_PITX1_DBD_cycle2_rep1


title: 1_C9_PITX1_DBD_cycle3_rep1


title: X41_E_1_A


title: X41_E_2_C


title: 1_C9_PITX1_DBD_cycle1_rep1


title: X32_E_2_D


title: X28_E_3_D


title: X32_E_1_B


title: 1_C8_NCOA3_DBD_cycle4_rep1


title: X28_E_2_C


title: 1_C8_NCOA3_DBD_cycle3_rep1


title: 1_C8_NCOA3_DBD_cycle2_rep1


title: X26_E_2_B


title: X26_E_3_I


title: X26_E_1_A


title: 1_C8_NCOA3_DBD_cycle1_rep1


title: 1_C9_PITX1_DBD_cycle4_rep1


title: X25_E_2_D


title: X25_E_3_F


title: 1_C7_HOXD12_DBD_cycle4_rep1


title: X25_E_1_I


title: X24_E_3_H


title: X24_E_2_E


title: 1_C7_HOXD12_DBD_cycle2_rep1


title: X23_E_3_E


title: X32_E_3_I


title: X23_E_1_A


title: X23_E_2_J


title: 1_C7_HOXD12_DBD_cycle1_rep1


title: 1_C6_EBF2_DBD_cycle4_rep1


title: X22_E_3_E


title: X24_E_1_G


title: 1_C6_EBF2_DBD_cycle3_rep1


title: X22_E_1_B


title: X19_E_3_D


title: X19_E_2_B


title: 1_C6_EBF2_DBD_cycle2_rep1


title: X19_E_1_A


title: X14_E_2_C


title: 1_C6_EBF2_DBD_cycle1_rep1


title: X13_E_3_H


title: X14_E_1_B


title: 1_C5_VENTX_DBD_cycle4_rep1

value: VENTX


title: X28_E_1_A


title: X13_E_2_D


title: 1_C7_HOXD12_DBD_cycle3_rep1


title: X13_E_1_C


title: 1_C5_VENTX_DBD_cycle3_rep1


title: 1_C5_VENTX_DBD_cycle2_rep1


title: 1_C5_VENTX_DBD_cycle1_rep1


title: X9_E_3_H


title: X22_E_2_I


title: X9_E_2_F


title: liver erythrodiol 4 (fourth-erythrodiol replicate)

city: Zaragoza

first: Roubi

middle: Hamid

last: AbuObeid

state: Spain

address: calle de Miguel Servet, 177

department: Biochemistry and Molecular Biology

country: Spain

institute: university of Zaragoza

data_processing:
After reads filtering from reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, clean reads were mapped  to reference genome (assembly ID 334509) using HISAT.
StringTie was used to reconstruct transcripts, and with genome annotation information, novel transcripts were identified using Cuffcompare(a tool of Cufflinks) and predict the coding ability of those new transcripts using CPC . In total, 14,920 novel transcripts were identified.
GATK was used to call  SNP  and  INDEL  variant for each sample. Final results are stored in VCF format.
rMATS then detected differentially splicing gene (DSG) between samples. DSGs are regulated by alternative splicing (AS), five types of AS events were screened, including Skipped Exon (SE), Alternative 5' Splicing Site (A5SS), Alternative 3' Splicing Site (A3SS), Mutually exclusive exons (MXE) and Retained Intron (RI).
After novel transcript detection, novel coding transcripts were merged with reference transcripts to get complete reference, then clean reads were mapped to it using Bowtie2, followed by calculating gene expression level for each sample with RSEM

source_name: liver samples

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep kit (Cat.No:R1055, ZYMO Research, Irvine, CA, USA).
The first step involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: PBS wash of liver sections

value: male

value: 8 weeks

value: Apoe-deficient

value: liver

value: Test group:fed  for 8 weeks with 10 mg/kg erythrodiol-enriched Western diet.


title: liver erythrodiol 7 (erythrodiol replicate 7)


title: liver erythrodiol 5 (erythrodiol replicate 5)


title: liver erythrodiol 2 (second-erythrodiol replicate)


title: 1_C4_RXRA_DBD_cycle4_rep1

value: RXRA


title: liver erythrodiol 6 (sixth-erythrodiol replicate 6)


title: X9_E_1_A


title: 1_C4_RXRA_DBD_cycle3_rep1


title: X8_E_3_F


title: liver erythrodiol 3 (third-erythrodiol replicate)


title: 1_C4_RXRA_DBD_cycle2_rep1


title: liver erythrodiol 1 (erythrodiol replicate 1)


title: X8_E_1_D


title: 1_C3_RORA_DBD_cycle4_rep1

value: RORA


title: liver control 7 (seventh-control replicate)

value: Control group:fed for 8 weeks with Western diet.


title: X8_E_2_E


title: 1_C4_RXRA_DBD_cycle1_rep1

value: SELEX

value: DBD


title: X7_E_3_J

value: postnatal day 56-106

value: whole brain


title: liver control 4 (sample 4-control)


title: liver control 6 (number-6 control)


title: liver control 5 (fifth-control sample)


title: X7_E_2_B

value: ethanol (5 g/kg, ip)


title: 1_C3_RORA_DBD_cycle3_rep1


title: 1_C3_RORA_DBD_cycle1_rep1


title: 1_C3_RORA_DBD_cycle2_rep1


title: liver control 3 (aliquot control 3)


title: X5_E_3_E


title: 1_C2_GSX1_DBD_cycle4_rep1


title: 1_C2_GSX1_DBD_cycle3_rep1


title: liver control 1 (control replicate 1)


title: 1_C2_GSX1_DBD_cycle2_rep1


title: X5_E_2_D


title: X5_E_1_I


title: X3_E_3_J


title: X3_E_2_C


title: 1_C1_TGIF2_DBD_cycle3_rep1


title: Leaves, RB-3 (WGBS)

city: Hangzhou

first: Linying

last: Li

state: Zhejiang

address: 198 Shiqiao Road

country: China

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Firstly, Cutadapt were used to remove the reads that contained adapter contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads that passed quality control were mapped to reference genome using Bismark.
After alignment, reads were further deduplicated using samtool. For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using MethPipe.
Differentially methylated regions (DMRs) were calculated by R package-MethylKit with default parameters (1000 bp slide windows, 500 bp overlap, p value<0.05).
Genome_build: Osativa_323_v7.0
Supplementary_files_format_and_content: Differentially methylated regions (DMRs) were calculated by R package-MethylKit with default parameters (1000 bp slide windows, 500 bp overlap, p value<0.05).

organism: Oryza sativa

source_name: Leaves, RB

growth_protocol: Rice plants were then grown in a glasshouse with a condition of a 14/10 light/dark cycle under artificial light at 28-30 °C

extract_protocol:
Total DNA was extracted using QIAamp Fast DNA Tissue Kit (Qiagen, Dusseldorf, Germany) following the manufacturer's procedure. The quantity of DNA was measured by reading A260/280 ratios by spectrophotometer. When A260/280 ratios located range 1.8 to 2.0, DNA was available.
The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI, USA) was utilized for attaching adapters to single-stranded DNA fragments. Briefly, as protocol shown below, the Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3’ ends, and ligation of the first truncated adapter complement to 3’ ends. The Extension step is used to incorporate truncated adapter 1 by a primer extension reaction. The Ligation step is used to add the second truncated adapter to the bottom strand only. The Indexing PCR step increases yield and incorporates full length adapters. Bead-based SPRI clean-ups are used to remove both oligonucleotides and small fragments, as well as to change enzymatic buffer composition.

treatment_protocol: RBSDV were transmitted experimentally to 10-day-old seedlings by the small brown plant hopper (Laodelphax striatellus) for 3 days.

