title: B3 Control _ day 12 for Patient H8_replicate3

description:
replicate3
readcount.txt

value: Control


title: WGSB of RPE obtained from eye tissue #4

status: Public on Sep 04 2019

type: SRA

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
WGBS reads were mapped to the human reference genome sequence (hg19) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Methylation levels were calculated for individual CG, CHG and CHH sites.
Genome_build: hg19
Supplementary_files_format_and_content: BED files include chrmosome, position, strand, the number of mC reads and the number of total reads.

molecule: genomic DNA

organism: Homo sapiens

source_name: Retinal pigment epithelum obtained from eye tissue

growth_protocol: We cultured cells according to manufacturer's instructions.

extract_protocol:
The DNA samples analyzed in this study were prepared as described previously (Mandai et al., N Engl J Med., 2017).
All WGBS libraries were prepared using the PBAT method from ~100 ng of genomic DNA without using any global PCR amplification (Miura et al., Nucleic Acids Res., 2012; Miura and Ito, DNA Res., 2018). Illumina sequencing was conducted on HiSeq2500 using 100-nt single-read mode.

tag: cell type

value: RPE derived from eye tissue


title: WGSB of RPE obtained from eye tissue #3


title: WGSB of RPE obtained from eye tissue #2


title: HiC_MJ6_wt_2A3_8h

city: San Francisco

first: Geoffrey

last: Fudenberg

state: CA

address: 1650 Owens

department: Data Science and Biotechnology

country: USA

institute: Gladstone Institutes

description: Wild type

data_processing:
HiC-pro (Servant et al., Genome Biology, 2015, 16:259, DOI 10.1186/s13059-015-0831-x) with mapping to SK1Mod (Crawford et al., bioRxiv 496182; doi: https://doi.org/10.1101/496182) genome and with parameters for DpnII and binned to 2 and 5 kb
Genome_build: SK1MOD (Crawford et al., bioRxiv 496182; doi: https://doi.org/10.1101/496182)
Supplementary_files_format_and_content: HiC-pro sparse matrices, bed file is from the default output of the Hi-C-pro pipeline, and shows the chromosomal positions of bins in the sparse matrices.

organism: Saccharomyces cerevisiae

source_name: Hi-C, wt meiotic timecourse1 8h

growth_protocol: S. cerevisiae diploid SK1 cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to saturation for meiotic timecourses and into exponential phase for mitotic experiments.

extract_protocol:
For meiotic samples: 5 ml aliquots (20-30 ODs) of S. cerevisiae diploid SK1 cells were fixed with Formaldehyde at 3% final concentration for 20 minutes at 30 °C, 250 rpm, then quenched by incubating with a final concentration of 0.35 M Glycine (2x the volume of Formaldehyde added) for an additional 5 minutes. Cells were washed with water, split into two samples and stored at -80 ̊C ready for library preparation. For mitotic samples: 100ml (50-80 OD) of S. cerevisiae diploid SK1 cells were fixed with Formaldehyde as described above and used for one library.  The Hi-C protocol used was amended from Belton and Dekker (2015, Cold Spring Harb Protoc; doi:10.1101/pdb.prot085209) by ~5-fold reduction in all materials and volumes. Briefly, cells were thawed, washed in spheroplasting buffer (SB, 1 M Sorbitol, 50 mM Tris pH 7.5) and digested for 15-20 min at 35 ˚C with 100 micrograms/ml 100T Zymolyase in SB containing 1% beta-Mercaptoethanol. Cells were washed in restriction enzyme buffer, chromatin was solubilised by adding SDS to 0.1% and incubating at 65 ˚C for 10 minutes. Excess SDS was quenched by addition of Triton X100 to 1%, and chromatin was incubated with 2.07U/ul of DpnII overnight at 37 ˚C. DNA ends were filled-in with nucleotides, substituting dCTP for biotin-14-dCTP using Klenow fragment DNA polymerase I at 37 ˚C for 2 h followed by addition of SDS to 1.5% and incubation at 65 ˚C for 20 minutes to inactivate Klenow and further solubilise the chromatin. The sample volume was diluted 15-fold, crosslinked DNA ends ligated at 16 ˚C for 8 h using 0.024U/ul of T4 DNA ligase, and crosslinks reversed by overnight incubation at 65 ˚C in the presence of proteinase K. DNA was precipitated with ethanol, dissolved in TE and passed through an Amicon 30 kDa column. DNA was further purified by phenol:chloroform:isoamylalcohol extraction and precipitated again before treating with RNaseA at 37 ˚C for 1 h. Biotin was removed from unligated ends by incubation with T4 DNA polymerase at 20˚C for 4 h and at 75 ˚C for 20 minutes for inactivation of the enzyme. DNA was subsequently fragmented using a Covaris M220 (Duty factor 20%, 200 cycles/burst, 350s, 20 ˚C). After purification with with Qiagen MinElute Columns, DNA ends were repaired using T4 DNA polymerase, T4 Polynucleotide Kinase and Klenow fragment DNA polymerase I at 20˚C for 30 minutes. The DNA was purified with Qiagen MinElute Columns and 3’ ends were A-tailed with dATP using Klenow Fragment (exo-) at 37˚C for 30 min and then at 65˚C for 20 min to inactivate the enzyme.
The Hi-C protocol used was amended from Belton and Dekker (2015, Cold Spring Harb Protoc; doi:10.1101/pdb.prot085209) by ~5-fold reduction in all materials and volumes. Briefly, the end-repaired and A-tailed fragments were fractionated using a Blue Pippin (Sage) and the 100-250bp fraction was used for further processing. Biotinylated fragments were enriched using streptavidin magnetic beads (C1) and NextFlex (Bioo Scientific) barcoded adapters were ligated while the DNA was on the beads. Resulting libraries were minimally amplified by PCR and sequenced using paired-end 42 bp reads on a NextSeq500 (Ilumina; Brighton Genomics).

treatment_protocol: For meiotic samples: S. cerevisiae diploid SK1 cells were synchronised in G1 by growth at 30 ˚C for 16-18 h in 30 ml YPA (1% Yeast extract, 2% Peptone, 1% KAc) to OD600 of ~4, harvested, washed, and resuspended in prewarmed sporulation medium (2% KAc with 0.2x nutritional supplements). 5 ml aliquots (20-30 ODs, sufficient for 2 Hi-C libraries) of relevant meiotic timepoints were collected. For mitotic samples: S. cerevisiae diploid SK1 cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to exponential phase, 10 micrograms/ml of nocodazole were added and 100ml of cells (50-80 OD, sufficient for 1 Hi-C library) were harvested after 2h.

tag: background strain

tag: genotype

tag: phenotype

value: Wild type


title: WGBS of cultured RPE #4

source_name: Cultured retinal pigment epithelum

value: Epithelial cells derived from the outer layer of the embryonic optic cup, obtained from Lonza


title: WGSB of RPE obtained from eye tissue #1


title: WGBS of cultured RPE #2


title: WGBS of cultured RPE #3


title: WGBS of cultured RPE #1


title: A15 E2+MPA+cAMP _ day 12 for Patient H7_replicate3

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description:
replicate3
readcount.txt

library_source: transcriptomic

data_processing:
Raw sequences (fastq) were subjected to quality control using windowed adaptive quality triming approach implemented in fqtrim (https://ccb.jhu.edu/software/fqtrim/).
Read quallity was checked by FastQC and quality control was performed by fqtrim.
The quality reads were then mapped to the human reference genome (GRCh38) using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/).
Read counts mapping to each gene were determined from the mapping data using FeatureCounts
Differential expression analysis between sample groups was performed by robustly fitting the expression data to a generalized linear model using edgeRrobust
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-limited text file of read count data.

molecule: total RNA

source_name: uterine organoids

growth_protocol: We used the protocol of Matrigel and WNT-activating conditions to generate three-dimensional human uterine gland organoid (HUGO) cultures from endometrial biopsies.

extract_protocol:
Total RNA was extracted from hormone-treated organoids using a standard TRIzol-based protocol and Direct-zol RNA MiniPrep Plus isolation kit (Zymo Research, R2070). To eliminate genomic DNA contamination, isolated RNA was treated with DNase I (RNase-Free DNase Set (Qiagen, 79256).
RNA library preparation and sequencing was conducted by Novogene, California.

treatment_protocol: After passage, HUGO were grown for 4 days in expansion medium and then treated with estrogen (E2) for 2 days and then either nothing (Control), E2 and medroxyprogesterone acetate (MPA) or E2+MPA+cAMP for a further 6 days (n=3 replicates per patient and treatment).

tag: treatment

tag: days of culture

tag: patient id

value: Patient H7


title: DOHH2-DMSO-8H-1

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
Alignment: STAR 2-pass, GRCh38.p10, GENCODEv27
Quantification: htseq-count, GENCODEv27
Differential Expression: edgeR
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: text file with raw read count

molecule: polyA RNA

source_name: DLBCL cell line

extract_protocol:
Qiagen RNEasy followed by DNAse treatment
Fragmentation and standard Illumina barcode, primer ligation followed by sequencing.

value: DMSO

tag: duration

tag: cell line


title: DOHH2-DMSO-8H-2


title: DOHH2-DMSO-8H-3


title: DOHH2-DMSO-18H-1


title: DOHH2-DMSO-18H-3


title: DOHH2-TK-8H-1

value: TK


title: DOHH2-TK-8H-2


title: DOHH2-TK-8H-3


title: B4 E2+MPA _ day 12 for Patient H8_replicate1

description:
replicate1
readcount.txt

value: Patient H8


title: A5 Estrogen _ day 6 for Patient H7_replicate2

description:
replicate2
readcount.txt

value: Estrogen


title: A2 Control _ day 6 for Patient H7_replicate2

description:
replicate2
readcount.txt


title: A8 Control _ day 12 for Patient H8_replicate2

description:
replicate2
readcount.txt


title: B2 Control _ day 12 for Patient H8_replicate2

description:
replicate2
readcount.txt


title: A3 Control _ day 6 for Patient H7_replicate3

description:
replicate3
readcount.txt


title: A9 Control _ day 12 for Patient H8_replicate3

description:
replicate3
readcount.txt


title: B8 E2+MPA+cAMP _ day 12 for Patient H8_replicate2

description:
replicate2
readcount.txt


title: A11 E2+MPA _ day 12 for Patient H7_replicate2

description:
replicate2
readcount.txt


title: A14 E2+MPA+cAMP _ day 12 for Patient H7_replicate2

description:
replicate2
readcount.txt


title: A4 Estrogen _ day 6 for Patient H7_replicate1

description:
replicate1
readcount.txt


title: B5 E2+MPA _ day 12 for Patient H8_replicate2

description:
replicate2
readcount.txt


title: A13 E2+MPA+cAMP _ day 12 for Patient H7_replicate1

description:
replicate1
readcount.txt


title: A10 E2+MPA _ day 12 for Patient H7_replicate1

description:
replicate1
readcount.txt


title: DOHH2-TK-18H-1


title: A7 Control _ day 12 for Patient H8_replicate1

description:
replicate1
readcount.txt


title: DOHH2-TK-18H-2


title: U2932-DMSO-8H-1


title: B1 Control _ day 12 for Patient H8_replicate1

description:
replicate1
readcount.txt


title: B7 E2+MPA+cAMP _ day 12 for Patient H8_replicate1

description:
replicate1
readcount.txt


title: U2932-DMSO-8H-2


title: U2932-DMSO-8H-3


title: U2932-DMSO-18H-2


title: K562_LTR2BgRNAs_RNA-3

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to hg38 using HISAT2 v2.0.5 with --no-softclip.
Raw read counts for each gene were generated in Seqmonk with the RNA-seq quantitation pipeline. Normalized gene expression values were calculated with the variance stabilizing transformation in DESeq2.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 200 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: Biwig tracks; tab-delimited text file containing normalised gene expression values (log2) for each sample.

