title: ImR90−NPC−rep4

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

institute: The University of Hong Kong

data_processing:
The libraries were sequenced at the Centre for Genomics Sciences (CGS), The University of Hong Kong
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes

source_name: differentiations from iPSC cell-line (ImR90)

growth_protocol: hESC3/ESC9/IMR90-iPSC were cultured on a six-well culture plate (Corning Cellgro) coated with Geltrex (Thermo Fisher). Essential 8 medium (Thermo Fisher) was changed daily to sustain cell growth. Y-27632 (Sigma) was added after cell passage, thawing and nucleofection (Lonza).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For NC-like cell differentiation, ESC3/ESC9/IMR90-iPSC were passaged and seeded on a 0.1% Geltrex-coated 6-well plate at a density of 50,000 cells/cm2 with Essential 8 medium. One day later, Essential 8 medium was replaced by DMEM/F12 medium supplemented with N2, B27, ITS, 0.1mM NEAA, 2 mM L-glutamine, and 0.1 mM 2-mercaptoethanol (Thermo Fisher) and Activin A (10ng/mL) for two days at step1. Then, other cell growth factors containing Activin A (10ng/mL), FGF2 (10ng/mL), Noggin (50ng/mL), CHIR (3μM) and AGN193109 (10μM) were added for a further three days differentiation (Cell growth factor from PeproTech, chemicals from Sigma) at step 2. For NP-like cell differentiation, the medium at step 2 was changed to DMEM-HG supplemented with 1% ITS+, 1% NEAA, 1% penicillin/streptomycin, 50μg/ml ascorbic acid-2-phosphate (Sigma), 40μg/ml L-proline (Sigma), and 10ng/ml TGF-β3 (R&D) for 15 days at step3.

tag: cell type

value: iPSC-derived NPCs

tag: passages


title: sample 135b

status: Public on Dec 31 2019

type: SRA

country: Hong Kong

description: invivoNPC.gene.expression.tables.FPKM.txt [CDS_135_T12_L1]

library_source: transcriptomic

data_processing:
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes

molecule: polyA RNA

organism: Homo sapiens

source_name: human in vivo nucleus pulposus in young scoliotic individuals 2b

extract_protocol:
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: nucleus pulposus

tag: age

tag: gender

value: female

tag: ivd level

tag: date of surgery

tag: surgical procedures

value: discectomy

tag: condition

value: scoliosis


title: sample 147

description: invivoNPC.gene.expression.tables.FPKM.txt [CDS_147_L1_L2]

source_name: human in vivo nucleus pulposus in young scoliotic individuals 3

value: L1 fracture


title: sample 124

description: invivoNPC.gene.expression.tables.FPKM.txt [CDS_124]

source_name: human in vivo nucleus pulposus in young scoliotic individuals 1


title: ImR90−NPC−rep2


title: sample135a

description: invivoNPC.gene.expression.tables.FPKM.txt [CDS_135_L1_L2]

source_name: human in vivo nucleus pulposus in young scoliotic individuals 2a


title: ImR90−NPC−rep3


title: Scramble_S18_2_S30

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

country: USA

institute: University of California San Francisco

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
For publication purposes, sample IDs were renamed as follows: S1=S1, S2=S2, S18=S3, S19=S4, AB1=AB1, AB10=AB2, AB17=AB3, AB22=AB4
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values files including FPKM values for each sample.

molecule: total RNA

source_name: CCRF-CEM leukemia cell line

growth_protocol: CCRF-CEM cells were cultured as recommended by ATCC guidelines

extract_protocol:
Total RNA was prepared using Trizol based extraction. Samples were purified and concentrated using the RNeasy Mini Kit. RNA concentration was determined using a NanoDrop spectrophotometer. RNA quality was assessed using an Agilent 2200 Bioanalyzer.
Libraries were prepared using the TruSeq RNA Exome RNA kit. Libraries were sequenced on a NextSeq 500 using 150bp paired-end chemistry.

treatment_protocol: Cells were exposed to vehicle, dexamethasone, IL-7, or the combination for 4 or 16 hours

tag: knockout

tag: treatment condition

tag: drug exposure time

value: 16 hours


title: STAT5_KO_AB22_6_S49

value: STAT5A and STAT5B

value: 4 hours


title: ImR90−NPC−rep1


title: E9−NPC−rep4

source_name: differentiations from ESC cell-line (ESC9)

value: ESC-derived NPCs


title: STAT5_KO_AB1_6_S39


title: STAT5_KO_AB1_5_S41


title: STAT5_KO_AB1_7_S21


title: STAT5_KO_AB1_3_S54


title: STAT5_KO_AB1_4_S34


title: STAT5_KO_AB1_1_S39

value: VEH


title: STAT5_KO_AB1_2_S47


title: STAT5_KO_AB17_7_S30


title: E9−NPC−rep3


title: E9−NPC−rep1


title: E3−NPC−rep4

source_name: differentiations from ESC cell-line (ESC3)


title: E9−NPC−rep2


title: STAT5_KO_AB17_6_S44


title: E3−NPC−rep3


title: STAT5_KO_AB22_1_S44


title: STAT5_KO_AB17_5_S50


title: E3−NPC−rep2


title: STAT5_KO_AB17_4_S31


title: STAT5_KO_AB17_3_S43


title: STAT5_KO_AB17_2_S42


title: ImR90-iPSC

source_name: iPSC cell-line

value: iPSC


title: STAT5_KO_AB17_1_S48


title: E3−NPC−rep1


title: STAT5_KO_AB10_7_S38


title: ESC3

source_name: ESC cell-line

value: hESC


title: ESC9


title: STAT5_KO_AB10_5_S46


title: STAT5_KO_AB10_4_S53


title: STAT5_KO_AB10_3_S35


title: STAT5_KO_AB10_6_S46


title: STAT5_KO_AB10_2_S31


title: STAT5_KO_AB10_1_S45


title: Sperm, H3RS_V3

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description: results.vin.rs.csv.gz

library_source: genomic

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DHRs, the reference genome was broken into 100 bp windows. Genomic windows with less than 100 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than 10-4 were considered DHRs. The DHR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DHR.
CpG density and other information was then calculated for the DHR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ obtained from Harlan/Envigo (Indianapolis, IN)  at about 70 to 100 days of age were maintained in ventilated (up to 50 air exchanges/hour) isolator cages (cages with dimensions of 10 ¾″ W×19 ¼″ D×10 ¾″ H, 143 square inch floor space, fitted in Micro-vent 36-cage rat racks; Allentown Inc., Allentown, NJ) containing Aspen Sani chips (pinewood shavings from Harlan) as bedding, and a 14 h light: 10 h dark regimen, at a temperature of 70 F and humidity of 25% to 35%. The mean light intensity in the animal rooms ranged from 22 to 26 ft-candles. Rats were fed ad lib with standard rat diet (8640 Teklad 22/5 Rodent Diet; Harlan) and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (i.e. sperm plug present) (day 0) rats were monitored for diestrus and body weight. The control, vinclozolin, and DDT lineages were housed in the same room and racks with lighting, food and water

extract_protocol:
The epididymis was dissected free of connective tissue, a small cut made to the cauda and tissue placed in 5 ml of 1x PBS solution for up to 2 hours at 4°C. The epididymal tissue was minced and the released sperm was centrifuged at 6,000 x g, then the supernatant was removed, and the pellet was resuspended in NIM buffer, to be stored at -80O C until further use. One hundred μl of sperm suspension was sonicated to destroy somatic cells and tissue, spun down at 6,000 x g, the sperm pellet was washed with 1x PBS once. Germ cells were isolated exclusively from males. To isolate round spermatids, testes were collected from 12 month old rats suspended in F-12 culture medium (Gibco-Life Technologies, USA. Ref 11765-054) and shipped overnight on ice to Dr. John McCarrey. A StaPut gradient method was used to isolate the developing germ cell stages. Three pools of cells of each cell type were prepared for each treatment group, with each pool derived from testes of three rats from different litters. DNA was isolated from round spermatids using the same procedure as was used for sperm, with the omission of sonication and DTT treatments. Individual rat sperm collections were generated and the sperm counts were determined for each individual. Equal numbers of sperm were added from each individual for a total of 1.5 million sperm per pool, and 3 pools with different individual rats for each pool for the control, vinclozolin and DDT lineage animals. The control pools contained equal numbers of sperm for each of 5–6 individuals for a total of n = 17 rats, and the vinclozolin and DDT pools contained equal numbers of sperm for each of 4 individuals in each pool for a total of n = 12 rats per exposure group. To remove any somatic cell contamination sperm samples from each animal were sonicated for 10 seconds using a Sonic Dismembrator Model 300 (Thermo Scientific Fisher, USA) then centrifuged 1800 g for 5 min at 4 °C then resuspended and counted individually on a Neubauer counting chamber (Propper manufacturing Co., Inc., New York, USA) prior to pooling. The sperm pools were reconstituted up to 1 ml with PBS (phosphate buffered saline). To reduce disulfide bonds, 50 μl of 1 M DTT was added to each pool and the pools were then incubated for 2 hours at room temperature under constant rotation. To quench any residual DTT (dithiothreitol, Fisher Scientific, NY USA) in the reaction, 120 μl of fresh 1 M NEM (N-Ethylmaleimide, Thermo Scientific, Rockford, USA) was then added and the samples were incubated for 30 min at room temperature under constant rotation. The sperm cells were pelleted at 450 g for 5 min at room temperature and the supernatant was discarded. Pellets were resuspended in PBS and then spun again at 450 g for 5 min at room temperature. The supernatant was discarded and resuspended in 130 μl of complete buffer supplemented with tergitol 0.5% and DOC 1%. The samples were then sonicated using the Covaris M220. Covaris was set to a 10 min “Chromatin shearing” program and the program was run for each tube in the experiment.  After the Covaris sonication, 10 μl of each sample was run on a 1.5% agarose gel to verify fragment size. Samples were then centrifuged at 12,500 g for 10 min at room temperature. The supernatant was transferred to a fresh microfuge tube. 65 μl of protease inhibitor cocktail (1 tablet dissolved in 500 μl, 20 × concentrated) (Roche, cat. no. 11 873 580 001) were added in each sample as well as 3 μl of antibody (anti-histone H3 pan- monoclonal antibody, cat no. 05–928, or anti-trimethyl-histone H3 (Lys27) polyclonal antibody, cat no. 07–449, both with broad spectrum species specifically form Millipore Corp, Temecula CA USA). The DNA-antibody mixture was incubated overnight on a rotator at 4 °C. The following day, magnetic beads (ChIP-Grade protein G magnetic beads, Cell Signaling 9006) were pre-washed as follows: the beads were resuspended in the vial, then 30 μl per sample was transferred to a microfuge tube. The same volume of Washing Buffer (at least 1 ml) was added and the bead sample was resuspended. The tube was then placed into a magnetic rack for 1–2 min and the supernatant was discarded. The tube was removed from the magnetic rack and the beads were washed once. The washed beads were resuspended in the same volume of IP buffer as the initial volume of beads. 30 μl of beads were added to each DNA-antibody mixture from the overnight incubation, then incubated for 2 h on a rotator at 4 °C. After the incubation, the bead-antibody-DNA complex was washed three times with IP buffer as follows: the tube was placed into a magnetic rack for 1–2 min and the supernatant was discarded, then washed with IP buffer 3 times. The washed bead-antibody-DNA solution was then resuspended in 300 μl of digestion buffer (1 M Tris HCI, pH 8.0, 0.5 M EDTA, 10% SDS) and 3 μl proteinase K (20 mg/ml). The sample was incubated for 3 h on a rotator at 56 °C. After incubation the samples were extracted with Phenol-Chloroform-Isoamyalalcohol and precipitated with 2 μl of Glycoblue (20 mg/ml), a one-tenth volume of 3 M sodium acetate and two volumes of ethanol overnight at −20 °C.  The precipitate was centrifuged at 18,000 g for 30 min at 4 °C and the supernatant was removed, while not disturbing the pellet. The pellet was washed with 500 μl cold 70% ethanol, then centrifuged again at 18,000 g for 10 min at 4 °C and the supernatant was discarded. The tube was spun briefly to collect residual ethanol to bottom of tube and as much liquid as possible was removed with a gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 min), then resuspended in 20 μl H20. DNA concentration was measured in the Qubit (Life Technologies) with the BR dsDNA kit (Molecular Probes Q32853).
The ChIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, Ipswich, MA). The manufacturer protocol was followed. Each pool received a separate index primer. NGS was performed at the WSU Spokane Genomics Core using Ilumina HiSeq. 2500 with a read size of approximately 50 bp PE and approximately 20 million reads per pool. Eleven or twelve libraries were run in one lane.