value: NIP

value: leaves

tag: infection

value: Rice black-streaked dwarf virus (RBSDV)

tag: Stage

value: 30 days after inoculation


title: X123_S_3_F

value: saline (0.01 ml/g, ip)


title: Leaves, RB-1 (WGBS)


title: 1_C1_TGIF2_DBD_cycle4_rep1

tag: library strategy


title: X7_E_1_A


title: X3_E_1_A


title: 1_C1_TGIF2_DBD_cycle2_rep1

tag: tf


title: 1_C1_TGIF2_DBD_cycle1_rep1

tag: tf type


title: X123_S_2_E


title: X123_S_1_C


title: 1_C12_HES5_DBD_cycle4_rep1

tag: cycle


title: Leaves, RB-3 (Transcriptome)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Osativa_323_v7.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Osativa_323_v7.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM expression values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Leaves, MOCK-3 (WGBS)

source_name: Leaves, MOCK

value: mock


title: Leaves, MOCK-1 (WGBS)


title: Leaves, MOCK-2 (WGBS)


title: X122_S_3_F


title: Leaves, RB-2 (Transcriptome)


title: liver control 2 (replicate control 2)

value: male

value: 8 weeks

value: Apoe-deficient


title: 1_C12_HES5_DBD_cycle3_rep1

tag: plate


title: 1_C2_GSX1_DBD_cycle1_rep1

tag: replicate


title: X122_S_2_D


title: Leaves, RB-2 (WGBS)


title: 1_C12_HES5_DBD_cycle1_rep1


title: 1_C12_HES5_DBD_cycle2_rep1


title: X122_S_1_C


title: Leaves, RB-1 (Transcriptome)


title: 1_C11_GSX2_DBD_cycle4_rep1


title: X115_S_3_F


title: Leaves, MOCK-3 (Transcriptome)


title: X115_S_2_E


title: 1_C11_GSX2_DBD_cycle3_rep1


title: Leaves, MOCK-1 (Transcriptome)


title: X115_S_1_C


title: 1_C11_GSX2_DBD_cycle2_rep1


title: X114_S_3_F


title: Leaves, MOCK-2 (Transcriptome)


title: 1_C11_GSX2_DBD_cycle1_rep1


title: 3336

city: Iowa City

first: Keyan

last: Zarei

state: IA

address: 6330 PBDB

department: Internal Medicine

institute: University of Iowa Carver College of Medicine

description: bulk RNA-Seq

data_processing:
Bulk RNA-seq: Alignment with Kallisto (v0.45.0); Parameters: bootstrapping=100.
Single cell RNA-seq: Illumina software HCS HD version 3.4.0 was used for basecalling.
Single cell RNA-seq: Alignment of raw fastq files to pig genome assembly Sscrofa11.1, filtering, barcode counting, and UMI counting were performed with 10x CellRanger software version 3.0.2 with the argument --expect-cells=5000.
Genome_build: Sus scrofa reference genome 11.1 (Sscrofa11.1)
Supplementary_files_format_and_content: Bulk RNA-seq: HDF5 format file containing transcript ID, transcript length, effective length, estimated counts, transcripts per million, and bootstrap estimates.
Supplementary_files_format_and_content: Single cell RNA-seq: HDF5 format file containing counts for each gene (row) and cell barcode (column).

organism: Sus scrofa

source_name: gallbladder

extract_protocol:
Bulk RNA-Seq: Total RNA was isolated from whole gallbladder using a RNeasy Lipid Tissue Kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA was digested using DNase I (Qiagen). RNA samples were then quantified using fluorimetry (Qubit 2.0 fluorometer; Life Technologies), and RNA quality was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). Only samples with RNA integrity numbers >9 were used.
Bulk RNA-Seq: Libraries generated with Illumina TruSeq LT kit and standard Illumina library-generating protocols.

value: gallbladder

value: newborn

tag: genotype

value: CFTR-/-


title: WT-GB

description: Single Cell RNA-Seq

extract_protocol:
Single cell RNA-seq: Whole gallbladder from a non-CF pig was excised and cut open to reveal the lumen. The outermost layer of cells facing the lumen were mechanically scraped into DPBS-DTT. Cells were dissociated for 1 hour in 1.4 mg/ml pronase and 40 U DNase and then filtered through a 40 μm tissue strainer. Density gradient centrifugation was performed with Iodixanol (OptiPrep) to separate live and dead cells. Cells were stained with trypan blue, counted using a hemocytometer, and submitted for sequencing in DPBS with 0.04% BSA.
Single cell RNA-seq: 10x Genomics Chromium Single Cell 3’ Reagent Kits v3 system.

value: CFTR+/+


title: X114_S_2_E


title: 1_C10_ESR2_DBD_cycle3_rep1

value: SELEX

value: DBD


title: 3335

description: bulk RNA-Seq


title: X112_S_3_E

value: postnatal day 56-106

value: whole brain


title: X114_S_1_E


title: 1_C10_ESR2_DBD_cycle4_rep1


title: 1_C10_ESR2_DBD_cycle2_rep1


title: 3329

description: bulk RNA-Seq


title: X112_S_2_D


title: 1_C10_ESR2_DBD_cycle1_rep1


title: 3274

description: bulk RNA-Seq


title: X112_S_1_A


title: 1_B9_ASCL2_DBD_cycle4_rep1


title: 3273

description: bulk RNA-Seq


title: 1_B9_ASCL2_DBD_cycle3_rep1


title: 3271

description: bulk RNA-Seq


title: 1_B9_ASCL2_DBD_cycle2_rep1


title: X107_S_3_E


title: X107_S_2_D


title: X103_S_3_F


title: 1_B8_BSX_DBD_cycle4_rep1

value: BSX


title: X107_S_1_A


title: 1_B9_ASCL2_DBD_cycle1_rep1


title: X103_s_2_C


title: 3331

description: bulk RNA-Seq


title: 1_B8_BSX_DBD_cycle3_rep1


title: M2_24h replicate3

city: Haikou

first: Li

last: Wei

state: Hainan

address: No. 99 Longkun South Road, Haikou

department: Colleage of life science

institute: Hainan normal university

description:
processed data file: M2_24h-FPKM.txt, M2_WT_24h-FPKM.txt
M2_24h-3

data_processing:
To ensure quality, the raw data (2×90bpPE reads) was modified by following 2 steps: first the adapter pollutions in reads were deleted, and then because the sequence qualities of Illumina reads degrade quickly toward the 3’ end, all reads were trimmed from the 3’ end until the 3’-end-most position with Phred-equivalent score was 20 or greater. These filtered Illumina reads with 75bp length were aligned to the N.oceanica draft genome with Tophat (version 2.0.4, allowed no more than two segment-mismatches) and reads mapped to more than one location were excluded. Thirdly, the short read mapping results from TopHat was used for the following differential gene expression analysis with Cufflinks (version 2.0.2).
Genome_build: GCA_001870945.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: M2_24h_whole cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into modified f/2 liquid medium, which was prepared as follows:35 g/l sea salt, 1 g/l NaNO3, 67 mg/1 NaH2PO4*H2O, 3.65 mg/l FeCl3*6H2O, 4.37 mg/l Na2EDTA*2H2O, trace metal mix (0.0196 mg/l CuSO4*5H2O, 0.0126 mg/l NaMoO4*2H2O, 0.044 mg/l ZnSO4*7H2O, 0.01mg/l CoCl2, 0.36 mg/l MnCl2*4H2O) and vitamin mix(5 mg/l VB12, 5 mg/l Biotin and 1 mg/l Thiamine HCl). The cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air or 0.01% CO2.

extract_protocol: Algal total RNAs under the above conditions were extracted using Trizol reagents (Invitrogen). For RNA-Seq, the poly (A) containing mRNA molecules were purified using Sera-mag Magnetic Oligo(dT) Beads (Thermo Scientific) and was fragmented into 200- to 300-bp fragments by incubation in RNA Fragmentation Reagent (Ambion)according to the manufacturer’s instructions. The fragmented mRNA was then purified away from the fragmentation buffer by Agencourt®RNAClean beads (Beckman Coulter). The purified, fragmented mRNA was then converted into double-stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) by priming with random hexamers. Strand nonspecific transcriptome libraries were prepared using NEBNext® mRNA Library Prep Reagent Set(New England Biolabs) and sequenced for 2×90bprun(paired-end, PE) using Illumina HiSeq2000.

