title: alternative MED19-LNCaP 2

city: New York

first: Michael

last: Garabedian

state: NY

address: 550 First Avenue

department: Microbiology

institute: NYU School of Medicine

description:
Sample 11
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment two - 12-24-17

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Genome_build: hg19

source_name: LNCaP cells

growth_protocol: LNCaP cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Hyclone; Fisher Scientific) and 1% penicillin-streptomycin (Cellgro; Mediatech, Inc.) For assays under androgen deprivation, cells were cultured in androgen-depleted RPMI: phenol red- and L-glutamine-free RPMI-1640 supplemented with 10% FBS dextran charcoal-stripped of androgens (c-FBS, Hyclone) and 1% L-glutamine (Cellgro Mediatech, Inc.). Cells were cultured on poly-d-lysine-coated plates.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen)
Libraries were prepared with ribodepletion using Illumina TruSeq stranded total RNA with RiboZero Gold library preparation kit. Sequencing was performed using the Illumina HiSeq4000 Sequencing system (Paired-End 50 Cycle Lane).

treatment_protocol: Cells were with 10 nM R1881 or ethanol vehicle for 16 hours

value: EtOH vehicle

value: MED19 overexpression

tag: time course

value: androgen deprivation 3 days

tag: cell line

value: LNCaP

tag: disease

value: prostate cancer


title: control LNCaP 3

status: Public on Jan 20 2021

type: SRA

country: USA

description:
Sample 9
control LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment three - 12-9-17

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: treatment

tag: genotype

value: control


title: alternative MED19-LNCaP 3

description:
Sample 12
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment three - 12-9-17


title: X26_RFP5

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
Reads were trimmed for adaptors and low-quality bases using Trimmomatic and were aligned with the reference genome (Human-hg38) and the annotated transcripts (Gencode_v24) using STAR (https://github.com/alexdobin/STAR).
The gene expression quantification analysis was performed using STAR/RSEM tools (http://deweylab.github.io/RSEM/) to obtain raw read counts and normalized read counts (RPKM) for each gene.
Differentially expressed genes were identified using DESeq2 in R with a false discovery rate (FDR) cutoff of 0.01, and analyzed by gene enrichment analysis for KEGG (https://www.genome.jp/kegg/) and Reactome Pathways (https://reactome.org/) using DAVID v6.8 (https://david.ncifcrf.gov/).

molecule: total RNA

source_name: Cell line

extract_protocol:
RNA samples were treated with DNase I (no. 18068015, Thermo Fisher Scientific), followed by purification with RNeasy MinElute Cleanup kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA).

tag: tissue

value: Cell line

tag: genotype/variation


title: alternative MED19-LNCaP 1

description:
Sample 10
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment one - 12-17-17


title: VO-pop1-2

city: Melbourne

first: Ana Rita

last: Leitoguinho

state: VIC

address: 50 Flemington road

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description: Population (Pop.) 1

data_processing:
FASTQ samples sequenced 2 times were pooled into a single file. Compressed (gzipped) FASTQ files  were aligned to the Human genome using STAR software (v2.5.2a) in a 2 pass mode (Dobin et al., 2013).
Uniquely mapped reads were indexed, sorted and summarised using Samtools (v1.8) and FeatureCounts (v1.4.6) using Gencode Release 19 comprehensive annotation (Liao, Smyth and Shi, 2014).
Genes lowly expressed were excluded (less than 10 counts per million in fewer than 3 samples). The data was TMM normalised, voom transformed and differential gene expression was assessed using moderate t-tests from the R (v3.3.2) Bioconductor limma (v3.30.13) package and edgeR (v3.16.5) (Robinson, McCarthy and Smyth, 2009; Robinson and Oshlack, 2010; Ritchie et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: ESC derived PGC-like cells were generated using Spin Embryoid body (EB). For each experiment, 3-4 × 10^6 cells in a T75 flask were seeded in 10x 96-well plates. Cells were left in PGC differentiation media until day 4 when Ebs were dissociated and cell sorrted into different fractions (populations)

extract_protocol:
Cells samples were lysed in RLY buffer (Bioline) supplemented with 2-Mercaptoethanol (Life Technologies) and subsequently frozen at -80C. All RNA extraction was performed simultaneously using the Isolate II RNA Micro kit (Bioline) to avoid artificial batch effects.
RNA libraries were prepared for sequencing using  Illumina TruSeq Stranded mRNA kit according to manufacturers' protocol or using an adjusted protocol for less than 100ng total RNA input. Sequencing was performed using the Illumina NextSeq 550 (Illumina) platform with using the 2x75 bp run setting (single indexing reads) and an average of 20 million reads per sample.

treatment_protocol: Day 0: 1.25 ng/ml ACTIVIN A; 40ng/ml BMP4; 100ng/ml SCF. Day 1: 280ng/ml BMP4. Day 2: 1microMolar of CHIR.

tag: cell type

value: ES-derived primordial germ cells

tag: sorting profie

value: GFP+ mCHERRY+ EPCAM+ CD49f+

value: VENTX Wild type (VO)

tag: day

value: Day 4


title: MED19-LNCaP R1881 3

description:
Sample 6
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment three - 12-9-17

value: 10 nM R1881 overnight


title: KO-pop5-5

description: Population (Pop.) 5

value: GFP+ mCHERRY+ EPCAM+ CD49f-

value: VENTX Knock-out (KO)


title: VO-pop1-1

description: Population (Pop.) 1


title: VO-pop2-4

description: Population (Pop.) 2

value: GFP- mCHERRY+ EPCAM+ CD49f-


title: VO-pop2-5

description: Population (Pop.) 2


title: KO-pop5-4

description: Population (Pop.) 5


title: MED19-LNCaP R1881 2

description:
Sample 4
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment two - 12-24-17


title: KO-pop5-2

description: Population (Pop.) 5


title: control LNCaP R1881 2

description:
Sample 3
control LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment two - 12-24-17


title: control LNCaP R1881 1

description:
Sample 1
control LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment one - 12-17-17


title: MED19-LNCaP R1881 1

description:
Sample 2
alt MED19-LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment one - 12-17-17


title: KO-pop4-4

description: Population (Pop.) 4

value: GFP- mCHERRY+ EPCAM+ CD49f+


title: KO-pop4-5

description: Population (Pop.) 4


title: control LNCaP 2

description:
Sample 8
control LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment two - 12-24-17


title: input MED19-LNCaP CS R1881 3

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19 - 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, input sample - input used for normalization/control

library_source: genomic

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Homo sapiens genome build hg19 using bowtie23.
Per-sample quality assessment plots were generated with HOMER4 and Mosaics5. Peaks were called using MACS26 (with input/IgG controls background subtracted, if provided).
Peak overlaps and differential binding were calculated using the DiffBind R library7. Differential binding was calculated at gene promoter sites.
Read distribution percentages, identity heatmaps, and FRiP plots were generated as part of the QC step using ChIPQC R library8 and HOMER.
HOMER was also used to generate known and de novo motifs and perform functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies.
Genome_build: hg19

molecule: genomic DNA

source_name: LNCaP

growth_protocol: LNCaP cell lines were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) (Hyclone; Fisher Scientific) and 1% penicillin-streptomycin (Cellgro; Mediatech, Inc.)  For assays under androgen deprivation, cells were cultured in androgen-depleted RPMI: phenol red- and L-glutamine-free RPMI-1640 supplemented with 10% FBS dextran charcoal-stripped of androgens (c-FBS, Hyclone) and 1% L-glutamine (Cellgro Mediatech, Inc.).  Cells were cultured on poly-d-lysine-coated plates.

extract_protocol:
Cell pellets were resuspended in nuclei isolation buffer (50 mM Tris–pH 8.0, 60 mM KCl, 0.5% NP40), nuclei collected, and resuspended in sonication buffer (RIPA buffer).  Samples were sonicated in TPX PMP tubes (Diagenode) for 60 min (30 sec. on, 30 sec. off) in a Bioruptor sonicator (Diagenode). Inputs (10%) were collected and supernatants were then incubated overnight with the following antibodies pre-incubated with Protein A and Protein G Dynabeads (Invitrogen): a mixture of AR antibodies (AR 441 mouse monoclonal, Santa Cruz Biotechnology, cat # sc-7305) and (AR D6F11 rabbit monoclonal, Cell Signaling Technology, cat # 5153); DYKDDDDK Tag (FLAG epitope) (Cell Signaling Technology, cat # 14793); or H3K27 acetylation (Active Motif, cat # 39034).  Control ChIPs were performed with normal mouse IgG (Santa Cruz Biotechnology, cat # sc-2025) and normal rabbit IgG (Sigma Aldrich, cat # 12-370). Immunocomplexes were then washed and cross-linking reversed overnight at 65 °C with 5 M NaCl. DNA was isolated with the Zymo Chip DNA Clean and Concentrator kit (Zymo Research).
libraries were prepared according to the protocol described in PMID: 30679424.  Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from a 10% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Sequencing was performed using Illumina HiSeq4000 Sequencing (HiSeq 4000 Single Read 50 Cycle Lane).

treatment_protocol: Cells treated with 100 nM R1881 (a synthetic androgen diluted from a 1,000x stock in 100% ethanol) or an equivalent volume ethanol vehicle for 4 hours.