treatment_protocol: On days 8 through 14 of gestation, the females received daily intraperitoneal injections of DDT (25 mg/kg body weight/day), vinclozolin, or dimethyl sulfoxide (DMSO). The DDT (dichlorodiphenyltrichloroethane) was obtained from Chem Service Inc. (West Chester, PA) and reported to have a purity of 98.2%. DDT were dissolved and injected in DMSO vehicle as previously described. Treatment lineages are designated ‘control’, ‘vinclozolin’, or ‘DDT’ lineages. The treated gestating female rats were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from the F1 generation of control, vinclozolin, or DDT lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring. Individuals were maintained for 12 months and euthanized for sperm collection. The F1- F3 generation offspring were not themselves treated directly with DDT or vinclozolin.

tag: treatment

value: vinclozolin

tag: development stage

value: round spermatids

value: sperm

tag: chip antibody

value: anti-histone H3 panmonoclonal


title: Sperm, H3RS_D2

description: results.ddt.rs.csv.gz

value: DDT


title: Sperm, H3RS_D1

description: results.ddt.rs.csv.gz


title: Sperm, H3RS_D3

description: results.ddt.rs.csv.gz


title: Sperm, H3RS_V1

description: results.vin.rs.csv.gz


title: Sperm, H3meCP_C3

description:
results.ddt.h3caput.csv.gz
results.vin.h3caput.csv.gz
results.c.h3caput.h3cauda.csv.gz

value: control

value: caput

value: anti-trimethyl-histone H3 (Lys27) polyclonal


title: Sperm, H3meCP_C2


title: Sperm, H3meCP_D1


title: Sperm, H3meCP_C1


title: Sperm, H3RS_V2

description: results.vin.rs.csv.gz


title: Sperm, H3meCP_D2


title: Sperm, H3meCP_V2


title: Sperm, H3meCP_V3


title: Sperm, H3RS_C2

description:
results.ddt.rs.csv.gz
results.vin.rs.csv.gz
results.c.rs.caput.csv.gz


title: Sperm, H3RS_C1


title: Sperm, H3meCP_V1


title: Sperm, H3RS_C3


title: Sperm, H3meCP_D3


title: Sperm, H3meCD_V3

value: cauda


title: Sperm, H3meCD_V1


title: hSynI-creER+LSL-SmoM2+LSL-BRPF1 TR_2

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

description:
ATAC-seq
Synapsin_lsl-tomato_lsl-Brpf1_lsl-SmoM2_TOTAL.NORM_peaks.bed

data_processing:
Sequenced reads from all independent sequenced libraries were quality assessed by using fastQC and trimmed with Trimmomatic. Reads from biological replicates were merged for all analysis. Total reads were aligned to either the mouse genome NCBI37/mm9 or the human genome GRCh37/hg19 using Bowtie2, using the parameters ‘--very-sensitive -k 1’, thus discarding ambiguous reads mapping at multiple sites. Duplicated reads and reads mapping on mitochondrial DNA were discarded for further analysis with SAMtools.
Normalized BigWig tracks of ATAC-seq signals were generated with BEDtools 2.24.0 and the bedGraphToBigWig program and visualized on the UCSC Genome Browser.
The HOMER software was further used to analyze ATAC-seq data. The command ‘findPeaks’ was used for peak calling with these parameters ‘-size 150 -minDist 1000’; the command ‘get-DifferentialPeaks’ was used to find peaks with differential ATAC-seq signals between two conditions (‘-F 2 -P 0.001’); the command ‘findMotifsGenome.pl’ was used for motifs enrichment analysis; the command ‘annotatePeaks.pl’ was used to annotate peaks to related genes and genomic regions and to count the number of normalized reads on specific regions.
Genome_build: mouse genome NCBI37/mm9 and the human genome GRCh37/hg19
Supplementary_files_format_and_content: BED files of peaks called with HOMER on normalized ATAC-seq data

source_name: AF22 neuroephitilial-like stem cells

growth_protocol: Human iPSC-derived neuroepithelial-like stem cells AF22 at passage 30, were cultured in a 1:1 ratio mixture of Neurobasal and DMEM/F12 media supplemented with N2 (1:100), B27 (1 µl/ml), 10 ng/ml EGF and 10 ng/ml FGF2. Cerebella were dissected from P7 mice.

extract_protocol:
Nuclei were isolated by transferring 400 ul of supernatant in a plastic tube and sequentially added 400 ul of 50% Iodixanol solution (homogenization buffer and 50% Iodixanol solution), 600 ul of 29% Iodixanol (homogenization buffer, 160 mM and 29% Iodixanol solution) and 600 ul of 35% Iodixanol solution (homogenization buffer, 160 mM and 35% Iodixanol solution) to the bottom of the tube, avoiding mixture of layers.   We centrifuged for 20 min at 3,000 RCF and we discarded upper layers of the gradient in order to collect 200 ul from the nuclei band. We counted nuclei and transferred 50.000 into a tube with 1 ml of ATAC-Resuspension Buffer (RSB) + 0.1% Tween-20 (10 mM  Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). We pelleted nuclei by centrifuging for 10 minutes at 500 RCF and resuspended in 50 ul cold ATAC-RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin,. We lysed for 3 minutes on ice and washed with 1 ml of cold ATAC-RSB + 0.1% Tween-20.
We transposed the samples by resuspending nuclei in 50 ul of transposition mix (25 ul 2x TD buffer, 100nM transposase, 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) and incubated at 37°C for 30 minutes. We purified the transposed DNA using the Qiagen MinElute PCR Purification Kit (cat. # 28004) and eluted in 10 μl elution buffer. Next we amplified the transposed DNA fragments in the PCR mix (10 μl transposed DNA, 10 μl nuclease-free H2O, 2.5 μl 25 μM PCR Primer 1, 2.5 μl 25 μM Barcoded PCR Primer 2 and 25 μl NEB Next High-Fidelity 2× PCR Master Mix cat. # M0541L). The final ATAC-seq libraries were purified using the Qiagen MinElute PCR Purification Kit, quantified at the Qubit Fluorometer (Invitrogen, cat. #Q33226) and quality controlled with the High Sensitivity DNA Assay at the 2100 Bioanalyzer (Agilent, cat. # G2939BA). Four and three independent biological replicates, sequenced as independent libraries, were performed for Gabra6-cre;LSL-SmoM2 and control Gabra6-cre, respectively. Two independent biological replicates, sequenced as independent libraries, were performed for hSynI-creER+LSL-tdTomato, hSynI-creER+LSL-BRPF1 TR, hSynI-creER+LSL-SmoM2 and hSynI-creER+LSL-SmoM2+LSL-BRPF1 TR cell lines.
All libraries were sequenced as single reads of 50 bp with the Illumina HiSeq2500.

treatment_protocol: Frozen cerebella were dounced in 2 ml cold homogenization buffer (0.017 mM PMSF, 0.17 mM β-mercaptoethanol, 320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8) and pelleted at 100 RCF for 1 min.

value: induced pluripotent stem cells (iPSCs) generated from reprogrammed adult fibroblasts (ADF)


title: hSynI-creER+LSL-SmoM2+LSL-BRPF1 TR_1


title: hSynI-creER+LSL-SmoM2_2

description:
ATAC-seq
Synapsin_lsl-tomato_lsl-SmoM2_TOTAL.NORM_peaks.bed


title: Sperm, H3meCD_D3


title: hSynI-creER+LSL-SmoM2_1


title: Sperm, H3meCD_C3

description:
results.ddt.h3cauda.csv.gz
results.vin.h3cauda.csv.gz
results.c.h3caput.h3cauda.csv.gz


title: Sperm, H3meCD_D1


title: Sperm, H3meCD_C2


title: hSynI-creER+LSL-BRPF1 TR_2

description:
ATAC-seq
Synapsin_lsl-tomato_lsl-Brpf1_TOTAL.NORM_peaks.bed


title: Sperm, H3meCD_C1


title: hSynI-creER+LSL-tdTomato_2

description:
ATAC-seq
Synapsin_lsl-tomato_TOTAL.NORM_peaks.bed


title: Sperm, H3CP_V3

description: results.vin.caput.csv.gz


title: hSynI-creER+LSL-BRPF1 TR_1


title: Sperm, H3meCD_V2


title: Sperm, H3CP_V2

description: results.vin.caput.csv.gz


title: Pericyte_3

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
gene_count_matrix.csv
RLECPC9

data_processing:
The libraries underwent 76-bp paired-end sequencing using an Illumina HiSeq 2500. Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were mapped to the human reference genome (hg38) with HISAT2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts and reporting alignments tailored for transcript assemblers. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with StringTie v1.3.3b and the Python script “prepDE.py” provided in the package. StringTie was limited to reads matching the reference annotation GENCODE v27. After obtaining the matrix of read counts, differential expression analysis was conducted and normalized counts were produced using DESeq2. P-values were adjusted for multiple testing using the Benjamini-Hochberg procedure.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts per gene for each sample. Direct output from python script "prepDE.py" included in StringTie

source_name: Human placenta

growth_protocol: Human lung fibroblasts were purchased from Lonza (Walkersville, MD, USA) and used between subculture 2-15. Fibroblasts were serially cultured in Medium 199 (Gibco, Grand Island, NY, USA) plus 20% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin (all from Invitrogen, Carlsbad, CA, USA). Confluent fibroblasts from three different donors for each cell type were grown in one well of a 12-well plate.

extract_protocol:
Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) with an on-column DNase treatment.
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

value: Human placenta pericyte

tag: passage

value: Placenta


title: Pericyte_2

description:
gene_count_matrix.csv
RLECPC8


title: Sperm, H3meCD_D2


title: Sperm, H3CP_D3

description: results.ddt.caput.csv.gz


title: Sperm, H3CP_V1

description: results.vin.caput.csv.gz


title: Bacteria_rG4seq_M_Li_rep2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

institute: City University of Hong Kong

description:
Ecoli_K_hits.bed
single-ended rG4-seq data of Escherichia coli str. K-12 substr. MG1655 in Li+ rich buffer
instrument model: MiSeq V3 (Illumina).

data_processing:
Bacterial rG4-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
Calculate the coverage of each base
Calculate the reverse transcriptase stalling sites
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516.2) and Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Supplementary_files_format_and_content: bed file containing the significant RNA reverse transcriptase stalling sites
Column names:  Refseq, W_Start, W_End, hgnc, RTS_Score,  strand, P_Value, genomic_location, hgnc_genomic_location.
RTS_Score was used to measure the RNA reverse transcriptase stalling degree.