treatment_protocol: Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 80±5 µmol photons m-2 s-1) at 25℃ and aerated by bubbling with a mixture of 5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in fresh medium and cultured under 5% CO2 for preadaption for one hour, and then two samples (from biological replicates) were collected as 0h samples. After the preadaption for one hour, half of them were sequentially grown under 5% in air (High carbon or HC) and other half of them were grown under 0.01% CO2   (Very low carbon or VLC) with 80±5 µmol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 6h, 12h and 24h. Three biological replicates of algal cultures were established under each of the above “VLC” and “HC” conditions, respectively. Two biological replicates were randomly selected to prepare mRNA-Seq library. In total, 18 samples collected at 5 time points (0h, 3h, 6h, 12h, and 24h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.

tag: genotype/variation

value: M2 (RNAi-knockdown line of carbonic anhydrase (CA2))

value: whole cells

tag: molecule subtype

value: nuclear RNA


title: X103_S_1_A

tag: age

value: saline (0.01 ml/g, ip)


title: M2_24h replicate2

description:
processed data file: M2_24h-FPKM.txt, M2_WT_24h-FPKM.txt
M2_24h-2


title: X101_S_3_E

tag: strain name


title: 1_B8_BSX_DBD_cycle2_rep1


title: 1_B8_BSX_DBD_cycle1_rep1


title: M2_12h replicate3

description:
processed data file: M2_12h-FPKM.txt, M2_WT_12h-FPKM.txt
M2_12h-3

source_name: M2_12h_whole cells


title: X101_S_2_C

tag: strain number


title: 1_B7_SOX8_DBD_cycle4_rep1


title: M2_12h replicate1

description:
processed data file: M2_12h-FPKM.txt, M2_WT_12h-FPKM.txt
M2_12h-1


title: X101_S_1_A

tag: treatment


title: 1_B7_SOX8_DBD_cycle3_rep1


title: WT_24h replicate3

description:
processed data file: WT_24h-FPKM.txt, M2_WT_24h-FPKM.txt
WT_24h-3

source_name: WT_24h_whole cells

value: wild type

tag: tissue


title: 1_B7_SOX8_DBD_cycle2_rep1

source_name: Synthesized DNA


title: X100_S_3_F


title: 3269

description: bulk RNA-Seq


title: WT_24h replicate2

description:
processed data file: WT_24h-FPKM.txt, M2_WT_24h-FPKM.txt
WT_24h-2

tag: strain


title: M2_24h replicate1

description:
processed data file: M2_24h-FPKM.txt, M2_WT_24h-FPKM.txt
M2_24h-1


title: WT_12h replicate3

description:
processed data file: WT_12h-FPKM.txt, M2_WT_12h-FPKM.txt
WT_12h-3

source_name: WT_12h_whole cells


title: 1_B6_SOX4_DBD_cycle3_rep1


title: X99_S_3_E


title: 1_B6_SOX4_DBD_cycle4_rep1


title: X99_S_2_D


title: M2_12h replicate2

description:
processed data file: M2_12h-FPKM.txt, M2_WT_12h-FPKM.txt
M2_12h-2


title: WT_12h replicate1

description:
processed data file: WT_12h-FPKM.txt, M2_WT_12h-FPKM.txt
WT_12h-1


title: X99_S_1_C


title: 1_B6_SOX4_DBD_cycle2_rep1


title: 1_B5_SOX12_DBD_cycle3_rep1


title: X94_S_3_E


title: 1_B5_SOX12_DBD_cycle4_rep1


title: X98_S_2_J


title: 1_B6_SOX4_DBD_cycle1_rep1


title: X100_S_1_I


title: Ctr4_Shoot_Zhongshuang

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

country: Germany

institute: University Bayreuth

description:
Ctr4_SZS
Brassica napus cv. Zhongshuang 9

data_processing:
Fastq files were used for transcript quantification by use of kallisto (Bray et al. 2016), with 30 bootstrap samples. The reference genome build v5 from Genoscope was used (http://www.genoscope.cns.fr/brassicanapus/). This genome built included 101 040 transcripts.
Differential expression analysis was performed with the edgeR and limma Bioconductor packages in R. Log2 Fold Changes and Benjamini-Hochberg-corrected P-values were calculated fitting a negative binomial generalized log-linear model with a full factorial design matrix of treatment and genotype.
Genome_build: AST_PRJEB5043_v1
Supplementary_files_format_and_content: _abundance.tsv: Tab-separated text files include length of transcript, est_counts and TPM for each sample.

organism: Brassica napus

source_name: first true leaf of 16-day-old seedlings

growth_protocol: Seeds were germinated on moist filter paper for 24 h at 30°C in the dark. Subsequently, they were transferred to a sand:soil (1:3) mixture. Plants grew in a growth chamber under short-day conditions (8 h light, 16 h darkness) with about 23°C and 100 µmol photons m-2 s-1.

extract_protocol:
RNA was extracted from the ground plant tissue by use of the ISOLATE II RNA plant kit according to the manual, including a DNase treatment (Bioline, Luckenwalde, Germany).
RNA was further processed by Eurofins Genomics Europe Shared Services GmbH (Ebersberg, Germany). Integrity and quantity of the RNA were determined by measurement of volume and quantity, gel electrophoresis and fluorimeter measurements. Library preparation incorporated adaptor sequences and indexing compatible for Illumina sequencing technology, using proprietary methods of Eurofins Genomics Europe Shared Services GmbH. The cDNA library preparation was performed following optimized protocols. After first strand synthesis, the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next, the sequencing adapters were ligated to the DNA fragments, and the dUTP containing second strand was removed. Determination of size distribution and quantification of the sequencing library was accomplished with appropriate methods according to optimized protocols. Sequencing was performed on the Illumina HiSeq 4000 platform.

treatment_protocol: On the 15th day after germination, 2 h after the start of the photoperiod, plants were fully submerged in tap water (equilibrated to room temperature overnight). The plants were kept in the normal short-day rhythm. After 24 h, leaves were harvested and analyzed further. Control plants were kept in similar boxes without water.

tag: cultivar

value: Zhongshuang 9

value: 16 days

value: First true leaf

value: Air

tag: treatment duration


title: WT_12h replicate2

description:
processed data file: WT_12h-FPKM.txt, M2_WT_12h-FPKM.txt
WT_12h-2


title: 1_B5_SOX12_DBD_cycle2_rep1

tag: library strategy


title: X98_S_3_H

source_name: brain


title: 1_B5_SOX12_DBD_cycle1_rep1

tag: tf


title: X94_S_2_D


title: 1_B7_SOX8_DBD_cycle1_rep1

tag: tf type


title: X100_S_2_D


title: X94_S_1_A


title: WT_24h replicate1

description:
processed data file: WT_24h-FPKM.txt, M2_WT_24h-FPKM.txt
WT_24h-1


title: Sub4_Shoot_Zhongshuang

description:
Sub4_SZS
Brassica napus cv. Zhongshuang 9

value: Submergence


title: Sub3_Shoot_Zhongshuang

description:
Sub3_SZS
Brassica napus cv. Zhongshuang 9


title: Ctr3_Shoot_Zhongshuang

description:
Ctr3_SZS
Brassica napus cv. Zhongshuang 9


title: 1_B4_BHLHE23_DBD_cycle4_rep1

tag: cycle


title: Sub4_Shoot_Avatar

description:
Sub4_SAV
Brassica napus cv. Avatar

value: Avatar


title: 1_B4_BHLHE23_DBD_cycle3_rep1

tag: plate


title: 1_B4_BHLHE23_DBD_cycle2_rep1

tag: replicate


title: Sub3_Shoot_Avatar

description:
Sub3_SAV
Brassica napus cv. Avatar


title: 1_B4_BHLHE23_DBD_cycle1_rep1


title: Sub1_Shoot_Zhongshuang

description:
Sub1_SZS
Brassica napus cv. Zhongshuang 9


title: X92_S_3_I


title: X93_S_1_A


title: 1_B3_SOX11_DBD_cycle4_rep1


title: X92_S_2_I


title: X92_S_1_A


title: 1_B3_SOX11_DBD_cycle3_rep1


title: Sub1_Shoot_Avatar

description:
Sub1_SAV
Brassica napus cv. Avatar


title: Ctr4_Shoot_Avatar

description:
Ctr4_SAV
Brassica napus cv. Avatar


title: 1_B3_SOX11_DBD_cycle2_rep1


title: Ctr1_Shoot_Avatar

description:
Ctr1_SAV
Brassica napus cv. Avatar


title: Ctr3_Shoot_Avatar

description:
Ctr3_SAV
Brassica napus cv. Avatar


title: X89_S_3_I


title: X89_S_1_A


title: X89_S_2_D


title: 1_B3_SOX11_DBD_cycle1_rep1


title: X87_S_3_G


title: 1_B2_SCXB_DBD_cycle4_rep1

value: SCXB


title: 1_B2_SCXB_DBD_cycle3_rep1

value: SELEX


title: X93_S_2_D


title: Ctr1_Shoot_Zhongshuang

description:
Ctr1_SZS
Brassica napus cv. Zhongshuang 9


title: Young adults purified DNA worm-wide DamID RPB-6, replicate 1

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in entire animals
Worm_Wide_Starved_pass_barcode02.sorted_damid-vs-Dam.gatc.bedgraph
Worm_Wide_Starved_pass_barcode02.genes.details.csv

