title: ZF4-18-30d cold2

city: shanghai

first: xiangqin

last: ji

address: hucheng ring road 999

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean reads were obtained from raw sequences after removing all low-quality reads (N% > 5%, or with ploy A), contaminants, reads smaller than 17 nt or longer than 35 nt, and trimming the adapters.
Clean reads were mapped to zebrafish reference non-coding RNA sequences (danRer10, ftp://ftp.ensembl.org/pub/release-91/fasta/ danio_rerio/ncrna/) using bowtie 2.3.0
To identify the miRNAs associated with cold acclimation, clean reads were aligned to known zebrafish miRNAs database miRBase22 (http://www.mirbase.org/) using bowtie2.3.0.
The  miRNAs expression levels were estimated by TPM (Transcripts per million)
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for novel micRNAs

organism: Danio rerio

source_name: embryonic fibroblast cells

growth_protocol: ZF4 cell line was from the American Type Culture Collection (ATCC, CRL 2050). Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix (SH30023.01B, Hyclone, Thermo Scientific) supplemented with 10% fetal bovine serum (10099141, Gibco, Life technologies),1% penicillin-streptomycin-glutamine solution (SV30082.01, Hyclone, Thermo Scientific)at 28°C, 5% CO2.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (217004, Qiagen) and purified by RNAClean XP Kit (A63987, Beckman Coulter) and RNase-Free DNase Set (79254, Qiagen).
Libraries were pooled and sequenced using the Illumina HiSeq machine as 50-bp single-end sequencing reads.

treatment_protocol: For cold acclimation, ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C, 5% CO2, in the same medium for 30 days.

tag: cell line

value: fibroblast cell line

tag: growth temperature

value: cultured at 18 C for 30 days

value: cold treatment for 30 days


title: ZF4-18-30d cold1

status: Public on Dec 17 2019

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: treatment


title: CUTRUN Eed flfl GOII H3K27me3 rep1

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

description: CUTRUN Eed flfl GOII H3K27me3 rep1

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment analysis are done as previously described (Lieberman et al., 2009)
TAD calling is done with insulation score as previously described ( Crane et al., 2015)
CUT&RUN reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together. And the mouse profiles were normalized to the yeast reads.
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

molecule: genomic DNA

organism: Mus musculus

source_name: CUTRUN Eed flfl GOII H3K27me3

extract_protocol:
To isolate PGCs, germinal ridges were isolated from E11.5 and E13.5 embryos. To obtain the single cell su¬spension, the germinal ridges were digested with 0.25% trypsin-EDTA at 37°C for 10min. For E13.5 embryos, the germinal ridges were digested separately based on the gender. GFP-positive PGCs were sorted and collected by FACS.WT oocytes were collected from wild-type C57BL/6N females. Briefly, growing oocytes were isolated by mechanical dissection using a 26 gauge needle in M2 medium. Growing oocytes I were isolated from 7 or 10d old mice and growing oocytes II were from 14d old mice. Full-grown oocytes were isolated from superovulated 8-week-old mice 46 h after PMSG injection. The whole ovaries were clipped mechanically with a razor blade. To remove the granulosa cells, the dissociated oocyte-granulosa cell complexes were transferred into M2 medium containing 0.1% hyaluronidase and digested for 5 min. Oocytes were then crosslinked with 1% formaldehyde after removing the zona pellucida by acidic Tyrode’s solution treatment. Eedfl/wt and EedmNull late 2-cell embryos were harvested by mating Eedfl/fl  or Eedfl/fl;Gdf9-Cre females with PWK/PhJ males.
sisHi-C libraries were produced as described (Du et al., 2017). Briefly, PGCs, oocytes or embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Then formaldehyde was quenched with glycine for 10 min at RT. After being washed with 1 × PBS, the samples were incubated in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min and the chromatin was solubilized with 0.5% SDS. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP, the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, Cat # 65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Extaq (Takara), and the products were purified and size-selected with AMPure XP beads （Beckman Coulter, Cat # A63881）  RNA-seq libraries of Ring1-/-Rnf2fl/fl and Ring1/Rnf2 dKO oocytes were prepared as follows. Cumulus oocyte complexes were isolated from ovaries of approx. 3 months old females. Granulosa cells were removed by repeated pipeting using a fine-pulled capilary glass needle in M2 medium. Oocytes were washed twice in M2 medium and subsequently washed twice in DNA suspension Buffer (TEKnova, Cat # PNT0221). For RNA isolation, 15 GV oocytes from one mouse were pooled and RNA was extracted using the RNAEasy Micro Kit (Qiagen,Cat # 74004) according to the manufacturer’s instructions. RNA was amplified and converted to cDNA using the Ovation v2 Kit (NuGen, Cat # 7102). Sequencing libraries were prepared with the Truseq DNA LT kit (Illumina, Cat # FC-121-2001).  CUT&RUN libraries of Eedfl/fl and Eed-/- oocytes were conducted as previously described (Skene and Henikoff, 2017). A low constant amount of yeast DNA was added to each reaction as spike-in DNA.

treatment_protocol: To collect oocytes undergoing germinal vesicle break down (GVBD), the full-grown oocytes with granulosa cells removed were firstly cultured in M2 medium supplemented with 5μM milrinone. Then half of the FGOs were washed out of milrinone and cultured at 37℃ to allow synchronized resumption of meiosis. After 2-4hours of incubation, oocytes that exit meiosis arrest and lose the GV were collected. The other half of the FGOs cultured with milrinone were collected at the same time as control.

tag: developmental stage

value: Growing oocytes II


title: Tumor specimen 091

type: RNA

city: Detroit

first: Kristen

last: Purrington

state: MI

address: 4100 John R St.

department: Oncology

country: USA

institute: Wayne State University

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: All statistical analyses were performed in R (https://cran.r-project.org/). Raw probe intensity data were normalized separately by batch as implemented by the “rma” function to perform background subtraction, quantile normalization, summarization of probe sets using median-polish, and log2-transformation. We evaluated batch effects using principal components analysis as implemented by the “princomp function. Batch effects were corrected by standardization of probes (subtracting the mean expression value and dividing by standard deviation) by batch (Batch 1 n=60, Batch 2 n=166). There was no evidence for batch effects after standardization.

organism: Homo sapiens

source_name: FFPE tumor

label_protocol: Affymetrix

extract_protocol: Qiagen RNeasy FFPE Kit

tag: race

value: Black/African American (AA)

tag: batch

tag: age

tag: vital status


title: Progeny2-AF275 [a550818-4325018-051918-779_B03]

type: genomic

city: Gainesville

first: Jianping

last: Wang

state: Florida

address: 2033 Mowry Road

department: Agronomy

institute: University of Florida

description:
processed data file: AxiomGT1.calls.batch2.txt
Hybridized to Axiom Sugarcane100K SNP array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The Affymetrix bioinformatics team processed the raw intensities in cell intensity files (.CEL) to obtain normalized intensities for each probe set. Further, these normalized intensities were converted to genotype calls with the Axiom Genotyping Algorithm version one
primary data description: Genotype Call (SNP call): AA=0, AB=1, BB=2, NoCall="-"; 'Signal' = Summarized signal

label: Biotin

organism: Saccharum officinarum

source_name: Progeny from selfing CP80-1827

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: These plant samples were maintained at the United States Department of Agriculture (USDA), Agricultural Research Service (ARS) Sugarcane Field Station at Canal Point, FL, which were under nature condition.

extract_protocol: Genomic DNA samples were extracted using MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific, MA, USA).

treatment_protocol: Young leaf tissues were collected and stored at -80 °C for DNA extraction.

tag: tissue

value: Sugarcane yellow leaf virus infected


title: ZF4-18-30d cold3


title: Progeny2-AF268 [a550818-4325018-051918-779_B02]

value: Sugarcane yellow leaf virus free


title: Tumor specimen 003

value: Systemic therapy before surgery

value: Dead


title: Progeny2-AF261 [a550818-4325018-051918-779_A12]


title: Tumor specimen 191

value: Systemic therapy after surgery


title: Tumor specimen 179


title: MG_glc

city: San Diego

first: Anand

last: Sastry

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2 with parameters -X 1000 -n 2
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package, with strand inversion for the dUTP protocol and “IntersectionStrict” mode
Transcripts per Million (TPM) were calculated using DESeq2’s fpkm function, then normalizing for library size.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-separated text files include TPM (Transcripts per million) for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 MG1655

growth_protocol: glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2.

extract_protocol:
After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: media

value: M9 minimal media w/ 0.2% glucose

tag: knock-out


title: ZF4-28 con3

value: normal cultured (28 C)

value: control


title: Hi-C Ring1 Rnf2 dKO FGO rep1

description:
Hi-C Ring1 Rnf2 dKO FGO rep1
processed data file:
Ring1_Rnf2_dKO_FGO_rep123_allValidPairs.txt.gz

source_name: Hi-C Ring1 Rnf2 dKO FGO

value: Full-grown oocytes


title: ZF4-28 con1


title: Hi-C Ring1 KO Rnf2 flfl FGO rep2

description:
Hi-C Ring1 KO Rnf2 flfl FGO rep2
processed data file:
Ring1_KO_Rnf2_flfl_FGO_rep123_allValidPairs.txt.gz

source_name: Hi-C Ring1 KO Rnf2 flfl FGO


title: ZF4-28 con2


title: Control_a for 11PP16 Plants

city: MALAGA

first: FERNANDO

last: DE LA TORRE

state: MALAGA

address: CAMPUS DE TEATINOS SN

department: BIOLOGIA MOLECULAR Y BIOQUIMICA

country: Spain

institute: UNIVERSIDAD MALAGA

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 mL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the microarrays. They were incubated in SureHyb microarray hybridization chambers with gasket slides (Agilent Technologies) at 65ºC for 17 h in an rotary oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 s with acetonitrile and 30 s in Agilent's stabilization and drying solution, then air dried.