source_name: Chronic Myelogenous Leukemia

growth_protocol: OCI-AML3 and K562 cells were  cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 2mM glutamax and 1% penicillin/streptomycin at 37°C in 5% carbon dioxide.

extract_protocol:
RNA was extracted using AllPrep DNA/RNA mini kit.
RNA-Seq libraries were generated from 500-1000 ng of total RNA using the NEBNext rRNA depletion kit and NEBNext ultra II directional RNA library prep kit.

treatment_protocol: OCI-AML3 and K562 cells were first transduced with lentiviral dCas9-KRAB-mCherry vector and then with a pool of four lentiviruses, each carrying a sgRNA (or an empty control) and a BFP reporter. After 48 hours, cells were sorted for mCherry and BFP expression.

tag: sgrna


title: K562_LTR2BgRNAs_RNA-2


title: K562_LTR2BgRNAs_RNA-1


title: A1 Control _ day 6 for Patient H7_replicate1

description:
replicate1
readcount.txt


title: K562_empty_RNA-2

value: empty vector


title: HiC_MJ6_wt_2A_0h

description: Wild type

source_name: Hi-C, wt meiotic timecourse1 0h/G1


title: U2932-TK-18H-3


title: DOHH2-TK-18H-3


title: U2932-TK-8H-2


title: U2932-TK-18H-1


title: U2932-TK-8H-1


title: U2932-TK-18H-2


title: GRO_EtOH

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

description: nuclear run on rna

data_processing:
Library strategy: GRO-Seq
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
Peaks are determined with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile

growth_protocol: MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM GIBCO/Invitrogen) with phenol red, supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).

extract_protocol:
GRO-seq experiments were performed as previously reported with a few modifications. Briefly, ∼10 millions of MCF7 cells treated with E2 for 1 hr were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-HCl pH7.5, 2mM MgCl2, 3mM CaCl2) for 10 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40, 20 units of SUPERase-In, and 10% glycerol). The resultant nuclei were washed two more times with 10ml lysis buffer and finally resuspended in 100 μl of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 100 μM A/GTP, 100 µM biotin-11-C/UTP (Perkin-Elmer) and incubated for 5 min at 30°C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol® LS reagent (Life Technologies, Cat# 10296-028) following manufacturer’s instructions. NRO-RNA was fragmented to ∼200-500nt by alkaline base hydrolysis on ice for 30 min and and neutralized by adding 1× volume of 1 M Tris-HCl pH 6.8, Excessive salt and residual NTPs were removed by using P-30 column (Bio-Rad, Cat# 732-6250), followed by treatment with DNase I (Promega Cat# M6101) and antarctic phosphatase (NEB Cat# M0289L). Fragmented nascent RNA was bound to 10 µl of MyOne Streptavidin C1 dynabeads (Invitrogen, Cat# 65001) following the manufacturer’s instructions. The beads were washed twice in high salt (2 M NaCl, 50 mM Tris-HCl pH 7.5, 0.5% Triton X-100, 0.5 mM EDTA), once in medium salt (1M NaCl, 5 mM Tris-HCl pH 7.5, 0.1% Triton X-100, 0.5 mM EDTA), and once in low salt (5 mM Tris-HCl pH 7.5, 0.1% Triton X-100). Bound RNA was extracted from the bead using Trizol (Invitrogen, Cat# 15596-018) in two consecutive extractions, and the RNA fractions were pooled, followed by ethanol precipitation. The RNA fragments were then subjected to poly-A tailing reaction by poly-A polymerase (NEB, Cat# M0276L) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223 primer and superscript III RT kit (Life Technologies, Cat# 18080-044).
The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those fragments migrating between 100-400bp were excised and recovered by gel extraction. Next, the first-strand cDNA was circularized by CircLigase (Epicenter, Cat# CL4115K) and relinearized by APE1 (NEB, Cat# M0282L). Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB, Cat# M0530L) according to the manufacturer’s instructions. The oligonucleotide primers oNTI200 and oNTI201 were used to generate DNA library for deep sequencing and the primer sequences were described in previous paper.

treatment_protocol: For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.1% in all samples. Cloning, mutagenesis, and generation of ERα wild type and P-box mutation biotin-tagged inducible MCF7 stable cell lines were described in a previous paper. We performed biotin ChIP or biotin ChIP-seq experiments for  ERα wild type (WT), and ERα P-box mutation stable cell lines following an earlier protocol. Briefly, cross-linked protein-DNA complexes were pulled down by M-280 Streptavidin Magnetic beads (Life Technologies, Cat# 11205D) and the washing was performed under much more stringent conditions that included 2 washes with 1% SDS in TE (20 min each) and two washes with 1% Triton X-100 in TE. The washed streptavidin beads were then subjected to AcTEV protease (Life Technologies, Cat# 12575-015) digestion twice for tagged protein and DNA complex elution before de-crosslinking at 65°C overnight.

tag: tissue

value: mammary gland

value: breast adenocarcinoma cell line MCF7

tag: passages

value: EtOH


title: GRO_E2

description: nuclear run on rna


title: GRO_siKdm2a5utr_KDM2A_WT_E2_Exp3

description: nuclear run on rna

data_processing:
Library strategy: GRO-Seq
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
Peaks are determined with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile,

value: human breast adenocarcinoma cell line


title: OCI-AML3_LTR2BgRNAs_RNA-1

source_name: Acute Myeloid Leukemia


title: K562_empty_RNA-1


title: OCI-AML3_empty_RNA-1


title: OCI-AML3_empty_RNA-2


title: OCI-AML3_LTR2BgRNAs_RNA-2


title: GRO_siKdm2a5utr_KDM2A_H212A_E2_Exp3

description: nuclear run on rna


title: Molm13_Dnase

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.3.4 with default paramaters. Uniquely aligned reads were extracted using a custom perl script.
Peaks were called using Fseq v1.84 with options -f 0 -t 6 -of npf
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 200 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig tracks; peak files (NarrowPeak)

growth_protocol: AML cell lines were  cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 2mM glutamax and 1% penicillin/streptomycin at 37°C in 5% carbon dioxide.

extract_protocol:
Cells were resuspended in RSB buffer (10 mM NaCl, 3mM MgCl2, 10mM Tris-Cl, pH 7.4). After cell lysis, the nuclei were digested with DNase I with 15 U for 10 min at 37oC. Digests were inactivated by the addition of 50 mM EDTA. RNA and proteins were digestion by RNase A (0.5 mg/ml) for 15 min at at 37°C and then by proteinase K (0.5 mg/ml) for 1 h at 65 oC. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.


title: OCI-AML3_Dnase


title: HL-60_Dnase


title: K562_Input

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.4.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.3.4 with default paramaters. Uniquely aligned reads were extracted using a custom perl script.
Peaks were called using MACS2 v2.1.1 with -q 0.05; --broad was used for histone modifications
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 200 bp bin size.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig tracks; peak files (BroadPeak or NarrowPeak)

growth_protocol: All cell lines were  cultured in RPMI 1640 supplemented with 10% fetal bovine serum, 2mM glutamax and 1% penicillin/streptomycin at 37°C in 5% carbon dioxide.

extract_protocol:
Chromatin was extracted from cross-linked cells, and sonicated to 200-700 bp fragments. Immunoprecipitation was performed with 15 µg of chromatin for 2.5 µg of anti-H3K27ac and H3K9me3 antibody or 75µg chromatin for 5µg Cas9 antibody. DNA was purified using the GeneJET PCR purification kit (Thermo Fisher).
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.

treatment_protocol: OCI-AML3 and K562 cells were first transduced with lentiviral dCas9-KRAB-mCherry vector and then with a pool of four lentiviruses, each carrying a sgRNA (or an empty control) and a BFP reporter. After 48 hours, cells were sorted for mCherry and BFP expression. No treatment was performed for HL-60 and Molm13 cells.

tag: chip antibody


title: K562_empty_dCas9

value: anti-Cas9 (Diagenode C15200229-100)


title: K562_LTR2BgRNAs_dCas9


title: GRO_siKdm2a5utr_KDM2A_H212A_E2_Exp2

description: nuclear run on rna


title: GRO_siKdm2a5utr_EtOH_Exp2

description: nuclear run on rna


title: OCI-AML3_LTR2BgRNAs_RNA-3


title: K562_LTR2BgRNAs_H3K9me3

value: anti-H3K9me3 (Diagenode C15410193)


title: GRO_siKdm2a5utr_KDM2A_WT_E2_Exp2

description: nuclear run on rna


title: K562_LTR2BgRNAs_H3K27ac-1

value: anti-H3K27ac (Active Motif 39133)


title: K562-empty_H3K27ac


title: K562_LTR2BgRNAs_H3K27ac-2


title: GRO_siCtrl_EtOH_Exp2

description: nuclear run on rna


title: PRO_siKdm2a_E2_Exp1

description: nuclear run on rna


title: PRO_siCtrl_E2_Exp1

description: nuclear run on rna


title: PRO_siKdm2a_EtOH_Exp1

description: nuclear run on rna


title: OCI-AML3_LTR2BgRNAs_H3K9me3-2


title: K562_empty_H3K9me3


title: PolII_siKdm2a_EtOH

data_processing:
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
Peaks are determined with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile,

extract_protocol:
ChIP was performed as previously described. Briefly, cells were cross-linked with 1% formaldehyde at room temperature for 10 min. For KDM2A ChIP, cells were double cross-linked with 2mM DSG (ProteoChem Cat# C1104) for 45 min and then for another 15 min with 1% formaldehyde (Sigma, F8775). In both situations, the cross-linking was quenched with 0.125M glycine for 5 min. Chromatin was fragmented using a Bioruptor (Diagenode) for 30 min at high power, with an interval of 30 s between pulses to get 200-500bp fragments and precleared using 20 μl Protein G Dynabeads (Life Technologies, Cat# 10009D). Subsequently, the soluble chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Immunoprecipitated complexes were collected using 20 μl Protein G Dynabeads per reaction. We performed biotin ChIP or biotin ChIP-seq experiments for BLRP-tagged KDM2A and ERα, and ERα P-box mutation stable cell lines following an earlier protocol. Briefly, cross-linked protein-DNA complexes were pulled down by M-280 Streptavidin Magnetic beads (Life Technologies, Cat# 11205D) and the washing was performed under much more stringent conditions that included 2 washes with 1% SDS in TE (20 min each) and two washes with 1% Triton X-100 in TE. The washed streptavidin beads were then subjected to AcTEV protease (Life Technologies, Cat# 12575-015) digestion twice for tagged protein and DNA complex elution before de-crosslinking at 65°C overnight.
For all ChIPs, after de-crosslinking overnight at 65°C, final ChIP DNA was extracted and purified using QIAquick spin columns (QIAGEN). The ChIP-seq libraries were constructed following Illumina’s ChIP-seq Sample prep kit. The library was amplified by 14 cycles of PCR.