source_name: liquid culture in LB (Luria-Bertani)  medium

growth_protocol: grow until mid-log phase in LB

extract_protocol:
To examine the effect of rG4 sites on the transcriptome of E. coli, 2 ml of mid-log-phase (OD600= 0.6) bacterial LB (Luria-Bertani) cultures (Escherichia coli str. K-12 substr. MG1655 strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the Ribo-ZeroTM rRNA Removal Kit (Bacteria) (Epicentre), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial rG4-seq reads were mapped to the  E. coli str. K-12 substr. MG1655 genome (NC_000913.3) by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses.  GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample inrG4-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

tag: genotype

value: Wild-type

tag: rts reaction buffer

value: Li


title: Sperm, H3CP_D2

description: results.ddt.caput.csv.gz

tag: cell type


title: Bacteria_rG4seq_M_Li_rep1

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


title: Fibroblast_2

description:
gene_count_matrix.csv
FIB-5

source_name: Human lung

value: Human lung fibroblast

tag: tissue

value: Lung


title: Fibroblast_1

description:
gene_count_matrix.csv
FIB-1


title: Sperm, H3CP_C2

description:
results.ddt.caput.csv.gz
results.vin.caput.csv.gz
results.c.caput.cauda.csv.gz
results.c.rs.caput.csv.gz


title: X08h

city: Dresden

first: Andreas

last: Androutsellis-Theotokis

address: Fetscherstr. 74

department: Department of Internal Medicine III

country: Germany

institute: University Hospital Carl Gustav Carus at the Technische Universität Dresden

data_processing:
basecalling: Bcl2fastq 2.17.1.14
alignment: Alignment to the human reference hg38 with the aligner GSNAP and the support of Ensembl annotation version 78 for splice site detection
read counting: featureCounts was used on the bam files and Ensembl annotation version 78 (as gtf) to detect fragments to genes
Genome_build: hg38
Supplementary_files_format_and_content: genecount.hg38.e78.txt.gz is a tab separated file from featureCounts, starting with EnsemblID, chromosome, start, end, strand, length, followed by the counts for the 24 samples

source_name: GBM cells treated with Hes3 siRNA

extract_protocol:
Total RNA was isolated using Roche High Pure RNA extraction kit as described by the manufacturer
Samples were subjected the standard workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB).

value: Glioblastoma multiforme

value: GBM cells treated with Hes3 siRNA

tag: cell line id

tag: culture condition

value: high Hes3 expression


title: Sperm, H3CP_C1

value: sperm


title: Sperm, H3CP_C3

value: anti-histone H3 panmonoclonal


title: Fibroblast_3

description:
gene_count_matrix.csv
FIB-6


title: 8h3


title: Sperm, H3CD_V3

description: results.vin.cauda.csv.gz

value: vinclozolin


title: 8h1


title: Sperm, H3CD_V1

description: results.vin.cauda.csv.gz


title: Bacteria_rG4seq_M_K_rep1

description:
Ecoli_K_hits.bed
single-ended rG4-seq data of Escherichia coli str. K-12 substr. MG1655 in K+ rich buffer
instrument model: MiSeq V3 (Illumina).

value: K


title: Sperm, H3CD_V2

description: results.vin.cauda.csv.gz


title: hSynI-creER+LSL-tdTomato_1


title: 8h2


title: X08c

source_name: GBM cells treated with control (scrambled) siRNA


title: 8c5

value: GBM cells treated with control (scrambled) siRNA


title: Sperm, H3CD_D3

description: results.ddt.cauda.csv.gz

value: DDT


title: Sperm, H3CP_D1

description: results.ddt.caput.csv.gz

value: caput


title: Bacteria_rG4seq_M_K_rep2


title: Sperm, H3CD_D2

description: results.ddt.cauda.csv.gz

value: cauda


title: Sperm, H3CD_D1

description: results.ddt.cauda.csv.gz


title: Sperm, H3CD_C3

description:
results.ddt.cauda.csv.gz
results.vin.cauda.csv.gz
results.c.caput.cauda.csv.gz

value: control


title: X04 Hes3 B


title: Sperm, H3CD_C2


title: 8c1


title: X04h


title: 4h2


title: Sperm, H3CD_C1


title: X04 Control B


title: DOM5

description: results.DNMvsDOM.csv.gz

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with less than 100 mapped reads summed across all samples were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than 10-5 were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

source_name: Adipocytes

growth_protocol: Female and male rats from an outbred strain of Harlan Sprague Dawley ®TM (Indianapolis, IN) were acquired at about 70 to 100 days of age and maintained in ventilated isolator cages with a 14 hour light: 10 hour dark regimen. The rats were fed ad lib. with a standard diet (8640 Teklad 22/5 Rodent Diet; Harlan) and ad lib. tap water for drinking.

extract_protocol:
Gonadal fat pads (epididymal and periovarian) from a total of 218 animals were dissected, weighed, and placed into 1X PBS on ice. The fat pads were dissected free of large pieces of vascular tissue or vas deferens and minced. The minced tissue was placed into a 1mg/ml collagenase solution in 1X PBS (Sigma-Aldrich® Collagenase from Clostridium histolyticum #C2139; St. Louis, MO) with 3 ml of collagenase solution per 1g of adipose tissue. The samples were shaken at 100 rpm at 37C for 45 minutes using New BrunswickTM Innova® 4000 (Edison, NJ), and then immediately placed on ice. The adipocytes were allowed to settle for 10 minutes on ice. The supernatant adipocyte layer was pipetted off and placed into microcentrifuge tubes. A portion of the isolated adipocyte sample was stored in 1 ml of RoboZolTM reagent at -20C. To isolate DNA, 200 μl of adipocytes in PBS were added to 820 μl of DNA extraction buffer (1M tris HCl, 0.5M EDTA, 10% sodium dodecyl sulfate) and 50 μl of proteinase K (20mg/ml). The samples were incubated at 55C for 2-3 hours under constant rotation. After incubation, 300 μl of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) was added to each sample, sample vortexed thoroughly, and incubated for 20 minutes on ice. The samples were centrifuged at 13,500 g for 30 minutes at 4C. Two 500 μl aliquots of the supernatant from each sample were transferred into two centrifuge tubes, ensuring the white protein pellet was not disturbed. 500 μl of phenol-chloroform-isoamyl alcohol was added to each tube and vortexed thoroughly. The samples were centrifuged at 16,250 g at room temperature for 5 minutes. Then, 500 μl of chloroform was added to each tube, vortexed thoroughly, then centrifuged for 5 minutes at 16,250 g. The supernatant was transferred to new tubes and then 2 μl of GlycoBlue (Invitrogen AM9516), 50 μl of 3M NaOAc pH 5.2, and 1 ml 100% ethanol was added to each tube. The samples were vortexed thoroughly and then incubated overnight at -20C. The samples were centrifuged at 13,500g for 20 minutes at 4C. The supernatant was discarded and 500 μl of 70% cold ethanol was added to each pellet and placed at -20C for 20 minutes. The samples were centrifuged for 10 minutes at 4C at 18,000 g, and the supernatant was discarded. The samples were centrifuged again in order to collect and discard the residual ethanol at the bottom of the tube. The samples were dried for 5 minutes, and then resuspended in 50 μl of nuclease free water in each tube. The adipocyte DNA from the control, F3 generation atrazine, and F3 generation DDT lineage rats were processed for MeDIP. Adipocyte DNA from 2-5 individuals were pooled into 5 pools per group: control obese male (COM), n=11; control normal male (CNM), n=17; control lean male (CLM), n=10; control obese female (COF), n=15; control normal female (CNF), n=17; control lean female (CLF), n=16; DDT obese male (DOM), n=14; DDT normal male (DNM), n=13; DDT obese female (DOF), n=14; DDT normal female (DNF), n=18; atrazine lean male (ALM), n=11; atrazine normal male (ANM), n=17; atrazine lean female (ALF), n=23; and atrazine normal female (ANF), n=10. Six μg of DNA from each pool was diluted with 130 μl TE buffer (10mM TrisHCl, pH7.5; 1mM EDTA) and sonicated to 300bp fragment size using the Covaris M220. 10 μl of each sample was run on a 1.5% agarose gel in order to verify fragment size. The volume of sonicated DNA was measured and diluted with TE buffer to 400 μl. The DNA was then denatured at 95C and immediately cooled in ice for 5 minutes. 100 μl of cold 5X IP buffer and 5 μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) was added. The samples were incubated overnight on a rotator at 4C. After incubation, magnetic beads (Dynabeads M-280 Sheep anti-Mouse IgG; Life Technologies 11201D) were prewashed by resuspending and placing 50 μl per sample into a tube on a magnetic rack in order to discard the supernatant. The beads were resuspended again in 1 ml of washing buffer and incubated for 1 minute. The beads were placed on the magnet again in order to discard the supernatant, and the beads were resuspended using 50 μl of 1x IP buffer per sample. 50 μl of beads were added to each sample of the DNA-antibody mixture. The samples were incubated on a rotating platform for 2 hours at 4C. Following incubation, the beads were washed three times with 1x IP buffer. The samples were placed on a magnet and the supernatant was discarded. The samples were washed with 1ml of cold 1x IP buffer, and mixed gently by inverting the tubes. The samples were placed on the magnet again and the supernatant was discarded. After the third wash, the beads were resuspended in 250 μl digestion buffer. 3.5 μl Proteinase K Mix (20mg/ml) were added to the resuspended beads. The beads were incubated for 2-3 hours on a rotating platform at 55C. After incubation, 250 μl of Phenol-Chloroform-Isoamylalcohol was added to each sample. The tubes were vortexed for 30 seconds and centrifuged at 18,000 g for 5 minutes at room temperature. The supernatant was removed, placed into new tubes, and 250 μl of chloroform was added. The tubes were vortexed again for 30 seconds and centrifuged at 18,000 g for 5 minutes at room temperature. The supernatant was removed and placed into a new tube. Then 2 μl of GlycoBlue (20 mg/ml) was added and tubes vortexed. The DNA was precipitated overnight at -20C. The following day, the samples were centrifuged for 18,000 g for 20 minutes at 4C. The supernatant was discarded and 500 μl cold 75% ethanol was added. The samples were placed at -20C for 15 minutes. The samples were centrifuged for 18,000 g for 5 minutes at 4C, and the supernatant was removed. The samples were allowed to dry for 5 minutes, and were then resuspended in 25 μl DNAse-free water. The DNA concentration were measured using the Qubit ssDNA kit (Life Technologies Molecular Probes Q10212).
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (San Diego, CA) starting at the second strand cDNA synthesis step of the manufacturer’s protocol in order to generate double stranded DNA from the single-stranded MeDIP DNA. Each individual sample received a separate index primer.

treatment_protocol: The females were mated and vaginally smeared to determine sperm positive status and to monitor for diestrus. Upon confirmed pregnancy, females were administered a daily intraperitoneal injection of DDT, atrazine, or vehicle control on days 8 through 14 of gestation. The gestating females treated were designated as either control, atrazine, or DDT lineages of the F0 generation. The offspring of the F0 gestating females were the F1 generation. The F2 generation rats were bred to create the F3 generation. No sibling or cousin breeding were used in either generation in order to avoid inbreeding depression. The F3 generations were not exposed directly to DDT or atrazine in order to see transgenerational effects.

value: Adipocytes

tag: Sex

value: male

tag: type

value: obese


title: 4h1


title: Pericyte_1

description:
gene_count_matrix.csv
RLECPC7

value: Human placenta pericyte

value: Placenta


title: STEMI patient, M-20

type: RNA

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

institute: Hospital of Parma

description: gene expression data from platelet of patient with ST-segment elevation myocardial infarction (STEMI)

hyb_protocol: Affymetrix gene chips, Human Transcriptome Array 2.0 (Affymetrix, Santa Clara, CA), were hybridized with 5 μg fragmented and biotin-labeled cDNA in 200 μl of hybridization cocktail. Target denaturation was performed at 99°C for 5 min. and then 45°C for 5 min, followed by hybridization with rotation 60 rpm for 16 hour at 45°C. Arrays were then washed and stained using Gene chip Fluidic Station 450, using Affymetrix GeneChip hybridization wash & stain kit.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Raw data were processed  by Affymetrix Expression Console software (v. 1.4.1) with the default parameters.  The SST-RMA normalization method was applied.