scan_protocol: Hybridized slides were scanned at 5 μm resolution and their signal intensities were detected by a GenePix 4100A microarray scanner (Molecular devices, Sunnyvale, CA, USA).

data_processing: Limma package for R.

organism: Pinus pinaster

source_name: Control plants

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by NucleoSpin® Gel and PCR Clean-up column purification (Macherey-Nagel, Düren, Germany). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Transgenic and control plants were cultivated in a greenhouse under controlled conditions (24 C 16 hours light/8 hours dark). Stem samples were collected after 16 months

extract_protocol: Total RNA was isolated following the method of Chang S et al. Plant Mol Biol Rep 1993, 11:113–116

treatment_protocol: Standard growth conditions without treatment

tag: line

value: Plantlet (16 month old)

tag: genotype

value: Stem


title: 11PP16_a Plants downregulated for PpMYB8m

source_name: 11PP16a Plants downregulated for PpMYB8

value: downregulated for PpMYB8


title: Tumor specimen 159


title: Tumor specimen 082


title: Tumor specimen 072


title: Tumor specimen 155


title: Tumor specimen 061


title: Tumor specimen 153


title: Progeny2-AF258 [a550818-4325018-051918-779_A10]


title: Progeny2-AF259 [a550818-4325018-051918-779_A11]


title: Hi-C Ring1 KO Rnf2 flfl FGO rep1

description:
Hi-C Ring1 KO Rnf2 flfl FGO rep1
processed data file:
Ring1_KO_Rnf2_flfl_FGO_rep123_allValidPairs.txt.gz


title: kidney_diabets_rep3 [H9]

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: gene expression data from kidney of diabetic rat

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Genespring v12.5 (Agilent Tchnologies, USA) for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 and a P value<0.05.

label: biotin

organism: Rattus norvegicus

source_name: diabetic, 17 weeks

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using total RNA Isolation Kit (mirVanaTM, ABI).

tag: strain background

value: Sprague Dawley

value: 17 week

value: kidney


title: Hi-C Eed mNull late 2cell rep2

description:
Hi-C Eed mNull late 2cell rep2
processed data file:
Eed_mNull_late_2cell_rep12_maternal_allValidPairs.txt.gz
Eed_mNull_late_2cell_rep12_paternal_allValidPairs.txt.gz
Eed_mNull_late_2cell_rep12_allValidPairs.txt.gz

source_name: Hi-C Eed mNull late 2cell

value: C57BL/6N x PWK/PhJ

value: late 2-cell embryos


title: Progeny2-AF250 [a550818-4325018-051918-779_A09]

value: Sugarcane yellow leaf virus infected


title: Hi-C Eed flwt late 2cell rep2

description:
Hi-C Eed flwt late 2cell rep2
processed data file:
Eed_flwt_late_2cell_rep12_maternal_allValidPairs.txt.gz
Eed_flwt_late_2cell_rep12_paternal_allValidPairs.txt.gz
Eed_flwt_late_2cell_rep12_allValidPairs.txt.gz

source_name: Hi-C Eed flwt late 2cell


title: Colon organoids, ATF2/7 fl 4

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

country: Netherlands

institute: AMC

description: ATF2 KO and ATF7 floxed mouse colon organoids

hyb_protocol: Fragmented cDNA was hybridized on mouse Clariom D pico assay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analyzed using Affimetrix expression console, RMA as normalization method

source_name: Colon organoids, ATF2 fl/fl / ATF7 KO

label_protocol: 400 ng RNA was amplified and labeled using 3' IVT nano kit (ThermoFisher) and Ovation RNA amplification system v2 kit (Nugen) according to manufacturers protocol

growth_protocol: Organoids were grown in a standard organoid growth medium ENR

extract_protocol: Bioline Isolate II RNA mini kit

treatment_protocol: 12 hour treatment with 50 ng/mL of recombinant TNF-alpha

value: ATF2 fl/fl / ATF7 KO

value: Colon organoids


title: Hi-C Eed CKO FGO rep2

data_processing:
Basecalls performed using CASAVA version 1.8
Hi-C reads are  processed using HiCPro version2.7.1b and replicates of same stage were pooled together
Cmpartment analysis are done as previously described. (Lieberman et al., 2009)
TAD calling is done with insulation score as previously described ( Crane et al., 2015)
Genome_build: mm9
Supplementary_files_format_and_content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format ;  read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

source_name: Full-grown oocytes

extract_protocol:
After removing the zona pellucida, oocytes were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C (Du et al., Nature, 2017)

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female Eedfl/fl;Gdf9-Cre mice was performed, followed by hyaluronidase treatment to remove cumulus cells.


title: Progeny2-AF246 [a550818-4325018-051918-779_A08]


title: Colon organoids, ATF2/7 fl 2


title: Progeny2-AF245 [a550818-4325018-051918-779_A07]

value: Sugarcane yellow leaf virus free


title: Hi-C Eed CKO FGO rep1


title: Progeny2-AF244 [a550818-4325018-051918-779_A06]


title: Hi-C Eed flfl FGO rep2

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female Eedfl/fl mice was performed, followed by hyaluronidase treatment to remove cumulus cells.


title: SARI3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

data_processing:
The quality of the reads was verified using FASTQC version 0.11.4
Paired-end sequences were pseudoaligned against a de novo transcriptome with kallisto (100 bootstraps) to create abundance-estimates (Bray et al., 2016, doi: 10.1038/nbt.3519).
Differential expression analyses were performed with sleuth 0.29.0 running on R 3.4.4 according to sleuth default settings, and by using the following R-packages; biomaRt 2.34.2, edgeR 3.20.9, limma 3.43.9, dplyr 0.7.6 and bindrcpp 0.2.2.   The Wald test in sleuth was used to analyze the kallisto bootstrap estimates (Pimentel et al., 2017, doi: 10.1038/nmeth.4324) while the transformation function log2(x + 0.5) (Sahraeian et al., 2017, doi: 10.1038/s41467-017-00050-4) option in the sleuth_prep command was used to calculate the effect size (β value) as log2-based fold changes.
Genome_build: The de novo transcriptome assembly consisted of 17,682 transcripts and was generated by merging the de novo transcriptome assembly (assembled using CLC Genomics Workbench 11) of each population followed by the removal of redundant transcripts using CD-HIT-EST (Li and Godzik 2006, doi: 10.1093/bioinformatics/btl158) and the removal of viral and Citrus sp. transcripts.
Supplementary_files_format_and_content: Tab-delimited text file includes kallisto estimated counts (est counts) and transcripts per million (tpm) for each sample

molecule: polyA RNA

organism: Panonychus citri

source_name: complete organism

growth_protocol: Mites were grown on leaves of lemon (Citrus limon (L.) Osbeck) in controlled condition, 25 ± 1°C, 60 % RH and 16:8 h (L:D) photoperiod, for at least three generations (48 ± 4 days).

extract_protocol:
Total RNA was extracted from 100-130 adult female mites of each P. citri population using the RNEasy Plus mini kit (Qiagen, Belgium) with four-fold biological replication for each population. The quality and quantity of the total RNA was analyzed by a DeNovix DS-11 spectrophotometer (DeNovix, USA) and by running an aliquot on a 1% agarose gel.
Illumina libraries were constructed with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA)

treatment_protocol: Both the Ramsar and Sari population were highly resistant against fenpyroximate compared to the susceptible population Rasht, while the Lahijan population was moderately resistant against fenpyroximate compared to the susceptible population Rasht.

tag: Stage

value: adult

tag: Sex

value: female

tag: population

value: SARI


title: SARI2


title: Progeny2-AF242 [a550818-4325018-051918-779_A05]


title: Hi-C Eed flfl FGO rep1


title: Hi-C GVBD rep2

source_name: GVBD oocytes

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female C57BL/6N mice was performed, followed by hyaluronidase treatment to remove cumulus cells. Then the full grown oocytes are cultured in M2 medium without milrinone. Oocytes were collected when the germinal vesicle break down.

value: GVBD oocytes


title: kidney_diabets_rep2 [E9]


title: SARI1


title: Colon organoids, ATF2/7 fl 3


title: kidney_diabets_rep1 [C9]


title: Progeny2-AF235 [a550818-4325018-051918-779_A03]


title: kidney_Shenqi Jiangtang Granule-treated_rep3 [E10]

description: gene expression data from kidney of Shenqi Jiangtang Granule-treated rat

source_name: Shenqi Jiangtang Granule, 17 weeks

value: Shenqi Jiangtang Granule (SJG)


title: Colon organoids, ATF2/7 fl 1


title: Colon organoids, ATF2/7 fl 4 + TNFa

description: ATF2 KO and ATF7 floxed mouse colon organoids treated with 50  ng/mL recombinant TNFa

source_name: Colon organoids, ATF2 fl/fl / ATF7 KO + TNFa

value: TNFa


title: RAMSAR4

value: RAMSAR


title: kidney_Shenqi Jiangtang Granule-treated_rep1 [C10]


title: Hi-C control for GVBD rep2

description: control_for_GVBD_rep12_allValidPairs.txt.gz

treatment_protocol: Collection of full grown oocytes from 5IU PMSG injected 8w-old female C57BL/6N mice was performed, followed by hyaluronidase treatment to remove cumulus cells. Then the full grown oocytes are cultured in M2 medium supplemented with 5uM milrinone.

value: Full-grown oocytes


title: Colon organoids, ATF2/7 fl 2 + TNFa


title: Colon organoids, ATF2/7 fl 3 + TNFa


title: Hi-C GO II alpha-amanitin 24h rep2

description: GOII_alpha_amanitin_24h_rep12_allValidPairs.txt.gz

source_name: Growing oocytes

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were cultured in KSOM medium at 37° with 250ug/ml alpha-amanitin for 24h.

value: Growing oocytes


title: Progeny2-AF231 [a550818-4325018-051918-779_A01]


title: RAMSAR3


title: RAMSAR2


title: Progeny2-AF237 [a550818-4325018-051918-779_A04]


title: Colon organoids, ATF2/7 fl 1 + TNFa


title: Hi-C GO II DMSO 24h rep2

description: GOII_DMSO_24h_rep12_allValidPairs.txt.gz

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were cultured in KSOM medium at 37° with DMSO for 24h.