value: anti-Pol II (N-20, sc-899, Santa Cruz Biotechnology)


title: PolII_siNedd4_EtOH


title: PolII_siCtrl_EtOH


title: OCI-AML3_Input


title: OCI-AML3_LTR2BgRNAs_H3K9me3-1


title: PolII_siNedd4_E2


title: PolII_siCtrl_E2


title: PRO_siCtrl_EtOH_Exp1

description: nuclear run on rna


title: PolII_siKdm2a_E2


title: GRO_siCtrl_E2_Exp2

description: nuclear run on rna


title: Molm13_Input


title: OCI-AML3_LTR2BgRNAs_H3K27ac-2


title: Molm13_H3K27ac


title: OCI-AML3-empty_H3K27ac


title: OCI-AML3_LTR2BgRNAs_H3K27ac-1


title: PolII_EtOH


title: OCI-AML3_empty_H3K9me3


title: HL-60_Input


title: GRO_siKdm2a5utr_E2_Exp2

description: nuclear run on rna


title: HL-60_H3K27ac


title: Nedd4_sc_siKdm2a_EtOH

value: anti-NEDD4 (D17, sc-14482, Santa Cruz Biotechnology)


title: Nedd4_sc_siKdm2a_E2


title: BC0708

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

address: kamakurashi

institute: Toray industries inc

description: miRNA

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetermined) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

source_name: Serum

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

value: Serum

tag: metastasis status

value: no-Metastasis

tag: age

tag: er(ps)

tag: pgr(ps)


title: Nedd4_sc_siCtrl_EtOH

tag: cell type


title: Nedd4_EtOH


title: PolII_E2


title: cKO_3

city: Shanghai

first: Huateng

last: Cao

state: Shanghai

address: 320 Yueyang Road

country: China

institute: Institute of Neuroscience, CAS, China

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts to obtained clean data (clean reads)
All the downstream analyses were based on the clean data with high quality.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene, and all groups showed over 90% unique_map ratios.
Then FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes readcount and FPKM values for each Sample ...

organism: Mus musculus

source_name: Cerebral cortex_S1BF

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
A  total  amount  of  3  µg  RNA  per  sample  was  used  as  input  material  for  the  RNA sample preparations. Sequencing libraries were generated using NEBNext®  UltraTM RNA Library  Prep  Kit  for  Illumina®  (NEB,  USA)  following  manufacturer’s  recommendations and  index  codes  were added  to  attribute  sequences  to  each  sample.

tag: strain

value: Cerebral cortex_S1BF

value: post natal day 17


title: BC0676

description: miRNA


title: cKO_2


title: cKO_1


title: Nedd4_E2


title: BC0524

description: miRNA

value: Metastasis


title: KDM2A_HA_EtOH_Exp2

value: anti-HA-tag (ab9110, abcam)


title: KDM2A_HA_EtOH_Exp1


title: BC0395

description: miRNA


title: Hetero_1


title: Loxp_4


title: KDM2A_HA_E2_Exp2


title: BC0393

description: miRNA


title: Loxp_3


title: Nedd4_sc_siCtrl_E2


title: cKO_4


title: Loxp_2


title: BC0342

description: miRNA


title: BC0666

description: miRNA


title: Hetero_2


title: KDM2A_HA_E2_Exp1


title: Loxp_1


title: Input_siNedd4_E2

value: Input DNA


title: Input_siNedd4_EtOH


title: IP_SMEDWI1 rep3

city: Bayreuth

first: Claus

last: Kuhn

address: Universitätsstr. 30

department: BIOmac Research Center, NW I

country: Germany

institute: University of Bayreuth

description:
Immunoprecipitated piRNAs bound to SMEDWI-1
small_rna_seq_weighted_counts.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

data_processing:
Base-calling was performed with Illumina Casava v1.8.2 software on HiSeq1000. RTA2 was used for base-calling on NextSeq 500
Degradome libraries were processed using piPipes (Han et al. 2014). Abundance of degradome reads was estimated with eXpress (Roberts and Pachter, 2012).
Before mapping reads to the planarian genome, 3’-adapters were removed with cutadapt, sequences mapping to planarian rRNA were discarded with SortMeRNA, and all duplicated reads were collapsed with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Large and small CLIP reads from separately prepared upper and down band of CLIP and CLASH libraries were pooled for their subsequent joint analysis. Reads were mapped to the planarian transcriptome using bowtie2 (Langmead and Salzberg, 2012) with -a option.  Weighted counts were used for multimapping CLIP reads, where read count was divided by the number of the read observations.
RNA-Seq reads after removal of 3’-adapters and quality filtering with Trimmomatic (0.36) were trimmed to a length of 50 nt. Next, sequences mapped to planarian rRNAs were removed with SortMeRNA. Reads were assigned to the reference transcriptome and consensus transposable element sequences (Bao et al., 2015) in strand-specific mode and quantified with kallisto (Bray et al., 2016) with “--single -l 350 -s 30 -b 30” for single-end libraries and “-b 30” for paired-end libraries.
Immunoprecipitated piRNAs were processed as following. 3’-adapters were trimmed using cutadapt (Martin, 2011) and filtered against planarian rRNA sequences with SortMeRNA (Kopylova et al., 2012). Only sequences longer than 18 nt and shorter than 40 nt were kept for the following analysis. Processed reads were mapped against the planarian genome using bowtie (1.1.2) (Langmead et al., 2009) with the following settings “-v 0 -a --best –strata”. Abundance of mapped piRNAs was estimated in weighted counts, where total read counts of multimapping reads were divided by the number of locations they map to.
Genome_build: dd_Smed_g4
Supplementary_files_format_and_content:
abundance_in_estCounts_DegradomeSeq.txt includes estimated counts of degradome reads assigned to the planarian transcriptome (Rozanski, 2018) and quantified with eXpress (Roberts and Pachter, 2012).
CLASH_and_CLIP_counts.txt contains weighted counts of CLIP and CLASH libraries (files from up and down band were merged and processed jointly) assigned to planarian transcriptome with bowtie2 (Langmead and Salzberg, 2012)
abundance_in_estCounts_upon_smedwi2_RNAi_RNAseq.txt was generated by assigning the sequenced reads from unc-22 (C. elegnas) and smedwi-2 (RNAi) knockdown libraries and consensus transposable element sequences with kallisto to planarian transcriptome and transposable elements consensus sequences (Bray et al., 2016).
abundance_in_estCounts_upon_smedwi3_RNAi_RNAseq.txt was generated by assigning the sequenced reads from unc-22 (C. elegnas) and smedwi-3 (RNAi) knockdown libraries and consensus transposable element sequences with kallisto to planarian transcriptome and transposable elements consensus sequences (Bray et al., 2016).
small_rna_seq_weighted_counts_to_genome.txt contains weighted counts of immunoprecipitated with SMEDWI-1, SMEDWI-3, SMEDWI-3 proteins piRNAs  mapped to planarian genome with 0 mismatches.

organism: Schmidtea mediterranea

source_name: whole worm

growth_protocol: Asexual S. mediterranea, clone CIW4, were maintained at 20 °C in Montjuic solution in the presence of 50 µg/ml gentamycin. Animals were fed weekly with homogenized calf liver and starved at least 7 days prior to experiments.

extract_protocol:
SMEDWI bound RNA was isolated from immunoprecipitated protein from whole worm lysate using protein-specific antibodies. Detailed protocol can be bound in the corresponding manuscript.
Libraries were prepared as described previously (Hauptmann et al., 2015).

tag: ip antibody

value: Anti-SMEDWI-1 (Guo et al., 2006)

tag: RNAi knockdown

value: WT


title: Input_siKdm2a_EtOH


title: IP_SMEDWI1 rep1


title: Negative Control experiment 1

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description:
NT 1.ga.cel
CB CD34+ cells transduced with Negative Control experiment 1

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

label: biotin

source_name: Cord Blood CD34+ cells_negative control

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from three independent experiments.  Briefly, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in 24-well plates at 5 x 10^5/mL in SYN-H (ABCell-Bio, Paris, France) supplemented with stem cell factor (SCF; 50 ng/mL), Fms-like tyrosine kinase 3 ligand (Flt3L; 50 ng/mL), thrombopoietin (TPO; 20 ng/mL), interleukin-6 (IL-6; 10 ng/mL), and interleukin-3 (IL-3; 10 ng/mL; all from Miltenyi).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: In order to achieve the overexpression of miR-382-5p in hematopoietic stem/progenitor cells (HSPCs), CD34+ cells were transfected by using the 4D-Nucleofector System (Lonza Group Ltd, Basel, Switzerland) as already described [Norfo R. et al, Blood 2014]. Briefly, 24 hours after immunoseparation CD34+ cells were electroporeted twice, once every 24 hours, with 3 µg of mirVana miR-382-5p mimic (382) or mirVana miRNA mimic Negative Control (NT) (Life Technologies, Carlsbad, CA, USA). For each electroporation, 4 × 10^5 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza) containing mimic miRNA, and pulsed with the program DS112. After each transfection, CD34+ cells were transferred into pre-warmed fresh medium in 24-well plates (Euroclone) and maintained in the same culture conditions as described above.

tag: tissue source

value: umbilical cord blood (CB)