data_processing:
Library strategy: DamID
Nanopore sequences were basecalled and demultiplexed using guppy 3.6 with the high accuracy model before mapping to the ce11 genome using minimap2 (Li 2018).
Reads were considered as DamID amplicons when both ends mapped +/- 8 bp from a genomic GATC motif. The bam files represent the filtered reads.
Filtered libraries were then used to call polymerase footprinting values using the damidseq_pipeline package (O. J. Marshall and Brand 2015) using bam files (parameters: --bamfiles --extend_reads=0). The output of this step are bedgraphs.
Gene values were extracted using polii.gene.call (https://owenjm.github.io/damidseq_pipeline/) using WS270 genes definition. The output of this steps are csv files.
Genome_build: ce11
Supplementary_files_format_and_content: bam file with valid DamID reads
Supplementary_files_format_and_content: Normalized begraph (Dam fusion over Dam only)
Supplementary_files_format_and_content: Gene-level DamID values in csv format, with number of GATC per gene and FDR

organism: Caenorhabditis elegans

source_name: Purified DNA

growth_protocol: Worms were grown on NGM seeded with Dam negative E. coli GM48 for at least two generations. Around 5,000 synchronized L1s were seeded onto 100 mm plates (1,000-1,200 per plate) and collected 53h later. Worms were washed extensively with M9 (at least 10 times) and distributed in aliquots of 30 μl removing the excess of liquid. Samples were snap-frozen and stored at −80 °C.

extract_protocol:
gDNA was extracted from the animals using DNeasy Blood and Tissue Kit (Qiagen #69504).
DamID amplicons were obtained as previously described (Gomez-Saldivar et al. 2016) with 20 PCR cycles for worm-wide DamID, 22 PCR cycles for muscle DamID, 22-24 for intestine DamID and  24-26 cycles for XXX cells DamID.
DamID PCR amplicons were directly used for nanopore library barcoding and preparation using NBD-104 and LSK-109 kits (Oxford Nanopore).

tag: developmental stage

value: Young adults

value: Whole animal

tag: sample type

value: Specific expression of Dam in target tissue

tag: expressing

value: Dam RPB-6 in entire animals


title: X87_S_2_G

tag: age

value: postnatal day 56-106

value: whole brain


title: Young adults purified DNA worm-wide DamID RPB-6, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in entire animals
Worm_Wide_Starved_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph
Worm_Wide_Starved_pass_barcode05.genes.details.csv


title: 1_B2_SCXB_DBD_cycle2_rep1

value: DBD


title: Young adults purified DNA worm-wide DamID GFP control, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam GFP in entire animals
Worm_Wide_Starved_pass_barcode02.sorted_damid-vs-Dam.gatc.bedgraph
Worm_Wide_Starved_pass_barcode02.genes.details.csv

value: Dam GFP in entire animals


title: Young adults purified DNA worm-wide DamID GFP control, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam GFP in entire animals
Worm_Wide_Starved_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph
Worm_Wide_Starved_pass_barcode05.genes.details.csv


title: Young adults purified DNA XXX-specific DamID RPB-6, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in XXX cells
XXX_DamID_pass_barcode07.sorted_damid-vs-Dam.gatc.bedgraph
XXX_DamID_pass_barcode07.genes.details.csv

value: XXX cells

value: Dam RPB-6 in XXX cells


title: X86_S_3_G

tag: strain name

value: saline (0.01 ml/g, ip)


title: 1_B1_SOX3_DBD_cycle4_rep1


title: X87_S_1_D

tag: strain number


title: 1_B1_SOX3_DBD_cycle3_rep1


title: 1_B1_SOX3_DBD_cycle2_rep1


title: X86_S_1_B

tag: treatment


title: X84_S_3_I

tag: tissue


title: Young adults purified DNA XXX-specific DamID GFP control, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam GFP in XXX cells
XXX_DamID_pass_barcode07.sorted_damid-vs-Dam.gatc.bedgraph
XXX_DamID_pass_barcode07.genes.details.csv

tag: strain

value: Dam GFP in XXX cells


title: 1_B1_SOX3_DBD_cycle1_rep1


title: 1_B12_NR2F1_DBD_cycle4_rep1


title: Young adults purified DNA muscle-specific DamID RPB-6, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in muscle cells
Muscle_DamID_pass_barcode09.sorted_damid-vs-Dam.gatc.bedgraph
Muscle_DamID_pass_barcode09.genes.details.csv

value: Muscle

value: Dam RPB-6 in muscle cells


title: Young adults purified DNA muscle-specific DamID RPB-6, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in muscle cells
Muscle_DamID_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph
Muscle_DamID_pass_barcode12.genes.details.csv


title: X84_S_1_A


title: 1_B12_NR2F1_DBD_cycle3_rep1


title: X84_S_2_D


title: X80_S_3_E


title: Young adults purified DNA muscle-specific DamID GFP control, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam GFP in muscle cells
Muscle_DamID_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph
Muscle_DamID_pass_barcode12.genes.details.csv

value: Dam GFP in muscle cells


title: X80_S_2_D


title: Young adults purified DNA intestine-specific DamID RPB-6, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in intestinal cells
Intestine_DamID_2_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph
Intestine_DamID_2_pass_barcode11.genes.details.csv

value: Intestine

value: Dam RPB-6 in intestinal cells


title: 1_B12_NR2F1_DBD_cycle1_rep1

value: SELEX


title: 1_B2_SCXB_DBD_cycle1_rep1

value: SCXB


title: Young adults purified DNA muscle-specific DamID GFP control, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam GFP in muscle cells
Muscle_DamID_pass_barcode09.sorted_damid-vs-Dam.gatc.bedgraph
Muscle_DamID_pass_barcode09.genes.details.csv

value: Young adults

value: Specific expression of Dam in target tissue


title: 1_B12_NR2F1_DBD_cycle2_rep1


title: Young adults purified DNA XXX-specific DamID RPB-6, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in XXX cells
XXX_DamID_pass_barcode10.sorted_damid-vs-Dam.gatc.bedgraph
XXX_DamID_pass_barcode10.genes.details.csv


title: X80_S_1_A

value: postnatal day 56-106


title: Young adults purified DNA intestine-specific DamID RPB-6, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam RPB-6 in intestinal cells
Intestine_DamID_2_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph
Intestine_DamID_2_pass_barcode05.genes.details.csv


title: X86_S_2_F

value: whole brain


title: X76_S_3_E


title: 1_B11_ISX_DBD_cycle3_rep1

value: ISX

value: DBD


title: X76_S_2_B


title: 1_B11_ISX_DBD_cycle2_rep1


title: Young adults purified DNA intestine-specific DamID GFP control, replicate 1

description:
DamID amplicons from total DNA of animals expressing Dam GFP in intestinal cells
Intestine_DamID_2_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph
Intestine_DamID_2_pass_barcode05.genes.details.csv

value: Dam GFP in intestinal cells


title: 1_B11_ISX_DBD_cycle1_rep1


title: X70_S_3_E


title: 1_B10_ESRRB_DBD_cycle4_rep1

value: ESRRB


title: 1_B10_ESRRB_DBD_cycle3_rep1


title: X70_S_2_D

value: saline (0.01 ml/g, ip)