tag: antibody

value: none (Input)

tag: phenotype


title: control LNCaP 1

description:
Sample 7
control LNCaP cells 3 days androgen deprivation with 16 h EtOH vehicle treatment overnight - experiment one - 12-17-17

value: EtOH vehicle


title: input MED19-LNCaP CS R1881 2

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19 - 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, input sample - input used for normalization/control

value: MED19 overexpression


title: KO-pop4-2

description: Population (Pop.) 4


title: input MED19-LNCaP CS media 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19 - 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, input sample - input used for normalization/control

value: EtOH vehicle 4 h


title: KO-pop3-5

description: Population (Pop.) 3

value: GFP+ mCHERRY+ EPCAM- CD49f-


title: input MED19-LNCaP CS R1881 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19 - 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, input sample - input used for normalization/control

value: prostate cancer

value: LNCaP


title: input MED19-LNCaP CS media 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19 - 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, input sample - input used for normalization/control


title: KO-pop3-2

description: Population (Pop.) 3


title: KO-pop3-1

description: Population (Pop.) 3


title: input MED19-LNCaP CS media 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19 - 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, input sample - input used for normalization/control


title: KO-pop3-4

description: Population (Pop.) 3


title: KO-pop2-5

description: Population (Pop.) 2


title: input control LNCaP CS R1881 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, input sample

value: control


title: KO-pop2-4

description: Population (Pop.) 2

value: ES-derived primordial germ cells


title: KO-pop2-2

description: Population (Pop.) 2


title: input control LNCaP CS R1881 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, input sample - input used for normalization/control


title: KO-pop2-1

description: Population (Pop.) 2


title: control LNCaP R1881 3

description:
Sample 5
control LNCaP cells 3 days androgen deprivation with 16 h 10 nM R1881 treatment overnight - experiment three - 12-9-17

value: androgen deprivation 3 days


title: KO-pop1-5

description: Population (Pop.) 1

value: GFP+ mCHERRY+ EPCAM+ CD49f+


title: input control LNCaP CS media 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, input sample - input used for normalization/control


title: input control LNCaP CS media 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, input sample - input used for normalization/control


title: input- control LNCaP CS media 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, input sample - input used for normalization/control


title: KO-pop1-4

description: Population (Pop.) 1

value: Day 4


title: KO-pop4-1

description: Population (Pop.) 4


title: FntbKO_eTreg1_ATACseq

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
Adapter sequences were removed using trimmomatic v.0.36
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.7.16, default parameter)
duplicated reads were then marked with Picard (version 2.9.4) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.1, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm10
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

organism: Mus musculus

source_name: Treg cells directly sorted from mixed bone marrow chimera

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: Spleen and lymph nodes

value: Treg


title: KO-pop1-2

description: Population (Pop.) 1

value: VENTX Knock-out (KO)


title: KO-pop1-1

description: Population (Pop.) 1


title: IgG ChIP MED19-LNCaP CS R1881 2

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, IgG ChIP - used as additional negative control

value: IgG mouse (Santa Cruz # sc-2025)


title: hESC-VO-2

description: hESC

value: human undifferentiated (hESC)

value: Unsorted

value: VENTX Wild type (VO)

value: Day 0


title: hESC-VO-3

description: hESC


title: input control LNCaP CS R1881 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, input sample

value: none (Input)


title: IgG ChIP MED19-LNCaP CS R1881 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, IgG ChIP - used as additional negative control

value: MED19 overexpression


title: hESC-KO-3

description: hESC


title: IgG ChIP MED19-LNCaP CS media 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, IgG ChIP - used as additional negative control

value: EtOH vehicle 4 h

value: prostate cancer


title: IgG ChIP MED19-LNCaP CS media 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, IgG ChIP - used as additional negative control

value: LNCaP


title: IgG ChIP control LNCaP CS R1881 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, IgG ChIP (additional negative control)

value: control


title: IgG ChIP MED19-LNCaP CS media 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, IgG ChIP - used as additional negative control


title: IgG ChIP control LNCaP CS media 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, IgG ChIP (additional negative control)


title: hESC-KO-1

description: hESC


title: IgG ChIP MED19-LNCaP CS R1881 3

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, IgG ChIP - used as additional negative control


title: IgG ChIP control LNCaP CS R1881 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, IgG ChIP (additional negative control)


title: IgG ChIP control LNCaP CS R1881 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, IgG ChIP (additional negative control)


title: IgG ChIP control LNCaP CS media 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, IgG ChIP (additional negative control)


title: IgG ChIP control LNCaP CS media 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, IgG ChIP (additional negative control)


title: H3K27ac ChIP MED19-LNCaP CS R1881 2

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, H3K27ac ChIP

value: H3K27ac (Active Motif, cat # 39034


title: H3K27ac ChIP MED19-LNCaP CS R1881 3

description: MED19-LNCaP - LNCaP cells stably expressing (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, H3K27ac ChIP


title: hESC-VO-1

description: hESC


title: Liver_CN65_D1_stdata

city: Stockholm

first: Franziska

middle: Frederike Annalena

last: Hildebrandt

state: Stockholms Lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
creation of count-matrices using ST pipeline (v 1.7.6) (Navarro J.F., 2017 , DOI: 10.1093/bioinformatics/btx211 )
Genome_build: GRCm38 v86 and corresponding GENCODE annotation file
Supplementary_files_format_and_content: compressed tab seperated count matrices
Supplementary_files_format_and_content: 10% scaled spot coordiantes under the tissue
Supplementary_files_format_and_content: output count matrices from ST pipeline

source_name: liver tissue

extract_protocol:
mice were euthanized between week 8 and 12, livers were collected, and four lobes were separated. Each lobe was segmented so cryosections would fit on the 6,200 x 6,400 µm areas of the Codelink-activated microscope slides and frozen in -30°C 2-Methylbutane (Merck, cat.no.: M32631-1L). The frozen liver samples were embedded in cryomolds (10x10 mm, TissueTek) filled with pre-chilled (4°C) OCT embedding matrix and frozen (CellPath, cat.no.: 00411243).
The sequencing libraries were prepared as described in Jemt et al. (DOI: 10.1038/srep37137 ).In short, the 2nd strand synthesis, cDNA purification, in vitro transcription, amplified RNA purification, adapter ligation, post-ligation purification, a second 2nd strand synthesis and purification were done using an automated MBS 8000+ system. To determine the number of PCR cycles needed for optimal indexing conditions, using qPCR as described previously 58. After determination of the optimal cycle number for each sample, the remaining cDNA was indexed and amplified. The indexed libraries were then purified using an automated system as previously described 60. The average length of the indexed cDNA libraries was determined with a 2100 Bioanalyzer using the Bioanalyzer High Sensitivity DNA kit (Agilent, cat.no.:5067-4626), concentrations were measured using a Qubit dsDNA HS Assay Kit (Thermofisher, cat.no:Q32851) and libraries were diluted to 4nM. Paired-end sequencing was performed on the Illumina NextSeq500 platform

tag: Sex

value: female

tag: strain

tag: liver lobe

value: caudate


title: Liver_CN65_C1_stdata


title: Liver_CN65_C2_stdata


title: H3K27ac ChIP MED19-LNCaP CS media 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, H3K27ac ChIP


title: hESC-KO-2

description: hESC


title: H3K27ac ChIP MED19-LNCaP CS R1881 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, H3K27ac ChIP


title: KO-pop3-3

description: Population (Pop.) 3

value: ES-derived primordial germ cells

value: GFP+ mCHERRY+ EPCAM- CD49f-

value: Day 4


title: Liver_CN16_D2_stdata

value: right


title: Liver_CN16_E1_stdata


title: Liver_CN73_E2_stdata


title: Liver_CN16_D1_stdata


title: H3K27ac ChIP MED19-LNCaP CS media 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, H3K27ac ChI


title: H3K27ac ChIP control LNCaP CS R1881 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two - H3K27ac ChIP


title: Liver_CN73_C1_stdata


title: Liver_CN73_D1_stdata


title: Liver_CN16_E2_stdata


title: H3K27ac ChIP control LNCaP CS media 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, H3K27ac ChIP


title: H3K27ac ChIP control LNCaP CS media 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, H3K27ac ChIP


title: H3K27ac ChIP control LNCaP CS media 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, H3K27ac ChIP


title: Liver_CN65_E1_stdata


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-M-BM-253_GT18-10921_CGAGGCTG-CTCCTTAC_S6

city: Farmington

first: Duygu

last: Ucar

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
trimmed reads were aligned to mouse genome (mm10) using BWA
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the samples of the same tissue were merged to generate one consensus peak set by using R package DiffBind.
Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized using the cpm function via the log option turned on from edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: Atacseq consensus peaks per tissue/cell type

source_name: Bone Marrow

extract_protocol:
Data is obtained from bone marrow of NZO/HILtJ mouse strain, hereafter NZO at ages 3 and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq
ATAC-seq libraries were prepared using 50,000 cells, as previously described (Buenrostro et al, 2015), with the following modifications: digitonin was added to the transposition reaction at a final concentration of 0.01%; the transposition reaction was purified using the Genomic DNA Clean & Concentrator-10 kit (Zymo Research Corporation); PCR amplification was carried out using the Nextera DNA Library Prep (Illumina) Index Adapters, Nextera PCR Master Mix, and PCR Primer Cocktail for 10 cycles of PCR; PCR reaction was purified using 1.7x SPRI beads (Agencourt AMPure XP, Beckman Coulter). Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies) and quantitative  PCR (KAPA Biosystems), according to the manufacturer's instructions. Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 reagents (Illumina).

value: NZO

value: Bone Marrow

tag: age

value: male


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-F-BM-244_GT18-10917_AAGAGGCA-TCTACTCT_S4