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

tag: transfected with

value: miRVana mimic Negative Control

tag: experiment

value: experiment 1


title: ChIP-Seq_unc_K4me3-2

description:
unc-22 RNAi H3K4me3 CHIP-Seq  replicate 2 was run on four lanes
unc-2_summits.bed

data_processing:
RTA2 was used for base-calling on NextSeq 500
H3K4me3 CHIPseq reads were aligned to the Schmidtea mediterranea genome with bowtie (version 1; parameters: -k 100 –strata) and formatted with samtools (version 1.8) (Grohme et al. 2018; Li et al. 2009; Langmead et al. 2009; Rozanski et al. 2019). Peaks were called with macs2 (version:2.1.1.20160309; parameters: -q 0.01) (Zhang et al. 2008).
Genome_build: dd_Smed_g4
Supplementary_files_format_and_content: BED files contain peaks generated with macs2. The 5th column in BED files is -log10pvalue of peak summits.

source_name: FACS-sorted neoblasts (X1 cells)

extract_protocol:
Worms were dissociated into single cells in cold calcium- and magnesium-free buffer with 1 % BSA (CMFB) as described (Duncan et al., 2015) and FACS-sorted to isolate X1 cell population.
CHIP-Seq libraries were prepared from X1 FACS-sorted cells as described (Duncan et al. 2015)

value: Anti-H3K4me3 (Millipore 07-473)

value: unc-22 RNAi (control)

value: FACS-sorted neoblasts (X1 cells)


title: mimic miR-382-5p experiment 1

description:
382 1.ga.cel
CB CD34+ cells transduced with mimic miR-382-5p experiment 1

source_name: Cord Blood CD34+ cells_miR-382-5p

value: miRVana mimic miR-382-5p


title: Input_siKdm2a_E2

value: human breast adenocarcinoma cell line


title: LN229 PTEN KO1

city: Nanjing

first: Chao

last: Chen

address: 101 Longmian Road

institute: Nanjing Medical University

description: total RNA

data_processing:
This project has  4 samples anlayzed using the BGISEQ-500 platform.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence use the filtering software SOAPnuke developed by BGI for statistics and filter using trimmomatic, then mapped to GRCh38.p11 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Gene expression levels of each sample was caculated using RSEM v1.2.8
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: PTEN KO LN229 GBM Xenograft tumor

growth_protocol: LN229 WT/PTEN KO cells(5×106) in PBS were injected into the flanks of male nude mice, and cultured 30 days in vivo.

extract_protocol:
Xenograft tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. BGISEQ-500 RNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

tag: host strain

value: BALB/c nude

tag: source cell type

value: PTEN KO LN229 glioblastoma multiforme (GBM) cells

value: Xenograft tumor

tag: time point

value: 30 days of tumor formation


title: LN229 WT1

description: total RNA

source_name: PTEN WT LN229 GBM Xenograft tumor

value: PTEN WT LN229 glioblastoma multiforme (GBM) cells

tag: tissue


title: LN229 PTEN KO2

description: total RNA


title: Negative Control experiment 2

description:
NT 2.ga.cel
CB CD34+ cells transduced with Negative Control experiment 2

value: experiment 2


title: ChIP-Seq_unc_input-1

description:
unc-22 RNAi DNA input replicate 1 was run on four lanes
unc-1_summits.bed


title: ChIP-Seq_unc_input-2

description:
unc-22 RNAi DNA input replicate 2 was run on four lanes
unc-2_summits.bed


title: ChIP-Seq_smedwi-3_K4me3-2

description:
smedwi-3 RNAi H3K4me3 CHIP-Seq  replicate 2 was run on four lanes
Smedwi3-2_summits.bed

value: smedwi-3 RNAi


title: ChIP-Seq_unc_K4me3-1

description:
unc-22 RNAi H3K4me3 CHIP-Seq  replicate 1 was run on four lanes
unc-1_summits.bed


title: ChIP-Seq_smedwi-3_K4me3-1

description:
smedwi-3 RNAi H3K4me3 CHIP-Seq  replicate 1 was run on four lanes
Smedwi3-1_summits.bed


title: LN229 WT2

description: total RNA


title: Input_siCtrl_E2

tag: passages

tag: cell line

value: Input DNA


title: H3K27Ac_EtOH

tag: chip antibody

value: anti-H3K27Ac (Abcam, ab4729)


title: IP_SMEDWI1 rep2

value: Anti-SMEDWI-1 (Guo et al., 2006)

value: WT


title: H3K27Ac_E2


title: ChIP-Seq_smedwi-3_inpt-2

description:
smedwi-3 RNAi DNA input replicate 2 was run on four lanes
Smedwi3-2_summits.bed


title: iKPC3-ED-USP21

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University

description: ED-USP21 rep3

data_processing:
BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool
FASTQ files of RNA samples are processed using both STAR (Dobin et. al. 2012) following the two-step alignment procedure and TopHat (Kim and Salzberg 2011) and Cufflinks (Trapnell et. al. 2010).
data followed CBS (Olshen et. al. 2004) segmentation. Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include Htseq count values for each Sample

source_name: mouse PDAC cells

extract_protocol:
RNA Extraction Kits (Qiagen) were used to extract RNA from cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse PDAC cells from iKPC GEMM

tag: background strain

tag: genotype

value: tetO_LKrasG12D, ROSA_rtTA, p48-Cre, ED-USP21


title: iKPC4-WT-USP21

description: WT-USP21 rep4

value: tetO_LKrasG12D, ROSA_rtTA, p48-Cre, WT-USP21


title: Input_siCtrl_EtOH


title: Negative Control experiment 3

description:
NT 3.ga.cel
CB CD34+ cells transduced with Negative Control experiment 3

value: umbilical cord blood (CB)

value: CD34+ hematopoietic stem/progenitor cells (HSPCs)

value: miRVana mimic Negative Control

value: experiment 3


title: mimic miR-382-5p experiment 3

description:
382 3.ga.cel
CB CD34+ cells transduced with mimic miR-382-5p experiment 3

value: miRVana mimic miR-382-5p


title: ChIP-Seq_smedwi-2_K4me3-1

description:
smedwi-2 RNAi H3K4me3 CHIP-Seq  replicate 1 was run on four lanes
Smedwi2-1_summits.bed

value: Anti-H3K4me3 (Millipore 07-473)

value: smedwi-2 RNAi

value: FACS-sorted neoblasts (X1 cells)


title: ERa_BLRP_WT_EtOH_Exp2

value: human breast adenocarcinoma cell line

value: Dynabeads M-280 Streptavidin


title: ERa_BLRP_WT_EtOH_Exp1


title: iKPC3-WT-USP21

description: WT-USP21 rep3


title: ChIP-Seq_smedwi-2_inpt-2

description:
smedwi-2 RNAi DNA input replicate 2 was run on four lanes
Smedwi2-2_summits.bed


title: ERa_BLRP_WT_E2_Exp2


title: CLIP_down rep3

description:
hitsclip1_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt

extract_protocol:
Worms were dissociated into single cells in cold calcium- and magnesium-free buffer with 1 % BSA (CMFB) as described (Duncan et al., 2015). Next, filtered, pelleted and resuspended in CMFB buffer cells were irradiated at 254 nm as described in the accompanying manuscript. Cross-linked protein-RNA complexes were immunoprecipitated with anti-SMEDWI-3 antibody.
Libraries were prepared as described  in Vourekas and Mourelatos, 2014.

value: Anti-SMEDWI-3 (raised polyclonal antibody)


title: ChIP-Seq_smedwi-2_inpt-1

description:
smedwi-2 RNAi DNA input replicate 1 was run on four lanes
Smedwi2-1_summits.bed


title: iKPC4-ED-USP21

description: ED-USP21 rep4


title: iKPC1-ED-USP21

description: ED-USP21 rep1


title: CLIP_up rep3

description:
hitsclip1_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: ChIP-Seq_smedwi-3_inpt-1

description:
smedwi-3 RNAi DNA input replicate 1 was run on four lanes
Smedwi3-1_summits.bed

value: smedwi-3 RNAi


title: ERa_BLRP_WT_E2_Exp1


title: ERa_BLRP_pbox_E2_Exp2


title: iKPC1-WT-USP21

description: WT-USP21 rep1


title: CLASH_down 6

description:
clash6_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt

extract_protocol:
Worms were dissociated into single cells in cold calcium- and magnesium-free buffer with 1 % BSA (CMFB) as described (Duncan et al., 2015). Next, filtered, pelleted and resuspended in CMFB buffer cells were irradiated at 254 nm as described in the accompanying manuscript. Cross-linked protein-RNA complexes were immunoprecipitated with anti-SMEDWI-3 antibody.
Libraries were prepared as described in the manuscript.


title: ERa_BLRP_pbox_EtOH_Exp2


title: ERa_BLRP_pbox_EtOH_Exp1


title: iKPC2-WT-USP21

description: WT-USP21 rep2


title: ERa_BLRP_pbox_E2_Exp1


title: iKPC2-ED-USP21

description: ED-USP21 rep2


title: CLASH_down 4

description:
clash4_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: CLASH_down 5

description:
clash5_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: CLASH_down 3

description:
clash3_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: CLASH_down 2

description:
clash2_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: CLASH_down 1

description:
clash1_down
CLIP reads from the shorter size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: mimic miR-382-5p experiment 2

description:
382 2.ga.cel
CB CD34+ cells transduced with mimic miR-382-5p experiment 2

value: experiment 2


title: siNF90-1

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

hyb_protocol: Following fragmentation and terminal biotin-labeling, 5.5 ug of biotin-labeled ss-DNA fragment were hybridized for 20 hr at 48C on GeneChip Mouse Gene 2.1 ST Array Strip. GeneChips were washed and stained in the Fluidics Station in GeneAtlas system (Affymetrix).

scan_protocol: GeneChips were scanned using the imaging station in GeneAtlas system (Affymetrix).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software (ThermoFisher, USA).

source_name: Beta-TC-6 cells, a pancreatic cell lines, transfected with siRNA targeted to NF90

label_protocol: ssDNA were prepared according to the standard Affymetrix protocol from 250 ng of total RNA (GeneChip WT PLUS Reagent Kit, Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays, Affymetrix).

growth_protocol: Beta-TC6 cells were cultrured in  Dulbecco’s Modified Eagle’s Medium (DMEM) containing with 25 mM glucose supplemented with 15% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol: Total RNAs were prepared from Beta-TC6 cells transfected with siRNAs by miRNeasy kit (QIAGEN).

treatment_protocol: Mixture of three RNAi duplexes that targeted to NF90 and siRNA negative control were transfected into Beta-TC6 cells by Lipofectamin RNAi MAX reagent (Invitrogen, USA).