title: Young adults purified DNA XXX-specific DamID GFP control, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam GFP in XXX cells
XXX_DamID_pass_barcode10.sorted_damid-vs-Dam.gatc.bedgraph
XXX_DamID_pass_barcode10.genes.details.csv

value: XXX cells

value: Dam GFP in XXX cells


title: 1_B10_ESRRB_DBD_cycle2_rep1


title: FACS-sorted Y embryonic Y cells DamID GFP control, replicate 2

description:
DamID amplicons from sorted muscle embryonic Y cells expressing Dam fusion to GFP
YGR_rpb-6_DamID_pass_barcode04.genes.details.csv
YGR_rpb-6_DamID_pass_barcode04.sorted_damid-vs-Dam.gatc.bedgraph

data_processing:
Library strategy: DamID
Nanopore sequences were basecalled and demultiplexed using guppy 3.6 with the high accuracy model before mapping to the ce11 genome using minimap2 (Li 2018).
Reads were considered as DamID amplicons when both ends mapped +/- 8 bp from a genomic GATC motif. The bam files represent the filtered reads.
Filtered libraries were then used to call polymerase footprinting values using the damidseq_pipeline package (O. J. Marshall and Brand 2015) using bam files (parameters: --bamfiles --extend_reads=0 --rpm). The output of this step are bedgraphs.
Gene values were extracted using polii.gene.call (https://owenjm.github.io/damidseq_pipeline/) using WS270 genes definition. The output of this steps are csv files.
Genome_build: ce11
Supplementary_files_format_and_content: bam file with valid DamID reads
Supplementary_files_format_and_content: Normalized begraph (Dam fusion over Dam only)
Supplementary_files_format_and_content: Gene-level DamID values in csv format, with number of GATC per gene and FDR

source_name: Embryonic Y cell

growth_protocol: Synchronized gravid adult hermaphrodites containing 8-10 eggs were treated with hypochlorite. Eggs were then incubated for 3 hours in M9 at 25°C until they reached the 1.5 fold stage. Eggs were then transferred to 500 μl egg buffer and pelleted 1 min at 2000 rpm. The supernatant was then aspirated, leaving 100 μl of buffer with the pellet. 500 U of chitinase (Sigma-Aldrich;C8241-25U) were added and the mixture resuspended and further incubated for one hour at room temperature. Chitinase was then neutralized with 800 μl Leibovitz medium. Digested embryos were then recovered by centrifugation at 3000 rpm for 5 minutes at 4°C. Embryos were then dissociated into isolated blastomeres by pipetting up and down with a P1000 pipette, up to 150 times until dissociation was complete. The cell population was then filtered with a Millex-SV syringe 5 μm filter (Millipore;SLSV025LS). 500 fluorescent cells were sorted using a BD FACSAria Fusion (8000 events/second; 85µm nozzle) in sterile PCR tubes containing 1ul of pick buffer (50mM Tris-HCl pH 8.3; 75mM KCl; 3mM MgCl2; 137mM NaCl). Collected samples were then frozen in liquid nitrogen before further processing. After DamID processing and PCR (see below), two technical replicates were pooled for sequencing library preparation.

extract_protocol:
For sorted cells, frozen samples were lysed by addition of 2 ul of lysis buffer (10mM TrisAc, 10 mM MgAc, 50 mM KA, 0.67% Tween 20, 0.67% Igepal + 1mg/ml Proteinase K) and incubated during 2 hours at 60ºC before Proteinase K inactivation at 95ºC for 15 minutes. DamID amplicons were obtained as previously described (Gomez-Saldivar, Meister, and Askjaer 2016) using 30 PCR cycles.
DamID PCR amplicons were therefore sequenced using nanopore sequencing. After AMPure XP (Beckman-Coulter) purification with 1.8 beads volume, DamID PCR amplicons were directly used for nanopore library barcoding and preparation using NBD-104 and LSK-109 kits (Oxford Nanopore).
Libraries were sequenced to obtain at least 1 million reads per library on MinION using flow cells R9.4.1.

value: Embryonic blastomeres

value: Y cell

value: FACS-sorted

value: Dam fusion to GFP


title: Young adults purified DNA intestine-specific DamID GFP control, replicate 2

description:
DamID amplicons from total DNA of animals expressing Dam GFP in intestinal cells
Intestine_DamID_2_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph
Intestine_DamID_2_pass_barcode11.genes.details.csv

value: Intestine


title: X52_S_3_G


title: 1_B10_ESRRB_DBD_cycle1_rep1

value: SELEX


title: X52_S_2_F


title: 1_B11_ISX_DBD_cycle4_rep1


title: 1_A9_ATOH7_DBD_cycle4_rep1


title: 1_A9_ATOH7_DBD_cycle3_rep1


title: FACS-sorted muscle embryonic blastomeres DamID RPB-6, replicate 2

description:
DamID amplicons from sorted muscle embryonic blastomeres expressing Dam fusion to RPB-6
Intestine_Muscle_pass_barcode11.genes.details.csv
Intestine_Muscle_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph

source_name: Muscle embryonic blastomeres

value: Muscle

value: Dam fusion to RPB-6


title: FACS-sorted muscle embryonic blastomeres DamID RPB-6, replicate 1

description:
DamID amplicons from sorted muscle embryonic blastomeres expressing Dam fusion to RPB-6
Intestine_Muscle_pass_barcode10.genes.details.csv
Intestine_Muscle_pass_barcode10.sorted_damid-vs-Dam.gatc.bedgraph


title: FACS-sorted muscle embryonic blastomeres DamID GFP control, replicate 2

description:
DamID amplicons from sorted muscle embryonic blastomeres expressing Dam fusion to GFP
Intestine_Muscle_pass_barcode11.genes.details.csv
Intestine_Muscle_pass_barcode11.sorted_damid-vs-Dam.gatc.bedgraph


title: X52_S_1_D

value: postnatal day 56-106


title: X48_S_3_H

value: whole brain


title: 1_A9_ATOH7_DBD_cycle2_rep1


title: FACS-sorted muscle embryonic blastomeres DamID GFP control, replicate 1

description:
DamID amplicons from sorted muscle embryonic blastomeres expressing Dam fusion to GFP
Intestine_Muscle_pass_barcode10.genes.details.csv
Intestine_Muscle_pass_barcode10.sorted_damid-vs-Dam.gatc.bedgraph


title: FACS-sorted Y embryonic Y cells DamID RPB-6, replicate 2

description:
DamID amplicons from sorted muscle embryonic Y cells expressing Dam fusion to RPB-6
YGR_rpb-6_DamID_pass_barcode04.genes.details.csv
YGR_rpb-6_DamID_pass_barcode04.sorted_damid-vs-Dam.gatc.bedgraph


title: 1_A9_ATOH7_DBD_cycle1_rep1


title: X48_S_2_F


title: X76_S_1_A


title: X43_S_3_E


title: 1_A8_ZGLP1_DBD_cycle4_rep1


title: FACS-sorted Y embryonic Y cells DamID RPB-6, replicate 1

description:
DamID amplicons from sorted muscle embryonic Y cells expressing Dam fusion to RPB-6
YGR_rpb-6_DamID_pass_barcode01.genes.details.csv
YGR_rpb-6_DamID_pass_barcode01.sorted_damid-vs-Dam.gatc.bedgraph


title: X70_S_1_B


title: FACS-sorted Y embryonic Y cells DamID GFP control, replicate 1

description:
DamID amplicons from sorted muscle embryonic Y cells expressing Dam fusion to GFP
YGR_rpb-6_DamID_pass_barcode01.genes.details.csv
YGR_rpb-6_DamID_pass_barcode01.sorted_damid-vs-Dam.gatc.bedgraph


title: FACS-sorted intestinal embryonic blastomeres DamID RPB-6, replicate 2

description:
DamID amplicons from sorted intestinal embryonic blastomeres expressing Dam fusion to RPB-6
Intestine_Muscle_pass_barcode05.genes.details.csv
Intestine_Muscle_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph

source_name: Intestinal embryonic blastomeres


title: X43_S_2_I


title: 1_A8_ZGLP1_DBD_cycle3_rep1


title: FACS-sorted intestinal embryonic blastomeres DamID GFP control, replicate 2

description:
DamID amplicons from sorted intestinal embryonic blastomeres expressing Dam fusion to GFP
Intestine_Muscle_pass_barcode05.genes.details.csv
Intestine_Muscle_pass_barcode05.sorted_damid-vs-Dam.gatc.bedgraph


title: FACS-sorted intestinal embryonic blastomeres DamID RPB-6, replicate 1

description:
DamID amplicons from sorted intestinal embryonic blastomeres expressing Dam fusion to RPB-6
Intestine_Muscle_pass_barcode12.genes.details.csv
Intestine_Muscle_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph


title: 1_A8_ZGLP1_DBD_cycle2_rep1


title: F: Exs-Ad-P2X7-3

city: Xi'an

first: Xinyue

last: Xu

state: Shannxi

address: Changle west road

institute: The Fourth Military Medical University

description: Gene expression of exosomes which were derived from Ad-P2X7 transfected PDLSCs.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number G2505C).