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-M-BM-252_GT18-10920_GCTACGCT-CTCCTTAC_S1


title: 20180911_17-ucar-001-run29_FASTQ_NZO-3mo-M-BM-251_GT18-10919_CAGAGAGG-CTCCTTAC_S4


title: FLAG ChIP MED19-LNCaP CS R1881 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three,FLAG-MED19 ChIP

value: FLAG  (Cell Signaling ,cat # 14793)


title: 20180911_17-ucar-001-run29_FASTQ_NZO-3mo-F-BM-243_GT18-10916_CGAGGCTG-TCTACTCT_S3


title: H3K27ac ChIP MED19-LNCaP CS media 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, H3K27ac ChIP


title: H3K27ac ChIP control LNCaP CS R1881 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, H3K27ac ChIP


title: FLAG ChIP MED19-LNCaP CS R1881 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two,FLAG-MED19 ChIP


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-F-BM-245_GT18-10918_GTAGAGGA-TCTACTCT_S2


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-BM-40_GT18-03809_AAGAGGCA-AGGCTTAG_S3


title: FLAG ChIP MED19-LNCaP CS media 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three,FLAG-MED19 ChIP


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-BM-39_GT18-03808_CGAGGCTG-AGGCTTAG_S1


title: FLAG ChIP MED19-LNCaP CS media 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two,FLAG-MED19 ChIP


title: FLAG ChIP MED19-LNCaP CS media 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one,FLAG-MED19 ChIP


title: H3K27ac ChIP control LNCaP CS R1881 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, H3K27ac ChIP


title: FLAG ChIP control LNCaP CS R1881 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three,FLAG ChIP (negative control forFLAG-MED19)


title: FLAG ChIP control LNCaP CS R1881 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two,FLAG ChIP (negative control forFLAG-MED19)


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-F-BM-35_GT18-03804_AAGAGGCA-TACTCCTT_S4


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-F-BM-36_GT18-03805_CTCTCTAC-AGGCTTAG_S3


title: FLAG ChIP control LNCaP CS R1881 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one,FLAG ChIP (negative control forFLAG-MED19)


title: FLAG ChIP control LNCaP CS media 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three,FLAG ChIP (negative control forFLAG-MED19)


title: FLAG ChIP control LNCaP CS media 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two,FLAG ChIP (negative control forFLAG-MED19)


title: FLAG ChIP MED19-LNCaP CS R1881 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one,FLAG-MED19 ChIP


title: Liver_CN65_D2_stdata


title: AR ChIP MED19-LNCaP CS R1881 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, AR ChIP

value: AR 441 mouse monoclonal, Santa Cruz, cat # sc-7305) and (AR D6F11 rabbit monoclonal, Cell Signaling Technology, cat # 5153)


title: FLAG ChIP control LNCaP CS media 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one,FLAG ChIP (negative control forFLAG-MED19)


title: P0 proprioceptors [JJ003]

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

description:
JJ003
single cell RNAseq
Sequencing platform: Plate-seq

data_processing:
Cell (8bp) and UMI barcodes were extracted from the Read1 sequence (fastq) files.
Transcript read (R2 sequence files) were aligned to the GRCm38 (mm10) reference using the STAR aligner.
Distinct UMI barcodes were summed by gene within each cell barcode, allowing for a Hamming distance of 1 for aggregation.
Additional filtering step, applied only to aggregated counts table compiled from all plates: remove cells with total UMI sums <2000.
Genome_build: GRCm38
Supplementary_files_format_and_content: Counts tables (csv).

source_name: proprioceptors

extract_protocol:
DRG from adult (p>56), adolescent (p12), neonatal (p0), and embryos (e14.5) of either sex were dissected (1 hour maximal) in ice-cold Hank’s balanced salt solution (HBSS) and collected, on ice, in HBSS supplemented with 0.75% horse serum (HS). The total number of animals (of either sex) used for experiments was six for adult samples, four for p12, six for p0, and two for e14.5. Following dissection, DRGs were centrifuged at low speed and washed once with ice cold HBSS prior to dissociation though enzymatic digestion using Papain followed by Collagenase/Dispase35,57. Papain digestion step consisted of 3 ml HBSS with ~16 units/ml Papain (Worthington), 0.83 mM L-Cysteine, 0.42 mM EDTA, and 20 units DNase I/ml (Roche). Collagenase/Dispase digestion was with 3 ml HBSS containing 1,066 units/ml Collagenase IV (Wortington), 4 units/ml Dispase (Wortington), and 20 units/ml DNase I (Roche). Duration of digestion incubation times was 16 min for adult, 12 min for p12, 10 minutes for p0 and e14.5 (for both enzyme digestion steps). Solutions were exchanged by a low speed centrifuge step (4’ at 800 rpm in table top Eppendorf centrifuge) and aspiration. After Collagenase/Dispase digestion, enzyme solution was replaced with 500 ml HBSS supplemented with 20% HS and 20 units DNase I, and DRG/cell suspension was dissociated by slow mechanical trituration using a 200 ul pipetman (~50 times). Following dissociation, cell suspension was incubated with 2 mM Calcein Blue (CellTrace™ Calcein Blue, AM; Invitrogen) for 15 minutes at room temperature. After Calcein Blue labeling, cells were spun down (4’ at 800 rpm) and resuspended in 500 ml sorting solution (HBBS, 1% HS, 20 units/ml DNase I) supplemented with 0.01 mM Sytox red (SYTOX™ Red Dead Cell Stain; Invitrogen). Just prior to FACS, dissociated cells were passed through 40-70 mm gauze filters to clear remaining cellular aggregates. FACS of fluorescently-labelled (tdTomato+) neurons was performed at 12 psi, using a Becton Dickinson FACSAria (SORP model, 5-laser, 20 parameter), equipped with a 130 mm nozzle, and using 586/15 (tdTomato), 450/50 (Calcein Blue), and 670/30 (Sytox red) filter sets. Fluorescent neurons were directly deposited in 96-well LoBind plates (Eppendorf) prefilled with 7.5 ml lysis buffer/well. Lysis buffer contained 0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (ThermoFisher), 2 mM deoxyribonucleotides (dNTPs) (ThermoFisher), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)58. Plates were stored at -80oC until processed for cDNA generation, library preparation and RNA sequencing. After primer annealing (72°C for 3 min), reverse transcription (RT) was performed by adding 7.5 μl of RT mix to each well. RT mix contained 2 M betaine (Affymetrix), 2× Protoscript Buffer (New England Biolabs), 12 mM MgCl2 (ThermoFisher), 10 mM dithiothreitol (ThermoFisher), 5.3 U of Protoscript II Reverse Transcriptase (New England Biolabs), 0.53 U of SUPERaseIN (ThermoFisher), and 2 μM Template Switching Oligo (Integrated DNA Technologies). Reverse transcription was performed at 42°C for 90 min, followed by 10 cycles of 50°C for 2 min, 42°C for 2 min, 70°C for 10 min, followed by a 4°C hold. Excess primers were removed by adding 2 μl of Exonuclease I (ThermoFisher) mix to each well (1.875 U of ExoI in water) and incubating at 37°C for 30 min, 85°C for 15 min, 75°C for 30 s, and 4°C hold. Following RT reactions, all wells were pooled into a single 15-ml falcon tubes, and complementary DNA (cDNA) was purified and concentrated using Dynabeads MyOne Silane beads (ThermoFisher) according to the manufacturer’s instructions. The cDNA was split into duplicate reactions containing 25 μl of cDNA, 25 μl of 2× HIFI HotStart Ready Mix (Kapa Biosystems), and 0.2 M SMART PCR Primer and polymerase chain reaction (PCR) mix. cDNA was amplified as above, and duplicate reactions were combined and purified using 0.7 volume of AMPure XP beads (Beckman Coulter). The amplified cDNA was visualized on an Agilent TapeStation and quantified using a Qubit II fluorometer (ThermoFisher).
Sequencing libraries were constructed using Nextera XT (Illumina). A custom i5 primer was used (Nextera PCR) with 0.6 ng of input cDNA, and 10 cycles of amplification were performed. Unique i7 indexes were used for each plate. After amplification, the library was purified with two rounds of AMPure XP beads, visualized on the TapeStation, and quantified using the Qubit II fluorometer. Libraries were sequenced on an Illumina NextSeq 500 using the 75-cycle High Output Kit [read lengths 26(R1) × 8(i) × 58(R2)]. Custom sequencing primers were used for Read 1 (SMART_R1seq and ILMN_R1seq; see ref.58). With each plate, we targeted ~70 million reads. Library pools were loaded at 1.8 pM with 30% PhiX (Illumina).

value: genetically labeled (tdTomato) proprioceptors

tag: genetic strategy

tag: developmental stage


title: E14.5 proprioceptor progenitors [JJ015]

description:
JJ015
single cell RNAseq
Sequencing platform: Plate-seq


title: E14.5 proprioceptor progenitors [JJ016]

description:
JJ016
single cell RNAseq
Sequencing platform: Plate-seq


title: P12 proprioceptors [JJ018]

description:
JJ018
single cell RNAseq
Sequencing platform: Plate-seq


title: AR ChIP MED19-LNCaP CS R1881 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, AR ChIP

value: MED19 overexpression

tag: cell line


title: P0 proprioceptors [JJ004]

description:
JJ004
single cell RNAseq
Sequencing platform: Plate-seq


title: AR ChIP MED19-LNCaP CS R1881 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, AR ChIP

tag: disease

value: prostate cancer


title: P12 proprioceptors [JJ014]

description:
JJ014
single cell RNAseq
Sequencing platform: Plate-seq


title: P12 proprioceptors [JJ013]

description:
JJ013
single cell RNAseq
Sequencing platform: Plate-seq


title: P12 proprioceptors [JJ017]

description:
JJ017
single cell RNAseq
Sequencing platform: Plate-seq


title: adult proprioceptors [JJ011]

description:
JJ011
single cell RNAseq
Sequencing platform: Plate-seq

value: adult


title: AR ChIP MED19-LNCaP CS media 2

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, AR ChIP

tag: treatment

value: EtOH vehicle 4 h

value: LNCaP


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-BM-38_GT18-03807_GCTACGCT-AGGCTTAG_S4