value: Pancreatic beta cell line


title: CLASH_up 6

description:
clash6_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt

value: WT


title: siNF90-2


title: siNTC-2

source_name: Beta-TC-6 cells, a pancreatic cell lines, transfected with siRNA negative control


title: CLASH_up 5

description:
clash5_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: siNTC-1


title: CLASH_up 3

description:
clash3_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: CLASH_up 4

description:
clash4_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: siNF45-002

source_name: Beta-TC-6 cells, a pancreatic cell lines, transfected with siRNA targeted to NF45

treatment_protocol: Mixture of three RNAi duplexes that targeted to NF45 and siRNA negative control were transfected into Beta-TC6 cells by Lipofectamin RNAi MAX reagent (Invitrogen, USA).


title: ChIP-Seq_smedwi-2_K4me3-2

description:
smedwi-2 RNAi H3K4me3 CHIP-Seq  replicate 2 was run on four lanes
Smedwi2-2_summits.bed


title: CD8-AtmKO-lymphoma_3

city: Cologne

first: Filippo

last: Beleggia

address: Kerpener Str. 62

institute: University Hospital Cologne

data_processing:
quantification of transcript abundance with Salmon v0.11.3
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix of sample by gene counts

source_name: T lymphocytes

extract_protocol:
splenic T cells were isolated with the EasySep™ Mouse T Cell Isolation Kit, Stem Cell Technologies and RNA was isolated with the RNeasy Kit, Qiagen
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina; 3’ RNA seq

value: T lymphocytes

tag: co-receptor

tag: mouse identifier

tag: transplantation

value: B-cell lymphoma

value: Atm-/-


title: iTSCM_3

city: Tokyo

first: Taisuke

last: Kondo

department: Medicine

institute: Keio University

description:
Gene expression of T cells after OP9-hDLL1 cell co-culture for 11 days
SAMPLE 12

hyb_protocol: Biotin-labelled cDNA was hybridized with Gene ST 1.0 Array gene chip at 45°C, 17 hours, 60 rpm. Slides were scanned immediately after washing on the Scan ner 3000 7G (Thermo Fisher Scientific) using one color scan setting.

scan_protocol: The scanned images were analyzed with Expression Console™ Software (Thermo Fisher Scientific).

data_processing: Normalized by RMA method.

label: Biotin

source_name: CD8+ T cells

label_protocol: 2.726 ug of cRNA was fragmented fragmentation enzyme following the manufacturers instructions and labelled with biotin.

growth_protocol: We activated CD8+ T cells by aCD3/28 dynabeads for 7 days. To induce iTSCM cells,  activated T cells were co-cultured with OP9-hDLL1 cells after TCR stimulation. To induce TSCM-like (NICD) or TSCM-like (FOXM1ΔN) cells, NICD- or FOXM1-transduced T cells were cultured in OP9-hDLL1 conditioned medium after TCR stimulation.

extract_protocol: 75 ug of RNA was amplified as cDNA using GeneChip TM WT PLUS Reagent Kit according to the manufacturer's instructions and then amplified as cRNA. RNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. Single strand cDNA was synthesized by cRNA.

treatment_protocol: RNA was prepared using the QIAzol Lysis Reagent, QIAshredder and mi RNeasy Micro Kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell type

value: CD8+ T cells

tag: gender

value: male

tag: donor age


title: siNTC-002


title: CLASH_up 2

description:
clash2_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt

tag: strain

tag: ip antibody

tag: RNAi knockdown


title: Activated_3

description:
Gene expression after aCD3/28 activation
SAMPLE 9


title: iTSCM_2

description:
Gene expression of T cells after OP9-hDLL1 cell co-culture for 11 days
SAMPLE 8


title: CD8-AtmKO-lymphoma_2


title: siNF45-001


title: TSCM-like (FOXM1ΔN)_2

description:
Gene expression of FOXM1ΔN-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 7


title: TSCM-like (NICD)_2

description:
Gene expression of NICD-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 6


title: siNTC-001


title: CD8-AtmKO-lymphoma_1


title: TSCM-like (FOXM1ΔN)_3

description:
Gene expression of FOXM1ΔN-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 11


title: Activated_2

description:
Gene expression after aCD3/28 activation
SAMPLE 5


title: TSCM-like (FOXM1ΔN)_1

description:
Gene expression of FOXM1ΔN-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 3


title: TSCM-like (NICD)_3

description:
Gene expression of NICD-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 10


title: CD8-AtmWT-lymphoma_3

value: Atmwt/wt


title: Degradome_Seq 3

description:
Deg3
rRNA depleted total RNA from neoblasts upon unc-22 (C. elegans)  RNAi knockdown
processed data file:
abundance_in_estCounts_DegradomeSeq.txt

extract_protocol:
Total RNA was extracted from 2 million  FACS-sorted cells  using TriFast reagent  (peqlab) according to manufacturer extraction. Small RNA (< 200 nt) was discarded from total extracted RNA with Zymo-spin IC columns (RNA Clean and Concentrator-5, Zymo Research). Next, rRNA was depleted using custom DNA probes against planarian rRNA (as described in the manuscript).
RNA libraries from 2.5 µg total planarian RNA from X1 FACS-sorted cells were constructed as described (Wang et al., 2014).


title: iTSCM_1

description:
Gene expression of T cells after OP9-hDLL1 cell co-culture for 11 days
SAMPLE 4


title: Degradome_Seq 2

description:
Deg2
rRNA depleted total RNA from neoblasts upon unc-22 (C. elegans)  RNAi knockdown
processed data file:
abundance_in_estCounts_DegradomeSeq.txt


title: Degradome_Seq 1

description:
Deg1
rRNA depleted total RNA from neoblasts upon unc-22 (C. elegans)  RNAi knockdown
processed data file:
abundance_in_estCounts_DegradomeSeq.txt


title: CD8-AtmKO-control_3


title: BC0697

description: miRNA

value: Serum

tag: metastasis status

value: Metastasis

tag: age

tag: er(ps)

tag: pgr(ps)


title: DMSO_SHAPE-map

description:
DMSO-treated total RNA (negative control)
shape_reactivities.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

extract_protocol:
Total RNA was extracted from worms under non-denaturing conditions as described in the manuscript. Briefly, worms were dissociated into single cells in cold calcium- and magnesium-free buffer with 1 % BSA, pelleted, treated with Proteinase K and Dnase I. Next, total RNA was extracted twice with phenol and once with chloroform. RNA buffer was exchanged to the folding buffer (100 mM HEPES, pH 8.0, 100 mM NaCl, 10 mM MgCl2). After incubation in the folding buffer at 37 C for 20 min, RNA was treated with 1M7 in DMSO or with neat  DMSO (negative control).
SHAPE-MaP library construction were performed according to the amplicon workflow (Smola et al., 2015) using Nextera XT Kit (Illumina).


title: TSCM-like (NICD)_1

description:
Gene expression of NICD-transduced T cells after culture in OP9-hDLL1 conditioned medium for 11days
SAMPLE 2


title: CD8-AtmKO-control_2


title: RNA-Seq_Xins_sm2_exp2_pe rep3

description:
rRNA depleted total RNA from differentiated cells  upon smedwi-2  RNAi knockdown
abundance_in_est.counts_upon_smedwi2_RNAi_Xins_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

source_name: FACS-sorted differentiated cells (Xins cells)

extract_protocol:
Total RNA was extracted from 100 000 FACS-sorted cells  using TriFast reagent  (peqlab) according to manufacturer extraction. Small RNA (< 200 nt) was discarded from total extracted RNA with Zymo-spin IC columns (RNA Clean and Concentrator-5, Zymo Research). Next, rRNA was depleted using custom DNA probes against planarian rRNA (as described in the manuscript).
RNA libraries from 100,000 FACS-sorted planarian X1 and Xins cells were constructed as described (Zhang et al., 2012).

value: Smedwi-2 RNAi


title: 1M7_SHAPE-map

description:
1M7-treated total RNAs
shape_reactivities.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz


title: Activated_1

description:
Gene expression after aCD3/28 activation
SAMPLE 1


title: CD8-AtmKO-control_1


title: RNA-Seq_Xins_sm2_exp2_pe rep2


title: RNA-Seq_Xins_sm2_exp2_pe rep1


title: CD8-AtmWT-control_3


title: ileal mucosa from postnatal growth retardation pig 6

city: Changsha

first: Ming

last: Qi

state: Hunan

address: 644 Yuanda 2nd Rd

institute: Insititute of Subtropical Agriculture

description: Test

data_processing:
All samples were tested in triplicate. The relative expression levels of the selected genes normalized against the reference gene (β-actin) were calculated by using the 2－△△Ct method. Data are expressed as the relative values to those for healthy pigs.
Matrix normalized worksheet reports normalized signal (against housekeeping genes). Fold Change worksheet reports test/control (i.e., jejunal mucosa from postnatal growth retardation pig/jejunal mucosa from healthy pig) ratios.

label: SYBR Green

organism: Sus scrofa

source_name: ileal mucosa

label_protocol: Synthesis of the first strand (cDNA) was performed with 5 × PrimeScript Buffer 2 and PrimeScript reverse transcriptase Enzyme Mix 1(Takara Biotechnology (Dalian) Co., Ltd, Dalian, China).  The resulting cDNA was diluted and used as a PCR template to evaluate gene expression. The reaction was performed in a volume of 10 μL (LightCycler® 480 Real-Time PCR System, Roche, Switzerland). 1 μL cDNA template was added to a total volume of 10 μL containing 5 μL SYBR Premix Ex Taq II (Takara, Dalian, China), 3.2 μl distilled H2O, and 0.4 μmol/L each of forward and reverse primer. Reactions were incubated in a 384-well optical plate (Roche, Switzerland). We used the following protocol: (i) predenaturation program (30 s at 95°C), (ii) amplification and quantification program, repeated 40 cycles (5 s at 95°C and 20 s at 60°C for annealing), and (iii) melting curve program (60 to 95°C with a heating rate of 0.1°C per second and ﬂuorescence measurement).

growth_protocol: Samples of the jejunal and ileal mucosa were scraped and immediately snap-frozen in liquid nitrogen and stored at −80°C

extract_protocol: Total RNA was extracted from the intestinal mucosa samples with the TRIZOL reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions and  followed by DNase I treatment.