label: biotin

source_name: Platelets

label_protocol: biotin-labelled cDNA (from 10 ng of RNA) was synthesised using the GeneChip WT Pico kit (Affymetrix, Santa Clara, CA).

growth_protocol: Citrate anti-coagulated blood samples (50 mL) were taken from each subject and collected in vacutainers (BD Vacutainer, Becton Dickinson, San Diego, CA) at a final sodium citrate concentration of 3.8%. The blood samples were centrifuged at 160 g for 20 minutes at room temperature in order to obtain platelet-rich plasma, and the platelets were then purified by immunomagnetic negative selection using magnetic beads coated with anti-CD45 antibodies (DynabeadsH, Invitrogen, Carlsbad, CA) to deplete the nucleated cells. The purified platelets were washed three times in PBS/BSA solution, counted, and tested for purity. Finally, the purified platelets were treated with an appropriate amount of TRIzolTM (Invitrogen) for cell lysis and RNA cryopreservation.

extract_protocol: RNA was extracted by TRIzolTM (Invitrogen) in accordance with the manufacturer’s protocol.

value: Platelets

tag: diagnosis

value: STEMI


title: 8c2

value: Glioblastoma multiforme

value: high Hes3 expression


title: DOM4

description: results.DNMvsDOM.csv.gz


title: STEMI patient, M-18


title: X04c


title: STEMI patient, M-16


title: STEMI patient, M-19


title: 4c4


title: DOM3

description: results.DNMvsDOM.csv.gz


title: STEMI patient, M-15


title: STEMI patient, M-14


title: DOM2

description: results.DNMvsDOM.csv.gz


title: STEMI patient, M-17


title: STEMI patient, M-12


title: STEMI patient, M-10


title: DOM1

description: results.DNMvsDOM.csv.gz


title: X01 Hes3 B

value: GBM cells treated with Hes3 siRNA


title: DOF5

description: results.DNFvsDOF.csv.gz

value: female


title: X01h


title: DOF4

description: results.DNFvsDOF.csv.gz


title: 1h2


title: 1h1


title: STEMI patient, M-11


title: STEMI patient, M-09


title: 4c3


title: DOF2

description: results.DNFvsDOF.csv.gz


title: DOF1

description: results.DNFvsDOF.csv.gz


title: STEMI patient, M-08


title: STEMI patient, M-05


title: STEMI patient, M-04


title: STEMI patient, M-06


title: STEMI patient, M-07


title: STEMI patient, M-03


title: X01c


title: DNM5

description: results.DNMvsDOM.csv.gz

value: normal


title: 1c4

value: GBM cells treated with control (scrambled) siRNA


title: DOF3

description: results.DNFvsDOF.csv.gz

value: DDT


title: 1c3


title: DNM2

description: results.DNMvsDOM.csv.gz


title: DNF5

description: results.DNFvsDOF.csv.gz


title: X01 Control B


title: DNF4

description: results.DNFvsDOF.csv.gz


title: DNF2

description: results.DNFvsDOF.csv.gz


title: DNM4

description: results.DNMvsDOM.csv.gz


title: DNF1

description: results.DNFvsDOF.csv.gz


title: COM4

description: results.CNMvsCOM.csv.gz


title: COM5

description: results.CNMvsCOM.csv.gz


title: STEMI patient, M-01


title: COM3

description: results.CNMvsCOM.csv.gz


title: input DNA

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
library strategy:5hMethylCap-seq
The 5hMethylCap-Seq raw reads were trimmed for Illumina TruSeq adapters and low quality bases.  Trimmed and filtered fastq were mapped to hg19 reference genome using bowtie 1.1.2. Alignment will be converted to bam with SAMtools 1.3.1, and duplicate reads removed with picard v2.4.1. For peak calling, the 5hmC sample bam files were downsampled to 4 million reads.  The histone methylation regions were called using a Model-based Analysis of ChIP-Seq (MACS2) using the full Input sample as a control. Complete peak files are included for download.  For comparison purposes, peaks within 1 kb were merged with samples and across samples.
To determine the relationship between H3K9 and DNA methylation, we correlated the genome-wide 5mC/5hmC profiles with histone modification profiles from ChIP-Seq (DONOR_ID: 27, clear cell type), as well as with genomic features and data from the publicly available histone database (NIH Roadmap Epigenomics Mapping Consortium, JASPAR motif database and UCSC Genome Browser database). Average profile plots from sequencing reads of regions with differential 5hmC marks and histone modifications were generated using ngs.plot (version 2.0.8).  DiffBind was used for differential binding analysis of ChIP-seq peak data.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: NARROWPEAK files generated with MACS2 comparing each downsampled 5hmC sample to Input

source_name: input DNA

growth_protocol: Human renal clear cell carcinoma cell lines VHL-WT Caki-1 and VHL-null Caki2 were purchased from the American Type Culture Collection (ATCC). The cells were passaged in RPM11640 medium with 10% FBS and 1% Penicillin Streptomycin. To systematically study the association between H3K9me3 and 5hmC in RCC cells, we established stable SUV39H1 knockdown VHL-WT Caki-1 cells and VHL-null Caki-2 cells using short hairpin RNA.

extract_protocol:
Tissue and cell line DNA were processed by DNeasy Blood & Tissue kit (Qiagen) according to manufacturer’s requirement. Total DNA was extracted from urine samples using ZR Urine DNA Isolation Kit (Zymo Research).
The DNA samples were sheared by sonication using the Covaris S220 (COVARIS, INC.) to achieve an averaged DNA fragment size around 300 bp. The immunoprecipitation was performed using the Methylated DNA Capture Kit (Diagenode) and the IP-Star Compact Automated System (Diagenode). The libraries were generated using PrepX ILM DNA Library Kit (Illumina) per manufacturer’s instructions. Library quantification is performed using Qubit (Invitrogen) and Labchip GX HS (PerkinElmer) system for library fragment analysis. The libraries were subjected to massively parallel sequencing using HiSeq 2500 (Illumina) platform with the single-end 50 bp read option, according to the manufacturer’s instructions.

tag: tissue source

value: kidney

tag: tissue/cell type

value: clear cell renal cell carcinoma

tag: sample type

value: cell line


title: COM2

description: results.CNMvsCOM.csv.gz

value: Adipocytes

value: control


title: STEMI patient, M-02


title: healthy donor, H-15

description: gene expression data from platelet of patient healthy donor  (HDs)

value: healthy


title: DNM3

description: results.DNMvsDOM.csv.gz

value: male


title: COM1

description: results.CNMvsCOM.csv.gz

value: obese


title: healthy donor, H-14

value: Platelets


title: COF5

description: results.CNFvsCOF.csv.gz


title: healthy donor, H-16


title: healthy donor, H-20


title: healthy donor, H-11


title: healthy donor, H-12


title: healthy donor, H-09


title: healthy donor, H-17


title: healthy donor, H-18


title: healthy donor, H-10


title: COF1

description: results.CNFvsCOF.csv.gz


title: COF2

description: results.CNFvsCOF.csv.gz


title: DNF3

description: results.DNFvsDOF.csv.gz


title: COF3

description: results.CNFvsCOF.csv.gz


title: CNM4

description:
results.CLMvsCNM.csv.gz
results.CNMvsCOM.csv.gz


title: healthy donor,  H-06


title: COF4

description: results.CNFvsCOF.csv.gz


title: CaCo2 BRAF V600E + shSFPQ, 48 hrs, replicate 1

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

description:
V600E_shSFPQ_1
ext_L6921-1_KKN-7_S14

data_processing:
Quality control was performed using FastQC
Reads were mapped using STAR aligner v2.5.0c
Mapped reads were counted using subread featureCounts
Read counts were normalised using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimeted file of DESeq2 normalised read counts

source_name: CaCo2 BRAF V600E + shSFPQ

growth_protocol: Caco2 wt shRen, Caco2 wt shSFPQ and Cacc2 BRAFV600E shRen, Caco2 BRAFV600E shSFPQ were grown in DMEM supplemented with 10% FCS, Pen/Strep (100 U/ ml / 100µg/ml) and Ultraglutamine (2 mM) at 37°C with 5 % CO2

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit
Illumina TruSeq® Stranded Total RNA Library Prep

treatment_protocol: Upon attachment doxycycline (2 µg/ml) was added to induce transgene expression

tag: cell line

tag: genotype/variation

tag: shRNA

value: shSFPQ

tag: treated with

value: doxycycline for 48h


title: CNM5

tag: treatment


title: healthy donor, H-04


title: healthy donor, H-05


title: CNM1


title: CNM3


title: healthy donor, H-01


title: healthy donor, H-08


title: CNM2


title: sCAD patient, C-20

description: gene expression data from platelet of patient stable coronary artery disease (sCAD)

value: sCAD


title: healthy donor,  H-03


title: sCAD patient, C-19


title: sCAD patient, C-17


title: sCAD patient, C-18


title: healthy donor, H-02


title: sCAD patient, C-16


title: sCAD patient, C-15


title: CaCo2 BRAF V600E + shRen, 48 hrs, replicate 1

description:
V600E_shRen_1
ext_L6919-1_KKN-5_S10

source_name: CaCo2 BRAF V600E + shRen

value: shRen


title: CNF4

description:
results.CLFvsCNF.csv.gz
results.CNFvsCOF.csv.gz

value: female


title: CaCo2 BRAF V600E + shRen, 48 hrs, replicate 2

description:
V600E_shRen_2
ext_L6920-1_KKN-6_S13


title: CNF5

value: normal


title: CaCo2 BRAF wt + shSFPQ, 48 hrs, replicate 2

description:
wt_shSFPQ_2
ext_L6917-1_KKN-4_S12

source_name: CaCo2 BRAF wt + shSFPQ

value: BRAF wildtype


title: healthy donor, H-07


title: CNF2


title: CaCo2 BRAF wt + shSFPQ, 48 hrs, replicate 1

description:
wt_shSFPQ_1
ext_L6916-1_KKN-3_S9


title: sCAD patient, C-14


title: CaCo2 BRAF wt + shRen, 48 hrs, replicate 2

description:
wt_shRen_2
ext_L6915-1_KKN-2_S8

source_name: CaCo2 BRAF wt + shRen


title: CLM5

description: results.CLMvsCNM.csv.gz

value: lean


title: CNF1


title: OCI-Ly7 sgPRMT5 6-2

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

data_processing:
RNAseq fpkm were generated by HISAT, StringTie and Ballgown by following Pertea et al.(2016).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq (txt file: gene fpkm)

source_name: OCI-Ly7 sgPRMT5 6 days

growth_protocol: DLBCL cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
Total mRNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
cDNA library was construbuted by using Illumina Truseq RNA Library Prep Kit (RS-122-2002).

treatment_protocol: For RNAseq experiments, sgRNA was induced by Doxycycline for 0, 2 or 3 days.

value: GCB DLBCL cell line

value: expressing sgRNA targeting PRMT5

value: 20ng/ml doxycycline for 6 days.


title: CNF3

value: Adipocytes


title: CLM3

description: results.CLMvsCNM.csv.gz

value: control


title: CLM2

description: results.CLMvsCNM.csv.gz


title: sCAD patient, C-09


title: OCI-Ly7 sgPRMT5 6-1


title: CaCo2 BRAF wt + shRen, 48 hrs, replicate 1

description:
wt_shRen_1
ext_L6914-1_KKN-1_S7


title: sCAD patient, C-12


title: OCI-Ly7 sgPRMT5 3-2

source_name: OCI-Ly7 sgPRMT5 3 days

value: 20ng/ml doxycycline for 3 days.