title: kidney_Shenqi Jiangtang Granule-treated_rep2 [A10]

value: Sprague Dawley

value: 17 week


title: mRNA levels in Cap-G knockdown (with nSyb-GAL4) 3rd instar brains_rep3

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
For RNA-seq, sequencing data was mapped to the Drosophila genome using STAR.
STAR aligned files are collected in a matrix using featureCounts from the Rsubread package.
Differential expression analysis and MA plots were carried out using the Deseq2 R package.
Genome_build: BDGP6
Supplementary_files_format_and_content: bigwig (bw) files with RPKM values.

organism: Drosophila melanogaster

source_name: x35 dissected 3rd instar larval brains

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
For Targeted DamID experiments, genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016). For RNA-seq experiments, total RNA was extracted from dissected 3rd instar larvae CNS, 35 per replicate, using a standard TRIzol extraction protocol. RNA libraries and sequencing was performed by BGI (www.bgi.com).
Targeted DamID libraries were generated using the Illumina Truseq Library Kit. RNA-seq libraries were generated by BGI (www.bgi.com).

treatment_protocol: For Targeted DamID experiments, animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction. For RNA-seq experiments, animals were raised at 25 degrees.

value: brain

tag: cell type

value: whole brain

value: 3rd instar larvae


title: RAMSAR1


title: mRNA levels in Cap-G knockdown (with nSyb-GAL4) 3rd instar brains_rep2


title: Progeny2-AF234 [a550818-4325018-051918-779_A02]

source_name: Progeny from selfing CP80-1827


title: SARI4


title: Colon organoids, WT 1 + TNFa

description: WT mouse colon organoids treated with 50 ng/mL recombinant TNFa

source_name: Colon organoids, WT + TNFa

value: WT

tag: treatment


title: Hi-C GO II before treatment rep2

description: GOII_before_treatment_rep12_allValidPairs.txt.gz

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min.

tag: developmental stage


title: LAHIJAN4

value: LAHIJAN


title: Hi-C FGO rep3

treatment_protocol: Collection of FGOs oocytes from 5IU PMSG injected C57BL/6N mice was performed 44-48h after hCG injection, followed by hyaluronidase treatment to remove cumulus cells.


title: LAHIJAN3


title: Hi-C FGO rep2


title: LAHIJAN2


title: mRNA levels in wild type 3rd instar brains_nSyb_control_rep2


title: Hi-C GO II alpha-amanitin 24h rep1


title: Colon organoids, WT 3

description: WT mouse colon organoids

source_name: Colon organoids, WT

value: Colon organoids


title: Colon organoids, WT 4

description: WT mouse colon organoids


title: Hi-C GOII rep2

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then cross-linked with 1% formaldehyde after removing the zona pellucida by pronase treatment.

value: Growing oocytes II


title: Colon organoids, WT 3 + TNFa


title: mRNA levels in wild type 3rd instar brains_nSyb_control_rep1


title: RASHT4

value: adult

value: female

value: RASHT


title: Hi-C GOI rep2

treatment_protocol: Follicles were isolated from 7-day or 10-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then cross-linked with 1% formaldehyde after removing the zona pellucida by pronase treatment.

value: Growing oocytes I


title: year_2 rep2

city: Chengdu

first: Zhou

last: rui

state: Sichuan

address: 211 huimin road, wenjiang district

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

description:
domestic pig
Y2_2

data_processing:
Illumina CASAVA ver.1.8.2 software was used for basecalling.
We removed low-quality reads including those with ≥ 10% unidentified nucleotides, > 10 nt aligned to the adapter, allowing ≤ 10% mismatches, and with > 50% of bases with phred quality < 5. Then, high-quality reads of ten strand-specific libraries were mapped to the pig reference genome (Suscrofa.11.1 from Ensemble) with Hisat2 (v.2.0.4)
mRNA expression levels of fragments per kilobase per million mapped reads (FPKM) were obtained using Stringtie (v.1.3.3).
Transcripts were assembled by Stringtie version 1.3.3.
Cuffmerge (part of Cufflinks, version 2.2.1) was used to merge the assembled transcripts.
Coffcompare (part of Cufflinks, version 2.2.1) was used to remove transcripts annotated in the reference sequence (marked by ‘c’ for partial match or ‘=’ for full match).
Each transcript sequence was translated in all six possible frames with Transeq (part of EMBOSS version 6.5.7) and the transcript with translated protein sequences that had a significant hit in the Pfam (release27) database with HMMER (v3.1b2) were excluded.
Remaining transcripts were compared with human and mouse genomes, and the UniRef database with BLASTX, then, potential coding transcripts were removed.
The Coding Potential Calculator (CPC) was used to assess the coding potential of the remaining transcripts.
Genome_build: Suscrofa.11.1 from Ensemble
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

organism: Sus scrofa

source_name: Whole-blood tissue

extract_protocol:
Total RNA was isolated from each sample with Trizol reagent (Life Technologies, Beijing, China) according to the manufacturer's instruction.
Approximately 1 µg total RNA and the Ribo-Zero™ kit (Epicentre, Madison, WI, USA) were used to generate RNA-Seq cDNA libraries from each sample, and then, RNA sequencing was performed following the manufacturer's standard procedures.

tag: development stage

value: Whole-blood

value: 2 years after birth


title: mRNA levels in wild type 3rd instar brains_nSyb_control_rep3


title: mRNA levels in Cap-G knockdown (with elav-GAL4) 3rd instar brains_rep3


title: Colon organoids, WT 2

description: WT mouse colon organoids


title: Colon organoids, WT 2 + TNFa

value: TNFa


title: Colon organoids, WT 4 + TNFa


title: LAHIJAN1


title: year_2 rep1

description:
domestic pig
Y2_1


title: mRNA levels in Cap-G knockdown (with elav-GAL4) 3rd instar brains_rep2


title: Colon organoids, WT 1

description: WT mouse colon organoids


title: Hi-C GO II before treatment rep1

value: Growing oocytes


title: Hi-C GOI rep1


title: day_180 rep2

description:
domestic pig
D180_2

value: sexual maturity

value: 180 days after birth


title: mRNA levels in Cap-G knockdown (with elav-GAL4) 3rd instar brains_rep1

value: brain


title: RASHT2


title: day_180 rep1

description:
domestic pig
D180_1


title: Hi-C E13.5 male PGC rep2

description: E13.5_male_PGC_rep12_allValidPairs.txt.gz

source_name: Primordial germ cells (PGCs)

extract_protocol:
PGCs were washed with PBS and fixed with 1% formaldehyde for 10min at RT.
HiC libraries were prepared using sisHi-C (Du et al., Nature, 2017)

treatment_protocol: Germinal ridges, collected from E13.5 male embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: OG2 x PWK/PhJ

value: E13.5 male PGC


title: RASHT1


title: mRNA levels in wild type 3rd instar brains_elav_control_rep3

value: whole brain

value: 3rd instar larvae


title: Hi-C E13.5 female PGC rep2

description: E13.5_female_PGC_rep12_allValidPairs.txt.gz

treatment_protocol: Germinal ridges, collected from E13.5 female embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: E13.5 female PGC


title: mRNA levels in Cap-G knockdown (with nSyb-GAL4) 3rd instar brains_rep1


title: day_28 rep2

description:
domestic pig
D28_2

value: weaning

value: 28 days after birth


title: Hi-C E11.5 PGC rep2

treatment_protocol: Germinal ridges, collected from E11.5 embryos by mating the PWK/PhJ mice with OG2 strain (with Oct4-GFP reporter), were digested with trypsin-EDTA (0.25%) at 37℃ for 10min. GFP-positive PGCs were sorted and collected by FACS and then cross-linked with 1% formaldehyde.

value: E11.5 PGC


title: RASHT3

value: adult

value: female

value: RASHT


title: mRNA levels in wild type 3rd instar brains_elav_control_rep2


title: N2_NHS_rep3

city: La Jolla

first: Jacob

last: Garrigues

address: 9500 Gilman Dr.

description:
N2_5_S17_L004
Control sample replicate 3
processed data file: Cel_N2_NHS.HS_normalized.counts.txt

data_processing:
Default base-calling software for the Illumina HiSeq 4000 platform was used
Sequenced reads were aligned to the mRNA transcriptome using Salmon v0.13.1 with default parameters and automatic library type detection enabled
Salmon-derived counts (TPMs) for each transcript were processed using DESeq2 v1.18.1 with default parameters and a parametric fit type to obtain gene-level normalized counts
Genome_build: ce11 for C. elegans, cb4 for C. briggsae
Supplementary_files_format_and_content: tab-delimited text files include DESeq2-normalized counts for protein-coding genes

organism: Caenorhabditis elegans

source_name: N2_NHS_whole L2 stage worm

growth_protocol: Worms were grown under standard conditions at 20 C until heat shock was performed

extract_protocol:
L2 stage worms were collected and washed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
Illumina TruSeq Stranded Total RNA Library Prep Gold Kit was used with 1 ug of total RNA for the construction of sequencing libraries

treatment_protocol: Control (NHS) worms were maintained at 20 C, while heat-shocked (HS) worms were placed in a 34 C water bath for 30 minutes before collection

value: L2 stage

value: control (NHS)

value: Whole worm


title: day_7 rep2

description:
domestic pig
D7_2

value: suckling

value: Whole-blood

value: 7 days after birth


title: mRNA levels in wild type 3rd instar brains_elav_control_rep1

value: brain


title: N2_HS_rep3

description:
N2_6_S18_L004
Heat-shocked sample replicate 3
processed data file: Cel_N2_NHS.HS_normalized.counts.txt

source_name: N2_HS_whole L2 stage worm

value: heat-shocked (HS)


title: day_28 rep1

description:
domestic pig
D28_1


title: N2_HS_rep2

description:
N2_4_S16_L004
Heat-shocked sample replicate 2
processed data file: Cel_N2_NHS.HS_normalized.counts.txt


title: day_7 rep1

description:
domestic pig
D7_1


title: N2_NHS_rep2

description:
N2_3_S15_L004
Control sample replicate 2
processed data file: Cel_N2_NHS.HS_normalized.counts.txt


title: BW_cra

organism: Escherichia coli BW25113

source_name: E. coli BW25113 cra KO

value: M9 minimal media w/ 0.2% glucose

value: cra


title: metJ_meio_1_ChIPexo

first: Ye

last: Gao

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from ChIP-exo were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
MACE program  was used to define peak candidates from biological duplicates for each experimental condition with sequence depth normalization.
To reduce false-positive peaks, peaks with signal-to-noise (S/N) ratio less than 1.5 were removed
The noise level was set to the top 5% of signals at genomic positions because top 5% makes a background level in plateau and top 5% intensities from each ChIP-exo replicates across conditions correlate well with the total number of reads.The calculation of S/N ratio resembles the way to calculate ChIP-chip peak intensity where IP signal was divided by Mock signal. Then, each peak was assigned to the nearest gene.
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli K-12

source_name: bacteria cells

growth_protocol: glycerol stocks of E. coli strains were inoculated into glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated uncharacterized transcripton factors-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked E. coli cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously [42]. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method [11]. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65oC. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously [12] were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using HiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.