tag: tissue

value: ileal mucosa

tag: growth status

value: Postnatal growth retardation

value: 42 days


title: CD8-AtmWT-control_1


title: CD8-AtmWT-control_2


title: ileal mucosa from postnatal growth retardation pig 5

description: Test


title: CD4-AtmKO-lymphoma_3


title: Glis2KD-1

city: Iowa City

first: Massimo

last: Attanasio

state: IA

address: 285 Newton Road

department: Internal medicine

institute: University of Iowa Carver College of Medicine

description: replicate 1

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Glis2 knckdown

label_protocol: Standard Illumina hybridization protocol

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: anti-Glis2 shRNA or anti GFP shrna (control cells)

tag: strain  background

value: Immortalized proximal tubular cells

tag: genotype/variation

value: Glis2 knockdown; anti-Glis2 shRNA


title: RNA-Seq_Xins_unc_exp2_pe rep2

description:
rRNA depleted total RNA from differentiated cells  upon unc-22 (C. elegans)  RNAi knockdown
abundance_in_est.counts_upon_smedwi2_RNAi_Xins_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

value: Unc-22 RNAi (control)


title: Control-1

description: replicate 1

source_name: control

value: control; anti-GFP shRNA


title: Control-3

description: replicate 3


title: CD4-AtmKO-lymphoma_1

tag: co-receptor

tag: genotype


title: ileal mucosa from postnatal growth retardation pig 4

description: Test


title: Glis2KD-2

description: replicate 2


title: fluconazole resistant Candida auris strain_3

first: Jian

last: Bing

address: Songhu Road, Yangpu District

department: School of Life Sciences

institute: Fudan University

description:
B1-3
DESeq_WT_B1.txt

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
FPKM method is used in calculated expression level, the formula is shown as follows, and the formula is shown as follows: FPKM=106C/(NL/103). Given to be the expression of gene A , C to be number of fragments that are uniquely aligned to gene A , N to be total number of fragments that are uniquely aligned to all genes, and L to be number of bases on gene A.
Genome_build: Candida auris B8441 genome (GCA_002759435.2)
Supplementary_files_format_and_content: text files containing FPKM values for each Sample

organism: Candidozyma auris

source_name: candida auris

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: fluconazole resistance


title: RNA-Seq_Xins_unc_exp2_pe rep3


title: fluconazole resistant Candida auris strain_2

description:
B1-2
DESeq_WT_B1.txt


title: Glis2KD-3

description: replicate 3

tag: cell type


title: RNA-Seq_X1_sm2_exp2_pe rep2

description:
rRNA depleted total RNA from neoblasts upon smedwi-2  RNAi knockdown
abundance_in_est.counts_upon_smedwi2_RNAi_X1_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz


title: ileal mucosa from postnatal growth retardation pig 2

description: Test


title: RNA-Seq_Xins_unc_exp2_pe rep1


title: CD4-AtmKO-lymphoma_2

value: T lymphocytes

tag: mouse identifier

tag: transplantation


title: ileal mucosa from postnatal growth retardation pig 1

description: Test


title: fluconazole resistant Candida auris strain_1

description:
B1-1
DESeq_WT_B1.txt


title: RNA-Seq_X1_sm2_exp2_pe rep3

tag: strain


title: CD4-AtmWT-lymphoma_3

value: B-cell lymphoma


title: ileal mucosa from healthy pig 6

description: Control

source_name: jejunal mucosa

value: jejunal mucosa

value: Healthy


title: RNA-Seq_X1_sm2_exp2_pe rep1


title: RNA-Seq_X1_unc_exp2_pe rep3

description:
rRNA depleted total RNA from neoblasts upon unc-22 (C. elegans)  RNAi knockdown
abundance_in_est.counts_upon_smedwi2_RNAi_X1_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz


title: CD4-AtmWT-lymphoma_2


title: fluconazole sensitive Candida auris strain_3

description:
WT-3
DESeq_WT_B1.txt

value: fluconazole sensitive


title: ileal mucosa from healthy pig 5

description: Control


title: CD4-AtmWT-lymphoma_1

value: Atmwt/wt


title: fluconazole sensitive Candida auris strain_2

description:
WT-2
DESeq_WT_B1.txt


title: CD4-AtmKO-control_3

value: Atm-/-


title: CD4-AtmKO-control_2


title: fluconazole sensitive Candida auris strain_1

description:
WT-1
DESeq_WT_B1.txt


title: RNA-Seq_X1_unc_exp2_pe rep1


title: RNA-Seq_X1_unc_exp2_pe rep2


title: CD4-AtmKO-control_1


title: RNA-Seq_Xins_sm3_exp1 rep3

description:
rRNA depleted total RNA from differentiated cells  upon smedwi-3  RNAi knockdown
abundance_in_est.counts_upon_smedwi3_RNAi_Xins_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

value: smedwi-3 RNAi


title: ileal mucosa from healthy pig 3

description: Control


title: RNA-Seq_Xins_sm3_exp1 rep2


title: Seedling, Salt_12h

city: Nanchang

first: Jianbo

last: Song

state: Jiang Xi

address: Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China

institute: Jiang Xi Agricultural University

data_processing:
The raw data comprised 100-bp paired-end sequences, and the cleaned reads were then mapped to M. truncatula genome (Mt4.0) using default settings of TOPHATv2.0.8.
The duplicated reads were removed and alignments with MAPQ score > 20 were used for further analysis.
RNA-seq alignments were processed using HTSeq-count, and differentially expressed genes were identified using DESeq with |log2 fold change| > 3.5
Genome_build: M. truncatula genome (Mt4.0)
Supplementary_files_format_and_content: FPKM

organism: Medicago truncatula

source_name: seedling

growth_protocol: Plants were grown under long day (14 h light/ 10 h darkness) conditions at 22-24°C

extract_protocol:
Medicago truncatula seedlings were collected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNA was isolated at each time point for each treatment using the TRIzol purification system (Invitrogen). The 3’-tag digital gene expression libraries were prepared using the Illumina Gene Expression Sample Prep Kit. The library was sequenced on an Illumina HiSeq3000.

value: Jemalong A17

value: seedling

value: 4 weeks

value: Wild type

tag: stress

value: Salt

tag: time


title: CD4-AtmWT-control_3


title: ileal mucosa from healthy pig 2

description: Control

value: 42 days


title: ileal mucosa from healthy pig 1

description: Control


title: CD4-AtmWT-control_2


title: Seedling, Salt_6h


title: jejunal mucosa from postnatal growth retardation pig 5

description: Test

value: ileal mucosa

value: Postnatal growth retardation


title: jejunal mucosa from postnatal growth retardation pig 6

description: Test


title: ileal mucosa from postnatal growth retardation pig 3

description: Test


title: RNA-Seq_Xins_sm3_exp1 rep1

tag: RNAi knockdown


title: RNA-Seq_X1_sm3_exp1 rep2

description:
rRNA depleted total RNA from neoblasts upon smedwi-3  RNAi knockdown
abundance_in_est.counts_upon_smedwi3_RNAi_X1_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

source_name: FACS-sorted neoblasts (X1 cells)


title: Seedling, Drought_12h

tag: age

value: Drought


title: ileal mucosa from healthy pig 4

description: Control


title: Seedling, Salt_2h


title: WZS3

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

description: miniature pig

data_processing:
The remaining clean reads were then aligned to Sus scrofa reference genome build 10.23 by using SOAP aligner v2.21 (http://soap.genomics.org.cn/)
Annotation information of the porcine reference genome was obtained from the Ensembl public FTP site (ftp://ftp.ensembl.org/pub/release-78/gtf/sus_scrofa/Sus_scrofa.Sscrofa10.2.78.gtf.gz)
Genome_build: Sus scrofa reference genome build 10.23
Supplementary_files_format_and_content: wig files were generated using default settings35.  Wig files are included in tar archives.

source_name: muscle tissue

extract_protocol:
Total Genomic DNA (gDNA) were extracted from the same frozen tissue samples by using the All Prep DNA Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. DNA concentration was detected by NanoDrop spectrophotometer and quality was assessed by 1% agarose gel by electrophoresis.
DNA was fragmented by using sonication into 100-500 bp in size, and then followed by end blunting, dA addition at the 3’end and ligation of adapters. The adapter sequence had multiple methyl cytosines so as to allow monitoring of the bisulfite conversion efficiency. Unmethylated cytosines were converted to uracils after bisulfite treatment by a modified protocol from previously described. DNA fragments with size range of 320 to 380 bp were gel-purified for sequencing. All procedures were carried out by the manufacturer’s instructions. Converted DNA was subjected to 50 bp paired end sequencing by Illumina Solexa GA sequencer (Illumina, San Diego, CA, USA). All the raw data was processed by the Illumina Pipeline v1.3.1 (Illumina, San Diego, CA, USA).

tag: breed

value: Wuzhishan

tag: Stage

value: 28 dpc

value: longissimus dorsi muscle


title: RNA-Seq_X1_sm3_exp1 rep1


title: jejunal mucosa from postnatal growth retardation pig 4

description: Test

tag: tissue


title: Seedling, Drought_6h


title: Seedling, Salt_0h


title: RNA-Seq_X1_sm3_exp1 rep3


title: Seedling, Drought_2h


title: jejunal mucosa from postnatal growth retardation pig 3

description: Test

tag: growth status


title: jejunal mucosa from postnatal growth retardation pig 2

description: Test


title: Seedling, Drought_0h


title: LR3

description: miniature pig

value: Landrance


title: WZS2

description: miniature pig

value: 21 dpc


title: Seedling, Cold_12h

value: Cold


title: WZS1

description: miniature pig

value: 18 dpc


title: RNA-Seq_Xins_unc_exp1 rep1

description:
rRNA depleted total RNA from differentiated cells  upon unc-22 (C. elegans)  RNAi knockdown
abundance_in_est.counts_upon_smedwi3_RNAi_Xins_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

value: Unc-22 RNAi (control)


title: Seedling, Cold_6h

value: Jemalong A17


title: CD4-AtmWT-control_1

value: T lymphocytes

value: Atmwt/wt


title: LR1

description: miniature pig


title: jejunal mucosa from healthy pig 5

description: Control

value: jejunal mucosa

value: Healthy


title: jejunal mucosa from healthy pig 6

description: Control

value: 42 days


title: RNA-Seq_X1_unc_exp1 rep2

description:
rRNA depleted total RNA from neoblasts upon unc-22 (C. elegans)  RNAi knockdown
abundance_in_est.counts_upon_smedwi3_RNAi_X1_Cells.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz


title: jejunal mucosa from postnatal growth retardation pig 1

description: Test

value: ileal mucosa


title: Seedling, Cold_2h

value: seedling

value: 4 weeks

value: Wild type


title: RNA-Seq_Xins_unc_exp1 rep2


title: jejunal mucosa from healthy pig 3

description: Control


title: Seedling, Cold_0h


title: RNA-Seq_Xins_unc_exp1 rep3


title: RNA-Seq_X1_unc_exp1 rep1


title: CLIP_down rep2

description:
CLIP reads from the shorter size UV-cross-linked RNA
short_CLIP_seq.length.txt.gz

source_name: whole worm

tag: ip antibody

value: Anti-SMEDWI-3 (raised polyclonal antibody)

value: WT


title: jejunal mucosa from healthy pig 4

description: Control


title: CLIP_down rep1


title: jejunal mucosa from healthy pig 2

description: Control


title: RNA-Seq_X1_unc_exp1 rep3


title: V07-EGM2

city: TOULOUSE

first: Frederic

last: Deschaseaux

state: HAUTE-GARONNE

address: 4 BIS AVENUE HUBERT CURIEN, BATIMENT INCERE

department: Research

country: France

institute: EFS-Occitanie, Inserm U1031

hyb_protocol: cDNA were fragmented and biotinylated using the Encore™ Biotin Module (NuGEN®) and hybridized (48°C, 20h) to Affymetrix® HuGene1.1STArray Strip Kit (Affymetrix®, Santa Clara, CA, USA)

scan_protocol: The arrays were scanned using the Affymetrix GeneAtlas imaging station. The scanned images (DAT files) were processed using the AGCC (Affymetrix GeneChip Command Console) software,

data_processing: The CEL files were imported and manipulated into Partek® Genomics Suite™ software (Partek, Inc. MO, USA).