title: sCAD patient, C-10


title: sCAD patient, C-08


title: sCAD patient, C-11


title: CLM4

description: results.CLMvsCNM.csv.gz

value: male


title: CLM1

description: results.CLMvsCNM.csv.gz


title: sCAD patient, C-06


title: CaCo2 BRAF V600E + shSFPQ, 48 hrs, replicate 2

description:
V600E_shSFPQ_2
ext_L6922-1_KKN-8_S15


title: CLF5

description: results.CLFvsCNF.csv.gz


title: OCI-Ly7 sgPRMT5 0-2

source_name: OCI-Ly7 sgPRMT5 0 day

value: 20ng/ml doxycycline for 0 days.


title: OCI-Ly7 sgPRMT5 3-1


title: CLF4

description: results.CLFvsCNF.csv.gz


title: OCI-Ly7 sgPRMT5 0-1


title: DNM1

description: results.DNMvsDOM.csv.gz

value: DDT


title: TMD8 sgPRMT5 6-2

source_name: TMD8 sgPRMT5 6 days

value: ABC DLBCL cell line


title: CLF2

description: results.CLFvsCNF.csv.gz


title: CLF3

description: results.CLFvsCNF.csv.gz


title: TMD8 sgPRMT5 6-1


title: CLF1

description: results.CLFvsCNF.csv.gz


title: ANM5

description: results.ALMvsANM.csv.gz

value: atrazine


title: TMD8 sgPRMT5 0-2

source_name: TMD8 sgPRMT5 0 day


title: ANM4

description: results.ALMvsANM.csv.gz


title: TMD8 sgPRMT5 3-2

source_name: TMD8 sgPRMT5 3 days


title: TMD8 sgPRMT5 0-1


title: sCAD patient, C-05

value: Platelets

value: sCAD


title: sCAD patient, C-04


title: healthy donor, H-19

value: healthy


title: sCAD patient, C-02


title: sCAD patient, C-07


title: sCAD patient, C-01


title: ANM2

description: results.ALMvsANM.csv.gz

value: normal


title: cal27_0

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

data_processing:
Real-Time Analysis software was used for base calling
Raw reads were aligned to human genome version hg38 using Bowtie2 version 2.2.6 and Tophat version 2.1.0
Differential expression analysis was performed using CuffDiff version 2.2.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: human cancer cell line

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% (v/v) fetal bovine serum, and maintained at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Cells were harvested at 70% confluency and total RNA purified suing miRNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit from Illumina

tag: disease

value: squamous cell carcinoma

value: tongue


title: cal27_sh_grk2_2


title: cal27_1


title: ANF5

description: results.ALFvsANF.csv.gz

value: female


title: ANM1

description: results.ALMvsANM.csv.gz


title: ANF3

description: results.ALFvsANF.csv.gz


title: cal27_sh_grk2_1


title: ANF1

description: results.ALFvsANF.csv.gz


title: C4: TNFSG_3

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

data_processing:
Data were analysed by GATC Biotech (Konstanz, Germany).
Reads were aligned to the reference genome or reference transcriptome using Bowtie (version 2.2.9). Splice junctions were mapped using TopHat (version 2.0.14).
Normalized abundances of transcripts were obtained and annotated using Cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file merged from cufflinks output include FPKM values for all samples

source_name: CML Cell line

growth_protocol: Cell were cultivated in RPMI medium supplemented with 10% FCS and antibiotics/antimycotics.

extract_protocol:
RNA were extracted using the Trizol kit, and cleaned using the Qiagen Rnase kit.
RNA sequencing, including library preparation, was carried out by GATC Biotech (Konstanz, Germany) following optimized standard operating procedures, using an Illumina HiSeq sequencer (single read mode, 1 x 50 base pair read length).

treatment_protocol: K562 cells were transfected with Si623/Gap01 or SiCt+GapCt (Mock transfection) under the experimental conditions mentioned above, then cells were treated or not with TNF_ (20ng/mL) for 6 hours.

value: CML

value: TNFSG

tag: replicate


title: cal27_2


title: ANF2

description: results.ALFvsANF.csv.gz

tag: cell type

value: Adipocytes


title: ALM5

description: results.ALMvsANM.csv.gz

value: lean


title: cal27_sh_grk2_0

tag: tissue


title: ANF4

description: results.ALFvsANF.csv.gz


title: ALM3

description: results.ALMvsANM.csv.gz


title: C3: SG_3

value: SG


title: ANM3

description: results.ALMvsANM.csv.gz

value: male


title: ALM4

description: results.ALMvsANM.csv.gz


title: C2: TNF_3

value: TNF


title: TMD8 sgPRMT5 3-1

value: expressing sgRNA targeting PRMT5

value: 20ng/ml doxycycline for 3 days.


title: C1: control_3

value: control


title: B4: TNFSG_2


title: B2: TNF_2


title: ALM2

description: results.ALMvsANM.csv.gz

value: atrazine


title: ALF5

description: results.ALFvsANF.csv.gz


title: ALM1

description: results.ALMvsANM.csv.gz


title: A4: TNFSG_1


title: A1: control_1


title: A2: TNF_1


title: B1: control_2


title: ALF3

description: results.ALFvsANF.csv.gz


title: A3: SG_1


title: PANC-1_Ctrl 24hrs-II

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

description:
P3404_116
Ctrl 24hrs-II

data_processing:
Mapping:  Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37.
Merging:  Bamfiles from samples run on different lanes were merged with samtools.
Sorting and Marking duplicates:  Merged bam files were sorted and duplicates removed using picard-tools/1.29.
Counts for genes:  Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts: FPKMs for genes and transcripts were generated using  cufflinks/2.1.1 on bamfiles with duplicates included.
Genome_build: Homo Sapiens, GRch37
Supplementary_files_format_and_content: [count_table.txt ]  Counts per gene and sample (duplicates included).
[fpkm_table.txt]  A single file containing all of the FPKM values per gene and sample (duplicates included).
[isoform_fpkm_table.txt]  A single file containing all of the FPKM values per isoform and sample (duplicates included).

source_name: Ctrl 24hrs-II

growth_protocol: DMEM/10 FBS media was used to culture both cell lines

extract_protocol:
Qiagen RNAasy kit. We have done an extra on-colum DNAase treatment step.
Illumina TruSeq Stranded mRNA, Poly-A selection

value: Pancreas

tag: genistein (um)

tag: gemcitabine (nm)


title: ALF2

description: results.ALFvsANF.csv.gz

tag: Sex


title: PANC-1_50uM Gen + 40nM Gem2 24hrs-I

description:
P3404_111
50uM Gen + 40nM Gem2 24hrs-I

source_name: 50uM Gen + 40nM Gem2 24hrs-I


title: PANC-1_50uM Gen + 40nM Gem2 24hrs-II

description:
P3404_112
50uM Gen + 40nM Gem2 24hrs-II

source_name: 50uM Gen + 40nM Gem2 24hrs-II


title: PANC-1_50uM Gen 24hrs-I

description:
P3404_109
50uM Gen 24hrs-I

source_name: 50uM Gen 24hrs-I


title: PANC-1_50uM Gen 24hrs-II

description:
P3404_110
50uM Gen 24hrs-II

source_name: 50uM Gen 24hrs-II


title: ALF1

description: results.ALFvsANF.csv.gz

source_name: Adipocytes

tag: type


title: Mia-PaCa-2_Ctrl 24hrs-II

description:
P3404_108
Ctrl 24hrs-II


title: Mia-PaCa-2_50uM Gen + 40nM Gem2 24hrs-I

description:
P3404_103
50uM Gen + 40nM Gem2 24hrs-I


title: PANC-1_Ctrl 24hrs-I

description:
P3404_115
Ctrl 24hrs-I

source_name: Ctrl 24hrs-I


title: Mia-PaCa-2_50uM Gen + 40nM Gem2 24hrs-II

description:
P3404_104
50uM Gen + 40nM Gem2 24hrs-II


title: PANC-1_40nM Gem2 24hrs-I

description:
P3404_113
40nM Gem2 24hrs-I

source_name: 40nM Gem2 24hrs-I


title: Mia-PaCa-2_Ctrl 24hrs-I

description:
P3404_107
Ctrl 24hrs-I


title: Mia-PaCa-2_40nM Gem2 24hrs-I

description:
P3404_105
40nM Gem2 24hrs-I


title: Mia-PaCa-2_50uM Gen 24hrs-I

description:
P3404_101
50uM Gen 24hrs-I


title: Mia-PaCa-2_50uM Gen 24hrs-II

description:
P3404_102
50uM Gen 24hrs-II


title: ALF4

description: results.ALFvsANF.csv.gz


title: Iso_ctrl_AD5p2

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

description: Isogenic control cell line Iso ctrl AD4, derived from AD5 1.5 cell line. Ideally should correspond to healthy control.

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three  Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to human genome hg38 using STAR aligner, version 2.5.2  (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file containing unnormalized (raw) read counts per feature.

source_name: hiPSC-derived brain astrocytes

growth_protocol: The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 5–7 months before dissociation and plating the cells on Matrigel-coated dishes for maturation 7 days prior to experiments. The technical replicates are all from the same subclone and differentiation batch but for the final 7 day maturation stage the replicates were plated and collected for RNA isolation on different days. The experiments were approved by the committee on Research Ethics of Northern Savo Hospital district (license no. 123/2016).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

tag: hipsc source

value: skin fibroblasts

tag: derived cell type

value: hiPSC-derived brain astrocytes

tag: psen1 genotype

value: Corrected

tag: patient age

tag: patient gender

tag: apoe genotype

tag: disease status

value: mutation corrected

tag: biological replicate

tag: technical replicate


title: Iso_ctrl_AD5p1

value: female


title: AD5_1.5p3

description: Alzheimer’s disease cell line AD 5 1.5

value: Presymptomatic


title: AD5_1.5p2

description: Alzheimer’s disease cell line AD 5 1.5


title: PANC-1_40nM Gem2 24hrs-II

description:
P3404_114
40nM Gem2 24hrs-II

source_name: 40nM Gem2 24hrs-II

tag: cell line


title: Control serum EV RNA - 3

city: Frankfurt am Main

first: Ricardo

middle: Mamede

last: Figueiredo

address: Altenhöferallee 3

institute: GenXPro GmbH

description: Sample 6 - 25539

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
PCR duplicates were cleaned using TrueQuant technology (UMI) and in-house GenXPro GmbH script.
Small RNA sequencing data was processed using omiRas (Müller S et al., Bioinformatics, 2013). In short, reads were summarized to UniTags, singletons were removed and the remaining tags were mapped to the human genome (hg19) with bowtie. The mapped tags were annotated using coding and non-coding RNAs retrieved from the UCSC table browser. The DESeq package was used to normalize the data and to independently calculate differential expression between the two conditions.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample, mean of normalized counts for each group, fold changes, pvalues and adjusted pvalues.

source_name: Serum extracellular vesicles

extract_protocol:
RNA was isolated using the ExoRNeasy Midi kit (Qiagen, Hilden, Germany) with a starting volume of 100 µl serum.
SncRNA libraries were prepared using the TrueQuant technology (GenXPro, Frankfurt am Main, Germany) for elimination of PCR bias. Modified 3′ and 5′ TrueQuant adapters were successively ligated to small RNA (<200 nt) using T4 RNA Ligase 2 and T4 RNA Ligase 1 (NEB, Frankfurt am Main, Germany), respectively. Adapter-ligated RNA was reverse transcribed with SuperScript III (Life Technologies, Darmstadt, Germany) and amplified by PCR with KAPA HiFi Hot-Start Polymerase (KAPA Biosystems, Wilmington, USA).