tag: myc-tagging

value: metJ myc-tagging cells

tag: medium

value: M9 minimal media w/ 2g/L glucose

tag: supplement

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1,sc-40, lot#J2413, Santa Cruz Biotechnology


title: metJ_meio_2_ChIPexo

tag: strain


title: ILC3_DSS

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

description: DSS-activated ILC3s

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: standard Agilent protocol

source_name: primary mouse ILC3s in the small intestine

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNAs were isolated from ILC3s using Trizol reagent. The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: ILC3s were isolated from Rag1-/- mice treated with DSS or vehicle.

value: DSS


title: ILC3_vehicle

description: control ILC3s

value: vehicle


title: day_0 rep2

description:
domestic pig
D0_2

value: newborn

tag: tissue

tag: age

value: 0 days after birth


title: N2_NHS_rep1

description:
N2_1_S13_L004
Control sample replicate 1
processed data file: Cel_N2_NHS.HS_normalized.counts.txt

value: L2 stage


title: cysB_taur_1_ChIPexo

value: cysB myc-tagging cells

value: Taurine (0.25mM)


title: AACG6

status: Public on Dec 16 2019

city: Wuhan

first: Dong

last: Chen

state: Hubei

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

department: Center for Genome Analysis

institute: ABLife, Inc.

description:
tisssue of patient with glaucoma
AACG6_mRNA_raw
processed data file: clin_expressed_gene_*.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue < =0.05
Genome_build: GRCH38
Supplementary_files_format_and_content: txt; abundance measurements

source_name: Human trabecular meshwork tissue

extract_protocol:
Total RNA was extracted by the hot phenol method. The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1.5μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.

tag: subject source

value: acute angle-closure glaucoma

tag: tissue/cell type

value: Human trabecular meshwork (HTM) tissue


title: cysB_taur_2_ChIPexo


title: CCGA3

description:
tisssue of patient with glaucoma
CCGA3-mRNA_raw
processed data file: clin_expressed_gene_*.txt

value: chronic angle-closure glaucoma


title: AACG5

description:
tisssue of patient with glaucoma
AACG5-mRNA_raw
processed data file: clin_expressed_gene_*.txt


title: CCAG2

description:
tisssue of patient with glaucoma
CCAG2-mRNA_raw
processed data file: clin_expressed_gene_*.txt


title: Regulatory T cells from leukemia mice injected with leukemia cells

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

description: Regulatory T cells from acute myeloid leukemia mice

data_processing:
Base calling was done by BGIseq-500
Read pairs with low quality in either read were filtered out (10% bases with N or 50% bases with Q5)
Alignment was performed against RefSeq by bowtie2 (version 2.2.5) with parameters as: -q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200
FPKM values of each gene for each sample was measured via RSEM
Supplementary_files_format_and_content: text file with FPKM values

source_name: Regulatory T cells

extract_protocol:
sorted regulatory T cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGIseq-500

treatment_protocol: Leukemia cells (8×10^5 cells) were transplanted into B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J host mouse without irradiation. Mice suffered leukemia with a survival time of 30-40 days. CD4+FOXP3-GFP+ regulatory T cells were sorted from spleen of leukemia mice at day18 or healthy B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J mice injected with PBS

value: Spleen

value: Treg

tag: disease state

value: acute myeloid leukemia


title: CCAG1

description:
tisssue of patient with glaucoma
CCAG1-mRNA_raw
processed data file: clin_expressed_gene_*.txt


title: AACG4

description:
tisssue of patient with glaucoma
AACG4-mRNA_raw
processed data file: clin_expressed_gene_*.txt


title: POAG1

description:
tisssue of patient with glaucoma
POAG1-mRNA_raw
processed data file: clin_expressed_gene_*.txt

value: primary open-angle glaucoma


title: LC_6_CRISPR_IRF4KD_1000

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

institute: University of Southampton

description: human skin primary migratory LCs

data_processing:
R1 read: contains the cell barcode (first 12 nt) and UMI (next 8 nt).
R2 read: contains the RNA sequence.
Samples were de-multiplexed with bcl2fastq tool from Illumina
Alignment, read filtering, barcode and UMI counting were performed using kallisto-bustools
Filtering: High quality barcodes were selected based on the overall UMI distribution using emptyDrops, To remove low quality cells, we filtered cells with a high fraction of counts from mitochondrial genes (20% or more)
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files with annotated, aligned, normalized, filtered reads, TPMs

source_name: epidermis

growth_protocol: Human primary LCs were migrated out of epidermal sheets, following digest with dispase o/n at +4C and enriched for LCs over density gradient OPTIPREP (AxisShield, Noway)

extract_protocol: cDNA libraries were  tagmented and PCR-amplified (Nextera tagmentation kit, Illumina)

treatment_protocol: Highly purified human LCs (> 80% of CD1a+HLADR+) were unbanked from cryo-storage, and processed on ice to enable the co-encapsulation of single cells with genetically-encoded beads (Drop-seq, 90). Monodisperse droplets at 1 nl in size were generated using the microfluidic devices fabricated in the Centre for Hybrid Biodevices, University of Southampton. To achieve single cell/single bead encapsulation barcoded Bead SeqB [Chemgenes, USA], microfluidics parameters (pump flow speeds for cells and bead inlets, cell buoyancy) were adjusted to optimise cell-bead encapsulation and the generation of high quality cDNA libraries. Following encapsulation, ~4500 STAMPS (beads exposed to a single cell) from 1.2 ml cell suspension were generated in the Faculty of Medicine University of Southampton Drop-seq Facility. Based on encapsulation frequencies and bead counts up to 1000 STAMPS were taken further for library prep (High Sensitivity DNA Assay, Agilent Bioanalyser, 12 peaks with the average fragment size 500 bp). The resulting libraries were run on a shared NextSeq run (1.5x10e5 reads for maximal coverage) at the Wessex Investigational Sciences Hub laboratory, University of Southampton, to obtain single cell sequencing data.

tag: genotype

tag: condition

tag: time


title: day_0 rep1

description:
domestic pig
D0_1

value: Whole-blood


title: Regulatory T cells from healthy mice injected with phosphate buffered saline

description: Regulatory T cells from normal mice

tag: cell type

value: normal


title: AACG1

description:
tisssue of patient with glaucoma
AACG1-mRNA_raw
processed data file: clin_expressed_gene_*.txt


title: N2_HS_rep1

description:
N2_2_S14_L004
Heat-shocked sample replicate 1
processed data file: Cel_N2_NHS.HS_normalized.counts.txt

tag: treatment

value: heat-shocked (HS)

value: Whole worm


title: B_M0

city: Calgary

first: Matthew

last: Workentine

state: Alberta

address: 3280 Hospital Drive NW

country: Canada

institute: University of Calgary

data_processing:
Raw reaqds were quantified using cDNA from Homo sapiens GRCh38 with kallisto 0.43.1
Kallisto output was imported in R using sleuth 0.30.0, with gene mode turned on
Genome_build: GRCh38
Supplementary_files_format_and_content: scaled reads per base, output by sleuth 0.30.0, rows are Ensembl gene IDs and columns are samples

source_name: blood-derived macrophages_control

extract_protocol:
Macrophage RNA was isolated using the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Hercules, Ca), quantified using the Nanodrop 1000 Spectrophotometer (Thermo Fisher), and 0.5 g of RNA converted to cDNA using an iScript kit (Bio-Rad Laboratories Canada, Mississauga, ON, Canada).
RNA sequencing was performed at the Centre for Health Genomics and Informatics, Univ. Calgary, where samples were made into libraries using the Illumina TruSeq Stranded mRNA LT library preparation kit

tag: donor line

value: B

value: blood-derived macrophages

value: Control


title: B_IL4

source_name: blood-derived macrophages_IL4


title: A_M0

value: A


title: A_IL4


title: LC_5_T0_1000

description: human skin primary migratory LCs

value: unstimulated


title: C_34.4 kPa

description:
under substrate stiffness treatment
1_human-xlw_C_5
processed data file: cell_expressed_gene_*.txt

source_name: Human trabecular meshwork cells

value: Human trabecular meshwork (HTM)cells

value: 34.4 kPa for five day cultivation


title: C_2.5 kPa

description:
under substrate stiffness treatment
1_human-xlw_C_2
processed data file: cell_expressed_gene_*.txt

value: 2.5 kPa for five day cultivation


title: C_11.9 kPa

description:
under substrate stiffness treatment
1_human-xlw_C_4
processed data file: cell_expressed_gene_*.txt

value: 11.9 kPa for five day cultivation


title: C_M0

value: C


title: C_1.1 kPa

description:
under substrate stiffness treatment
1_human-xlw_C_1
processed data file: cell_expressed_gene_*.txt

value: 1.1 kPa for five day cultivation


title: C_50 kPa

description:
under substrate stiffness treatment
1_human-xlw_C_6
processed data file: cell_expressed_gene_*.txt

value: 50 kPa for five day cultivation


title: A_50 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_6
processed data file: cell_expressed_gene_*.txt

value: 50 kPa for three day cultivation


title: C_IL4


title: A_11.9 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_4
processed data file: cell_expressed_gene_*.txt

value: 11.9 kPa for three day cultivation


title: A_2.5 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_2
processed data file: cell_expressed_gene_*.txt

value: 2.5 kPa for three day cultivation


title: A_4.2 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_3
processed data file: cell_expressed_gene_*.txt

value: 4.2 kPa for three day cultivation


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1843]

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Ribosomal-bound RNA
1843_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep5_S18

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Accumbens nucleus

growth_protocol: Not applicable

extract_protocol:
The accumbens nucleus was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: Saline self-administration. Cocaine self-administration.