scan_protocol: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

label: Cyanine 3-pCp

organism: Homo sapiens

source_name: Ad-P2X7 transfected PDLSCs

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase. The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Human periodontal ligament stem cells were firstly transfected with Ad-P2X7 or Ad-control. Culture these cells with a-MEM medium supplemented without fetal bovine serum for 24 hours at 37 ºC in a humidified incubator with 5% CO2.Then, we isolated the exosomes from the culture medium of these gene modified stem cells.

tag: adenovirus

value: Ad-P2X7 transfected

tag: donor

value: donor 3

value: periodontal ligament stem cells (PDLSCs)


title: 1_A8_ZGLP1_DBD_cycle1_rep1

tag: library strategy

value: DBD


title: E: Exs-Ad-control-3

description: Gene expression of exosomes which were derived from Ad-control transfected PDLSCs.

source_name: Ad-control transfected PDLSCs

value: Ad-control transfected


title: 1_A7_LASS6_DBD_cycle4_rep1

tag: tf


title: 1_A7_LASS6_DBD_cycle3_rep1

tag: tf type


title: X41_S_1_A

value: saline (0.01 ml/g, ip)


title: X41_S_3_H


title: X41_S_2_C


title: D: Exs-Ad-P2X7-2

value: donor 2


title: X32_S_3_E


title: C: Exs-Ad-control-2


title: 1_A7_LASS6_DBD_cycle2_rep1

tag: cycle


title: 1_A7_LASS6_DBD_cycle1_rep1

tag: plate


title: B: Exs-Ad-P2X7-1

value: donor 1


title: 1_A6_SOX14_DBD_cycle4_rep1

tag: replicate


title: X32_S_1_B


title: A: Exs-Ad-control-1


title: X28_S_3_D


title: 1_A6_SOX14_DBD_cycle3_rep1


title: X43_S_1_A


title: X28_S_1_A


title: X28_S_2_C


title: 1_A6_SOX14_DBD_cycle1_rep1


title: 1_A6_SOX14_DBD_cycle2_rep1


title: X26_S_3_I


title: X26_S_2_B


title: ter119_rep3

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library strategy: Nu Capture-C-seq
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (CCseqBasic)
Alignment: Bowtie
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (https://github.com/Hughes-Genome-Group/CCseqBasicS)
Processing: Combining data from multiple replicates (CCseqBasic)
Processing: Removal of ploidy regions and off target capture (CCseqBasic)
Processing: Interaction counts were normalised to 100,000 cis-interactions per viewpoint (https://github.com/Hughes-Genome-Group/CaptureCompare)
Genome_build: mm9
Supplementary_files_format_and_content: custom format (chr start stop rep1_interactions rep2_interactions rep3_interactions viewpoint)

source_name: Mouse erythroid cells

growth_protocol: Murine erythroid cells were obtained from spleens of C57BL/6-cross-CBA/J F1 hybrid mice treated with phenylhydrazine (40 mg g-1 body weight per dose, with three doses given 12 h apart; mice were killed on day 5). Spleens, consisting of >80 % CD71+ ter119+ erythroid cells due to hemolytic anemia, were dissociated in Phosphate buffered solution (PBS) and strained through a 30 µM filter (Miltenyi Biotec) to remove clumps. For ter119+ selection, 3×108 cells were resuspended in 3 ml of FACS buffer (PBS with 10% FBS) and stained with 0.9 µg anti-ter119-PE (130-102-338; Miltenyi Biotec). Stained cells were conjugated to anti-PE microbeads (130-048-801; Miltenyi Biotec) and passed through 3 LS Columns (Miltenyi Biotec)

extract_protocol:
For Nu-3C, cells were lysed on ice in 5 ml lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2% Igepal NP-40 (Sigma), 1× cOmplete protease inhibitor (Roche) then pelleted by centrifugation (15 min, 4ºC, 500 rcf). Lysis buffer was discarded and nuclei were resuspended in 1 ml PBS before snap freezing and storage at -20ºC for up to 12 months. For digestion, up to 5×106 nuclei were defrosted, pelleted (15 min, 4ºC, 500 rcf) then resuspended in 215 µl 1× DpnII buffer. Nuclei were then permeabilized with 0.28% SDS in a single reaction (200 µl nuclei, 60 µl 10× DpnII buffer, 434 ml PCR grade water, 10 µl 20% vol/vol SDS) and one undigested control (15 µl nuclei, 28.5 µl 10× DpnII buffer, 227.5 ml PCR grade water, 4 µl 20% vol/vol SDS) for 1 hour at 37ºC on a thermomixer (500 rpm). SDS was quenched into micelles for one hour by addition of 20% Triton-X (1.67% final concentration, 66 µl for digest and 25 µl for the undigested control). DpnII was added to digests in three aliquots of 10µl (500 U) spaced several hours apart for a total digest time of 16-24 hours at 37ºC. DpnII was neutralized by incubation at 65ºC for 15 minutes and then immediate transfer to ice to reduce potential for de-crosslinking. 100 µl was removed from the digestion reaction and combined with 200 µl PCR grade water as an un-ligated control. Controls were de-crosslinked, Proteinase-K treated, RNAse A treated, and phenol chloroform extracted as described below. Crosslinked digested DNA was re-ligated by addition of 240 U T7 ligase (500 ml PCR grade water, 134 ml 10× ligation buffer, 8 µl ligase) and incubated overnight at 16ºC on a thermomixer (500 rpm). Following ligation, nuclei were isolated by centrifugation (15 min, 4ºC, 500 rcf) and the supernatant, containing both freed DNA and the high levels of DTT from the ligation buffer, discarded. Nuclei were resuspended in 300 µl of TRIS-EDTA and de-crosslinked overnight at 65ºC with 5 µl Proteinase-K (3 U). RNA was removed by treatment with 5 µl RNAse A (7.5 mU) for 30 minutes at 37ºC. DNA was extracted by addition of 310 µl phenol-chloroform-isoamylalcohol with thorough vortexing before transfer to a phase lock tube and centrifugation (10 min, 12,600 rcf, room temp). The upper layer was transferred to a new tube and DNA precipitated overnight at -20ºC (30 µl 3M sodium acetate, 1 µl glycoblue, 900 µl 100% ethanol). DNA was pelleted by centrifugation (30 min, 21,000 rcf, 4ºC) and washed twice with 70% ice cold ethanol before resuspension in 150 µl water (30 µl for controls). Samples and controls were quantified using Qubit (Invitrogen), run on a 1% agarose gel and tested by qPCR to determine library quality. Only libraries with a digestion efficiency >70% were used for Capture-C.
Libraries were either indexed with NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). 3 µg 3C material was sonicated to 200 bp as previously described8, and purified using Ampure XP SPRI beads (Beckman Coulter). DNA was eluted into 53 µl with 1 µl used for D1000 TapeStation analysis (Agilent) and 2 µl used for Qubit quantification (Invitrogen). 50 µl of DNA (≤2 µg) was then indexed with the following modifications; for the End Prep reaction, the 20ºC incubation was lengthened to 45 min, 5 µl of NEBNext Adaptor was added and incubated for 30 min at 20ºC, the USER Enzyme incubation was extended to 30 min (37ºC), and indexing was performed in two reactions with Herculase II Fusion Polymerase (Agilent) using 6 cycles of amplification.

tag: cell type

value: Erythroid

value: F1 hybrid (C57BL/6-cross-CBA/J)

tag: cell markers


title: ter119_rep1


title: 1_A5_TCF23_DBD_cycle4_rep1


title: X26_S_1_A


title: FACS-sorted intestinal embryonic blastomeres DamID GFP control, replicate 1

description:
DamID amplicons from sorted intestinal embryonic blastomeres expressing Dam fusion to GFP
Intestine_Muscle_pass_barcode12.genes.details.csv
Intestine_Muscle_pass_barcode12.sorted_damid-vs-Dam.gatc.bedgraph

tag: developmental stage

value: Embryonic blastomeres

tag: sample type

value: FACS-sorted

tag: expressing

value: Dam fusion to GFP


title: YTN16 anti-CTLA-4 3weeks-5

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Sequence reads were mapped to mm10 using STAR(version 2.5.2b).
Mapped reads were counted by HTSeq(version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts.