title: AR ChIP MED19-LNCaP CS media 3

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, AR ChIP


title: adult proprioceptors [JJ007]

description:
JJ007
single cell RNAseq
Sequencing platform: Plate-seq


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-F-BM-42_GT18-03806_CAGAGAGG-AGGCTTAG_S2

value: female


title: AR ChIP MED19-LNCaP CS media 1

description: MED19-LNCaP - LNCaP cells stably expressingFLAG-tagged (alternative) MED19, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, AR ChIP


title: AR ChIP control LNCaP CS R1881 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment three, AR ChIP

value: control


title: adult proprioceptors [JJ006]

description:
JJ006
single cell RNAseq
Sequencing platform: Plate-seq


title: adult proprioceptors [JJ002]

description:
JJ002
single cell RNAseq
Sequencing platform: Plate-seq


title: adult proprioceptors [JJ001]

description:
JJ001
single cell RNAseq
Sequencing platform: Plate-seq


title: AR ChIP control LNCaP CS R1881 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment two, AR ChIP


title: AR ChIP control LNCaP CS R1881 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with 100 nM R1881 4 h, experiment one, AR ChIP


title: AR ChIP control LNCaP CS media 3

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment three, AR ChIP


title: AR ChIP control LNCaP CS media 2

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment two, AR ChIP


title: P90 Rho-/- Txnip cones 3

city: Boston

first: Yunlu

last: Xue

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description:
S083_J-L3-G11_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv

data_processing:
Smart-Seq2 libraries were constructed and sequenced by the Broad Institute Genomics Platform on an Illumina NextSeq 500
Reads were aligned using STAR and quantified using featureCounts
Analysis of differential gene expression was performed using DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: P90 Rho-/- Txnip cones

extract_protocol:
Retinas were dissected, dissociated with papain, and subjected to cell sorting. Cones were isolated in Buffer TCL by antibody staining.
Libraries were constructed by the Broad Institute Genomics Platform using a modified Smart-Seq2 protocol

treatment_protocol: AAVs were injected to neonatal eyes of mice at P0.

tag: strain/genotype

value: Rho-/-

value: post natal day 90

value: Txnip

value: retinal cones

tag: labeling

value: cone-specific H2BGFP for FACS sorting


title: P90 Rho-/- Txnip cones 4

description:
S084_J-L4-G12_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv


title: P90 Rho-/- Txnip cones 2

description:
S082_J-L2-G10_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv


title: AR ChIP control LNCaP CS media 1

description: control LNCaP stably expressing empty plenti vector, 3 d androgen deprivation (CS media), treated with EtOH vehicle 4 h, experiment one, AR ChIP


title: P90 Rho-/- Txnip cones 1

description:
S081_J-L1-G09_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv


title: P90 Rho-/- control cones 3

description:
S079_J-R3-G07_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv

source_name: P90 Rho-/- control cones

value: Control


title: Total_small_RNA_eri1(mg366)_nol56_RNAi

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

country: China

institute: University of Science & Technology of China

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at Novogene (Beijing). Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
Genome_build: WS243
Supplementary_files_format_and_content: the number of reads targeting each transcript

organism: Caenorhabditis elegans

source_name: young adult stage

growth_protocol: L3 or young adult stage on OP50 NGM

extract_protocol:
(1) Total RNAs were isolated from L3 stage worm using a dounce homogenizer (pestle B) in TRIzol solution (Invitrogen) followed by DNase I digestion (Fermentas, no. 18068015). The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP. (2) 3xFLAG::GFP::NRDE-3-associated siRNAs were isolated from L3 stage worm lysates. The worm lysates were generated via Bioruptor UCD-200 (Diagenode). The lysate was pre-cleared with protein G-agarose beads (Roche) and incubated with anti-FLAG M2 agarose beads (Sigma #A2220). The beads were washed extensively and were eluted with 100 μg/ml 3xFLAG peptide (Sigma). The eluates were incubated with TRIzol reagent followed by isopropanol precipitation and DNase I digestion (Fermentas). To facilitate 5′-phosphate-independent deep sequencing, the precipitated RNAs were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by Novogene (Beijing, China). sRNAs ranging from 18 to 40 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

treatment_protocol: at 20℃

value: young adult

tag: genotype


title: Total_small_RNA_eri1(mg366)_mtr4_RNAi


title: NRDE3_IP_small_RNA_eri1(mg366)_exos10(ok2269)_GFPNRDE3

source_name: L3 stage

tag: rip antibody

value: anti-FLAG M2 agarose beads (Sigma #A2220)


title: P90 Rho-/- control cones 2

description:
S078_J-R2-G06_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv

tag: cell type


title: P90 Rho-/- control cones 4

description:
S080_J-R4-G08_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv


title: NRDE3_IP_small_RNA_eri1(mg366)_exos1(ust57)_GFPNRDE3


title: P21 rd1 Txnip cones 3

description:
S094_D-L3-H10_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv

source_name: P21 rd1 Txnip cones

value: rd1 (FVB)

value: post natal day 21


title: NRDE3_IP_small_RNA_eri1(mg366)_dis3(ust56)_rrf1(pk1417)_rrf2(ok210)_GFPNRDE3


title: P21 rd1 Txnip cones 1

description:
S092_D-L1-H08_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: P90 Rho-/- control cones 1

description:
S077_J-R1-G05_p3merged
processed data file: res_P90_Rho-KO_Txnip_sig.csv


title: Total_small_RNA_eri1(mg366)_fib1_RNAi


title: P21 rd1 Txnip cones 2

description:
S093_D-L2-H09_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: NRDE3_IP_small_RNA_eri1(mg366)_dis3(ust56)_GFPNRDE3


title: P21 rd1 control cones 5

description:
S068_A2-5-F08_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv

source_name: P21 rd1 control cones


title: NRDE3_IP_small_RNA_eri1(mg366)_GFPNRDE3


title: P21 rd1 control cones 6

description:
S069_A2-6-F09_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: Total_small_RNA_eri1(mg366)_exos10(ok2269)


title: Total_small_RNA_eri1(mg366)_dis3(ust56)_rrf1(pk1417)_rrf2(ok210)


title: P21 rd1 control cones 4

description:
S067_A2-4-F07_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: Total_small_RNA_eri1(mg366)_L4440_RNAi


title: P21 rd1 control cones 3

description:
S066_A2-3-F06_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: P21 rd1 control cones 1

description:
S064_A2-1-F04_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: P21 rd1 control cones 2

description:
S065_A2-2-F05_p3merged
processed data file: res_P21_rd1_Txnip_sig.csv


title: Total_small_RNA_exos1(ust57)


title: Total_small_RNA_eri1(mg366)


title: Total_small_RNA_dis3(ust56)


title: Total_small_RNA_N2 wildtype


title: Total_small_RNA_eri1(mg366)_dis3(ust56)


title: 25652_None_RNAseq

city: Ithaca

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.3 with the following setting: q-value (0.01) and the rest of the options as recommended defaults.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig format, gene abundance values

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells treated with 0.3 mM H2O2 for 6 minutes and then crosslinked with formaldehyde to a final concentration of 1.0%.

tag: assaytype

value: RNA-seq


title: DRN-18462

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description:
Microglia from APP-SAA homozygous animal
dst150_processed.xlsx

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer (version 0.2.2). Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the –sjdbGTFfile argument. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6. Gene level counts were obtained using feature Counts from the subread package (version 1.6.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package.
Genome_build: GRCm38_p6
Supplementary_files_format_and_content: Excel (XLSX) file with sample annotations, raw counts and TMM-normalized counts per million (CPM)

source_name: microglia from brain (cortex & hippocampus)

growth_protocol: Mice were maintained on the C57BL/6J genetic background and heterozygous KI mice were intercrossed to obtain homozygous and heterozygous KI mice and littermate controls. All mouse husbandry and experimental procedures were reviewed and approved by Denali Institutional Animal Care and Use Committee and were conducted in full compliance with regulatory statutes, Institutional Animal Care and Use Committee policies, and National Institutes of Health guidelines. Housing conditions included standard pellet food and water, a 12-h light–dark cycle at temperature of 22°C with maximal 5 mice per cage and cage replacement once per week, and regular health monitoring. At time of sacrifice, animals are deeply anesthetized via intraperitoneal (i.p.) injection of 2.5% Avertin prior to tissue collection.