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum

tag: agent

value: Cocaine

tag: animal line

value: Drd2-TRAP CP101

tag: antibody

value: anti-EGFP Immunopurified (IP)


title: Saline self-administration input Rep1 [1824]

description:
Total RNA
1824_Drd2_TRAP_CP101_saline_input_S19

value: Saline

value: Input


title: LC_6_CRISPR_CTRL_1000

description: human skin primary migratory LCs

value: unstimulated


title: Saline self-administration withdrawl IP Rep3 [1838]

description:
Ribosomal-bound RNA
1838_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep3_S13


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1840]

description:
Ribosomal-bound RNA
1840_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep2_S15


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1839]

description:
Ribosomal-bound RNA
1839_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep1_S14


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1841]

description:
Ribosomal-bound RNA
1841_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep3_S16


title: Cocaine self-administration, nonescalating group input Rep1 [1825]

description:
Total RNA
1825_Drd2_TRAP_CP101_cocaine_nonescalating_input_S20


title: Saline self-administration withdrawl IP Rep1 [1836]

description:
Ribosomal-bound RNA
1836_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep1_S11


title: Saline self-administration withdrawl IP Rep2 [1837]

description:
Ribosomal-bound RNA
1837_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep2_S12


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1821]

description:
Ribosomal-bound RNA
1821_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep2_S16


title: Saline self-administration withdrawl IP Rep2 [1818]

description:
Ribosomal-bound RNA
1818_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep2_S13


title: Cocaine self-administration, nonescalating group IP Rep5 [1814]

description:
Ribosomal-bound RNA
1814_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep5_S9


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1820]

description:
Ribosomal-bound RNA
1820_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep1_S15


title: Saline self-administration withdrawl IP Rep3 [1819]

description:
Ribosomal-bound RNA
1819_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep3_S14


title: Cocaine self-administration, escalating group IP Rep1 [1815]

description:
Ribosomal-bound RNA
1815_Drd2_TRAP_CP101_cocaine_escalating_IP_Rep1_S10


title: Cocaine self-administration, nonescalating group IP Rep4 [1813]

description:
Ribosomal-bound RNA
1813_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep4_S8


title: Cocaine self-administration, nonescalating group IP Rep3 [1812]

description:
Ribosomal-bound RNA
1812_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep3_S7


title: Cocaine self-administration, nonescalating group IP Rep2 [1811]

description:
Ribosomal-bound RNA
1811_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep2_S6


title: Saline self-administration withdrawl IP Rep1 [1817]

description:
Ribosomal-bound RNA
1817_Drd2_TRAP_CP101_saline_withdrawl_IP_Rep1_S12


title: A_1.1 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_1
processed data file: cell_expressed_gene_*.txt

value: Human trabecular meshwork (HTM)cells

value: 1.1 kPa for three day cultivation


title: Cocaine self-administration, escalating group IP Rep2 [1816]

description:
Ribosomal-bound RNA
1816_Drd2_TRAP_CP101_cocaine_escalating_IP_Rep2_S11


title: A_34.3 kPa

description:
under substrate stiffness treatment
1_human-xlw_A_5
processed data file: cell_expressed_gene_*.txt

value: 34.3 kPa for three day cultivation


title: Cocaine self-administration, nonescalating group IP Rep1 [1810]

description:
Ribosomal-bound RNA
1810_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep1_S5


title: Saline self-administration IP Rep4 [1809]

description:
Ribosomal-bound RNA
1809_Drd2_TRAP_CP101_saline_IP_Rep4_S4


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1823]

description:
Ribosomal-bound RNA
1823_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep4_S18


title: Saline self-administration IP Rep3 [1808]

description:
Ribosomal-bound RNA
1808_Drd2_TRAP_CP101_saline_IP_Rep3_S3


title: Saline self-administration IP Rep1 [1806]

description:
Ribosomal-bound RNA
1806_Drd2_TRAP_CP101_saline_IP_Rep1_S1


title: Drd1-EGFP/Rpl10a (CP73) accumbens older mouse IP Rep3 [1616]

description:
Ribosomal-bound RNA
1616_Drd1_TRAP_CP73_accumbens_IP_old mouse_Rep3_S13

extract_protocol:
The dorsal striatum and accumbens nucleus were dissected  and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

treatment_protocol: No treatment

value: aged to >20 months

value: Drd1-TRAP CP73


title: Drd1-EGFP/Rpl10a (CP73) accumbens older mouse IP Rep2 [1615]

description:
Ribosomal-bound RNA
1615_Drd1_TRAP_CP73_accumbens_IP_old mouse_Rep2_S12


title: Drd1-EGFP/Rpl10a (CP73) dorsal striatum older mouse IP Rep2 [1611]

description:
Ribosomal-bound RNA
1611_Drd1_TRAP_CP73_dorsal striatum_IP_old mouse_Rep2_S2

source_name: Dorsal striatum


title: Drd1-EGFP/Rpl10a (CP73) dorsal striatum older mouse IP Rep3 [1612]

description:
Ribosomal-bound RNA
1612_Drd1_TRAP_CP73_dorsal striatum_IP_old mouse_Rep3_S3


title: Drd1-EGFP/Rpl10a (CP73) accumbens older mouse IP Rep1 [1614]

description:
Ribosomal-bound RNA
1614_Drd1_TRAP_CP73_accumbens_IP_old mouse_Rep1_S11


title: Drd1-EGFP/Rpl10a (CP73) dorsal striatum older mouse IP Rep4 [1613]

description:
Ribosomal-bound RNA
1613_Drd1_TRAP_CP73_dorsal striatum_IP_old mouse_Rep4_S4


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1842]

description:
Ribosomal-bound RNA
1842_Drd2_TRAP_CP101_cocaine_nonescalating_withdrawl_IP_Rep4_S17


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1604]

description:
Ribosomal-bound RNA
1604_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep4_S15

tag: background strain

tag: protocol

value: nonescalating group; approx. 1 month following self administration

tag: application

value: RNA-seq

tag: sample type

value: Immunopurified (IP)

value: Accumbens nucleus


title: Cocaine self-administration, escalating group withdrawl IP Rep2 [1607]

description:
Ribosomal-bound RNA
1607_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep2_S18

value: escalating group; approx. 1 month following self administration

tag: tissue


title: Drd1-EGFP/Rpl10a (CP73) dorsal striatum older mouse IP Rep1 [1610]

description:
Ribosomal-bound RNA
1610_Drd1_TRAP_CP73_dorsal striatum_IP_old mouse_Rep1_S1

tag: age


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1601]

description:
Ribosomal-bound RNA
1601_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep1_S12

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum


title: Cocaine self-administration, escalating group withdrawl IP Rep4 [1609]

description:
Ribosomal-bound RNA
1609_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep4_S20


title: Htr3a-Cre (NO176) x Rosa26-LSL-TRAP cerebral cortex IP Rep1 [1479]

description: 1479_Htr3a_CRE_NO176::Rosa26_LSL_cerebral cortex_IP_Rep1_S7

source_name: Cerebral cortex

extract_protocol:
The whole cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: cerebral cortex

tag: molecule

value: Ribosomal-bound RNA


title: Cocaine self-administration, nonescalating group withdrawl IP Rep6 [1600]

description:
Ribosomal-bound RNA
1600_Drd1_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep6_S11


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1599]

description:
Ribosomal-bound RNA
1599_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep5_S10


title: Cocaine self-administration, escalating group withdrawl IP Rep1 [1606]

description:
Ribosomal-bound RNA
1606_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep1_S17


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1598]

description:
Ribosomal-bound RNA
1598_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep4_S9


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1605]

description:
Ribosomal-bound RNA
1605_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep5_S16


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1597]

description:
Ribosomal-bound RNA
1597_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep3_S8


title: Drd1-EGFP/Rpl10a (CP73) accumbens older mouse IP Rep4 [1617]

description:
Ribosomal-bound RNA
1617_Drd1_TRAP_CP73_accumbens_IP_old mouse_Rep4_S14

value: anti-EGFP Immunopurified (IP)


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1596]

description:
Ribosomal-bound RNA
1596_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep2_S7