source_name: EGM2 ASCs from subcutaneous adipose tissue

label_protocol: stained on a GeneAtlas™ System according to the Affymetrix GeneChip® Expression Analysis Technical Manual (P/N 08-0306 Rev. A).

growth_protocol: Adipose stromal cells were generated from prmary cultures in two types of medium: standard or EGM2. After 7 days of expansion, cells were harvested.

extract_protocol: RNA were extracted with RNeasy Plus Mini kit (Qiagen). cDNA synthesis and amplification were performed on high quality RNA (RQI>9.8) by the Ovation®PicoSL WTA System V2 protocol (NuGEN®).

treatment_protocol: Cells were resuspended by trypsination and  were lysed with RLT (Qiagen; Hilden, Deutschland)

tag: gender

value: Female

value: adipose-derived stem/stromal cells

tag: growth


title: V08-EGM2


title: V06-EGM2


title: Control-2

description: replicate 2

tag: strain  background

value: Immortalized proximal tubular cells

tag: genotype/variation

value: control; anti-GFP shRNA


title: keratinocytes_miR-Ctrl_rep3

city: Stockholm

first: Ning

last: Xu

address: CMM L8:02

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from keratinocytes transfected with control oligos with scrambled sequence.

hyb_protocol: The samples were hybridized to a Clariom_S_Human_HT Array Plate according to standard Affymetrix GeneTitan protocol.

scan_protocol: The array plate was scanned using the Affymetrix GeneTitan Scanner.

data_processing: Generated CEL files were analyzed using Affymetrix Expression Console v. 1.4 and the RMA method

source_name: keratinocytes transfected with miR-con

label_protocol: Total RNA was labeled using the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s (Affymetrix) instructions.

growth_protocol: Human adult epidermal keratinocytes were purchased from Cascade Biologics and cultured in EpiLife® serum-free keratinocyte growth medium including Human Keratinocyte Growth Supplement at a final Ca2+ concentration of 0.06mM (Cascade Biologics) at 37°C in 5% CO2.

extract_protocol: 48 hours after transfection, the total RNA was extracted with miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The third passage keratinocytes at 30-50% confluence were transfected with 20nM miR-34a, miR-34c mimics or control oligos (Ambion) using Lipofectamine 2000 (Invitrogen).

value: skin

tag: cell type

value: keratinocytes

tag: genotype

value: control


title: 50uM rep1

city: Uppsala

first: Feifei

address: Husargatan 3

institute: Uppsala University

data_processing:
Illumina HiSeq 2500, Demultiplexing and conversion to FASTQ performed using the bclfastq2
FASTQ were mapped Giardia WB genome using STAR v020201. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R using edgeR v3.6.8 workflow. Quasi-likelihood F test was sed to determine significant differential gene expression.
Genome_build: Giardia WB, AACB03000000
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts from STAR mapping for each sample

organism: Giardia duodenalis

source_name: trophozoites

growth_protocol: A trohphozoite culture was diluted in TYDK and seeded as single cells into the wells of a 96-well plate. Upon reaching 70-80% confluence, a clonal culture was selected to seed 10 ml tubes containing TYDK, TYDK without added ferric, and TYDK without ferric and supplemented with 50 uM of the iron chelator 2,2'-Dipyridyl (Sigma-Aldrich)

extract_protocol:
Performed according to the instructions provided with the Trizol reagent. RNAs were then treated with DNaseI and extracted by phenol chlororform.
Libraries were prepared from 400 ng total RNA using the TruSeq stranded mRNA library prepartion kit inlcuding polyA selection. The library preparation was performed according to the manufacturer's protocol no. 15031047

treatment_protocol: Upon reaching 80% confluence, trophozoites were detached on ice (10m), washed with ice-cold PBS, pelletedand lysed in 1.5ml of Trizol and collected in Eppendorf tubes. Samples were frozen immediatedly in dry ice and kept at -80 util RNA extraction

value: WB

value: TYDK without ferric with 50µM iron inhibitor


title: 50uM rep2


title: 50uM rep3


title: LR2

description: miniature pig

value: Landrance

value: 21 doc

value: longissimus dorsi muscle


title: CLIP_up rep2

description:
CLIP reads from the longer size UV-cross-linked RNA
raw_reads_SMEDWI3_HITS_CLIP_uniquely_mapped.txt.gz
TMM_fitted_abundance_SMEDWI3_HITS_CLIP_vs_SMEDWI3_piRNAs_IP.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz


title: CD8-AtmWT-lymphoma_2

value: T lymphocytes

tag: co-receptor

tag: mouse identifier

tag: transplantation

value: B-cell lymphoma

value: Atmwt/wt


title: CLIP_up rep1

tag: strain

value: Anti-SMEDWI-3 (raised polyclonal antibody)


title: NOFERRIC rep3

value: TYDK without ferric


title: R016-EGM2

value: Female


title: NOFERRIC rep2


title: IP_SMEDWI3 rep2

description:
Immunoprecipitated piRNAs bound to SMEDWI-3
small_rna_seq_weighted_counts.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

extract_protocol:
SMEDWI bound RNA was isolated from immunoprecipitated protein from whole worm lysate using protein-specific antibodies. Detailed protocol can be bound in the corresponding manuscript.
Libraries were prepared as described previously (Hauptmann et al., 2015).

tag: RNAi knockdown

value: WT


title: CD8-AtmWT-lymphoma_1


title: jejunal mucosa from healthy pig 1

description: Control

value: jejunal mucosa

value: Healthy

tag: age

value: 42 days


title: IP_SMEDWI3 rep3


title: V08-10%FGF

source_name: standard ASCs from subcutaneous adipose tissue

value: adipose-derived stem/stromal cells

value: standard media


title: keratinocytes_miR-Ctrl_rep1

value: skin

value: keratinocytes

value: control


title: R012-EGM2


title: keratinocytes_miR-Ctrl_rep2


title: NOFERRIC rep1

value: WB


title: CLASH_up 1

description:
clash1_up
CLIP reads from the longer size UV-cross-linked RNA
processed data file:
CLASH_and_CLIP_counts.txt


title: IP_SMEDWI3 rep1


title: IP_SMEDWI2 rep3

description:
Immunoprecipitated piRNAs bound to SMEDWI-2
small_rna_seq_weighted_counts.txt.gz
final_dd_Smed_g4.maker.genes.gff.gz

value: Anti-SMEDWI-2 (raised polyclonal antibody)


title: TYDK rep3

value: TYDK


title: TYDK rep2


title: R46_W43RTO

status: Public on Sep 03 2019

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Standard Illumina pipeline including CASSAVA
Sequenced reads were aligned to 56,044 gene models, build Wm82.a2.v1 DNA soybean cDNA gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

organism: Glycine max

source_name: seedling roots from 5 day greenhouse grown seedlings

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated mg fresh weight, length (for leaves), or days after planting (for roots), or at maturity. Whole seeds were dissected by hand into cotyledons,  seed coats, and embryo axis for some samples.

extract_protocol:
Total RNA was extracted from freeze-dried tissues using phenol:chloroform and a lithium chloride precipitation (Gonzalez and Vodkin 2007). Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar/genotype

value: Williams (PI548631)

value: roots

value: 5 days


title: R104_DrySC

source_name: seed coat dissected from mature dry seed

value: mature seed coat

tag: Stage

value: Mature dry seed


title: R016-10%FGF

value: Female


title: R49_5-6mgSC.

source_name: seed coat dissected from 5-6mg immature seed

tag: tissue

value: immature seed coat


title: keratinocytes_miR-34c_rep1

description: Gene expression data from keratinocytes with miR-34c.

source_name: keratinocytes transfected with miR-34c

value: miR-34c overexpression


title: keratinocytes_miR-34c_rep4


title: keratinocytes_miR-34a_rep3

description: Gene expression data from keratinocytes with miR-34a.