treatment_protocol: Serum was collected at the time of study enrolment before any invasive or surgical procedure using EDTA as an anticoagulant followed by centrifugation at 3000×g for 10 min and samples were then frozen at –80°C until analysis.

tag: sample type

value: serum


title: Iso_ctrl_AD4p3

description: Isogenic control cell line Iso ctrl AD4, derived from AD4 1.6 cell line. Ideally should correspond to healthy control.


title: Iso_ctrl_AD4p1


title: Control serum EV RNA - 2

description: Sample 5 - 22622


title: B3: SG_2

tag: cell type

value: CML

tag: treatment

tag: replicate


title: Mia-PaCa-2_40nM Gem2 24hrs-II

description:
P3404_106
40nM Gem2 24hrs-II

tag: tissue

tag: genistein (um)

tag: gemcitabine (nm)


title: AD5_1.5p1

description: Alzheimer’s disease cell line AD 5 1.5

tag: hipsc source


title: AD4_1.6p3

description: Alzheimer’s disease cell line AD 4 1.6

tag: derived cell type

value: Alzheimer's disease


title: CTEPH serum EV RNA - 3

description: Sample 3 - 175147


title: Iso_ctrl_AD4p2

tag: psen1 genotype


title: teachey-75

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 using Bowtie v2
Transcript quantification was performed with RNA-seq by Expectation Maximization (RSEM) protocol.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values files including Log CPM values for each sample.

source_name: Bone Marrow

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: Leukemia

tag: leukemia subtype

value: T-cell lymphoblastic


title: teachey-73


title: teachey-74


title: teachey-72


title: CTEPH serum EV RNA - 2

description: Sample 2 - 174187


title: Iso_ctrl_AD5p3

tag: patient age

tag: patient gender


title: teachey-71


title: Control serum EV RNA - 1

description: Sample 4 - 22159


title: HCT-116 cell culture replicate 2

city: Vilnius

first: Raimundas

last: Ražanskas

address: Sauletėkio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Biological replicate 2 of 3

data_processing:
Basecalls performed using CASAVA version 1.8
Short sequences in paired-end FASTQ files were joined with Adapter Removal v1.5.4. Next, files were processed with custom R scripts. Briefly, identical sequences were counted and collapsed, adapter sequences were trimmed and reads shorter than 16 nt and longer than 28 nt were removed. Remaining reads were aligned to human miRNA hairpin sequences from miRBase v22 using Bowtie v1.1.2 with parameters -a -v 0. Additional alignment cycles with modified parameter --3 X were performed to include miRNA sequences with 1, 2 or 3 non-template 3’-terminal nucleotides. Any aligned sequence was accepted as mature miRNA if its 5’-terminal mapped to hairpin no further than 1 nt in either direction from the 5’ start position of corresponding mature miRNA.
Data normalization and differential miRNA expression analyses were performed with R package DeSeq2.
Genome_build: hs_ref_GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and DeSeq2 normalized values of mature miRNAs in each sample.

source_name: colorectal carcinoma HCT116

growth_protocol: HCT116  and colorectal cancer sublines, resistant  to oxaliplatin or 5-fluoruracil,  were cultured in RPMI 1640 medium supplemented with 10% fetal bovine seum and penicillin (100µg/ml) and streptomycin (100µg/ml).

extract_protocol:
RNA was extrated with RNAzol® RT  reagent.
cDNA libraries for sequencing were prepared using NEXTflex Small RNA-Seq v3 kit. Ligation reactions of 3′ and 5′ adapters were performed using 1,2 µg of total RNA. The cDNA was amplified 16 PCR cycles.

treatment_protocol: Resistant cell lines were selected  by continuous permanent treatment by gradually increasing concentrations of 5-fluoruracil or oxaliplatin.

tag: resistance to

value: no resistance to 5-FU or Oxa


title: HCT-116 cell culture replicate 3

description: Biological replicate 3 of 3


title: HCT-116 cell culture replicate 1

description: Biological replicate 1 of 3


title: teachey-69

extract_protocol:
Total RNA was prepared using Trizol based extraction. Samples were purified and concentrated using the RNeasy Mini Kit. RNA concentration was determined using a NanoDrop spectrophotometer. RNA quality was assessed using an Agilent 2200 Bioanalyzer.
Libraries were prepared using the TruSeq RNA Exome RNA kit. Libraries were sequenced on a NextSeq 500 using 150bp paired-end chemistry.


title: teachey-70


title: AD4_1.6p2

description: Alzheimer’s disease cell line AD 4 1.6

value: male

tag: apoe genotype

tag: disease status

tag: biological replicate


title: HCT_Oxa cell culture replicate 3

description: Biological replicate 3 of 3

source_name: colorectal carcinoma HCT116 subline, resistant to Oxa

tag: cell line

value: Oxaliplatin


title: HCT_Oxa cell culture replicate 2

description: Biological replicate 2 of 3


title: teachey-68

tag: cell type


title: CTEPH serum EV RNA - 1

description: Sample 1 - 168598

tag: sample type


title: AD4_1.6p1

description: Alzheimer’s disease cell line AD 4 1.6

tag: technical replicate


title: teachey-67


title: HCT_Oxa cell culture replicate 1

description: Biological replicate 1 of 3


title: teachey-64


title: teachey-65


title: HCT_FU cell culture replicate 3

description: Biological replicate 3 of 3

source_name: colorectal carcinoma HCT116 subline, resistant to 5-FU


title: teachey-63


title: teachey-66


title: HCT_FU cell culture replicate 1

description: Biological replicate 1 of 3


title: teachey-61


title: HCT_FU cell culture replicate 2

description: Biological replicate 2 of 3


title: teachey-62


title: teachey-59


title: teachey-60


title: teachey-58


title: teachey-57


title: teachey-56


title: teachey-55


title: teachey-54


title: teachey-53


title: teachey-52


title: teachey-48


title: teachey-50


title: teachey-51


title: teachey-47


title: teachey-46


title: teachey-45


title: teachey-44


title: teachey-43


title: teachey-42


title: Microglia 3

city: Charlottesville

first: Hui

last: Zong

state: VA

address: 7046 Jordan Hall, 7th Floor, 1340 JPA

department: Microbiology, immunology and cancer biology

institute: University of Virginia

data_processing:
Adaptor Trimming by bioconductor
Initial quality assessment of sequencing reads using FastQC
Transcript abundance was estimated with Sailfish
Counts of reads mapping to GENCODE genes using the tximport package
Differential gene expression by Deseq2 Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: TPM

organism: Mus musculus

source_name: Microglia 3

extract_protocol: Tumor associated microglia and normal microglia was purified from tumor and cerebral cortex separately. In briefly, tumor mice were anaesthetized (60mg/kg ketamine; 12 mg/kg xylazine). Tumor tissue or cerebral cortex was dissected. After cutting into pieces, tissue was dissociated in enzyme solution (100 U papain, 4mg L-cysteine and 200U DNase I) for 45 minutes. Digested tumor pieces were triturated in enzyme inhibitor solution. After depletion of myelin, the microglia was incubated and captured with CD11b magnetic beads for one hour on ice. The cell suspension was added into purification column. After washing three times with washing buffer, the microglia was eluted into suspension buffer. Cells were spin down at 1000g for 5 minutes.

tag: mouse age

value: postnatal  day 60

tag: strain

tag: rna extraction methods

value: Trizol method

value: normal microglia


title: Microglia 2

source_name: Microglia 2


title: teachey-41

city: San Francisco

first: Benjamin

last: Huang

institute: University of California San Francisco


title: Microglia 1

source_name: Microglia 1


title: sCAD patient, C-03

source_name: Platelets

tag: tissue

value: Platelets

tag: diagnosis

value: sCAD


title: teachey-40


title: TAMs 5

source_name: TAMs 5

value: postnatal  day 62

value: tumor-associated microglia/macrophage


title: teachey-39


title: teachey-49


title: TAMs 3

source_name: TAMs 3

value: postnatal  day 61


title: teachey-38


title: monocytes.RA1

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

description:
CD11b+CD33+CD15neg cells
RA1_beta

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Rstudio

label: Cy3, Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from sorted monocytes using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

tag: Sex

value: F

tag: age

tag: patient cohort

value: discovery

tag: donor

value: RA

tag: batch


title: teachey-37

address: 1450 3rd Street

tag: leukemia subtype


title: TAMs 1

source_name: TAMs 1

value: postnatal  day 68


title: monocytes.RA2

description:
CD11b+CD33+CD15neg cells
RA2_beta


title: monocytes.RA16

description:
CD11b+CD33+CD15neg cells
RA16_beta


title: monocytes.RA46

description:
CD11b+CD33+CD15neg cells
RA46_beta

value: M

value: validation


title: teachey-36

value: Leukemia

value: T-cell lymphoblastic


title: TAMs 2

source_name: TAMs 2

value: postnatal  day 90


title: monocytes.RA9

description:
CD11b+CD33+CD15neg cells
RA9_beta


title: monocytes.RA41

description:
CD11b+CD33+CD15neg cells
RA41_beta


title: monocytes.RA45

description:
CD11b+CD33+CD15neg cells
RA45_beta


title: monocytes.RA39

description:
CD11b+CD33+CD15neg cells
RA39_beta


title: teachey-34


title: monocytes.RA4

description:
CD11b+CD33+CD15neg cells
RA4_beta


title: teachey-33


title: teachey-32


title: monocytes.RA50

description:
CD11b+CD33+CD15neg cells
RA50_beta


title: monocytes.RA20.2

description:
CD11b+CD33+CD15neg cells
RA20.2_beta


title: monocytes.RA5

description:
CD11b+CD33+CD15neg cells
RA5_beta


title: monocytes.RA35.2

description:
CD11b+CD33+CD15neg cells
RA35.2_beta


title: teachey-35


title: monocytes.RA8

description:
CD11b+CD33+CD15neg cells
RA8_beta


title: teachey-31


title: monocytes.RA11

description:
CD11b+CD33+CD15neg cells
RA11_beta


title: teachey-30


title: monocytes.RA49

description:
CD11b+CD33+CD15neg cells
RA49_beta


title: teachey-29


title: monocytes.RA33

description:
CD11b+CD33+CD15neg cells
RA33_beta


title: monocytes.RA34

description:
CD11b+CD33+CD15neg cells
RA34_beta


title: monocytes.RA13

description:
CD11b+CD33+CD15neg cells
RA13_beta


title: monocytes.RA13.2

description:
CD11b+CD33+CD15neg cells
RA13.2_beta


title: monocytes.RA28

description:
CD11b+CD33+CD15neg cells
RA28_beta


title: teachey-25


title: teachey-24


title: teachey-28


title: teachey-26


title: teachey-23


title: monocytes.RA36

description:
CD11b+CD33+CD15neg cells
RA36_beta


title: teachey-21


title: teachey-19


title: monocytes.RA40

description:
CD11b+CD33+CD15neg cells
RA40_beta


title: teachey-20


title: teachey-18


title: teachey-17


title: teachey-27


title: teachey-16


title: teachey-15


title: monocytes.RA3

description:
CD11b+CD33+CD15neg cells
RA3_beta


title: teachey-22


title: monocytes.RA14

description:
CD11b+CD33+CD15neg cells
RA14_beta


title: teachey-13


title: teachey-14


title: monocytes.RA18

description:
CD11b+CD33+CD15neg cells
RA18_beta


title: teachey-12


title: monocytes.RA9.2

description:
CD11b+CD33+CD15neg cells
RA9.2_beta


title: monocytes.RA29

description:
CD11b+CD33+CD15neg cells
RA29_beta


title: 191K_HF_HFS: GDM High fat sucrose 3

city: Winnipeg

first: Dr. Vernon

last: Dolinsky

state: Manitoba

address: 601 John Buhler Research Centre, 715 McDermot Avenue

department: Department of Pharmacology and Therapeutics

country: Canada

institute: University of Manitoba

data_processing:
The base calls are made by the RTA software on the computer that runs the instrument. The RTA for the Hiseq 4000 is v .2.7.7. Using default parameters.
After quality check the reads were aligned to Rattus norvegicus (Rnor_5) genome assembly  using STAR v2.5.1b .
All the "chrUn" were not considered in the downstrem analysis
For differential analysis software HOMER (v4.9) was used. First using homer script makeTagDirectory, the tag directories were made, which contains basic configuration information, such as the total number of reads, the total number of unique positions with aligned reads. Then homer script analyzeRepeats.pl was used to generate raw read counts based on exons and the counts were not adjusted and were condensed to genes. Further, the raw reads were subjected to homer script getDiffExpression.pl where we used DESeq2 18 to obtain the differentially regulated genes.  We used a cutoff of ≥1.5 fold and FDR of ≤0.05 to find the significant genes.
Genome_build: Rattus norvegicus (Rnor_5) genome assembly
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: islets