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1595]

description:
Ribosomal-bound RNA
1595_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep1_S6


title: Saline self-administration withdrawl IP Rep5 [1594]

description:
Ribosomal-bound RNA
1594_Drd1_TRAP_CP73_saline_withdrawl_Rep5_S5

value: control group; approx. 1 month following self administration


title: Htr3a-Cre (NO176) x Rosa26-LSL-TRAP cerebral cortex IP Rep3 [1481]

description: 1481_Htr3a_CRE_NO176::Rosa26_LSL_cerebral cortex_IP_Rep3_S9


title: Htr3a-Cre (NO176) x Rosa26-LSL-TRAP cerebral cortex IP Rep2 [1480]

description: 1480_Htr3a_CRE_NO176::Rosa26_LSL_cerebral cortex_IP_Rep2_S8


title: Saline self-administration withdrawl IP Rep4 [1593]

description:
Ribosomal-bound RNA
1593_Drd1_TRAP_CP73_saline_withdrawl_Rep4_S4


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1603]

description:
Ribosomal-bound RNA
1603_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep3_S14


title: Saline self-administration withdrawl IP Rep3 [1592]

description:
Ribosomal-bound RNA
1592_Drd1_TRAP_CP73_saline_withdrawl_Rep3_S3


title: Saline self-administration withdrawl IP Rep1 [1590]

description:
Ribosomal-bound RNA
1590_Drd1_TRAP_CP73_saline_withdrawl_Rep1_S1


title: Saline self-administration withdrawl IP Rep2 [1591]

description:
Ribosomal-bound RNA
1591_Drd1_TRAP_CP73_saline_withdrawl_Rep2_S2


title: Cocaine self-administration, escalating group IP Rep4 [1588]

description:
Ribosomal-bound RNA
1588_Drd1_TRAP_CP73_cocaine_escalating_Rep4_S19

value: escalating group; 24 hours following self administration


title: Cocaine self-administration, escalating group IP Rep5 [1589]

description:
Ribosomal-bound RNA
1589_Drd1_TRAP_CP73_cocaine_escalating_Rep5_S20


title: Cocaine self-administration, escalating group IP Rep3 [1587]

description:
Ribosomal-bound RNA
1587_Drd1_TRAP_CP73_cocaine_escalating_Rep3_S18


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1602]

description:
Ribosomal-bound RNA
1602_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep2_S13


title: Cocaine self-administration, escalating group IP Rep2 [1586]

description:
Ribosomal-bound RNA
1586_Drd1_TRAP_CP73_cocaine_escalating_Rep2_S17


title: Cocaine self-administration, escalating group IP Rep1 [1585]

description:
Ribosomal-bound RNA
1585_Drd1_TRAP_CP73_cocaine_escalating_Rep1_S16


title: Cocaine self-administration, nonescalating group IP Rep5 [1580]

description:
Ribosomal-bound RNA
1580_Drd1_TRAP_CP73_cocaine_nonescalating_Rep5_S11

value: nonescalating group; 24 hours following self administration


title: Cocaine self-administration, nonescalating group IP Rep6 [1581]

description:
Ribosomal-bound RNA
1581_Drd1_TRAP_CP73_cocaine_nonescalating_Rep6_S12


title: Cocaine self-administration, nonescalating group IP Rep4 [1579]

description:
Ribosomal-bound RNA
1579_Drd1_TRAP_CP73_cocaine_nonescalating_Rep4_S10


title: Cocaine self-administration, nonescalating group IP Rep2 [1577]

description:
Ribosomal-bound RNA
1577_Drd1_TRAP_CP73_cocaine_nonescalating_Rep2_S8


title: Cocaine self-administration, nonescalating group IP Rep2 [1583]

description:
Ribosomal-bound RNA
1583_Drd1_TRAP_CP73_cocaine_nonescalating_Rep2_S14


title: Cocaine self-administration, nonescalating group IP Rep1 [1582]

description:
Ribosomal-bound RNA
1582_Drd1_TRAP_CP73_cocaine_nonescalating_Rep1_S13


title: Saline self-administration IP Rep4 [1573]

description:
Ribosomal-bound RNA
1573_Drd1_TRAP_CP73_saline_IP_Rep4_S4

value: control group; 24 hours following self administration


title: Saline self-administration IP Rep2 [1571]

description:
Ribosomal-bound RNA
1571_Drd1_TRAP_CP73_saline_IP_Rep2_S2


title: Saline self-administration IP Rep1 [1570]

description:
Ribosomal-bound RNA
1570_Drd1_TRAP_CP73_saline_IP_Rep1_S1


title: Saline self-administration IP Rep3 [1572]

description:
Ribosomal-bound RNA
1572_Drd1_TRAP_CP73_saline_IP_Rep3_S3


title: Cocaine self-administration, nonescalating group IP Rep3 [1584]

description:
Ribosomal-bound RNA
1584_Drd1_TRAP_CP73_cocaine_nonescalating_Rep3_S15


title: Saline self-administration IP Rep6 [1575]

description:
Ribosomal-bound RNA
1575_Drd1_TRAP_CP73_saline_IP_Rep6_S6


title: Saline self-administration IP Rep5 [1574]

description:
Ribosomal-bound RNA
1574_Drd1_TRAP_CP73_saline_IP_Rep5_S5


title: Cocaine self-administration, nonescalating group IP Rep3 [1578]

description:
Ribosomal-bound RNA
1578_Drd1_TRAP_CP73_cocaine_nonescalating_Rep3_S9


title: Saline self-administration Input Rep1 [1618]

description:
Total RNA
1618_Drd1_TRAP_CP73_saline_input_Rep1_S5

extract_protocol:
The dorsal striatum was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Dorsal striatum

tag: strain

tag: group

value: control group; following self administration

value: Input


title: Saline self-administration Input Rep2 [1619]

description:
Total RNA
1619_Drd1_TRAP_CP73_saline_input_Rep2_S6

value: Drd1-TRAP CP73


title: Cocaine self-administration, escalating group withdrawl IP Rep2 [1567]

description:
Ribosomal-bound RNA
1567_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep2_S18


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1564]

description:
Ribosomal-bound RNA
1564_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep4_S15

value: nonescalating group; approx. 1 month following self administration


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1562]

description:
Ribosomal-bound RNA
1562_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep2_S13


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1563]

description:
Ribosomal-bound RNA
1563_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep3_S14


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1565]

description:
Ribosomal-bound RNA
1565_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep5_S16


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1561]

description:
Ribosomal-bound RNA
1561_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep1_S12


title: Cocaine self-administration, escalating group withdrawl IP Rep1 [1566]

description:
Ribosomal-bound RNA
1566_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep1_S17


title: Cocaine self-administration, nonescalating group withdrawl IP Rep6 [1560]

description:
Ribosomal-bound RNA
1560_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep6_S11

value: nonescalating group; approx. 1 month following extended self administration


title: Cocaine self-administration, nonescalating group withdrawl IP Rep5 [1559]

description:
Ribosomal-bound RNA
1559_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep5_S10

value: Immunopurified (IP)


title: Cocaine self-administration, nonescalating group IP Rep1 [1576]

description:
Ribosomal-bound RNA
1576_Drd1_TRAP_CP73_cocaine_nonescalating_Rep1_S7

value: RNA-seq

value: Accumbens nucleus


title: Cocaine self-administration, escalating group withdrawl IP Rep3 [1608]

description:
Ribosomal-bound RNA
1608_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep3_S19

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum

value: escalating group; approx. 1 month following self administration


title: Cocaine self-administration, nonescalating group withdrawl IP Rep2 [1556]

description:
Ribosomal-bound RNA
1556_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep2_S7


title: Cocaine self-administration, nonescalating group withdrawl IP Rep3 [1557]

description:
Ribosomal-bound RNA
1557_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep3_S8


title: Saline self-administration withdrawl IP Rep5 [1554]

description:
Ribosomal-bound RNA
1554_Drd1_TRAP_CP73_saline_withdrawl_Rep5_S5

value: control group; approx. 1 month following extended self administration


title: Saline self-administration withdrawl IP Rep3 [1552]

description:
Ribosomal-bound RNA
1552_Drd1_TRAP_CP73_saline_withdrawl_Rep3_S3


title: Cocaine self-administration, nonescalating group withdrawl IP Rep1 [1555]

description:
Ribosomal-bound RNA
1555_Drd1_TRAP_CP73_cocaine_nonescalating_withdrawl_Rep1_S6


title: Saline self-administration withdrawl IP Rep4 [1553]

description:
Ribosomal-bound RNA
1553_Drd1_TRAP_CP73_Saline_withdrawl_Rep4_S4


title: Saline self-administration withdrawl IP Rep1 [1550]

description:
Ribosomal-bound RNA
1550_Drd1_TRAP_CP73_saline_withdrawl_Rep1_S1


title: Cocaine self-administration, escalating group IP Rep1 [1545]

description:
Ribosomal-bound RNA
1545_Drd1_TRAP_CP73_cocaine_escalating_Rep1_S16

value: escalating group; 24 hours following extended self administration


title: Cocaine self-administration, escalating group IP Rep2 [1546]

description:
Ribosomal-bound RNA
1546_Drd1_TRAP_CP73_cocaine_escalating_Rep2_S17


title: Cocaine self-administration, escalating group withdrawl IP Rep3 [1568]

description:
Ribosomal-bound RNA
1568_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep3_S19


title: Cocaine self-administration, escalating group IP Rep5 [1549]

description:
Ribosomal-bound RNA
1549_Drd1_TRAP_CP73_cocaine_escalating_Rep5_S20


title: Cocaine self-administration, escalating group IP Rep3 [1547]

description:
Ribosomal-bound RNA
1547_Drd1_TRAP_CP73_cocaine_escalating_Rep3_S18


title: Saline self-administration withdrawl IP Rep2 [1551]

description:
Ribosomal-bound RNA
1551_Drd1_TRAP_CP73_saline_withdrawl_Rep2_S2


title: Cocaine self-administration, nonescalating group IP Rep3 [1544]

description:
Ribosomal-bound RNA
1544_Drd1_TRAP_CP73_cocaine_nonescalating_Rep3_S15

value: nonescalating group; 24 hours following extended self administration


title: Cocaine self-administration, nonescalating group IP Rep2 [1543]

description:
Ribosomal-bound RNA
1543_Drd1_TRAP_CP73_cocaine_nonescalating_Rep2_S14


title: Cocaine self-administration, escalating group IP Rep4 [1548]

description:
Ribosomal-bound RNA
1548_Drd1_TRAP_CP73_cocaine_escalating_Rep4_S19


title: Cocaine self-administration, nonescalating group IP Rep6 [1541]