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumor tissues using TRIzol (Life technologies) and RNeasy spin columns (Qiagen) according to manufacturers' protocols.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep (sample 1-30, 47-61) or VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina (sample 31-46) according to manufacturers' protocols.

tag: time point (days post tumor inoculation)


title: 1_A5_TCF23_DBD_cycle2_rep1

value: SELEX


title: 1_A5_TCF23_DBD_cycle3_rep1


title: X25_S_3_F

tag: strain name

tag: strain number

tag: age

tag: treatment


title: YTN16 anti-CTLA-4 3weeks-4

tag: strain


title: YTN16 anti-CTLA-4 3weeks-3


title: X25_S_2_D

tag: tissue


title: 1_A5_TCF23_DBD_cycle1_rep1

tag: library strategy

tag: tf


title: X25_S_1_I


title: YTN16 anti-CTLA-4 3weeks-2


title: 1_A4_SIM1_DBD_cycle4_rep1

tag: tf type

tag: cycle


title: X24_S_3_H


title: YTN16 anti-CTLA-4 3weeks-1


title: 1_A4_SIM1_DBD_cycle3_rep1

tag: plate

tag: replicate


title: ter119_rep2

tag: cell type

tag: cell markers


title: X24_S_2_E


title: 1_A3_HES2_DBD_cycle4_rep1


title: YTN16 anti-CTLA-4 2weeks-4


title: YTN16 anti-CTLA-4 2weeks-3


title: X23_S_2_J


title: X24_S_1_G


title: X23_S_1_A


title: X23_S_3_E


title: 1_A3_HES2_DBD_cycle3_rep1


title: YTN16 anti-CTLA-4 1week-5


title: X22_S_3_E


title: YTN16 anti-CTLA-4 1week-4


title: YTN16 anti-CTLA-4 2weeks-1


title: 1_A3_HES2_DBD_cycle2_rep1


title: 1_A3_HES2_DBD_cycle1_rep1


title: X22_S_2_I


title: YTN16 anti-CTLA-4 1week-3


title: X22_S_1_B


title: 1_A2_NPAS1_DBD_cycle3_rep1


title: 1_A2_NPAS1_DBD_cycle4_rep1


title: YTN16 anti-CTLA-4 1week-2


title: X19_S_2_B


title: YTN16 anti-CTLA-4 2weeks-5


title: 1_A2_NPAS1_DBD_cycle2_rep1


title: 1_A4_SIM1_DBD_cycle2_rep1


title: YTN16 anti-CTLA-4 1week-1


title: 1_A4_SIM1_DBD_cycle1_rep1


title: YTN16 anti-CTLA-4 2weeks-2


title: 1_A1_NPAS4_DBD_cycle4_rep1


title: 1_A2_NPAS1_DBD_cycle1_rep1


title: X19_S_1_A


title: 1_A1_NPAS4_DBD_cycle3_rep1


title: YTN16 untreated 3weeks-4

value: untreated


title: YTN16 untreated 3weeks-5


title: YTN16 untreated 3weeks-1


title: 1_A1_NPAS4_DBD_cycle2_rep1


title: 1_A12_MYCL2_DBD_cycle4_rep1


title: 1_A1_NPAS4_DBD_cycle1_rep1


title: X13_S_3_H

value: postnatal day 56-106


title: X13_S_1_C

value: whole brain


title: X14_S_2_C


title: YTN16 untreated 3weeks-2


title: 1_A12_MYCL2_DBD_cycle2_rep1


title: X9_S_3_F


title: YTN2 untreated 3weeks-4


title: X13_S_2_D


title: YTN2 untreated 3weeks-3


title: X9_S_2_F


title: YTN2 untreated 3weeks-2


title: 1_A12_MYCL2_DBD_cycle1_rep1


title: 1_A12_MYCL2_DBD_cycle3_rep1


title: YTN16 untreated 3weeks-3


title: 1_A11_E2F4_DBD_cycle4_rep1


title: YTN2 untreated 3weeks-1


title: 1_A11_E2F4_DBD_cycle2_rep1


title: 1_A11_E2F4_DBD_cycle3_rep1


title: YTN16 untreated 2weeks-4


title: X8_S_2_D


title: X8_S_1_D


title: X8_S_3_F


title: 1_A11_E2F4_DBD_cycle1_rep1


title: YTN16 untreated 2weeks-2


title: X14_S_1_B


title: X7_S_2_B


title: 1_A10_FIGLA_DBD_cycle3_rep1

value: FIGLA


title: 1_A10_FIGLA_DBD_cycle4_rep1


title: X7_S_3_I


title: YTN16 untreated 2weeks-3


title: 1_A10_FIGLA_DBD_cycle2_rep1


title: X7_S_1_A


title: 1_A10_FIGLA_DBD_cycle1_rep1


title: YTN2 untretaed 2weeks-5


title: X5_S_2_D


title: YTN2 untretaed 2weeks-4


title: YTN16 untreated 2weeks-1


title: X5_S_3_E


title: YTN2 untretaed 2weeks-3


title: X9_S_1_A


title: YTN16 untreated 2weeks-5


title: X5_S_1_C


title: X3_S_2_C


title: YTN2 untretaed 2weeks-2


title: YTN2 untretaed 2weeks-1


title: N7N5_H1


title: N7N5_G1


title: N7N5_F1


title: X3_S_1_A


title: YTN16 untreated 1week-5


title: N7N5_E1


title: YTN16 untreated 1week-4


title: N7N5_C1


title: YTN16 untreated 1week-3


title: YTN16 untreated 1week-2


title: YTN16 untreated 1week-1


title: N7N5_B1


title: N7A5_H1


title: YTN2 untreated 1week-5


title: YTN2 untreated 1week-4


title: N7N5_A1


title: YTN2 untreated 1week-2


title: N7A5_G1


title: YTN2 untreated 1week-3


title: N7A5_E1


title: YTN2 untreated 1week-1


title: p300_NK_S4KO_IL2_12_6h

extract_protocol:
FastATAC-Seq: FastATAC-Seq was performed according to a published protocol(Corces et al., 2016)
RNA-Seq: RNA-seq was performed as described previously with slight modification (Hirahara et al., 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
RNA-Seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
scRNA-seq: Freshly sorted NK cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
scRNA-seq: The generated scRNA-Seq libraries were sequenced using a 50 cycle (paired-end) with a HiSeq 3000 (Illumina).

value: Spleen

value: Natural killer cells

tag: surface marker

value: Miltenyi NK isolation Kit

tag: culture condition

value: ex vivo

tag: description for exp id

tag: chip antibody

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot/batch#


title: K27me3_NK_S4KO_IL2_12_6h_rep1

tag: strain

value: Millipore


title: N7A5_D1

extract_protocol: SELEX: Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5Âµg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).


title: N7N5_D1


title: K4me3_NK_S4KO_IL2_12_6h_rep1

tag: tissue


title: N7A5_B1

tag: library strategy


title: N7A5_C1


title: K27me3_NK_WT_IL2_12_6h_rep1


title: K4me3_NK_WT_IL2_12_6h_rep1


title: N7N5_H9


title: N7A5_F1


title: K27me3_NK_WT_exvivo_rep1


title: STAT4_NK_WT_IL2_12_6h_rep1


title: XEN41_MIC_Exp5_t=72 (DNA-seq)