source_name: keratinocytes transfected with miR-34a

value: miR-34a overexpression


title: R108_200_300YSC

source_name: seed coat dissected from 200-300 mg yellow desiccating seed

value: 200-300mg desiccating


title: R106_200_300YCot_A

source_name: Cotyledon without embryo axis from 200-300 mg yellow, desiccating seed

value: immature cotyledon without embryo axis


title: R109_300_400YAxis

source_name: embryo axis dissected from 300-400 mg yellow, desiccating seed

value: embryo axis

value: 300-400mg desiccating


title: V07-10%FGF

value: adipose-derived stem/stromal cells

value: standard media


title: R012-10%FGF


title: keratinocytes_miR-34c_rep2

value: skin

value: keratinocytes


title: keratinocytes_miR-34c_rep3


title: R015-10%FGF


title: R107_200_300YAxis

source_name: embryo axis dissected from 200-300 mg yellow, desiccating seed

value: Williams (PI548631)


title: keratinocytes_miR-34a_rep2


title: V06-10%FGF


title: IP_SMEDWI2 rep2

data_processing:
Base-calling was performed with Illumina Casava v1.8.2 software on HiSeq1000. RTA2 was used for base-calling on NextSeq 500
Degradome libraries were processed using piPipes (Han et al. 2014). Abundance of degradome reads was estimated with eXpress (Roberts and Pachter, 2012).
Before mapping reads to the planarian genome, 3’-adapters were removed with cutadapt, sequences mapping to planarian rRNA were discarded with SortMeRNA, and all duplicated reads were collapsed with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Large and small CLIP reads from separately prepared upper and down band of CLIP and CLASH libraries were pooled for their subsequent joint analysis. Reads were mapped to the planarian transcriptome using bowtie2 (Langmead and Salzberg, 2012) with -a option.  Weighted counts were used for multimapping CLIP reads, where read count was divided by the number of the read observations.
RNA-Seq reads after removal of 3’-adapters and quality filtering with Trimmomatic (0.36) were trimmed to a length of 50 nt. Next, sequences mapped to planarian rRNAs were removed with SortMeRNA. Reads were assigned to the reference transcriptome and consensus transposable element sequences (Bao et al., 2015) in strand-specific mode and quantified with kallisto (Bray et al., 2016) with “--single -l 350 -s 30 -b 30” for single-end libraries and “-b 30” for paired-end libraries.
Immunoprecipitated piRNAs were processed as following. 3’-adapters were trimmed using cutadapt (Martin, 2011) and filtered against planarian rRNA sequences with SortMeRNA (Kopylova et al., 2012). Only sequences longer than 18 nt and shorter than 40 nt were kept for the following analysis. Processed reads were mapped against the planarian genome using bowtie (1.1.2) (Langmead et al., 2009) with the following settings “-v 0 -a --best –strata”. Abundance of mapped piRNAs was estimated in weighted counts, where total read counts of multimapping reads were divided by the number of locations they map to.
Genome_build: dd_Smed_g4
Supplementary_files_format_and_content:
abundance_in_estCounts_DegradomeSeq.txt includes estimated counts of degradome reads assigned to the planarian transcriptome (Rozanski, 2018) and quantified with eXpress (Roberts and Pachter, 2012).
CLASH_and_CLIP_counts.txt contains weighted counts of CLIP and CLASH libraries (files from up and down band were merged and processed jointly) assigned to planarian transcriptome with bowtie2 (Langmead and Salzberg, 2012)
abundance_in_estCounts_upon_smedwi2_RNAi_RNAseq.txt was generated by assigning the sequenced reads from unc-22 (C. elegnas) and smedwi-2 (RNAi) knockdown libraries and consensus transposable element sequences with kallisto to planarian transcriptome and transposable elements consensus sequences (Bray et al., 2016).
abundance_in_estCounts_upon_smedwi3_RNAi_RNAseq.txt was generated by assigning the sequenced reads from unc-22 (C. elegnas) and smedwi-3 (RNAi) knockdown libraries and consensus transposable element sequences with kallisto to planarian transcriptome and transposable elements consensus sequences (Bray et al., 2016).
small_rna_seq_weighted_counts_to_genome.txt contains weighted counts of immunoprecipitated with SMEDWI-1, SMEDWI-3, SMEDWI-3 proteins piRNAs  mapped to planarian genome with 0 mismatches.

value: Anti-SMEDWI-2 (raised polyclonal antibody)

value: WT


title: mRNA 48h-M2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
RNA-seq: was performed using TopHat v2.1.0 and Cufflinks v2.2.1
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000004515.4
Supplementary_files_format_and_content: FPKM

source_name: root hair cells_312 hrs after sowing

growth_protocol: The soybean plants were growth with an ultrasound aeroponic system (Qiao et al., 2013) under controlled conditions.

extract_protocol: Truseq RNA-seq v2 (Illumina)

value: willam 82

value: 312 hours after sowing

value: root hair cells


title: R105_DryCot

source_name: Cotyledon from mature dry seed

value: mature cotyledon

value: Mature dry seed


title: TYDK rep1

value: WB

value: TYDK


title: mRNA 48h-M1


title: keratinocytes_miR-34a_rep1

value: miR-34a overexpression


title: mRNA 24h-M2

source_name: root hair cells_288 hrs after sowing

value: 288 hours after sowing


title: mRNA 24h-M1


title: mRNA 12h-M2

source_name: root hair cells_276 hrs after sowing

value: 276 hours after sowing


title: IP_SMEDWI2 rep1

first: Claus

institute: University of Bayreuth

source_name: whole worm


title: mRNA 12h-M1


title: R50_5-6mgCot.

source_name: cotyledon from 5-6mg immature seeds

value: immature cotyledon


title: monkeyPFC-control-9

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

description:
Coh7a_Ctrl_28
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.

hyb_protocol: Following fragmentation, cRNA samples were hybridized for 16 hr to GeneChip Rhesus Macaque Genome arrays by procedures outlined by Affymetrix.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin and scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Raw microarray expression data from monkeys underwent background correction and quantile normalization in a single group by the Robust Multi-array Average (RMA) method within the affy package for R (Gautier et al. 2004). RMA data was examined for batch effects by principal component analysis. Batch effects were evident for two factors with similar patterns of segregation: microarray processing batch and MATRR cohort. To remove batch effects, RMA data was adjusted using the ComBat method in R (Johnson, Li, and Rabinovic 2007), with microarray processing batch as the batch factor. Principal component analysis confirmed that ComBat removed the batch effects. Network analysis with WGCNA and bioinformatics analysis were used to identify modules of co-expressed genes representing specific biological pathways.

organism: Macaca mulatta

source_name: Brodmann brain areas 24, 25, and 32, water control

label_protocol: Biotinylated cRNA samples were prepared according to Affymetrix protocols.

extract_protocol: Brain samples were homogenized with a tissue homogenizer. RNA was extracted from brain tissue using either RNeasy Mini Kit (Qiagen, Valencia, CA; cohorts 4 & 5) or All Prep DNA/RNA/miRNA Universal Kit (Qiagen; cohorts 7a & 7b) following the manufacturer’s protocol.

treatment_protocol: Macaques individually housed at the Oregon National Primate Research Center were induced to drink ethanol by schedule-induced polydipsia per previously published methods (Grant et al. 2008, Helms, Park, and Grant 2014), and were then allowed 22 hours per day of ad libitum access to water and 4% (w/v) ethanol in water for a period of one year. Control animals were given daily maltose dextran solution (calorically matched to an ethanol drinker) and had access to water during all portions of the experiment.

tag: Sex

value: male

value: adult

value: brain, Brodmann areas 24, 25, 32 pooled

tag: treatment

value: water control


title: monkeyPFC-control-11

description:
Coh7b_Ctrl_38
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-22

description:
Coh7a_EtOH_31
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.

source_name: Brodmann brain areas 24, 25, and 32, ethanol drinker

value: ethanol consuming


title: monkeyPFC-ethanol-29

description:
Coh7b_EtOH_40
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-31

description:
Coh7b_EtOH_42
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-28

description:
Coh7b_EtOH_39
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-21

description:
Coh7a_EtOH_30
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-26

description:
Coh7a_EtOH_35
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-6

description:
Coh7a_Ctrl_25
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-25

description:
Coh7a_EtOH_34
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-20

description:
Coh7a_EtOH_29
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-23

description:
Coh7a_EtOH_32
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-10

description:
Coh7b_Ctrl_37
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-19

description:
Coh5_EtOH_24
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-30

description:
Coh7b_EtOH_41
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-18

description:
Coh5_EtOH_23
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-8

description:
Coh7a_Ctrl_27
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-24

description:
Coh7a_EtOH_33
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-32

description:
Coh7b_EtOH_43
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-13

description:
Coh5_EtOH_18
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-5

description:
Coh5_Ctrl_16
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-15

description:
Coh5_EtOH_20
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-27

description:
Coh7a_EtOH_36
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-14

description:
Coh5_EtOH_19
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-7

description:
Coh7a_Ctrl_26
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-16

description:
Coh5_EtOH_21
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-17

description:
Coh5_EtOH_22
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-12

description:
Coh5_EtOH_17
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-11

description:
Coh4_EtOH_11
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-1

description:
Coh5_Ctrl_12
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-control-2

description:
Coh5_Ctrl_13
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-7

description:
Coh4_EtOH_7
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-control-3

description:
Coh5_Ctrl_14
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-control-4

description:
Coh5_Ctrl_15
Gene expression data from male Rhesus macaque prefrontal cortex tissue, control animal.


title: monkeyPFC-ethanol-2

description:
Coh4_EtOH_2
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-9

description:
Coh4_EtOH_9
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-4

description:
Coh4_EtOH_4
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: K9162.CD38.p.sIgD.p._naive

city: Shinjuku-ku

first: Jun

last: Inamo

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University School of Medicine

hyb_protocol: Following fragmentation, cDNAs were hybridized on the Human Genome U133 Plus 2.0 Array using GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Fluidics Station 450Dx v.2

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000Dx v.2 with AutoLoaderDX.

data_processing: Probe set expression values were estimated using frozen RMA, and their presence call was calculated with the MAS5 algorithm. Stepwise quality control for probes was conducted. First, probes that did not match any genes or that targeted multiple genes were removed. Then, probes that were called absent in all samples, were filtered out. In the case where multiple probes hybridized the same gene and those probes were positively correlated with a Pearson’s correlation coefficient of more than 0.3, the probe exhibiting the maximum average signals across samples was kept. Lastly, less variable probes whose interquartile ranges were in the bottom 20% of all probes were filtered out.

source_name: pSS_Memory B cell

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted from B cell subsets and transcribed to cDNA using NucleoSpin RNA (Macherey Nagel) and ReverTra Ace qPCR RT Master Mix (TOYOBO).

tag: subject status

value: healthy control

tag: subject id

value: peripheral blood B cell

tag: cell subtype

value: Memory B cell


title: monkeyPFC-ethanol-3

description:
Coh4_EtOH_3
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: K4113.CD38.n.sIgD.p

source_name: pSS_Pre-GC B cell

value: Pre-GC B cell


title: K9162.CD38.dp.sIgD.p_pre_GC.B


title: monkeyPFC-ethanol-10

description:
Coh4_EtOH_10
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-5

description:
Coh4_EtOH_5
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-1

description:
Coh4_EtOH_1
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: monkeyPFC-ethanol-6

description:
Coh4_EtOH_6
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: K4113.CD38.p.n.sIgD.n_memory


title: monkeyPFC-ethanol-8

description:
Coh4_EtOH_8
Gene expression data from male Rhesus macaque prefrontal cortex tissue, ethanol consuming animal x 1 year.


title: K9162.CD38.p.n.sIgD.n_memory


title: K4113.CD38.p.sIgD.p._naive


title: K9162.CD38.n.sIgD.p


title: K5778.CD38.n.sIgD.p


title: K5778.CD38.p.n.sIgD.n_memory


title: K5778.CD38.dp.sIgD.p_pre_GC.B


title: K5778.CD38.p.sIgD.p._naive


title: K4113.CD38.dp.sIgD.p_pre_GC.B


title: K9920.CD38.p.n.sIgD.n_memory

source_name: pSS_Naive B cell

value: Naive B cell