description:
Ribosomal-bound RNA
1541_Drd1_TRAP_CP73_cocaine_nonescalating_Rep6_S12


title: Cocaine self-administration, nonescalating group IP Rep3 [1538]

description:
Ribosomal-bound RNA
1538_Drd1_TRAP_CP73_cocaine_nonescalating_Rep3_S9


title: Cocaine self-administration, nonescalating group IP Rep5 [1540]

description:
Ribosomal-bound RNA
1540_Drd1_TRAP_CP73_cocaine_nonescalating_Rep5_S11


title: Cocaine self-administration, nonescalating group IP Rep4 [1539]

description:
Ribosomal-bound RNA
1539_Drd1_TRAP_CP73_cocaine_nonescalating_Rep4_S10


title: Cocaine self-administration, nonescalating group IP Rep1 [1542]

description:
Ribosomal-bound RNA
1542_Drd1_TRAP_CP73_cocaine_nonescalating_Rep1_S13


title: Cocaine self-administration, nonescalating group IP Rep2 [1537]

description:
Ribosomal-bound RNA
1537_Drd1_TRAP_CP73_cocaine_nonescalating_Rep2_S8


title: Cocaine self-administration, nonescalating group IP Rep1 [1536]

description:
Ribosomal-bound RNA
1536_Drd1_TRAP_CP73_cocaine_nonescalating_Rep1_S7


title: Cocaine self-administration, nonescalating group withdrawl IP Rep4 [1558]

description:
Ribosomal-bound RNA
1558_Drd1_TRAP_CP73_Cocaine_nonescalating_withdrawl_Rep4_S9


title: Saline self-administration IP Rep2 [1531]

description:
Ribosomal-bound RNA
1531_Drd1_TRAP_CP73_saline_IP_Rep2_S2

value: control group; 24 hours following extended self administration


title: Saline self-administration IP Rep6 [1535]

description:
Ribosomal-bound RNA
1535_Drd1_TRAP_CP73_saline_IP_Rep6_S6


title: Saline self-administration IP Rep1 [1530]

description:
Ribosomal-bound RNA
1530_Drd1_TRAP_CP73_saline_IP_Rep1_S1


title: Saline self-administration IP Rep5 [1534]

description:
Ribosomal-bound RNA
1534_Drd1_TRAP_CP73_saline_IP_Rep5_S5


title: Saline self-administration IP Rep3 [1532]

description:
Ribosomal-bound RNA
1532_Drd1_TRAP_CP73_saline_IP_Rep3_S3


title: Arabidopsis leaf treated with water and DC3000 at 12h rep2

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
A reference genome sequence data of Arabidopsis thaliana was obtained from Illumina iGenome supporting site (assembly ID: TAIR10; http://support.illumina.com/sequencing/sequencing_software/igenome.html). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments per kilobase of transcript per million fragments mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with FPkM values

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: ecotype

value: leaf

tag: treatment time

value: Water, DC3000


title: Arabidopsis leaf treated with water and DC3000 at 12h rep1


title: Arabidopsis leaf treated with water at 0h rep2

value: Water


title: Arabidopsis leaf treated with Chlorella and DC3000 at 12h rep1

value: Chlorella, DC3000


title: Alveolar macrophages, KOCS_IVb2

first: Ken

middle: R

last: Bracke

address: Corneel Heymanslaan 10

department: Department of Respiratory Medicine

institute: Ghent University

data_processing:
sequencing reads were mapped to the murine reference genome (GRCm38.p6) using STAR v2.6.0c and GENCODE release M18 as guidance
read counts were quantified using the "--quantMode GeneCounts" option
genomic features with a zero read count across all samples and without read count greater or equal than four in at least sixty percent of the samples from one group were discarded
raw counts were transformed into log2-counts per million using limma-voom
Genome_build: GRCm38.p6 + GENCODE release M18
Supplementary_files_format_and_content: tab-delimited text file including log-CPM transformed values

source_name: FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)

extract_protocol:
RNA extraction of FACS sorted alveolar macrophages was performed with the miRNeasy Mini Kit (Qiagen).
libraries were prepared using the TruSeq mRNA library prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. A total of 25 ng of RNA was used as input for polyA selection, followed by fragmentation, reverse transcription and PCR amplification

treatment_protocol: wild-type and miR-155 knock-out mice to four weeks of air or cigarette smoke

tag: cell type

tag: treatment protocol

value: cigarette smoke

tag: genotype


title: Arabidopsis leaf treated with Chlorella and DC3000 at 12h rep2

tag: treatment


title: Alveolar macrophages, KOCS_IVb4

value: FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)


title: Arabidopsis leaf treated with Chlorella at 0h rep2

value: Chlorella


title: Alveolar macrophages, KOCS_IVa2


title: Drd1-EGFP/Rpl10a-CP73_Dorsal striatum_Input Rep 2

description: 1623_Drd1_TRAP_CP73_Old mouse_Rep2_S10

extract_protocol:
The dorsal striatum and accumbens nucleus were dissected and homogenized. Total RNA was purified with the Agilent Nanoprep kit following manufacturer's protocol.
RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Aged animal >20 months

tag: animal line

value: Drd1-TRAP CP73

value: Dorsal striatum

value: Input


title: Alveolar macrophages, KOAIR_IIIb4

value: air


title: Drd1-EGFP/Rpl10a-CP73_Accumbens_Input Rep 1

description: 1628_Drd1_TRAP_CP73_Old mouse_Rep1_S19

value: Accumbens nucleus


title: Alveolar macrophages, KOAIR_IIIb3


title: Drd1-EGFP/Rpl10a-CP73_Accumbens_Input Rep 2

description: 1629_Drd1_TRAP_CP73_Old mouse_Rep2_S20


title: Arabidopsis leaf treated with Chlorella at 0h rep1


title: Arabidopsis leaf BG11 at 0h

value: nothing


title: Alveolar macrophages, KOAIR_IIIb1


title: Alveolar macrophages, KOAIR_IIIb2


title: Alveolar macrophages, KOAIR_IIIa5


title: Alveolar macrophages, WTCS_IIb3

value: wild-type


title: Drd1-EGFP/Rpl10a-CP73_Dorsal striatum_Input Rep 1

description: 1622_Drd1_TRAP_CP73_Old mouse_Rep1_S9


title: Alveolar macrophages, WTCS_IIb2


title: Arabidopsis leaf treated with water at 0h rep1


title: Alveolar macrophages, KOCS_IVa4


title: Alveolar macrophages, WTCS_IIb1


title: Alveolar macrophages, KOCS_IVa5


title: LC_3_TNFa_24h

description: human skin primary migratory LCs

data_processing:
Quality control: FASTQC
ChIP-seq alignment: BioWardrobe
ChiP-seq Peak Calling: Biowardrobe (MACS2 version 2.1.1)
RNA-seq trimming: Trimmomatic
RNA-seq mapping and alignment: TopHat V 2.0.9 and HTSeq-count V.0.5.4
Genome_build: hg19
scRNA-seq: demultiplexing: bcl2fastq tool, Illumina
scRNA-seq: STAR
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: peak files. RNA-seq: aligned Htseq Reads

growth_protocol: Human primary LCs were migrated out of epidermal sheets, following digest with dispase o/n at +4C. CD1a+ cells were purified using fluorescence-activated cell sorting.

extract_protocol:
for ChIP-seq: Purified migratory LCs were fixed with 1% formaldehyde for 15 min and the reaction quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 100–200 bp (Covaris). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat to remove crosslinks, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. Genomic DNA regions of interest were isolated using appropriate antibodies. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation (at 37 °C for 1 h, followed by 4 h at 65 °C) overnight at 65 °C, and ChIP DNA was purified by phenol–chloroform extraction and ethanol precipitation.  For RNA-seq: RNA was isolated using RNeasy mini kit (Qiagen) as per the manufacturer’s protocol. RNA concentration and integrity was determined with an Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA). All the samples had a RNA integrity number of 7.0 or above and were taken forward for labelling.
for Chip-seq: Illumina sequencing libraries were prepared from the ChIP and input DNAs by the standard consecutive enzymatic steps of end- polishing, dA-addition, and adaptor ligation using TruplexTM –FD prep kit (Rubicon Genomics, USA). After a final PCR amplification step, the resulting DNA libraries were quantified using Qubit (Life technologies, USA) and 75 nucleotide single-end reads were sequenced Illumina HiSeq2500 in the DNA sequencing core of the Cincinnati Children's Hospital Medical Center.  For RNA-seq: RNA-seq libraries were generated from 300 ng total RNA with an RNA Sample Prep Kit (Illumina) according to a standard protocol. The libraries were sequenced with Illumina HiSeq2500 in the DNA sequencing core of the Cincinnati Children's Hospital Medical Center. Each sample was used to generate 2 × 107 reads with 75–base pair paired-end sequencing.

tag: condition

value: TNFa

tag: time


title: Alveolar macrophages, WTCS_IIa5


title: Arabidopsis leaf BG11 at 12h


title: LC_3_0h

description: human skin primary migratory LCs

value: unstimulated


title: LC_2_TNFa_24h

description: human skin primary migratory LCs


title: Alveolar macrophages, WTAIR_Ib4


title: LC_2_TNFa_2h

description: human skin primary migratory LCs


title: LC_3_TNFa_2h

description: human skin primary migratory LCs


title: Alveolar macrophages, WTAIR_Ia3


title: LC_1_TNFa_24h

description: human skin primary migratory LCs


title: Alveolar macrophages, WTAIR_Ib2


title: Alveolar macrophages, WTAIR_Ib1


title: Treated, Experiment 2

city: Wako

last: Matsumoto

state: Saitama

address: 2-1 Hirosawa

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: The fragmented cRNA was used for hybridization to the Genechip overnight at 45°C with rotation.