growth_protocol: Pancreatic islets were isolated from Rattus norvegicus (Sprague Dawley) as described in Li, et al. 2009, with modifications to accommodate the features of the rat anatomy.  After euthanizing the animal, the pancreas was localized and perfused via the bile duct in situ with 10mL of ice-cold Collagenase V solution (Sigma, St. Louis MO, USA) to achieve distension of the pancreas (approximately 90%).  After the pancreas was fully distended, pancreatectomy was performed and the excised pancreas was immersed into a 50-mL conical tube containing 2.5 mL ice-cold collagenase V solution.  All animal protocols were conducted in accordance with guidelines set by the Canadian Council on Animal Care and were approved by the University of Manitoba animal care committee.  The pancreas was digested in a water bath at 37 oC for 15 min with gentle manual shaking at 2-3 min intervals.  Solution was then immediately topped up to 30-35 mL with islet media (RPMI (11.1 mM glucose, Invetrogen) + 10% FBS + 1% P/S + 1% L-glutamine) and placed on ice.  Samples were inverted to create a homogenous solution and then centrifuged at 290 x g for 30 sec.  Carefully (without disturbing the soft pellet) the supernatant was decanted and the pellet was washed with 20 mL ice-cold 1XPBS by centrifuging at 290 x g for 30 sec.  After a 100 m cell strainer (VWR, Pennsylvania, USA) was pre-wet with 1-2 mL 1XPBS, tissue suspension was re-suspended to create a homogeneous solution and filtered by passing through the cell strainer over a 50-mL tube.  Strainer was tapped to enhance liquid flow and subsequently washed with 3 mL 1XPBS.  Captured islets on the strainer were washed with 10 mL 1XPBS.  Cell strainer was inverted over a sterile 100 mm tissue culture plate and the strainer was rinsed with 15 mL of ice-cold media collecting the released islets in the cell culture dish.  Using a dissection microscope (Olympus SZ61; NCL 150 Illuminator), individual clean, healthy looking islets were picked manually using a 20 L or 100 L pipettor.  Approximately about 200-300 islets were picked, centrifuged at 290 x g for 30 sec.  Supernatant was removed and pellets were re-suspended in 300 L RLT buffer (Qiagen, Valencia CA, USA) and stored at -80°C until needed.

extract_protocol:
Total RNA from the islets was extracted using RNAeasy Micro kit (Qiagen, Valencia CA, USA) as per manufacturer instructions. Subsequently, ribosomal RNA was removed from two micrograms total RNA by using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).  Total RNA and mRNA purity and integrity was assessed using Bioanalyzer 2000 Total RNA Pico and mRNA Pico, respectively (Agilent Technologies, Santa Clara CA, USA).
The library was prepared according to NEBNext Ultra II Directional RNA Library Prep for Illumina (NEB, Ipswich, MA, USA).  Ribosomal RNA depleted RNA (10-100 ng) was fragmented and random primed, converted to cDNA and ligated to sequencing adaptors.  PCR enrichment of adaptor-ligated libraries was performed and libraries were analyzed and measured using Bioanalyzer 2000 2100 Expert DNA 1000 chip (Agilent Technologies, Santa Clara CA, USA).

treatment_protocol: Briefly, female Sprague-Dawley rats were obtained at 3 weeks of age from the University of Manitoba colony and n=6 were randomly assigned to a low-fat (LF) diet (10% fat, Research Diets D12450B) and n=6 were randomly assigned to a high-fat and sucrose (HFS) diet (45% fat, Research Diets D12451) for a period of 6 weeks.  After 6 weeks of dietary intervention animals were mated with LF diet fed males and diets were continued in the same dams throughout pregnancy and suckling period. Food intake and body weight of the dams were measured weekly and a glucose test was performed at e15.5. Dams were allowed to deliver naturally and at birth, litters were reduced to eight pups to avoid competition for food

value: Sprague Dawley

value: islets

value: 15 weeks of age


title: teachey-11


title: monocytes.RA35

description:
CD11b+CD33+CD15neg cells
RA35_beta


title: monocytes.RA37

description:
CD11b+CD33+CD15neg cells
RA37_beta


title: teachey-10


title: 179G_HF_HFS: GDM High fat sucrose 2


title: monocytes.RA22.2

description:
CD11b+CD33+CD15neg cells
RA22.2_beta


title: monocytes.RA32.2

description:
CD11b+CD33+CD15neg cells
RA32.2_beta


title: teachey-08


title: 182G_HF_LF: GDM Low fat 3


title: monocytes.RA27

description:
CD11b+CD33+CD15neg cells
RA27_beta


title: monocytes.RA30

description:
CD11b+CD33+CD15neg cells
RA30_beta


title: 124G_HF_HFS: GDM High fat sucrose 1


title: monocytes.RA17

description:
CD11b+CD33+CD15neg cells
RA17_beta


title: teachey-07


title: monocytes.RA18.2

description:
CD11b+CD33+CD15neg cells
RA18.2_beta


title: monocytes.RA33.2

description:
CD11b+CD33+CD15neg cells
RA33.2_beta


title: monocytes.RA15

description:
CD11b+CD33+CD15neg cells
RA15_beta


title: teachey-06


title: teachey-05


title: monocytes.RA30.2

description:
CD11b+CD33+CD15neg cells
RA30.2_beta


title: 172K_HF_LF: GDM Low fat 2


title: 165K_HF_LF: GDM Low fat 1


title: monocytes.RA12

description:
CD11b+CD33+CD15neg cells
RA12_beta


title: monocytes.HD80

description:
CD11b+CD33+CD15neg cells
HD80_beta

value: HD


title: monocytes.RA5.2

description:
CD11b+CD33+CD15neg cells
RA5.2_beta


title: monocytes.HD21

description:
CD11b+CD33+CD15neg cells
HD21_beta


title: teachey-04


title: monocytes.RA1.2

description:
CD11b+CD33+CD15neg cells
RA1.2_beta


title: teachey-03


title: 148G_LF_HFS: Lean High fat sucrose 2


title: 132G_LF_HFS: Lean High fat sucrose 1


title: teachey-02


title: monocytes.RA19

description:
CD11b+CD33+CD15neg cells
RA19_beta


title: 158G_LF_LF: Lean Low fat control 3


title: monocytes.RA6.2

description:
CD11b+CD33+CD15neg cells
RA6.2_beta


title: 142G_LF_LF: Lean Low fat control 2


title: 134G_LF_LF: Lean Low fat control 1


title: monocytes.RA10

description:
CD11b+CD33+CD15neg cells
RA10_beta


title: teachey-01


title: monocytes.RA28.2

description:
CD11b+CD33+CD15neg cells
RA28.2_beta


title: Tentacles_RNA_rep2

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

data_processing:
Adapter sequences and low quality base pairs from the paired-ends reads were trimmed using Trimmomatic v. 0.35 using the following parameters: “PE [read1.fastq] [read2.fastq] pe_read1.fastq.gz se_read1.fastq.gz pe_read2.fastq.gz se_read2.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:8:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:17 MINLEN:30”.
RNA-seq reads for each sample were mapped to the reference transcriptome (from Hydra 2.0 Genome Project) using Bowtie v. 1.2 with the following parameters: “-X 2000 -a -m 200 -S --seedlen 25 -n 2 -v 3”.
Gene expression levels and read counts were obtained using RSEM v. 1.2.31 with the following parameters: “--paired-end --num-threads 8 --calc-ci”.
Batch effects were removed from gene expression levels (TPM) using “ComBat” function from “sva” package in R. The TPM values were smooth quantile normalized using “qsmooth” package in R.
Genome_build: Hydra 2.0 Genome (https://research.nhgri.nih.gov/hydra/)
Supplementary_files_format_and_content: Tab-delimited text file includes batch-corrected and smooth quantile normalized TPM values for all samples.

organism: Hydra vulgaris

source_name: Tentacles

growth_protocol: Hydra vulgaris polyps were used for the isolation of RNA. They were fed freshly hatched Artemia salina nauplii twice per week.  Animals were starved for at least 1 day before any tissue manipulation or RNA isolation was carried out.

extract_protocol:
Each isolated tissue was dissolved in Qiagen RNeasy buffer RLT (with 2-betamercaptoethanol added) within 3 minutes of isolation. The dissolved tissue was immediately used for total RNA isolation using Qiagen RNeasy kit according to manufacturer’s protocol. The total RNA for each sample was treated with DNase from TURBO DNA-free kit to remove any genomic DNA contamination. RNA quality was checked with Agilent Bioanalyzer and samples with RIN scores ≥9 were used for RNA-seq library preparation.
Multiplexed RNA-seq libraries were built using the Smart-seq2 protocol with slight modifications. Briefly, mRNA from total RNA in each sample was converted to full-length cDNA using poly-dT primer and reverse transcriptase. cDNA was amplified using appropriate number of PCR cycles based on the initial amount of total RNA and as recommended by the Smart-seq2 protocol. 20 ng full-length cDNA for each sample was converted to sequencing library by tagmentation with the Illumina Nextera kit. 8 cycles of PCR were used for library amplification. Libraries were multiplexed and sequenced as 43 bp Illumina paired-end reads.

treatment_protocol: For regeneration, 1 animal per sample (with two biological replicates) was bisected at the region 1 (R1) and region 2 (R2) border and allowed to undergo head regeneration for a specific period of time (0, 2, 4, 6, 12, 24, or 48 hours). Then the R2-R3 region of the animal of a sample was isolated for RNA extraction. For the budding experiment, the head region of buds from animals at various stages of budding (S1, S3, S4, S5, S6, S7, S8, or S10) was bisected and used for total RNA extraction. Tissues from tentacles, budding zone, body column, hypostome, and foot were harvested for RNA extraction.