extract_protocol:
Mice were perfused with cold PBS and cortical and hippocampal tissues were dissected and dissociated into a single cell suspension using the Adult Brain Dissociation Kit (Miltenyi Biotec 130-107-677), according to the manufacturer’s protocol. Cell suspensions were stained with the following antibodies in FACS buffer (1% fatty acid-free BSA + 1mM EDTA in PBS) for 25 minutes on ice: Fixable Viability Stain BV510 (BD Biosciences, 564406), CD11b-BV421 (BioLegend 101251), CD45-APC (BD Biosciences, 559864), ACSA-2-PE (Miltenyi Biotec, 130-102-365), Mouse Fc blocker (anti-mouse CD16/32, BioLegend 101320). Cells were washed twice with FACS buffer and strained through a 100 μm filter before sorting CD11b+ microglia on a FACS Aria III (BD Biosciences) with a 100 μm nozzle. For bulk RNAseq analysis, cells were sorted directly into freshly prepared RLT-plus buffer (Qiagen) containing betamercaptoethanol. Live cells were sorted directly into RLT-plus buffer (Qiagen) with 1:100 betamercaptoethanol. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and resuspended in 14 μL nuclease-free water. RNA quantity and quality were assessed with a RNA 6000 Pico chip (Agilent) on a 2100 Bioanalyzer (Agilent).
cDNA synthesis was performed with the Clontech SMARTSeq v4 3′ DE kit (Takara Bio USA, Inc. 635040) kit. Two 3' tag RNA-seq libraries were generated per mouse, each consisting of 200 microglia cells isolated by FACS and dispensed directly into 11.5 microliters of 1X Reaction Buffer. Reverse transcription was followed by 15 cycles of cDNA amplification. cDNA was purified with 0.8X volume of SPRIselect beads (Beckman Coulter B23318), quantified on a Bioanalyzer 2100 System with a High Sensitivity DNA chip (Agilent 5067-4626). 300 pg of DNA from each sample was used as input for library preparation with the Nextera XT DNA Library Prep Kit (Illumina FC-131-1096). Fragmentation and adaptors insertion were performed by tagmentation, followed by 12 cycles of PCR amplification. The final libraries were purified using 0.6X SPRIselect beads. Library quantity and quality were assessed with Qubit 4 Fluorometer with the 1X dsDNA HS Assay Kit (Invitrogen Q33231) and on a Bioanalyzer 2100 System with a High Sensitivity DNA chip. 75 bp single end reads were generated on an Illumina NextSeq 500 sequencer by SeqMatic (Fremont, CA, USA)

tag: group

value: months

tag: batch

value: Microglia

value: Hom

value: male


title: 25651_None_RNAseq

tag: antibody


title: 25650_None_RNAseq


title: 25649_None_RNAseq


title: DRN-18455

tag: Sex


title: DRN-18461


title: DRN-18449


title: DRN-18450


title: DRN-18456


title: 19719_Pol2_ChIPexo

data_processing:
Library strategy: ChIP-exo
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file. using picard MarkDuplicates and samtools
peaks were called using ChExMix version: 0.3 with the following setting: q-value (0.01) and the rest of the options as recommended defaults.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig format, gene abundance values

value: ChIP-exo


title: Total_small_RNA_eri1(mg366)_exos1(ust57)


title: DRN-18441


title: DRN-18436

value: female


title: DRN-18435


title: 26270_Rpb3_ChIPexo

value: TAP-tag:Sigma i5006


title: 24884_Spt6_ChIPexo


title: DRN-18434


title: 24886_Spt6_ChIPexo


title: 22680_Swd3_ChIPexo


title: 19396_Ssl2_ChIPexo


title: DRN-18433


title: DRN-18463

description:
Microglia from APP-SAA heterozygous animal
dst150_processed.xlsx

value: Het


title: DRN-18464


title: 19975_Pob3_ChIPexo


title: DRN-18442


title: 19460_CTDSer7_ChIPexo

value: Millipore 04-1570-I


title: 22543_Set1_ChIPexo


title: DRN-18447


title: 26277_CTDSer7_ChIPexo


title: DRN-18454


title: DRN-18448


title: 26265_Rpb3_ChIPexo


title: 23993_Taf1_ChIPexo


title: DRN-18438


title: 19968_Spt5_ChIPexo


title: DRN-18437


title: DRN-18443


title: 18244_Rpb3_ChIPexo

value: TAP-tag:Sigma i5007


title: 19456_CTDSer5_ChIPexo

value: Millipore 04-1572-I


title: 24231_Spt4_ChIPexo


title: 26269_Rpb3_ChIPexo


title: 15926_Rpb3_ChIPexo


title: DRN-18460

description:
Microglia from WT animal
dst150_processed.xlsx

value: WT


title: DRN-18432


title: DRN-18431


title: 22699_Elf1_ChIPexo


title: DRN-18459


title: DRN-18458


title: 19980_Rpb3_ChIPexo


title: DRN-18457


title: DRN-18453


title: 23473_Cet1_ChIPexo


title: DRN-18444


title: 19457_CTDSer5_ChIPexo


title: DRN-18452


title: 28576_Sua7_ChIPexo


title: DRN-18451


title: DRN-18446


title: 18243_Rpb3_ChIPexo


title: GfpOff_1

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

data_processing:
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3 + ERCC92)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3 + ERCC92) and using "locus_tag" as the GFF gene identifier
Genome_build: NC_000964.3 and ERCC92
Supplementary_files_format_and_content: tabular files include raw counts for each gene/RNA features

organism: Bacillus subtilis

source_name: GfpOff

growth_protocol: Cells were cultured in 10 ml CH medium in 125 ml flasks to an OD660 of 0.5 and quickly cooled by adding 10 ml ice-cold PBS with 4 M NaCl, which preservers the mRNA

extract_protocol:
GFP-on/off cells were respectively broke using glass beads (0.1 mm) and RNA was extracted using 25:24:1 phenol/chloroform/isoamyl alcohol (P/C/I) mixture, and Dnase I was used to remove DNA from the RNA samples.
1 μl 1:1000 diluted ERCC RNA Spike-In mix 1 (Invitrogen) was added to 50 ng total RNA and the mixed RNA was subjected to sequencing library construction using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

treatment_protocol: Cells was directly sorted by BD FACSAriaTM III flow cytometer into GFP-on/off subsets.

tag: growth phase

value: Exponential growth

tag: strain


title: GfpOn_2

source_name: GfpOn


title: GfpOff_2


title: GfpOn_1


title: 26345_Sua7_ChIPexo


title: 26363_Sgv1_ChIPexo


title: S3 refed

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
QC performed usinf fastQC
Trimming applied using Trimmomatic
Alignment performed using Hisat2
Quantification with StringTie
Genome_build: hg38
Supplementary_files_format_and_content: gene expression result (FPKM)

extract_protocol:
Primary PBMCs were isolated from human blood by density centrifugation using Lymphocyte Separation Medium (MP Biomedicals). RNA was extracted from PBMCs by miRNeasy Micro Kit (Qiagen). RNA was quantified using a Qubit 3.0 fluorometer (Thermo Fisher Scientific) and its integrity confirmed using an Agilent Technologies 2100 Bioanalyzer (Agilent).
Dual index libraries were constructed with at least one unique index per each library using TruSeq Stranded Total RNA HT Kit (Illumina), to enable subsequent pooling of equal quantities of individual libraries. The integrity and ratio of pooled libraries was validated using Miseq system (Illumina) and then paired-end sequencing (2×75 bp) was performed on an HiSeq3000 sequencer (Illumina), with the Illumina HiSeq3000 SBS kit.

tag: individual

tag: bmi

tag: age

tag: gender

value: F

tag: time

tag: protocol

value: refed

value: PBMC


title: S3 fast

value: fast


title: S21 refed

value: M


title: S3 baseline

value: baseline


title: DRN-18445

value: months

value: Microglia


title: DRN-18440

value: male


title: DRN-18430


title: S20 fast


title: DRN-18429


title: S21 baseline


title: 24331_Rpb3_ChIPexo

value: ChIP-exo


title: S20 baseline


title: S19 baseline


title: S20 refed


title: 23971_Ssl1_ChIPexo

value: TAP-tag:Sigma i5006


title: Abu65_HKV7KBGX2_S4_R2

first: Heinz

last: Jacobs

address: Postbus 90203

department: Tumor Biology & Immunology

institute: The Netherlands Cancer Institute

data_processing:
Paired-end reads obtained by CEL-seq2 were aligned to the transcriptome using bwa mem (version 0.7.15) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode and UMI information: the first 6 bases correspond to the Unique Molecular Identifier (UMI), the next 8 basepairs to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.TranscriptCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. TranscriptCounts files show the estimated original transcript counts, based on the fact that you are randomly sampling from a small fraction of the original pool of molecules.
Supplementary_files_format_and_content: *.BarcodeCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. BarcodeCounts files show the number of UMI-corrected read counts.
Supplementary_files_format_and_content: *.ReadCounts.tsv: Tab-separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicates the cell number of the experiment. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore. ReadCounts files shows the number of raw read counts.

source_name: LSK cells

extract_protocol:
Cells were sorted into mineral oil (Sigma Aldrich) and cells were lysed at 65 ℃ for 5 minutes.
mRNA was processed using the previously described SORTseq method. Resulting DNA libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: Extraction of day 18.5 fetal liver of LSK cells through FACS.

tag: strain/background

tag: genotype (pcnak164r/k164r;rev1-/-)

value: WT;HOM

value: LSK cells

tag: day sorted

value: plate sorted 25/02/17


title: Abu66_HKV7KBGX2_S5_R2

tag: cell type


title: 22513_Set1_ChIPexo

tag: assaytype


title: S19 fast


title: S18 baseline


title: S2 refed


title: S18 refed


title: 23965_Taf10_ChIPexo


title: S17 fast


title: DRN-18439

tag: group

tag: genotype


title: Abu60-68_AHNGTJBGX2_S2_R2

value: HOM;HOM


title: 24328_Rpb3_ChIPexo

tag: antibody


title: S2 fast


title: S19 refed


title: S17 baseline


title: 24329_Rpb3_ChIPexo


title: 26342_Rpo21_ChIPexo


title: Abu56_HKV7KBGX2_S3_R2

value: WT;WT


title: S21 fast


title: 19974_Pob3_ChIPexo


title: S15 refed


title: S15 fast


title: S14 fast


title: 24187_Rpb7_ChIPexo


title: S18 fast


title: 26280_Rpb3_ChIPexo


title: S13 refed


title: S17 refed


title: Abu55_HKV7KBGX2_S2_R2


title: 19981_Rpb3_ChIPexo


title: S13 fast


title: 22512_Pcf11_ChIPexo


title: S16 refed


title: S12 fast


title: S16 fast


title: 26263_Rpb3_ChIPexo


title: S16 baseline


title: S15 baseline


title: 26275_CTDSer5_ChIPexo

value: Millipore 04-1572-I


title: 28580_Rpb1_ChIPexo


title: Abu36_AHKF77BGX2_S6_R2

value: plate sorted 07/02/17


title: Abu24_HKV7KBGX2_S1_R2

value: HOM;WT

value: plate sorted 17/01/17


title: S14 baseline

value: F

value: PBMC


title: S2 baseline

value: baseline


title: Abu22_AHJ2JFBGX2_S1_R2


title: 24330_Rpb3_ChIPexo


title: Abu10-11_AHJ2JFBGX2_S2_R2


title: Abu40-41_AHNGTJBGX2_S1_R2


title: Abu-32_HF5FWBGX2_S5_R2


title: S14 refed

value: refed


title: S13 baseline


title: S12 refed

value: M


title: Abu16-18_AHKF77BGX2_S5_R2


title: S12 baseline


title: S10 fast

value: fast


title: S11 fast


title: S11 refed


title: 26278_CTDSer7_ChIPexo

value: ChIP-exo

value: Millipore 04-1570-I


title: HZR412: Fntb KO Treg

type: RNA

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST Array. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: CD4+ YFP+ Cells from spleen and pLN of Foxp3CreFntbfl/fl chimeras