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Library strategy: WGS
Quality control assessment using FastQC
Data processing (trimming using AdapterRemoval, Alignment using BWA, variant calling using snippy)
Genome_build: GCF_000006765.1_ASM676v1
Supplementary_files_format_and_content: Variant call format (VCF)

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Hydroponic experiment in Growth Minimal medium (Rathnayake, I. V. N.; Megharaj, M.; Krishnamurti, G. S. R.; Bolan, N. S.; Naidu, R., Heavy metal toxicity to bacteria – Are the existing growth media accurate enough to determine heavy metal toxicity? Chemosphere. 2013, 90, (3), 1195-1200.

extract_protocol: DNA was harvested using QIAamp® DNA Mini Kit QIAGEN

treatment_protocol: solution was removed by centrifugation and bacteria were stored at -20°C prior to DNA extraction

value: Xen41 Tetracycline resistant

tag: treatment

value: MIC

tag: time


title: XEN41_MIC_Exp5_t=48 (DNA-seq)


title: XEN41_MIC_Exp5_t=24 (DNA-seq)


title: DR_D

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: diabetes-resistent

data_processing:
Raw-RNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Hisat2 v2.1.0, Cufflinks v2.2.1.
Raw-DNA-reads have been quality controlled and processed using Trimgalore v0.4.2, FastQC v0.11.5, Bismark v0.17.08 and MethPipe v3.4.2.
Genome_build: Reference genome file was generated by combining GRCm38.68 B6 reference and GRCm38p4 SNP file in order to exchange all B6 to NZO high quality SNPs. Non-symmetric CpGs have been withdrawn, p-values have been calculated using log-likelihood ratio test.
Supplementary_files_format_and_content: adjusted2.bed: statistic values (pval, neighbors,fdr) of all found CpGs merged by groups of all DNA samples
Supplementary_files_format_and_content: proportion_table2.txt: propotion values (found CpGs, methylated CpGs) for all DNA samples seperated
Supplementary_files_format_and_content: fpkm tracking

source_name: islet

extract_protocol:
Genomic DNA from NZO pancreatic islets was isolated with using Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol. One microgram of genomic DNA from each pool was bisulfite-converted using Zymo EZ DNA Methylation-Gold kit (Zymo Research Corporation, Irvine, CA, USA)
Carried by GATC (Konstanz, Germany)

value: NZO/HIBomDife

tag: age

value: 10 weeks

tag: Sex

value: female


title: XEN41_MIC/10_Exp5_t=72 (DNA-seq)


title: N7A5_A1

data_processing:
Sequencing data of each HT-SELEX cycle was aligned to the oligo library using BWA. More specific details to identify pbSNPs can be found in methods of associated manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Text file summarizing measurements of allelic TF binding to all SNPs tested was included.

tag: cycle

tag: plate


title: XEN41_MIC/10_Exp5_t=48 (DNA-seq)


title: DR_B

description: diabetes-resistent


title: DR_C

description: diabetes-resistent


title: X19_S_3_D

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini kits. Quantity and quality were determined using a NanoDrop™ spectrophotometer and an Agilent 2100 BioAnalyzer. Samples were enriched for poly-A RNA using the Invitrogen Dynabeads mRNA Purification kit.
Paired-end (2x100, expected size of 300 bp), strand-specific, cluster-ready libraries were prepared from the poly-A enriched RNA using the Illumina ScriptSeq RNA-Seq Library Preparation Kit v2.

tag: strain name

tag: strain number

value: saline (0.01 ml/g, ip)


title: PBS treated tumor EC

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 500 genes) and potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for PBS and STING injected tumor ECs

source_name: PBS injected CD31+ tumor EC

extract_protocol:
FACS sorted stromal cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Single cell 3' v2 Reagent Kit (10X genomics), cDNA libraries were constructed

tag: strain background

value: Adult

tag: cell type

value: Lewis Lung Carcinoma (LLC) tumor endothelial cells (Ecs)

value: PBS

tag: sample type

value: FACS sorted stromal cells


title: cGAMP treated tumor EC

source_name: cGAMP injected CD31+ tumor EC

value: cGAMP


title: MII_total_RNA_rep1

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat 2.1.1,  transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: mm9

source_name: Oocyte

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG.  MII oocytes were harvested in M2 medium 13 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.

value: Oocyte

tag: genotype

value: wild-type

tag: developmental stage

value: MII oocyte


title: K4me3_NK_WT_exvivo_rep1

city: Bethesda

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

institute: NIAMS

data_processing:
FastATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
FastATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used  in peak calling. Regions of open chromatin were identified by MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Only regions called in both replicates were used in downstream analysis.
RNA-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0. Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
RNA-Seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
scRNA-seq: Sequence reads from all samples were processed and aggregated using Cell Ranger. Aggregated data was further analyzed by Seurat(Macosko et al., 2015).Downstream analyses and heatmap generation were performed with R using Rstudio. To
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq; bedgraph for histone modification ChIP-seq

value: Spleen

value: Natural killer cells

tag: surface marker

value: Miltenyi NK isolation Kit

tag: culture condition

value: ex vivo

tag: description for exp id

tag: chip antibody

tag: chip antibody vendor

tag: chip antibody cat. #

tag: chip antibody lot/batch#


title: SN_spk_rep1

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 114bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.  To distinguish SN from NSN oocytes without staining DNA, a previously established method was used (Inoue et al., 2007), as SN oocytes show a perivitelline space (a space between zona pellucida and the surface of the oocyte).
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.17x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

tag: tissue

value: Full-grown oocyte SN

tag: antibody

value: Pol2(Active Motif 102660)


title: XEN41_MIC/10_Exp5_t=24 (DNA-seq)

tag: strain

value: Xen41 Tetracycline resistant

tag: treatment

tag: time


title: Sk-Hep1_scrambled siRNA_#2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from Sk-Hep1 cell line transfected with a nonsense siRNA as control for 48h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of human ClariomD-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, Kernel surface background correction and Medianpolish Probeset Summary

source_name: cell line Sk-Hep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Sk-Hep1 (ATCC; LGC Standards, Wesel, Germany) were cultured in DMEM (Sigma-Aldrich, Taufkirchen, Germany) supplemented with 10% FCS (Gibco/Life Technologies, Darmstadt, Germany) and 1 % penicillin/streptomycin (Sigma-Aldrich) at 37°C and 5% CO2.

extract_protocol: For isolation of total RNA from cultured cells, the NucleoSpin RNA II kit (Machery-Nagel, Düren, Germany) was applied.

treatment_protocol: Cells were seeded in 6-well plates one day prior to transfection with siRNAs. siRNAs were received from Eurofins MWG Operon (Ebersberg, Germany) and diluted in OptiMEM (Gibco/Life Technologies) to a final concentration of 20. Oligofectamine (Life Technologies) was used as transfection reagent according to the manufacturer's protocol. After incubation at room temperature for 15 minutes, the reagents were mixed, incubated for another 10 minutes at room temperature and distributed onto the cells covered with OptiMEM. One millilitre DMEM was added after 4 hours. The medium was replaced by FCS-free medium after 24 hours. Cells and supernatant were harvested 48 hours after transfection.

tag: sirna

value: NTC


title: DR_E

description: diabetes-resistent

value: NZO/HIBomDife

tag: age

value: 10 weeks

tag: Sex

value: female


title: Sk-Hep1_PAI-1 siRNA_#2

description: Gene expression data from Sk-Hep1 cell line transfected with a PAI-1 target siRNA for 48 hours


title: Sk-Hep1_PAI-1 siRNA_#1


title: SN_spk_rep2

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 115bp bin in the genome
Genome_build: mm9

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.  To distinguish SN from NSN oocytes without staining DNA, a previously established method was used (Inoue et al., 2007), as SN oocytes show a perivitelline space (a space between zona pellucida and the surface of the oocyte).
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.18x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

tag: genotype


title: Sk-Hep1_PAI-1 siRNA_#3


title: DP_E

description: diabetes-prone