scan_protocol: Using GeneChip Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX (Agilent). MAS5

source_name: Treated, Exp 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT PLUS Reagent protocol starting with 200 ng of total RNA

growth_protocol: HeLa S3 cells were inoculated in a 6-well plate the day before the compound treatment.

extract_protocol: RNA was purified by RNeasy mini kit (Qiagen).

treatment_protocol: Cells were treated with growth medium containing DMSO or 4 microM JBIR-140 for 6 h.

tag: cell line

value: HeLa S3

value: 4 microM JBIR-140 (prethioviridamide) for 6 h


title: C57BL/6_oocyte_RNApolII_rep2

city: Vancouver

last: Lorincz

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

institute: University of British Columbia

description: RNA polymerase II (CTD)

data_processing:
ChIP-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using Bowtie2 v.2.2.3 with soft-clipping enabled. Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1. PCR duplicates and alignments with mapping quality less than 10 were filtered out. Sequence alignment maps were converted to bedGraph and wiggle formats using Bedtools v2.22.1 and UCSC binary bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: GVO

extract_protocol:
ChIP-seq: purified ChIP DNA was extracted with Phenol:chloroform followed by ethanol precipitation. RNA-seq: total RNA was isolated from 100-200 mouse or rat oocytes using TriReagent, and ribosomal RNA was depleted using NEB Next rRNA Depletion kit according to manufacturer’s instruction. Double stranded cDNA was synthesized using NEB Next first strand and second strand synthesis modules.
Libraries were constructed using a custom protocol (Brind’Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer’s protocols.

value: oocyte

tag: antibody

value: RNA polymerase II (CTD)


title: Untreated, Experiment 2

source_name: Untreated, Exp 2

value: untreated


title: Treated, Experiment 1

source_name: Treated, Exp 1


title: LC_1_TNFa_2h

description: human skin primary migratory LCs


title: LC_4_T0_150SC

description: human skin primary migratory LCs


title: C57BL/6_oocyte_RNApolII_rep1

description: RNA polymerase II (CTD)


title: LC_1_0h

description: human skin primary migratory LCs


title: Untreated, Experiment 1

source_name: Untreated, Exp 1


title: BMHSC_iHiC_Rep2

city: PHILADELPHIA

first: Kai

last: Tan

state: PA

address: 3501 CIVIC CENTER BLVD.

institute: Children's Hospital of Philadelphia

data_processing:
Hi-C read mapping, detection of valid interactions, correction of systematic noise, and calculation of normalized contact matrices were performed using HiC-Pro with default parameters.
Paired-end reads were mapped to the mm9 version of the mouse genome. Normalized contact matrices at 10kb resolution were computed using  the ICE algorithm with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: TAD regions called by GMAP

source_name: 6-8 week-old bone marrow hematopoietic stem cells

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. Half million sorted cells were cross-linked with 1% formaldehyde for 10 min at RT and quenched with glycine (final concentration 0.125M). Nuclei were then permeabilized with 250 μL of cold lysis buffer (10 mM Tris, 10 mM NaCl, 0.2% Igepal CA630) and 50 μL of protease inhibitors (P8340, Sigma). Chromatin was digested with 100 units of MboI (R0147, NEB) overnight at 37°C with rotation. Restriction fragment ends were labelled with biotinylated nucleotides and proximity ligation in a small volume with 5 μL of 400 U/μL T4 DNA ligase (B0202, NEB). After reversal of cross-link, DNA was sheared to a length of 300~500 bp and size-selected using AMPure XP beads (A63881, Beckman Coulter). The ligated junctions were pulled down with 150 μL of Dynabeads MyOne Streptavidin C1 magnetic beads (65001, Thermo Scientific).
Libraries were constructed using NEB DNA quick ligase (NEB, M2200) and customized Illumina indexed adapters. Libraries were size-selected at 200-500 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

value: Adult bone marrow

value: 6-8 week-old


title: LC_3_TNFa_24h_Ac

description: human skin primary migratory LCs


title: BMHSC_iHiC_Rep1


title: LC_3_TNFa_2h_Ac

description: human skin primary migratory LCs


title: LC_3_0h_Ac

description: human skin primary migratory LCs


title: FLHSC_iHiC_Rep2

source_name: Embryonic day 14.5 fetal liver hematopoietic stem cells

value: Fetal liver

value: Embryonic day 14.5


title: LC_2_0h

description: human skin primary migratory LCs


title: LC_2_TNFa_24h_Ac

description: human skin primary migratory LCs


title: FLHSC_iHiC_Rep1


title: LC_2_TNFa_2h_Ac

description: human skin primary migratory LCs


title: BMHSC_Capture-C_SecondBatch_Rep2

data_processing:
Library strategy: Capture-C
Capture-C data were processed using the pipeline from Hughes et al. Briefly, Illumina Truseq adaptor sequences were trimmed from raw reads using trim galore version 0.41 with default parameter setting.
Paired-end reads were merged into one single fastq file to ensure each pair of reads interleaved in strict order. Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2).
Mapped reads were analyzed using the script CCanalyser2.pl (https://github. com/telenius/captureC/releases). Unique informative reads were extracted for each captured bait as the input for calling significant interactions.
Genome_build: mm9

extract_protocol:
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. Half million FACS-sorted cells were cross-linked, lysed and nuclei were digested using DpnII (R0543T, NEB) at 37°C with shaking at 1400 rpm overnight. The digested chromatin was proximally ligated with 100 U T4 DNA ligase (10799009001, Roche) at 16°C for 8 hrs with slow rotation. The samples were de-cross-linked followed by purification using phenol-chloroform extraction and precipitated using 70% ethanol. The purified 3C DNA was was sonicated to 200~300bp using Covaris S220 ultra-sonicator (6 min; duty cycle, 10%; intensity, 5; cycle per burst, 200). Sequencing libraries were constructed using NEBNext Ultra Kit (E7370, NEB). The libraries were size-selected using AMPure XP beads (A63881, Beckman Coulter). Oligonucleotide capture was performed using the SureSelect XT2 protocol (G9621A, Agilent). The libraries were quantified with Qubit, Agilent Bioanalyzer 2100 and KAPA qPCR (KK4844, Kapabiosystems). The captured libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq platform.
Libraries constructed using NEBNext Ultra Kit (E7370, NEB). The libraries were size-selected using AMPure XP beads (A63881, Beckman Coulter). The libraries were quantified with Qubit, Agilent Bioanalyzer 2100 and KAPA qPCR (KK4844, Kapabiosystems). The captured libraries were sequenced with 150 bp paired-end reads on an Illumina HiSeq platform.

tag: strain/cell type


title: LC_2_0h_Ac

description: human skin primary migratory LCs


title: LC_1_TNFa_24h_Ac

description: human skin primary migratory LCs


title: LC_1_TNFa_2h_Ac

description: human skin primary migratory LCs


title: FLHSC_Capture-C_SecondBatch_Rep2

tag: tissue


title: BMHSC_Capture-C_SecondBatch_Rep1

tag: age


title: Cocaine self-administration, escalating group withdrawl IP Rep4 [1569]

description:
Ribosomal-bound RNA
1569_Drd1_TRAP_CP73_cocaine_escalating_withdrawl_Rep4_S20

value: Dorsal striatum

value: FVB/N-Swiss Webster x 9 generations C57BL/6 minimum

value: escalating group; approx. 1 month following self administration

value: Drd1-TRAP CP73

tag: sample type

value: Immunopurified (IP)


title: LC_1_0h_Ac

description: human skin primary migratory LCs


title: LC_3_TNFa_24h_Me3

description: human skin primary migratory LCs


title: LC_3_TNFa_2h_Me3

description: human skin primary migratory LCs


title: Slc17a6-TRAP (JX883) midbrain IP Rep3 [1016]

description:
Ribosomal-bound RNA
1016_Slc17a6_TRAP_JX883_midbrain_IP3_ACAGTG_L003

source_name: Midbrain

extract_protocol:
The hypothalamus and midbrain were dissected seperately and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Midbrain

value: Slc17a6-TRAP JX883

tag: application

value: RNA-seq


title: Slc17a6-TRAP (JX883) midbrain input Rep3 [1017]

description:
Total RNA
1017_Slc17a6_TRAP_JX883_midbrain_Input3_GTGAAA_L003

value: Input


title: LC_3_0h_Me3

description: human skin primary migratory LCs

source_name: epidermis

value: unstimulated


title: Slc17a6-TRAP (JX883) midbrain input Rep2 [1011]

description:
Total RNA
1011_Slc17a6_TRAP_JX883_midbrain_Input2_GTGAAA_L007


title: Slc17a6-TRAP (JX883) hypothalamus IP Rep3 [1014]

description:
Ribosomal-bound RNA
1014_Slc17a6_TRAP_JX883_hypothalamus_IP3_ACAGTG_L002

source_name: Hypothalamus

value: Hypothalamus


title: Slc17a6-TRAP (JX883) midbrain IP Rep2 [1010]

description:
Ribosomal-bound RNA
1010_Slc17a6_TRAP_JX883_midbrain_IP2_ACAGTG_L007


title: LC_2_TNFa_2h_Me3

description: human skin primary migratory LCs

value: TNFa


title: LC_1_TNFa_24h_Me3

description: human skin primary migratory LCs


title: Slc17a6-TRAP (JX883) hypothalamus IP Rep2 [1008]

description:
Ribosomal-bound RNA
1008_Slc17a6_TRAP_JX883_hypothalamus_IP2_ACAGTG_L006


title: Slc17a6-TRAP (JX883) hypothalamus input Rep2 [1009]

description:
Total RNA
1009_Slc17a6_TRAP_JX883_hypothalamus_Input2_GTGAAA_L006


title: Slc17a6-TRAP (JX883) midbrain input Rep1 [983]

description:
Total RNA
983_Slc17a6_TRAP_JX883_midbrain_Input1_GTGAAA_L008


title: Alveolar macrophages, WTCS_IIa1

value: FACS sorted alveolar macrophages (CD45+SiglecF+CD11c+)

value: cigarette smoke

value: wild-type

tag: strain