value: tentacles


title: monocytes.HD22

description:
CD11b+CD33+CD15neg cells
HD22_beta


title: Tentacles_RNA_rep1


title: Hypostome_RNA_rep2

source_name: Hypostome

value: hypostome


title: Hypostome_RNA_rep1


title: Foot_RNA_rep2

source_name: Foot

value: foot


title: Foot_RNA_rep1


title: 162G_LF_HFS: Lean High fat sucrose 3


title: teachey-09

source_name: Bone Marrow


title: BuddingZone_RNA_rep1

source_name: BuddingZone

value: budding zone


title: monocytes.HD20

description:
CD11b+CD33+CD15neg cells
HD20_beta

value: F


title: IPF217_CD108_high

city: Los angeles

first: Xue

last: Liu

address: AHSP A9404, 127 S. San Vicente Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

description:
Reads were produced on both NextSeq 500 and NovaSeq 6000 instruments
Sample _IPF012_IPF217_SEMA7A_high_neg_FPKM.csv

data_processing:
Tophat2 (2.0.7) was applied to align sequencing reads to the reference human genome (GRCh38).
The relative gene expression RPKM (reads per kb of transcript, per million mapped reads) and read counts were estimated using SAMMate (2.7.4) and Ensembl database (Homo Sapiens.GRCh38.77). Protein-coding genes with at least 2 RPKM on average in either condition were used to perform the dif- ferential gene expression analysis using edgeR.
The P values of multiple tests were adjusted using the Benjamini-Hochberg method (56) and the significance level was set at FDR < 0.01 and |log2 FC| > 0.5.
Supplementary_files_format_and_content: CSV files were generated as the processed data

source_name: human lung of IPF patient

growth_protocol: Human lung fibroblasts were isolated from surgical lung biopsies or lung transplant explants obtained from patients with IPF. The diagnosis of IPF was arrived at by standard accepted American Thoracic Society recommendations (ATS/ERS, 2000). The tissues were minced, digested, and cultured in DMEM supplemented with 15% FBS and Antibiotic-An- timycotic (Thermo Fisher Scientific).

extract_protocol:
SEMA7A high and negative cells were lysated and RNA was extracted based on the protocol according to the manufacturer's instructions.
Library preparation and sequencing Library construction was performed using the Illumina TruSeq Stranded Total RNA-seq with Qiagen FastSelect rRNA removal kit.

treatment_protocol: IPF lung fibroblasts were trypsinized and stained with anti-human CD108 (SEMA7A)-PE antibody (BD biosciences, clone KS-2) and performed Fluorescence activated cell sortin (FACS) for SEMA7A high and negative cells

value: human lung fibroblasts

tag: passage

tag: patient diagnosis

value: Idiopathic pulmonary fibrosis (IPF)

tag: cd108 (sema7a) status

value: high


title: BodyColumn_RNA_rep2

source_name: BodyColumn

value: body column


title: BuddingZone_RNA_rep2


title: IPF012-14_CD108_high

tag: cell type


title: IPF012-14_CD108_low

value: low


title: IPF217_CD108_low


title: Reg_RNA_48hr_rep2

value: regenerating head


title: IPF11-15-CD108-low

description:
Reads were produced on both NextSeq 500 and NovaSeq 6000 instruments
Sample _IPF1_IPF11_SEMA7A_high_neg_FPKM.csv


title: monocytes.HD18

description:
CD11b+CD33+CD15neg cells
HD18_beta

value: discovery


title: Reg_RNA_48hr_rep1


title: monocytes.HD14

description:
CD11b+CD33+CD15neg cells
HD14_beta


title: monocytes.HD15

description:
CD11b+CD33+CD15neg cells
HD15_beta


title: IPF1-15-CD108-low


title: monocytes.HD3

description:
CD11b+CD33+CD15neg cells
HD3_beta


title: Reg_RNA_24hr_rep1


title: IPF11-15-CD108-high


title: IPF1-15-CD108-high


title: Reg_RNA_12hr_rep2


title: monocytes.RA20

description:
CD11b+CD33+CD15neg cells
RA20_beta

value: RA


title: monocytes.HD12

description:
CD11b+CD33+CD15neg cells
HD12_beta


title: monocytes.HD17

description:
CD11b+CD33+CD15neg cells
HD17_beta


title: monocytes.HD16

description:
CD11b+CD33+CD15neg cells
HD16_beta


title: YN14_020_PanTro_Olig2

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: Protocol 1

data_processing:
Single-end reads were aligned with STAR 2.5.2b using options "“--outFilterMultimapNmax 10 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 3 --twopassMode Basic" to the reference sequence (hg19, PanTro5, RheMac8 from UCSC)
Crossmap and Liftover tools were used to translate non-human priamte coordinates into human coordinates. Human reference was used for gene annotation and counting (gencode v19). Uniquely mapped reads were quantified using HTSeq python suite using high-scored orthologs' protein coding genes by exons.
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: tab separated files with raw counts

organism: Pan troglodytes

source_name: brain

extract_protocol:
nuclear extraction protocol: Tissue isolated from Brodmann Area 46 from 27 healthy humans, 11 healthy chimpanzee and 15 healthy rhesus macaque.700 mg of frozen postmortem brain was homogenized with lysis buffer using a dounce homogenizer. Brain lysate was placed on a sucrose solution to create a concentration gradient. Ultracentrifuge was used to separate nuclei and cytoplasmic fraction.
FANS protocol: Nuclei were resuspended in PBS plus RNase inhibitors and incubated with mouse Alexa488 conjugated anti-NeuN (1:200) (#MAB377X, Millipore, Billerica, MA) and rabbit Alexa555 conjugated anti-OLIG2 (1:75) (#AB9610-AF555, Millipore) antibodies with 0.5% BSA. Immuno-labeled nuclei were collected as NeuN-positive or OLIG2-positive populations by fluorescence-activated cell sorting (FACS).
total RNA extraction protocol: Total RNA were purified from each nuclei population using a ZR-Duet DNA/RNA MiniPrep (Plus) kit according to the manufacturer's instruction. 200 ng total RNA from each sample was treated for ribosomal RNA (rRNA) removal using the Low Input RiboMinus Eukaryote System v2 (#A15027, ThermoFisher) according to the manufacturer's instruction.
Total RNAs with an average RIN value of 7.5±0.16 were used for RNA-seq library preparation. 50 ng of total RNA after rRNA removal was subjected to fragmentation, first and second strand syntheses, and clean up by EpiNext beads (#P1063, EpiGentek, Farmingdale, NY). Second strand cDNA was adenylated, ligated and cleaned up twice by EpiNext beads. cDNA libraries were amplified by PCR, and cleaned up twice by EpiNext beads. cDNA library quality was quantified by a 2100 Bioanalyzer using an Agilent High Sensitivity DNA Kit (#5067-4626, Agilent, Santa Clara, CA). Barcoded libraries were pooled and underwent 75 bp single-end sequencing on an Illumina NextSeq 500.

value: brain

tag: nuclei

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

tag: sample id

tag: gender

value: M

tag: humanized age

tag: hemisphere

value: L

tag: pmi

tag: rin


title: N2: Control siRNA replicate 2

city: La Jolla

first: Michael

last: Hamilton

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

data_processing:
Kallisto – transcript quantification
Sleuth – gene differential expression analysis/gene normalized abundance measurements
HISAT2 - alignment of sequencing reads
edgeR - differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: .xls, TPM values, sleuth output, edgeR output

source_name: Caki-1 cells

extract_protocol:
Rneasy Mini kit
NEBNext Ultra II directional library kit

tag: tissue

value: Caki-1 cells

tag: genotype/variation

value: Control siRNA


title: YN14_020_PanTro_NeuN

description: Protocol 1

value: NeuN

tag: age


title: Reg_RNA_6hr_rep2


title: monocytes.HD8

description:
CD11b+CD33+CD15neg cells
HD8_beta

tag: Sex

value: F

tag: patient cohort

tag: donor

value: HD

tag: batch


title: Reg_RNA_24hr_rep2


title: monocytes.HD10

description:
CD11b+CD33+CD15neg cells
HD10_beta


title: monocytes.HD19

description:
CD11b+CD33+CD15neg cells
HD19_beta


title: BodyColumn_RNA_rep1


title: Reg_RNA_6hr_rep1


title: monocytes.raiv.3.tnfa

description:
CD11b+CD33+CD15neg cells
raiv.3.tnfa_beta

growth_protocol: PBMCs were cultured for 4 days in RMPI medium + 10% FBS

extract_protocol: Genomic DNA was extracted and purified from sorted CD11b+CD33+ cells using the Maxwell RSC Cell DNA kit (Promega) according to standard instructions

treatment_protocol: Cell were treated in vitro for 4 days with TNF-alpha (10 ng/mL), IFN-alpha (100 ng/mL), IFN-gamma (100 ng/mL) or control

tag: treatments

value: treatment with TNF-alpha


title: monocytes.raiv.3.ifng

description:
CD11b+CD33+CD15neg cells
raiv.3.ifng_beta

value: treatment with IFN-gamma


title: YN04_30_PanTro_NeuN

description: Protocol 1

tag: nuclei

value: R


title: monocytes.raiv.5.tnfa

description:
CD11b+CD33+CD15neg cells
raiv.5.tnfa_beta


title: P3: HOTAIRM1 siRNA replicate 3

value: HOTAIRM1 siRNA


title: monocytes.HD9

description:
CD11b+CD33+CD15neg cells
HD9_beta


title: monocytes.raiv.5.ifna

description:
CD11b+CD33+CD15neg cells
raiv.5.ifna_beta

value: treatment with IFN-alpha


title: Reg_RNA_4hr_rep2

value: regenerating head


title: N1: Control siRNA replicate 1


title: monocytes.raiv.2.tnfa

description:
CD11b+CD33+CD15neg cells
raiv.2.tnfa_beta


title: YN15_310_PanTro_Olig2

description: Protocol 1

tag: tissue preparation


title: YN04_30_PanTro_Olig2

description: Protocol 1

tag: region


title: Reg_RNA_4hr_rep1


title: monocytes.raiv.3.ifna

description:
CD11b+CD33+CD15neg cells
raiv.3.ifna_beta


title: N3: Control siRNA replicate 3


title: YN15_310_PanTro_NeuN

description: Protocol 1

tag: sample id


title: Reg_RNA_12hr_rep1


title: Reg_RNA_2hr_rep2


title: YN15_384_PanTro_Olig2

description: Protocol 1

tag: gender


title: P1: HOTAIRM1 siRNA replicate 1


title: Reg_RNA_0hr_rep2


title: Reg_RNA_2hr_rep1


title: Reg_RNA_0hr_rep1


title: YN06_147_PanTro_Olig2

description: Protocol 1

tag: humanized age


title: YN15_384_PanTro_NeuN

description: Protocol 1

tag: hemisphere


title: monocytes.HD7

description:
CD11b+CD33+CD15neg cells
HD7_beta

value: discovery


title: Bud_RNA_Stage10_rep2

value: developing bud


title: monocytes.raiv.5.ifng

description:
CD11b+CD33+CD15neg cells
raiv.5.ifng_beta


title: monocytes.raiv.5.c

description:
CD11b+CD33+CD15neg cells
raiv.5.c_beta

value: control


title: Bud_RNA_Stage10_rep1


title: YN06_147_PanTro_NeuN

description: Protocol 1

value: brain

value: Frozen Brain Tissue

value: Brodmann Area 46

tag: pmi


title: YN07_387_PanTro_NeuN

description: Protocol 1

value: M

value: L

tag: rin


title: monocytes.raiv.3.c

description:
CD11b+CD33+CD15neg cells
raiv.3.c_beta


title: Bud_RNA_Stage8_rep2

tag: tissue


title: YN14_056_PanTro_Olig2

description: Protocol 1


title: YN07_387_PanTro_Olig2

description: Protocol 1


title: YN07_147_PanTro_Olig2

description: Protocol 1


title: Bud_RNA_Stage8_rep1


title: monocytes.HD13

description:
CD11b+CD33+CD15neg cells
HD13_beta


title: Bud_RNA_Stage7_rep2


title: Bud_RNA_Stage7_rep1


title: YN07_147_PanTro_NeuN

description: Protocol 1

value: NeuN


title: monocytes.raiv.2.ifng

description:
CD11b+CD33+CD15neg cells
raiv.2.ifng_beta


title: Bud_RNA_Stage6_rep2


title: Bud_RNA_Stage6_rep1


title: Bud_RNA_Stage5_rep2


title: YN15_033_PanTro_Olig2

description: Protocol 1

value: F


title: Bud_RNA_Stage5_rep1