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were sort-purified using specificed markers from spleen and pLN of WT, Foxp3CreFntbfl/fl chimeras

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: Treg

value: Fntb KO


title: S11 baseline


title: S9 fast


title: S10 refed


title: S10 baseline


title: HZR411: Fntb KO Treg


title: 24327_Rpb3_ChIPexo

value: TAP-tag:Sigma i5006


title: S1 refed


title: HZR410: WT Treg

source_name: CD4+ YFP+ Cells from spleen and pLN of WT chimeras

value: WT


title: 24334_Rpb1_ChIPexo


title: 19969_Spt5_ChIPexo


title: S8 baseline


title: 21791_Rpb3_ChIPexo


title: S9 refed


title: S9 baseline


title: S8 fast


title: HZR408: WT Treg


title: 23996_Tfg1_ChIPexo


title: 19395_Ssl2_ChIPexo


title: S1 fast


title: S7 fast


title: S7 refed


title: S8 refed


title: S7 baseline


title: HZR413: Fntb KO Treg


title: 18242_Rpb3_ChIPexo


title: S6 fast


title: 26279_Rpb3_ChIPexo


title: S6 baseline


title: 19973_Elf1_ChIPexo


title: Sox5/6/9 rep3

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

country: Japan

institute: Osaka University graduate school of dentistry

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were mapped to mm10 using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
FPKMs was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

source_name: newborn rib chondrocytes

extract_protocol:
Total RNA was isolated using
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary chondrocytes were infected with mock and Sox5/6/9 adenovirus and cultured for 3day.

value: ICR

value: primary chondrocytes

value: Sox5/6/9 overexpression

value: newborn


title: S5 fast


title: S5 refed


title: 26268_Rpb3_ChIPexo


title: S5 baseline


title: Sox5/6/9 rep2


title: 21795_Rpb3_ChIPexo


title: S4 refed


title: Sox5/6/9 rep1


title: S4 fast


title: S4 baseline


title: S6 refed


title: S1 baseline


title: 22097_Spt5_ChIPexo


title: 19718_Pol2_ChIPexo


title: HZR406: WT Treg


title: 26361_Sgv1_ChIPexo


title: HZR404: WT Treg


title: ALL-Patient1

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were aligned to the hg19 genome assembly using TopHat v2.1.0
For each sample, reads counts of all genes were computed using HTSeq v0.6.0.Differentially-expressed genes between control and ALL were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: hg19
Supplementary_files_format_and_content: Reads count for each gene in four biological replicate for ALL patients and two replicates for controls.

source_name: Bone marrow

extract_protocol:
For RNA-seq, RNA was isolated from was isolated from Bone marrow as mentioned above using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read mode, creating reads with a length of 101 bp.

tag: tissue

value: Bone marrow tumor

tag: diagnosis

value: acute lymphoblastic leukemia (ALL)


title: ALL-Patient3


title: ALL-Patient4


title: ALL-Patient2


title: vivo_VE_day5_rep2

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

data_processing:
The raw sequences were cleaned using Trimmomatic (version 0.39)
Clean reads were mapped to mouse reference genome mm10 using STAR (version 2.7.3a)
High quality mapped reads were quantified using featureCounts
Raw counts were normalized to TPM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene TPM values for each sample

source_name: crypt after irradiation 5 day +VE

growth_protocol: Crypts were isolated and cultured as previously described.1 Briefly, proximal small intestine sections of approximately 20 cm were harvested, opened longitudinally, cut into 2–4mm pieces, rinsed with cold PBS and incubated in 2mM EDTA at 4 °C for 30 min with gentle shaking. Crypts were released after vigorous shaking in cold PBS and passed through a 70 μM cell strainer (BD Biosciences) for further enrichment. Approximately 500 crypts were embedded in 20 μL Matrigel (growth factor reduced; BD bioscience) and plated in 48-well plates. After Matrigel polymerization, 500 μL culture medium containing Advanced DMEM/F12 (Gibco), 10mM HEPES (Gibco), 1× GlutaMAX (Gibco), 1% penicillin/ streptomycin (Gibco), 1× N2 Supplement (Gibco), 1× B27 Supplement (Gibco), and 1mM N-Acetylcysteine (Sigma-Aldrich) was added. For ENR-organoids, culture medium containing 50 ng/mL murine EGF, 100 ng/mL murine Noggin and 500 ng/mL human R-Spondin 1 was used. For Hyper-organoids, culture medium containing 0.2 μM LDN193189, 0.1 μM GSK-3 Inhibitor XV, 1 μM Pexmetinib, 500 μM VPA, 2 μM EPZ6438, 50 ng/mL murine EGF, 10% R-Spondin 1 Conditioned Medium (Trevigen), and 20 ng/mL  FGF2 was used. The cell culture medium was changed every other day. Hyper-organoids can be generated from either ENRorganoids or primary crypts. For passage, organoids were removed from Matrigel, mechanically dissociated into singlecrypt domains and transferred to fresh Matrigel. Passage was  performed every 7 days with a 1:8 split ratio for ENR-organoids and a 1:30 split ratio for Hyper-organoids. 5% knockout serum replacement (KSR, GIBCO) was recommended to enhance expansion of Hyper-organoids after they were passaged. Six days after passage, the number of colonies containing typical organoid structures and expressing Lgr5-GFP was counted. Directed differentiation of organoid cultures was performed as previously reported.46 In brief, ENR- and Hyper-organoids were cultured under ENR conditions, supplemented with Notch inhibitor DAPT (10 μM) to induce enterocyte (alpi); with Notch inhibitor DAPT (10 μM) and Wnt inhibitor IWP2 (2 μM) to induce PC (lyz1), GC (muc2) and enteroendocrine cell (chga).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
RNA sequencing libraries were constructed using the NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB England BioLabs). Fragmented and randomly primed 2 × 150 bp paired-end libraries were sequenced using an Illumina HiSeq X Ten system.

value: crypt

tag: treatment in vivo

value: crypt after irradiation 5 day +VE

tag: repeat


title: HZR409: WT Treg


title: HZR407: Fntb KO Treg


title: HSPCs_5-FU_biological_rep2

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: HSPCs transplanted into 5-FU treated mice

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

growth_protocol: LSK cells in femurs and tibias were sorted from CAG-EGFP mice. Sorted cells (1×105 each) were transplanted into non-treated control or 5-FU treated WT mouse (n=2). 5-FU were intravenously administered 2 days before transplantation.

extract_protocol:
RNA was purified using miRNeasy mini kit (Qiagen, CA, USA)
cDNA was generated using a Clontech SMART-Seq Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200 - 500 bp) using the Covaris S220 (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA) for 75 bp single-end reads, according to the manufacturer’s instructions.

treatment_protocol: Twenty-four hours later, bone marrow mononuclear cells (BMMNCs) from femurs and tibias of each recipient were collected using Lymphoprep (Alere Technologies AS). Then, EGFP+ cells in the BM of each recipient mouse were re-sorted.

value: hematopoietic stem and progenitor cells


title: 24229_Spt4_ChIPexo


title: HSPCs_5-FU_biological_rep1

source_name: HSPCs transplanted into 5-FU treated mice


title: Control rep3

tag: strain

value: control


title: vivo_VE_day2_rep2

source_name: crypt after irradiation 2 day +VE

value: crypt after irradiation 2 day +VE


title: vivo_VE_day2_rep1


title: HZR405: Fntb KO Treg


title: vivo_VE_day5_rep1


title: vivo_VE_day3_rep2

source_name: crypt after irradiation 3 day +VE

value: crypt after irradiation 3 day +VE


title: Control rep2

tag: age


title: vivo_VE_day1_rep2

source_name: crypt after irradiation 1 day +VE

value: crypt after irradiation 1 day +VE


title: 26343_Sua7_ChIPexo

value: ChIP-exo


title: 23973_Ssl1_ChIPexo


title: vivo_VE_day1_rep1


title: HSPCs_ctrl_biological_rep1

description: HSPCs transplanted into control mice

source_name: HSPCs transplanted into control mice


title: 19392_Kin28_ChIPexo


title: Control rep1


title: 23467_Rpb1_ChIPexo


title: 24326_Rpb3_ChIPexo


title: 23472_Cet1_ChIPexo


title: HSPCs_ctrl_biological_rep2

description: HSPCs transplanted into control mice


title: vivo_IR_day5_rep2

source_name: crypt after irradiation 5 day

value: crypt after irradiation 5 day


title: vivo_Normal_rep1

source_name: normal crypt

value: normal crypt


title: vivo_VE_day3_rep1


title: vivo_IR_day3_rep1

source_name: crypt after irradiation 3 day

value: crypt after irradiation 3 day


title: 22098_Spt5_ChIPexo

value: TAP-tag:Sigma i5006


title: vivo_IR_day5_rep1


title: 26340_Rpo21_ChIPexo


title: 19972_Elf1_ChIPexo


title: vivo_IR_day3_rep2


title: 23466_Rpb1_ChIPexo


title: 23991_Taf1_ChIPexo


title: vivo_IR_day2_rep1

source_name: crypt after irradiation 2 day

value: crypt after irradiation 2 day


title: 28578_Sua7_ChIPexo


title: vivo_Normal_rep2


title: BRAIN_JHT_F_B13

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Mice were housed in a specific pathogen-free environment at the National Institute on Aging, Baltimore, MD. Mice were perfused with PBS for 20-30 minutes after euthanasia with CO2, and the brain and hippocampus were dissected  and rinsed in PBS.

extract_protocol: RNA was isolated with RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

value: brain

tag: Sex

value: F

value: 15-20 months

value: JHT


title: 9 days after treatment, biological rep 1

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description: Gene expression data from the heart of zebrafish at 9 days after 5-weeks of PHZ treatment

hyb_protocol: Arrays were hybridized, washed and stained using the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit.

scan_protocol: GeneChip Scanner 3000 according to the manufacturer’s standard procedure

data_processing: Microarray data were pre-processed by Oligo R package using the robust multi-chip analysis (RMA)

organism: Danio rerio

source_name: hearts from zebrafish at 9 days after 5-weeks of PHZ treatment

label_protocol: 250 ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs and labeled into biotinylated cRNA using the GeneChip WT Reagent kit (Affymetrix) according to the manufacturer’s standard protocols

extract_protocol: Total RNA from 3 biological replicates each containing 3 ventricles were isolated per time point using the RNeasy® micro kit (Qiagen). Potential contaminating genomic DNA was digested by DNase I treatment (Qiagen).

treatment_protocol: PHZ was added to the fish water of the treated group for 30 min every 3 days for 5 weeks. The 30 min incubation with PHZ was followed by a 30 min wash in fish water. PHZ was used at a concentration of 1.25 μg/mL the first week followed by 2.5 μg/mL for the rest of the protocol. The control group followed the same process without the addition of PHZ in the fish water.

tag: treatment

value: Heart


title: 9 days after treatment, biological rep 3

value: at 9 days after 5-weeks of PHZ treatment


title: 9 days after treatment, biological rep 2


title: 5 days after treatment, biological rep 3

description: Gene expression data from the heart of zebrafish at 5 days after 5-weeks of PHZ treatment

source_name: hearts from zebrafish at 5 days after 5-weeks of PHZ treatment


title: BRAIN_JHT_F_B14


title: BRAIN_WT_F_B12

value: WT


title: BRAIN_WT_F_B11


title: vivo_IR_day2_rep2

value: crypt


title: BRAIN_WT_F_B10


title: 5 days after treatment, biological rep 2

value: at 5 days after 5-weeks of PHZ treatment


title: 5 days after treatment, biological rep 1


title: BRAIN_JHT_3XTgAD_M_B9

value: M


title: 2 days after treatment, biological rep 2

description: Gene expression data from the heart of zebrafish at 2 days after 5-weeks of PHZ treatment

source_name: hearts from zebrafish at 2 days after 5-weeks of PHZ treatment


title: 2 days after treatment, biological rep 1

value: at 2 days after 5-weeks of PHZ treatment


title: 21794_Rpb3_ChIPexo

value: ChIP-exo


title: 24185_Rpb7_ChIPexo


title: 2 days after treatment, biological rep 3


title: vivo_IR_day1_rep2

source_name: crypt after irradiation 1 day

value: crypt after irradiation 1 day


title: 26266_Rpb3_ChIPexo


title: vivo_IR_day1_rep1


title: BRAIN_JHT_3XTgAD_M_B8


title: vitro_-Pex_rep2

source_name: organoid with 8C -Pex condition

value: organoid

tag: condition in vitro

value: organoid with 8C -Pex condition


title: BRAIN_JHT_3XTgAD_F_B6


title: 28583_Rpb1_ChIPexo


title: 5-week treatment, biological rep 3

description: Gene expression data from the heart of zebrafish after 5-weeks of PHZ treatment

source_name: hearts from zebrafish after 5-weeks of PHZ treatment

value: after 5-weeks of PHZ treatment


title: vitro_-Pex_rep3


title: 26276_CTDSer5_ChIPexo

value: Millipore 04-1572-I


title: vitro_NC_rep6

source_name: organoid with 8C -VE condition

value: organoid with 8C -VE condition


title: vitro_NC_rep7


title: BRAIN_JHT_3XTgAD_F_B7

value: brain

value: F


title: HSF WT TTR mice G2

city: Porto

first: João

last: Moreira

address: Rua Alfredo Allen, 208

country: Portugal

data_processing:
Read Alignment was performed with STAR aligner w/ options --outSAMtype BAM SortedByCoordinate --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
Quantification with cufflinks w/ -G option
Find significant changes in expression w/ cuffdiff
Genome_build: Ensembl genome of Mus musculus reference genome GRCm38

source_name: sciatic nerve

extract_protocol:
RNA from sciatic nerves was isolated with RNeasy Mini columns, following the manufacturer′s instructions (Qiagen, Hilden, Germany, catalog #74804). First-strand complementary DNA (cDNA) was synthesized using the SuperScript double-stranded cDNA Kit (Invitrogen). Subsequently, the cDNA samples were delivered to Bioinf2Bio Company for RNA sequence analysis.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols

value: sciatic nerve

value: 6 months

value: HSF WT TTR


title: 19459_CTDSer7_ChIPexo

value: Millipore 04-1570-I


title: 23994_Tfg1_ChIPexo

value: TAP-tag:Sigma i5006


title: vitro_NC_rep4


title: vitro_-Pex_rep1


title: HSF WT TTR mice G1


title: 5-week treatment, biological rep 2

value: Heart


title: BRAIN_3XTgAD_M_B3

value: M

value: 15-20 months


title: vitro_NC_rep5


title: 21793_Rpb3_ChIPexo

value: ChIP-exo


title: BRAIN_3XTgAD_M_B4


title: BRAIN_3XTgAD_M_B5


title: HSF V30M TTR mice A2

value: HSF V30M TTR


title: BRAIN_3XTgAD_F_B2


title: 5-week treatment, biological rep 1


title: vitro_NC_rep3

value: organoid


title: BRAIN_3XTgAD_F_B1


title: BRAIN_JHT_3XTgAD_M_B0


title: 28581_Rpb1_ChIPexo


title: control, biological rep 2

description: Gene expression data from the heart of zebrafish without PHZ treatment

source_name: hearts from zebrafish without PHZ treatment

value: without PHZ treatment


title: HIPP_JHT_F_H13

value: hippocampus

value: JHT


title: control, biological rep 3


title: HIPP_JHT_F_H14


title: control, biological rep 1


title: HSF V30M TTR mice A1


title: 21796_Rpb3_ChIPexo


title: 28577_Sua7_ChIPexo


title: vitro_NC_rep2

value: organoid with 8C -VE condition


title: vitro_NC_rep1


title: vitro_-GSK3i_rep3

source_name: organoid with 8C -GSK3i condition

value: organoid with 8C -GSK3i condition


title: 24335_Rpb1_ChIPexo


title: 19970_Spt16_ChIPexo


title: vitro_-GSK3i_rep2


title: 23464_Rpb1_ChIPexo


title: vitro_-GSK3i_rep1


title: 19393_Kin28_ChIPexo


title: vitro_ENR+VE_rep3

source_name: organoid with ENR +VE condition

value: organoid with ENR +VE condition


title: 23967_Taf10_ChIPexo


title: 28582_Rpb1_ChIPexo


title: vitro_ENR+VE_rep2


title: HIPP_WT_F_H10

value: F

value: WT


title: 22679_Swd3_ChIPexo


title: HIPP_WT_F_H11


title: HIPP_JHT_3XTgAD_M_H9


title: PG Fat Tbet KO Chow Rep 3

city: London

first: Paul

last: Lavender

address: 5th Floor, Tower Wing, Great Maze Pond

department: School of Immunology and Microbial Sciences

country: United Kingdom

institute: King's College London

hyb_protocol: Illumina arrays were hybridized using standard Illumina protocols at 48 C

scan_protocol: Standard Illumina scanning

data_processing: data was quantile normalized within Illumina Genome Studio

source_name: T cells

label_protocol: cDNA was labelled usin NuGen Encore Biotin IL kits

extract_protocol: Genomic DNA and RNA was isolated using Qiagen Allprep. 5pg total RNA was amplified using NuGen Ovation Pico WTA System V2

value: Tbetflox Foxp3Cre

tag: diet

value: chow

value: perigonadal adipose tissue

value: regulatory T cells


title: HIPP_JHT_3XTgAD_M_H8

value: M


title: vitro_ENR_rep7

source_name: organoid with ENR condition

value: organoid with ENR condition


title: PG Fat Tbet KO Chow Rep 2


title: HIPP_JHT_3XTGAD_F_H6

value: 15-20 months


title: HIPP_3XTGAD_M_H5


title: Spleen Control Chow Rep 3

value: spleen


title: Spleen TBetKO Chow Rep 3


title: HIPP_3XTGAD_M_H4


title: Spleen TBetKO Chow Rep 2


title: 21797_Rpb3_ChIPexo

value: ChIP-exo

value: TAP-tag:Sigma i5006


title: HIPP_WT_F_H12

value: hippocampus


title: HIPP_JHT_3XTgAD_F_H7


title: PG Fat Control Chow Rep 3


title: vitro_ENR_rep6

value: organoid


title: PG Fat Tbet KO Chow Rep 1


title: Spleen Control Chow Rep 2


title: HIPP_3XTGAD_M_H3


title: PG Fat Control Chow Rep 2


title: 21792_Rpb3_ChIPexo


title: HIPP_3XTGAD_F_H2


title: vitro_ENR+VE_rep1


title: PG Fat Control Chow Rep 1


title: 26264_Rpb3_ChIPexo


title: 26267_Rpb3_ChIPexo


title: vitro_ENR_rep5


title: 19465_Rpb3_ChIPexo


title: vitro_ENR_rep2


title: 26281_Rpb3_ChIPexo


title: vitro_ENR_rep1


title: vitro_ENR_rep4


title: 22542_Pcf11_ChIPexo


title: Anterior Cingulate cortex, sbb45, RNAseq

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

description:
ribosomal depletion RNA-seq
ACC_RNASeq.rawcounts.tsv.gz

data_processing:
Fastq files were aligned using TopHat
Genome_build: hg19
Supplementary_files_format_and_content: the "raw.counts" file contains counts gennerated using HTSeq-counts

source_name: Brain

extract_protocol: TrueSeq Stranded Total RNA Sample Preparation + Ribo-Zero Gold kits (Illumina)

value: Early-Life Adversity group

value: Anterior Cingulate cortex (human brain tissue)


title: vitro_ENR_rep3


title: 21798_Rpb3_ChIPexo


title: Anterior Cingulate cortex, sbb50, RNAseq

value: Control group


title: vitro_-bFGF_rep3

source_name: organoid with 8C -bFGF condition

value: organoid with 8C -bFGF condition


title: Anterior Cingulate cortex, sbb49, RNAseq


title: HIPP_3XTGAD_F_H1

value: F


title: Anterior Cingulate cortex, sbb48, RNAseq


title: Spleen TBetKO Chow Rep 1

value: Tbetflox Foxp3Cre


title: Anterior Cingulate cortex, sbb47, RNAseq


title: vitro_-EGF_rep3

source_name: organoid with 8C -EGF condition

value: organoid with 8C -EGF condition


title: Anterior Cingulate cortex, sbb44, RNAseq


title: vitro_-EGF_rep2


title: vitro_-EGF_rep1


title: 23465_Rpb1_ChIPexo


title: Spleen Control Chow Rep 1

value: chow


title: HIPP_JHT_3XTgAD_M_H0


title: vitro_-bFGF_rep1


title: Anterior Cingulate cortex, sbb42, RNAseq


title: Spleen T Reg H1FP3 Rep 1

value: high fat diet

value: regulatory T cells


title: Spleen Treg FP3 Rep 3


title: Spleen T Reg H1FP3 Rep 2


title: PGWAT H1FP3 Rep3

value: perigonadal adipose tissue


title: Spleen Treg FP3 Rep 1


title: Spleen T Reg H1FP3 Rep 3


title: Spleen Treg FP3 Rep 2


title: Anterior Cingulate cortex, sbb41, RNAseq


title: PGWAT H1FP3 Rep2


title: Anterior Cingulate cortex, sbb46, RNAseq


title: 28579_Sua7_ChIPexo


title: vitro_-bFGF_rep2


title: 19971_Spt16_ChIPexo


title: PGWAT H1FP3 Rep1


title: Anterior Cingulate cortex, sbb39, RNAseq


title: Anterior Cingulate cortex, sbb38, RNAseq


title: CZF1GADA 3

city: Würzburg

first: Joachim

last: Morschhäuser

address: Josef-Schneider-Str 2, Bau D15

department: Institute for Molecular Infection Biology

country: Germany

institute: University of Würzburg

data_processing:
Adapter and low quality end trimming using Trimmomatic (v0.36)
Mapping of reads to Candida albicans SC5314 genome assembly 22 using STAR (v2.6.1b) to produce BAM files
Raw read counts per feature generated using HTSeq (v0.6.1)
Normallization and determination of differentially expressed genes using DESeq2 (v1.14.1)
Genome_build: Candida albicans assembly 22
Supplementary_files_format_and_content: Processed data files for individual samples are tab delimited text files containing feature identifier (systematic orf name) and read counts

organism: Candida albicans

source_name: yeast cells

growth_protocol: Strains were grown overnight in YPD shaking at 30°C. The following day they were diluted 1:100 in YPD and grown for three hours shaking at 30°C.

extract_protocol:
Cells were broken by hot phenol and RNA was purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Samples were treated with TURBO DNase (Invitrogen GmbH, Darmstadt, Germany) to remove any residual genomic DNA, and remaining RNA was cleaned by a second purification using the RNeasy Mini kit.
Further steps to prepare for and conduct RNA sequencing were done by Eurofins Genomics (Konstanz, Germany). Such steps included purification of poly(A) mRNA molecules, mRNA fragmentation, preparation of strand-specific cDNA libraries, adapter ligation, and Illumina (HiSeq 2500) sequencing (single reads, 1x 50 base pair length).


title: 22697_Elf1_ChIPexo


title: CZF1GADB3


title: Anterior Cingulate cortex, sbb37, RNAseq


title: cKO_MZ2

city: birmingham

first: Etty (Tika)

last: Benveniste

state: Alabama

address: 1918 University Blvd., MCLM 31

department: CDIB

institute: UAB

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and demultiplexed using Illumina bcl2fastq v 2.17 program.
 After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: spleen

extract_protocol:
Spleens were harvested, marginal zone B cells were flow-sorted, and RNA was extacted using Qiagen RNeasy Mini Kit. Then RNA was submitted to GENEWIZ for RNA-seq and bioinformatics analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen


title: vitro_+VE_rep7

source_name: organoid with 8C condition

value: organoid with 8C condition


title: CZF1GADB2


title: vitro_+VE_rep6


title: CZF1GADA 1


title: PGWAT FP3 Rep2


title: PGWAT FP3 Rep1


title: vitro_+VE_rep1


title: PGWAT FP3 Rep3


title: CZF1GADB1


title: Anterior Cingulate cortex, sbb35, RNAseq


title: vitro_+VE_rep4


title: vitro_+VE_rep5


title: WT_MZ3

value: WT


title: cKO_MZ3


title: CZF1GADA 2


title: vitro_+V_rep7

source_name: organoid with 8C -E condition

value: organoid with 8C -E condition


title: Anterior Cingulate cortex, sbb34, RNAseq


title: Wild Type 1


title: vitro_+VE_rep3


title: Anterior Cingulate cortex, sbb40, RNAseq


title: vitro_+V_rep5


title: Anterior Cingulate cortex, sbb43, RNAseq


title: Anterior Cingulate cortex, sbb32, RNAseq


title: vitro_+VE_rep2


title: SHG_24h_2 miRNA-seq

city: Haikou

first: JunLong

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to pig reference genome with stringent criteria (0 mismatch in the first 18bp).
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: miRbase release 22
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Micropterus salmoides

source_name: liver

growth_protocol: To investigate the effects of hypoxia on largemouth bass, we simulated acute hypoxia caused by extreme weather, eutrophication and high-density aquaculture in actual aquaculture under laboratory conditions. At the beginning of the experiment, experimental fish were randomly distributed into 9 circulation closeness-tanks (30 fish per tank) connected with big reservoir barrel, the temperature of the tanks were still maintained at 20℃ and allowed to adapt for one day before the start of the experiment. The experiment was designed using three groups, namely severe hypoxia group (SHG) (DO: 1.2 ± 0.2 mg/L), moderate hypoxia group (MHG) (DO: 3.0 ± 0.2 mg/L) and control group (CG) (DO: 7.0 ± 0.2 mg/L), with three parallel tanks for each group. The DO treatments were regulated through the pumping of nitrogen and oxygen in the big reservoir barrel, filled with nitrogen (N2) to reduce the DO to the concentration required for the experiment within 2 h after the start of the experiment, and it was recorded as 0 h (Yang et al., 2017; Yang et al., 2019). Fish were subjected to acute hypoxic stress for 24 h (SHG and MHG) and fish in the CG were cultured simultaneously under normal oxygen conditions for 24 h, and they were recorded as 24 h. The fish were still fasted during the experiment. The DO level was monitored by measuring the water quality using the classic iodine quantity method in each experimental tank every hour (Beadle 1958) and making the appropriate adjustments.

extract_protocol:
The total RNA was harvested using Trizol-LS reagent.
The integrity of total RNA was determined by theAgilent 2100 Bioanalyzer and RNA 6000  Nano LabChip Kit with suitable RNA samples having an RNA integrity number > 6.5. Approximately, 15 μg of small RNA-enriched total RNA was prepared for high-throughput sequencing. For each library, small RNA ranging from 15 to 35 nt was purified by 15% Tris-bora-EDTA polyacrylamide gel electrophoresis, and 3´ and 5´ adaptors were ligated with unique small RNA fractions. The modified small RNA was then reverse-transcribed and amplified by reverse transcription-PCR. Finally, the enriched cDNA was sequenced on a Illumina HiSeq 2500 according to the manufacturer’s instructions.

treatment_protocol: Sampled after fasting for one days, the fish were anesthetized with MS-222. Their livers were collected from three groups in each five fish and immediately snap-frozen in liquid nitrogen, stored at -80℃ until use.

value: liver

tag: developmental stage

tag: sample group

value: severe hypoxia group (SHG) at 24h in acute hypoxic experiment


title: Anterior Cingulate cortex, sbb36, RNAseq

value: Early-Life Adversity group


title: cKO_MZ1


title: Wild Type 3


title: SHG_24h_1 miRNA-seq


title: SHG_24h_3 miRNA-seq